@article {pmid40630933,
year = {2025},
author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L},
title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf092},
pmid = {40630933},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; },
abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.},
}

Humans
*Metagenomics/methods
Algorithms
*Software
*Sequence Alignment/methods
*Metagenome
Microbiota/genetics

@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Phylogeny
Male
Female
*Oxidoreductases/metabolism/genetics
*Bacteria/enzymology/genetics/classification
*Steroids/metabolism
Biotransformation
Pregnenolone/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid40570246,
year = {2025},
author = {Ma, C and Bao, Y and Hereid, S and Zhang, H and Bai, X and Bai, Q and Zhao, L and Zhang, X and Lian, H and Dai, L and Bao, X and Bao, L},
title = {Mechanistic Elucidation of Tricholoma mongolicum Polysaccharides in Treating MAFLD via Regulation of the Gut Microbiota-Metabolite-Ferroptosis Axis: A Multi-Omics Perspective.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {27},
pages = {17040-17056},
doi = {10.1021/acs.jafc.5c05877},
pmid = {40570246},
issn = {1520-5118},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/administration & dosage/chemistry ; Animals ; Mice ; Male ; Humans ; *Tricholoma/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Iron/metabolism ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/genetics ; *Plant Extracts/administration & dosage/chemistry ; *Fatty Liver/drug therapy/metabolism/microbiology/genetics ; Multiomics ; },
abstract = {This study aimed to elucidate the modulatory effects and underlying molecular mechanisms of Tricholoma mongolicum polysaccharide (TMP) in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). High-performance gel permeation chromatography (HPGPC) analysis indicated a bimodal molecular weight distribution. Monosaccharide composition profiling revealed a predominance of glucose and galactose among other constituents. Scanning electron microscopy (SEM) illustrated a porous, aggregated colloidal microstructure. In a model of MAFLD, TMP intervention significantly attenuated serum levels of TC, TG, and AST, ALT, accompanied by notable histological improvements, including reduced hepatic steatosis and inflammatory cell infiltration. Metagenomic analysis demonstrated that TMP substantially enhanced gut microbial α-diversity, restructured microbial community composition, decreased the Firmicutes/Bacteroidetes ratio, enriched SCFAs-producing genera, and suppressed the excessive proliferation of pro-inflammatory bacterial genera. Integrated proteomic and lipidomic analyses revealed that TMP inhibited hepatic immune-inflammatory responses and ferroptosis pathways, enhanced pathways associated with metabolic homeostasis. Furthermore, TMP modulated hepatic iron metabolism by upregulating the Nrf2/GPx4 antioxidant axis and FPN1 while downregulating TFR1, thereby alleviating oxidative stress and iron overload. These findings demonstrate that TMP exerts therapeutic efficacy through a bidirectional gut-liver regulatory mechanism involving microbial modulation, ferroptosis inhibition, metabolic reprogramming, and activation of antioxidant defenses. This research provides novel insights and molecular targets for the development of natural polysaccharide-based interventions for MAFLD.},
}

*Gastrointestinal Microbiome/drug effects
*Polysaccharides/administration & dosage/chemistry
Animals
Mice
Male
Humans
*Tricholoma/chemistry
Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Mice, Inbred C57BL
Liver/metabolism/drug effects
Iron/metabolism
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/genetics
*Plant Extracts/administration & dosage/chemistry
*Fatty Liver/drug therapy/metabolism/microbiology/genetics
Multiomics

@article {pmid40556381,
year = {2025},
author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z},
title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {27},
pages = {17219-17232},
doi = {10.1021/acs.jafc.5c02308},
pmid = {40556381},
issn = {1520-5118},
mesh = {Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Guanidines/analysis/metabolism ; *Bacteria/genetics/isolation & purification/classification/metabolism ; Microbiota/drug effects ; Volatile Organic Compounds/chemistry/metabolism ; *Nitro Compounds/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Neonicotinoids/analysis ; *Pesticide Residues/analysis ; Taste ; Odorants/analysis ; *Fermented Foods/microbiology/analysis ; Metagenomics ; *Brassica/microbiology/chemistry ; },
abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.},
}

Fermentation
*Flavoring Agents/metabolism/chemistry
*Guanidines/analysis/metabolism
*Bacteria/genetics/isolation & purification/classification/metabolism
Microbiota/drug effects
Volatile Organic Compounds/chemistry/metabolism
*Nitro Compounds/analysis/metabolism
Gas Chromatography-Mass Spectrometry
*Neonicotinoids/analysis
*Pesticide Residues/analysis
Taste
Odorants/analysis
*Fermented Foods/microbiology/analysis
Metagenomics
*Brassica/microbiology/chemistry

@article {pmid40454811,
year = {2025},
author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM},
title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.},
journal = {mBio},
volume = {16},
number = {7},
pages = {e0110825},
doi = {10.1128/mbio.01108-25},
pmid = {40454811},
issn = {2150-7511},
support = {P20GM146584, P20GM139769/NH/NIH HHS/United States ; K01-DK111794/NH/NIH HHS/United States ; AI124255, AI090871/NH/NIH HHS/United States ; },
mesh = {Animals ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; Mice ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; Male ; Metagenomics ; Metabolomics ; },
abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.

IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.},
}

Animals
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
Mice
*Clostridioides difficile/physiology
*Gastrointestinal Microbiome
Humans
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Disease Models, Animal
Mice, Inbred C57BL
Female
Male
Metagenomics
Metabolomics

@article {pmid40285962,
year = {2025},
author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E},
title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {44},
number = {7},
pages = {1643-1657},
pmid = {40285962},
issn = {1435-4373},
support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; },
mesh = {Humans ; Male ; Female ; Child, Preschool ; Infant ; Child ; *Virome ; *Respiratory Tract Infections/virology/epidemiology ; Severity of Illness Index ; Bronchoalveolar Lavage Fluid/virology ; *Viruses/genetics/classification/isolation & purification ; Infant, Newborn ; Child, Hospitalized ; Sputum/virology ; High-Throughput Nucleotide Sequencing ; Adolescent ; *Virus Diseases/virology/epidemiology ; Metagenomics ; Hospitalization ; China/epidemiology ; },
abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.

METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).

RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.

CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
Female
Child, Preschool
Infant
Child
*Virome
*Respiratory Tract Infections/virology/epidemiology
Severity of Illness Index
Bronchoalveolar Lavage Fluid/virology
*Viruses/genetics/classification/isolation & purification
Infant, Newborn
Child, Hospitalized
Sputum/virology
High-Throughput Nucleotide Sequencing
Adolescent
*Virus Diseases/virology/epidemiology
Metagenomics
Hospitalization
China/epidemiology

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40624949,
year = {2025},
author = {Wu, M and Zhang, T and Han, S and Huan, S and Jiang, Y and Wang, Y and Cai, Z and Zhou, J},
title = {Structure and Function Features of Abundant and Rare Prokaryotic Communities Along Nearshore to Offshore Transitions.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70144},
doi = {10.1111/1462-2920.70144},
pmid = {40624949},
issn = {1462-2920},
support = {42476137//National Natural Science Foundation of China/ ; KCXFZ20230731093402005//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; SGDX20220530111204028//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; RCJC20200714114433069//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; ZDSYS20230626091459009//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; 2023KCXTD052//Innovation Team Project for Guangdong's Universities/ ; 2025A1515010643//Natural Science Foundation of Guangdong Province/ ; 2025A1515010519//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Microbiota ; Metagenome ; Metagenomics ; *Archaea/genetics/classification/isolation & purification ; },
abstract = {Abundant and rare taxa are crucial members of the marine microbial community. However, their biodiversity, assembly mechanisms, functional characteristics and ecological response strategies remain poorly understood. In this study, 16S rRNA and metagenomic sequencing were carried out to reveal the structural and functional features of abundant and rare taxa across the transition from nearshore to offshore. The results showed that the biodiversity of both abundant and rare taxa decreased with increasing distance from shore, with rare taxa exhibiting relatively higher diversity indices than abundant ones. Neutral model analysis revealed that the assembly process gradually changed from deterministic to stochastic from nearshore to offshore among abundant taxa. In contrast, among rare taxa, a stochastic process dominated nearshore, whereas a deterministic process was predominant in the offshore environment. Meanwhile, the proportion of variance that could be explained by environmental factors was relatively higher among abundant communities than among rare ones. A co-occurrence network analysis indicated that rare communities displayed greater complexity and a higher degree of modularity than abundant communities. Functionally, abundant communities tended to favour an r-strategy, whereas rare communities leaned towards a K-strategy. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns along coastal-to-open water transitions.},
}

Biodiversity
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Microbiota
Metagenome
Metagenomics
*Archaea/genetics/classification/isolation & purification

@article {pmid40624695,
year = {2025},
author = {Li, Q and Huang, J and Zhou, Y and Wu, Q and Zhou, J and He, F and He, L and Shi, Y and Guo, C and Dai, J},
title = {Virome profiling of Aedes albopictus across urban ecosystems in Guangdong reveals sex-specific diversity.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {264},
pmid = {40624695},
issn = {1756-3305},
support = {2024HK037//Scientific Research Project of General Administration of Customs/ ; 2024M760629//China Postdoctoral Science Foundation/ ; 2022YFC2302700//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Aedes/virology ; *Virome/genetics ; Female ; Male ; China ; *Mosquito Vectors/virology ; Phylogeny ; Ecosystem ; Metagenomics ; Cities ; Sex Factors ; Arboviruses/genetics/isolation & purification ; },
abstract = {BACKGROUND: Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne diseases. However, sex- and geography-specific virome profiles of Aedes albopictus populations in this area remain uncharacterized, limiting the development of targeted surveillance strategies and precise risk assessment.

METHODS: We performed a metagenomic analysis of 1269 adult Aedes albopictus collected from five cities across Guangdong Province during autumn 2021. Mosquito pools underwent viral particle enrichment followed by DNA and RNA sequencing. Bioinformatic analyses were employed to characterize viral communities, evaluate alpha/beta diversity, and conduct phylogenetic reconstruction.

RESULTS: A comparative analysis of virome profiles in male and female Aedes albopictus across five regions of Guangdong Province (Chaozhou, Guangzhou, Shaoguan, Shenzhen, Zhanjiang) revealed significant viral distribution patterns influenced by both sex and geographic location. Female mosquitoes predominantly hosted vertebrate-associated arboviruses, including Flavivirus, consistent with their blood-feeding behavior. RNA virome composition showed significant sex-specific clustering (permutational multivariate analysis of variance, PERMANOVA, P = 0.008), with coastal cities (Shenzhen, Zhanjiang) being dominated by RNA viruses, whereas inland areas (Shaoguan) exhibited a predominance of DNA viruses. DNA virome profiles displayed divergence between sexes but marked regional variation. Guangzhou emerged as an outlier, exhibiting exceptional bacteriophage diversity distinct from other regions. Phylogenetic analysis identified zoonotic pathogens with signatures of cross-species transmission and region-specific evolutionary adaptation. These findings highlight the interplay between mosquito ecology, geographic factors, and viral evolution in shaping virome diversity.

CONCLUSIONS: This study presents the inaugural comparative analysis of DNA/RNA viromes in Aedes albopictus populations across Guangdong Province, revealing distinct sex-specific and geographic patterns in viral composition. The identification of vertebrate-associated viruses in female mosquitoes reinforces their epidemiological significance as arboviral vectors, while male-specific environmental viral signatures suggest potential pathways for ecological spillover. Coastal-inland and urban-rural disparities in viral communities emphasize the need for regionally tailored surveillance. These findings provide essential baseline virome data for forecasting emerging arboviral threats and informing strategies to mitigate zoonotic spillover in subtropical urban ecosystems.},
}

Animals
*Aedes/virology
*Virome/genetics
Female
Male
China
*Mosquito Vectors/virology
Phylogeny
Ecosystem
Metagenomics
Cities
Sex Factors
Arboviruses/genetics/isolation & purification

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

Animals
*Dysbiosis/chemically induced/therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects
Humans
*Diarrhea/chemically induced/microbiology/therapy
Mice
*Bacteroides fragilis
Mice, Inbred C57BL
*Probiotics/therapeutic use
Mice, Inbred BALB C
*Antineoplastic Agents/adverse effects
Middle Aged
Fluorouracil/adverse effects
Feces/microbiology
Female
Aged

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation & purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

Humans
*Cholangiocarcinoma/microbiology/metabolism
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/metabolism
*Bile Acids and Salts/metabolism
Male
Middle Aged
Female
Metabolic Networks and Pathways
*Dysbiosis/microbiology
*Clostridiales/genetics/isolation & purification
Aged
Case-Control Studies
Adult
Feces/microbiology

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation & purification/genetics/growth & development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/classification/isolation & purification/genetics/growth & development/metabolism
*Microbial Interactions
Coculture Techniques
Metagenome
Healthy Volunteers
Feces/microbiology
China

@article {pmid40624535,
year = {2025},
author = {Zhao, Y and Niu, X and Zhang, Y and Zhao, L and Zhang, L and He, J and Zhang, Q and Mao, Y and Wang, F and Zhao, X and Wang, R},
title = {Impact of supplementing Limosilactobacillus fermentum MN-LF23 on the eradication of Helicobacter pylori with 14-day standard quadruple therapy: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {106},
pmid = {40624535},
issn = {1475-2891},
support = {2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Male ; Female ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/therapy ; Double-Blind Method ; Middle Aged ; Adult ; *Limosilactobacillus fermentum ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Dietary Supplements ; Dyspepsia ; },
abstract = {BACKGROUND: The effect of probiotics on Helicobacter pylori (Hp) infection demonstrates considerable heterogeneity. This study aims to elucidate the role of Limosilactobacillus fermentum MN-LF23 (MN-LF23) in Hp-infected populations.

METHODS: A total of 94 adult patients with confirmed Hp infection were enrolled in this study and randomly allocated to the placebo or MN-LF23 group. Patients initially received either placebo or probiotics along with standard quadruple therapy for 2 weeks, followed by continued administration of either placebo or probiotics for an additional 4 weeks. The eradication of Hp, serum levels of inflammatory factors, and alterations in gastrointestinal symptoms were assessed at weeks 0, 2, and 6, while fecal samples were collected for metagenomic sequencing.

RESULTS: The results showed no significant difference (P = 1) in the eradication rate between the placebo group (85.11%) and the probiotic group (82.98%). Following treatment, the incidence of constipation, dyspepsia, and Gastrointestinal Symptom Rating Scale (GSRS) scores in the probiotic group were markedly lower (P < 0.05) compared to those observed in the placebo group. Throughout the treatment process, there were no significant differences in TNF-α and IL-1β levels between the two groups. Compared to the placebo group, the probiotic group exhibited a significant increase in beneficial bacteria such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Bifidobacterium longum, Coprococcus caltus, and Clostridium butyricum.

CONCLUSION: MN-LF23 supplementation did not improve the eradication rate of standard quadruple therapy. However, it significantly reduced the overall GSRS score, improved digestive and constipation symptoms, and promoted the proliferation of beneficial bacteria in the intestine.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Male
Female
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/therapy
Double-Blind Method
Middle Aged
Adult
*Limosilactobacillus fermentum
Drug Therapy, Combination
Anti-Bacterial Agents/therapeutic use/administration & dosage
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome
Dietary Supplements
Dyspepsia

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification

@article {pmid40624236,
year = {2025},
author = {Wu, D and Niu, J and Hu, J and Wang, H and Kuang, H},
title = {Metabolomics combined with metagenomics analysis reveals the potential mechanism of Zhejiang psyllium polysaccharides against hyperuricemia in rats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24180},
pmid = {40624236},
issn = {2045-2322},
mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology ; *Metagenomics/methods ; *Metabolomics/methods ; Rats ; Uric Acid/blood ; Gastrointestinal Microbiome/drug effects ; Male ; *Psyllium/pharmacology/chemistry ; *Polysaccharides/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Blood Urea Nitrogen ; Creatinine/blood ; },
abstract = {This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus, thereby improving intestinal flora imbalance in rats with hyperuricemia.},
}

Animals
*Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology
*Metagenomics/methods
*Metabolomics/methods
Rats
Uric Acid/blood
Gastrointestinal Microbiome/drug effects
Male
*Psyllium/pharmacology/chemistry
*Polysaccharides/pharmacology/therapeutic use
Rats, Sprague-Dawley
Kidney/pathology/drug effects/metabolism
Blood Urea Nitrogen
Creatinine/blood

@article {pmid40557789,
year = {2025},
author = {Jones, KS and Pilliod, DS and Aunins, AW},
title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.},
journal = {Molecular ecology},
volume = {34},
number = {14},
pages = {e70003},
doi = {10.1111/mec.70003},
pmid = {40557789},
issn = {1365-294X},
support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Pollination ; *Flowers/genetics ; Bees/genetics/classification ; *Biodiversity ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; Sequence Analysis, DNA ; *Insecta/genetics/classification ; },
abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Pollination
*Flowers/genetics
Bees/genetics/classification
*Biodiversity
*DNA, Environmental/genetics
*Arthropods/genetics/classification
Sequence Analysis, DNA
*Insecta/genetics/classification

@article {pmid40415184,
year = {2025},
author = {Sheyn, U and Poff, KE and Eppley, JM and Leu, AO and Bryant, JA and Li, F and Romano, AE and Burger, A and Barone, B and DeLong, EF},
title = {Mesoscale eddies shape Prochlorococcus community structure and dynamics in the oligotrophic open ocean.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf106},
pmid = {40415184},
issn = {1751-7370},
mesh = {*Prochlorococcus/genetics/classification/growth & development ; *Seawater/microbiology/chemistry ; Phylogeny ; Pacific Ocean ; Ecosystem ; Temperature ; *Microbiota ; Ecotype ; },
abstract = {Mesoscale eddies, horizontally rotating currents sometimes referred to as "ocean weather," influence open ocean macronutrient distributions, primary production, and microbial community structure. Such eddies impact ecosystems like the North Pacific Subtropical Gyre, where year-round thermal stratification limits the mixing of subsurface macronutrients with surface waters. Populations of the dominant primary producer Prochlorococcus in the North Pacific Subtropical Gyre consist of genetic variants with differential adaptive traits to light intensity, temperature, and macronutrient availability. How Prochlorococcus population variants respond to transient, localized environmental changes, however, remains an open question. Leveraging microbial community phylogenetic, metagenomic, and metatranscriptomic data, we report here a consistent, specific enrichment of Prochlorococcus high-light I ecotypes around the deep chlorophyll maximum (DCM) in cyclonic eddies, but not adjacent anticyclonic eddies. The shallower DCM depths of cyclones had lower temperatures, higher light intensities, and elevated nutrient concentrations compared to adjacent anticyclones, which favored Prochlorococcus high-light I ecotype proliferation. Prochlorococcus high-light I ecotypes in the cyclone DCM exhibited unique genetic traits related to nitrogen metabolism and were enriched in gene transcripts associated with energy production, cell replication, and proliferation. Prochlorococcus gene transcripts involved in amino acid transport, metabolism, and biosynthesis were also elevated in the cyclone. These results suggest the potential importance of nitrogen metabolism in Prochlorococcus high-light I ecotype proliferation in cyclonic eddies. Our findings demonstrate how mesoscale eddies shape microbial community structure in the oligotrophic ocean and how Prochlorococcus communities respond to short-term localized environmental variability.},
}

*Prochlorococcus/genetics/classification/growth & development
*Seawater/microbiology/chemistry
Phylogeny
Pacific Ocean
Ecosystem
Temperature
*Microbiota
Ecotype

@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology
Pregnancy
Adult
Cross-Sectional Studies
Metagenomics/methods
*Microbiota/genetics
*Abortion, Spontaneous/microbiology
Mouth Mucosa/microbiology
Metagenome
*Mouth/microbiology
Young Adult

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40621956,
year = {2025},
author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC},
title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70329},
doi = {10.1111/gcb.70329},
pmid = {40621956},
issn = {1365-2486},
support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; },
mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; },
abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.},
}

*Biofilms/growth & development
*Plastics
*Nitrogen Cycle
*Estuaries
Transcriptome
Nitrogen/metabolism
Ecosystem
Seawater/microbiology
Bacteria/metabolism/genetics
Gene Expression Profiling
Metagenome

@article {pmid40619813,
year = {2025},
author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT},
title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf323},
pmid = {40619813},
issn = {1477-4054},
support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; },
abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.},
}

Humans
*Dysbiosis/microbiology
*Systems Biology/methods
*Microbiota
Metagenomics
Metabolomics
Proteomics

@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@article {pmid40615957,
year = {2025},
author = {Durand, K and Ogier, JC and Nam, K},
title = {The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {413},
pmid = {40615957},
issn = {1471-2180},
support = {ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-001-01//Agence Nationale de la Recherche/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche,France/ ; Resistome//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification ; *DNA-Directed RNA Polymerases/genetics ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Computational Biology/methods ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Bacterial Proteins/genetics ; High-Throughput Nucleotide Sequencing/methods ; Shotgun Sequencing ; },
abstract = {BACKGROUND: The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated.

RESULTS: For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values ​​and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method.

CONCLUSIONS: These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.},
}

*DNA Barcoding, Taxonomic/methods
*Bacteria/genetics/classification
*DNA-Directed RNA Polymerases/genetics
*Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
Computational Biology/methods
Phylogeny
*Microbiota/genetics
Metagenomics/methods
Bacterial Proteins/genetics
High-Throughput Nucleotide Sequencing/methods
Shotgun Sequencing

@article {pmid40499078,
year = {2025},
author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z},
title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {24},
number = {7},
pages = {3429-3446},
doi = {10.1021/acs.jproteome.5c00108},
pmid = {40499078},
issn = {1535-3907},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Polymorphism, Single Nucleotide ; *Amino Acids/genetics ; Metagenome/genetics ; Inflammatory Bowel Diseases/microbiology/genetics ; Diabetes Mellitus, Type 1/microbiology/genetics ; Proteome/genetics ; },
abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Polymorphism, Single Nucleotide
*Amino Acids/genetics
Metagenome/genetics
Inflammatory Bowel Diseases/microbiology/genetics
Diabetes Mellitus, Type 1/microbiology/genetics
Proteome/genetics

@article {pmid40456384,
year = {2025},
author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P},
title = {Gut and oral microbial profile associations to oral cancer.},
journal = {Journal of dentistry},
volume = {160},
number = {},
pages = {105848},
doi = {10.1016/j.jdent.2025.105848},
pmid = {40456384},
issn = {1879-176X},
mesh = {Humans ; *Mouth Neoplasms/microbiology/pathology ; Saliva/microbiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; Aged ; *Microbiota ; *Gastrointestinal Microbiome ; Adult ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor/analysis ; },
abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n = 30) divided into three groups based on histology; Benign (B) (n = 15), Potentially Malignant (PM) (n = 8), and Malignant (M) (n = 7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.},
}

Humans
*Mouth Neoplasms/microbiology/pathology
Saliva/microbiology
Male
Female
Middle Aged
*Mouth/microbiology
Aged
*Microbiota
*Gastrointestinal Microbiome
Adult
Fusobacterium nucleatum/isolation & purification
Biomarkers, Tumor/analysis

@article {pmid40015949,
year = {2025},
author = {Hu, M and Xu, Y and Wang, Y and Huang, Z and Wang, L and Zeng, F and Qiu, B and Liu, Z and Yuan, P and Wan, Y and Ge, S and Zhong, D and Xiao, S and Luo, R and He, J and Sun, M and Zhuang, X and Guo, N and Cui, C and Gao, J and Zhou, H and He, X},
title = {Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway.},
journal = {Gut},
volume = {74},
number = {8},
pages = {1230-1245},
doi = {10.1136/gutjnl-2024-332891},
pmid = {40015949},
issn = {1468-3288},
mesh = {*Colorectal Neoplasms/metabolism/microbiology ; Animals ; Humans ; *Gastrointestinal Microbiome/physiology ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Muramic Acids/metabolism/pharmacology ; Male ; Signal Transduction ; Female ; Peptidoglycan/metabolism ; Disease Models, Animal ; Carcinogenesis ; Feces/chemistry/microbiology ; },
abstract = {BACKGROUND: Gut microbial metabolites are recognised as critical effector molecules that influence the development of colorectal cancer (CRC). Peptidoglycan fragments (PGFs) produced by microbiota play a crucial role in maintaining intestinal homeostasis, but their role in CRC remains unclear.

OBJECTIVE: Here, we aimed to explore the potential contribution of PGFs in intestinal tumourigenesis.

DESIGN: The relative abundance of peptidoglycan synthase and hydrolase genes was assessed by metagenomic analysis. Specific PGFs in the faeces and serum of CRC patients were quantified using targeted mass spectrometry. The effects of PGF on intestinal tumourigenesis were systematically evaluated using various murine models of CRC and organoids derived from CRC patients. Downstream molecular targets were screened and evaluated using proteome microarray, transcriptome sequencing and rescue assays.

RESULTS: Metagenomic analysis across seven independent cohorts (n=1121) revealed a comprehensive reduction in peptidoglycan synthase gene relative abundance in CRC patients. Targeted mass spectrometry identified significant depletion of a specific PGF, N-acetylmuramic acid (NAM) in CRC patients, which decreased as tumours progressed (p<0.001). NAM significantly inhibits intestinal tumourigenesis in various models, including Apc [Min/+], AOM/DSS-treated and MC38 tumour-bearing mice. Additionally, NAM inhibits the growth of patient-derived CRC organoids in a concentration-dependent manner. Mechanistically, NAM inhibits the activation of AKT1 by directly binding to it and blocking its phosphorylation, which is a partial mediator of NAM's anticancer effects.

CONCLUSION: The PGF NAM protects against intestinal tumourigenesis by targeting the AKT1 signalling pathway. NAM may serve as a novel potential preventive and therapeutic biomarker against CRC.},
}

*Colorectal Neoplasms/metabolism/microbiology
Animals
Humans
*Gastrointestinal Microbiome/physiology
Mice
*Proto-Oncogene Proteins c-akt/metabolism
*Muramic Acids/metabolism/pharmacology
Male
Signal Transduction
Female
Peptidoglycan/metabolism
Disease Models, Animal
Carcinogenesis
Feces/chemistry/microbiology

@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; },
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}

Humans
*Hepatic Encephalopathy/microbiology/etiology/blood
*Liver Cirrhosis/microbiology/surgery/complications
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Portasystemic Shunt, Transjugular Intrahepatic/adverse effects
Ammonia/blood
Aged

@article {pmid40570762,
year = {2025},
author = {Pateriya, D and Malwe, AS and Sharma, VK},
title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.},
journal = {Computers in biology and medicine},
volume = {195},
number = {},
pages = {110592},
doi = {10.1016/j.compbiomed.2025.110592},
pmid = {40570762},
issn = {1879-0534},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Machine Learning ; Deep Learning ; Algorithms ; },
abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.},
}

*Gastrointestinal Microbiome
Humans
*Colorectal Neoplasms/microbiology/diagnosis
*Machine Learning
Deep Learning
Algorithms

@article {pmid40615598,
year = {2025},
author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J},
title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23957},
pmid = {40615598},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; },
abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.},
}

*Wastewater/microbiology
*Transcriptome
Ecosystem
Fresh Water/microbiology
*Eukaryota/genetics

@article {pmid40615445,
year = {2025},
author = {Di Gloria, L and Casbarra, L and Lotti, T and Ramazzotti, M},
title = {Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23997},
pmid = {40615445},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Sewage/microbiology ; *Metagenome ; },
abstract = {Biological wastewater treatment processes, such as activated sludge (AS) and aerobic granular sludge (AGS), have proven to be crucial systems for achieving both efficient waste purification and the recovery of valuable resources like poly-hydroxy-alkanoates. Gaining a deeper understanding of the microbial communities underpinning these technologies would enable their optimization, ultimately reducing costs and increasing efficiency. To support this research, we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community designed to provide a simplified yet comprehensive representation of the complex microbial ecosystems found in AS and AGS. Particular attention was given to the misclassification of eukaryotes as bacteria and vice versa, as well as the occurrence of false negatives. Notably, Kaiju emerged as the most accurate classifier at both the genus and species levels, followed by RiboFrame and kMetaShot. However, our findings highlight the substantial risk of misclassification across all classifiers and databases, which could significantly hinder the advancement of these technologies by introducing noises and mistakes for key microbial clades.},
}

*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Sewage/microbiology
*Metagenome

@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics

@article {pmid40613164,
year = {2025},
author = {Zhang, QL and Dong, LL and Zhang, LL and Wu, YJ and Li, M and Bo, J and Wang, LL and Jing, Y and Dou, LP and Liu, DH and Gu, ZY and Gao, CJ},
title = {[Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {3},
pages = {738-744},
doi = {10.19746/j.cnki.issn.1009-2137.2025.03.017},
pmid = {40613164},
issn = {1009-2137},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/drug therapy/microbiology ; *Induction Chemotherapy ; Feces/microbiology ; Male ; Female ; Middle Aged ; },
abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.

METHODS: Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.

RESULTS: During chemotherapy, the gut microbiota α-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).

CONCLUSION: During induction chemotherapy in AML patients, gut microbiota α-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.},
}

Humans
*Gastrointestinal Microbiome
*Leukemia, Myeloid, Acute/drug therapy/microbiology
*Induction Chemotherapy
Feces/microbiology
Male
Female
Middle Aged

@article {pmid40604345,
year = {2025},
author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB},
title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70417},
doi = {10.1002/alz.70417},
pmid = {40604345},
issn = {1552-5279},
support = {U01AG061359/AG/NIA NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; //Vilas Early-Career Investigator Award/ ; #2023-00356//Swedish Research Council/ ; #2022-01018//Swedish Research Council/ ; #2019-02397//Swedish Research Council/ ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; //Bluefield Project/ ; //Cure Alzheimer's Fund/ ; //Olav Thon Foundation/ ; //Erling-Persson Family Foundation/ ; #FO2022-0270//Familjen Rönströms Stiftelse, Stiftelsen för Gamla Tjänarinnor, Hjärnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; },
abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) ε4 status+ vs APOE ε4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.},
}

Humans
*Alzheimer Disease/microbiology/pathology/cerebrospinal fluid
*Gastrointestinal Microbiome/physiology
Male
Female
Aged
Biomarkers/cerebrospinal fluid
Feces/microbiology
Metagenomics
Amyloid beta-Peptides/cerebrospinal fluid
Aged, 80 and over

@article {pmid40604089,
year = {2025},
author = {Das, B and Desai, M and Bhagora, NJ and Koringa, P and Pathan, M and Thakor, JC and Savaliya, FP and Adil, S and Hati, S},
title = {Influence of fermented whey protein fractions on the growth performance, haematological traits, serum biochemistry, faecal and caeca microbiota of broiler chickens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23678},
pmid = {40604089},
issn = {2045-2322},
mesh = {Animals ; *Chickens/growth & development/microbiology/blood ; *Whey Proteins/pharmacology/metabolism ; *Feces/microbiology ; Fermentation ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; *Cecum/microbiology ; Male ; Limosilactobacillus fermentum/metabolism ; Female ; },
abstract = {Nowadays researchers and consumers are concerned about antibiotic resistance in poultry products causing antibiotic-resistant pathogens. Here, we investigated the effects of fermented whey peptides (FWP) with Limosilactobacillus fermentum (M4) as a nutraceutical supplement on growth performance, blood parameters, relative organs, and metagenomic analysis of broiler chickens, aiming to develop substitute for antibiotics in poultry feeds. An active culture of Lactobacillus fermentum (M4, GenBank Accession Number: MF951096) was inoculated into sterilized cheese whey at a rate of 2% (v/v) (10[7] CFU/ml) and incubated at 37 °C for 48 h. Ninety-six one-day-old mixed-sex commercial broiler chicks were randomly assigned in a Completely Randomized Design (CRD) experiment with four treatments, each having four replicates of six broiler chickens (6 × 4 × 4). One millilitre of liquid FWP fractions (> 10 kDa, < 10 kDa, and < 3 kDa) was freshly prepared and administered daily to the respective groups along with the basal diet from the 8th to the 15th day. Our current study revealed that supplementation with FWPs to broiler diets had no significant (p < 0.05) impact on body weight and FCR but numerically FCR value was high in control group. Blood cholesterol was significantly reduced in FWP fed groups. FWP had no significant impact on various blood parameters but influenced leukocytes and platelets. Metagenomic analysis showed no significant differences in microbial proportions. Histological analysis revealed no organ toxicity. The current findings suggest that broiler diets can substitute FWP for antibiotics to improve the growth performance and birds' health, without posing any biohazards. Furthermore, FWPs provide a variety of health benefits, potentially improving the health of humans who consume broiler meat or eggs.},
}

Animals
*Chickens/growth & development/microbiology/blood
*Whey Proteins/pharmacology/metabolism
*Feces/microbiology
Fermentation
Animal Feed
*Gastrointestinal Microbiome/drug effects
Dietary Supplements
*Cecum/microbiology
Male
Limosilactobacillus fermentum/metabolism
Female

@article {pmid40604039,
year = {2025},
author = {Meng, K and Bao, Y and Chen, G and Qu, J and Liang, S and An, S and Chen, Y and Liu, X and Fu, X},
title = {Metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23298},
pmid = {40604039},
issn = {2045-2322},
support = {GNK2023ZX06//Guangxi Academy of Agricultural Science and Technology Development Project/ ; GK-AA22117015-3//the Guangxi Major Science and Technology Program/ ; GNK2021YT117//Guangxi Academy of Agricultural Sciences Basic Research Project/ ; 2019E016//Guangdong 3D Orthopedics Biomimetic Translational Medicine Engineering Technology Research Center/ ; },
mesh = {Animals ; *Aspartame/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Glioblastoma/pathology/genetics/microbiology ; Mice ; Disease Models, Animal ; *Metagenomics/methods ; Disease Progression ; Gene Expression Profiling ; *Transcriptome/drug effects ; *Brain Neoplasms/pathology/genetics/microbiology ; Humans ; Gene Expression Regulation, Neoplastic/drug effects ; Male ; Sweetening Agents/pharmacology ; },
abstract = {Aspartame, a widely used artificial sweetener, has been extensively studied for its potential health effects. Emerging evidence suggests that aspartame intake may directly impact the composition and function of the intestinal microbiota, which could subsequently influence the risk, progression, and treatment of glioblastoma multiforme (GBM) within the tumor microenvironment. However, it remains unclear whether aspartame intake affects intestinal flora, gene expression, and epigenetic regulation during tumor progression. To address these gaps in knowledge, we conducted a comprehensive metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model. Using a well-established mouse model and a rigorous metagenomics and transcriptomics approach, our results demonstrated that although the aspartame diet did not significantly affect tumor growth, it induced changes in the composition of the gut microbiota, particularly a decrease in the relative abundance of the Rikenellaceae family. Additionally, key N6-methyladenosine (m[6]A)-regulated genes, such as cyclin-dependent kinase inhibitor 1A (CDKN1A), MYC (myelocytomatosis) oncogene, and transforming growth factor-β (TGFB1), were significantly upregulated in GBM tumors exposed to aspartame. Notably, the expression of TGFB1 (transforming growth factor-β) suggested a critical role in the progression of GBM mediated by aspartame-induced m[6]A modifications. Our integrative analysis offered novel perspectives on the intricate interplay between dietary aspartame intake, gut microbiota, and tumor biology.},
}

Animals
*Aspartame/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Glioblastoma/pathology/genetics/microbiology
Mice
Disease Models, Animal
*Metagenomics/methods
Disease Progression
Gene Expression Profiling
*Transcriptome/drug effects
*Brain Neoplasms/pathology/genetics/microbiology
Humans
Gene Expression Regulation, Neoplastic/drug effects
Male
Sweetening Agents/pharmacology

@article {pmid40603380,
year = {2025},
author = {Wang, R and Wang, J and Wang, L and Cai, Y and Wang, Y and Luo, H and Chen, B and Chen, J and Fang, J and Song, Z},
title = {A novel eco-friendly Acinetobacter strain A1-4-2 for bioremediation of aquatic pollutants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23207},
pmid = {40603380},
issn = {2045-2322},
support = {2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; },
mesh = {*Acinetobacter/metabolism/genetics/isolation & purification/classification ; *Biodegradation, Environmental ; Animals ; *Water Pollutants, Chemical/metabolism ; Zebrafish ; Phylogeny ; Metagenomics ; },
abstract = {The increasing accumulation of hydrocarbons and aromatic compounds in aquatic ecosystems, stemming from anthropogenic activities, poses severe ecological challenges, including disrupting biodiversity and threatening human health through the food chain. This study presents Acinetobacter strain A1-4-2, isolated from a hairy crab farming base, which could represent a novel Acinetobacter species. The metagenomic analysis of approximately 12,000 publicly available datasets revealed that this novel Acinetobacter species is widely distributed across various environments, particularly in those with high organic matter content, such as sludge, feces, and wastewater. Strain A1-4-2 exhibited exceptional metabolic capabilities, effectively degrading a diverse range of substrates, including amino acids, organic acids, oils, n-alkanes, lignin, and aromatic monomers. Genomic analysis, coupled with biological experiments, revealed that strain A1-4-2 exhibited resistance to a very limited kind of antibiotics. Moreover, the strain's biosafety, affirmed through zebrafish toxicity assays, underscores its suitability for environmental release. Additionally, the feasibility of genetic manipulation of strain A1-4-2 gives it the potential to become a chassis cell, enabling it to degrade organic pollutants more efficiently through genetic engineering. Our findings elucidate the strain's genomic and metabolic attributes, offering insights into its biodegradation potentials and developing effective strategies for ecological restoration in face of pollution.},
}

*Acinetobacter/metabolism/genetics/isolation & purification/classification
*Biodegradation, Environmental
Animals
*Water Pollutants, Chemical/metabolism
Zebrafish
Phylogeny
Metagenomics

@article {pmid40555791,
year = {2025},
author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y},
title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.},
journal = {Nature microbiology},
volume = {10},
number = {7},
pages = {1684-1697},
pmid = {40555791},
issn = {2058-5276},
mesh = {*Ammonia/metabolism ; *Renal Insufficiency, Chronic/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Mice ; Humans ; Aged ; Aged, 80 and over ; Escherichia coli/genetics/metabolism ; Male ; Female ; Metagenome ; Kidney ; Mice, Inbred C57BL ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.},
}

*Ammonia/metabolism
*Renal Insufficiency, Chronic/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Mice
Humans
Aged
Aged, 80 and over
Escherichia coli/genetics/metabolism
Male
Female
Metagenome
Kidney
Mice, Inbred C57BL
Bacterial Proteins/genetics/metabolism

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {10},
number = {7},
pages = {1570-1580},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
mesh = {*Microbiota/genetics ; Humans ; Biomass ; *Metagenomics/methods/standards ; Specimen Handling/standards/methods ; *DNA Contamination ; Guidelines as Topic ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

*Microbiota/genetics
Humans
Biomass
*Metagenomics/methods/standards
Specimen Handling/standards/methods
*DNA Contamination
Guidelines as Topic

@article {pmid40387372,
year = {2025},
author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X},
title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {25},
pages = {e00862},
pmid = {40387372},
issn = {2198-3844},
support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; },
mesh = {*Selenium/metabolism ; *Cadmium/metabolism ; Rhizosphere ; *Microbiota/physiology/genetics ; Soil Microbiology ; *Brassica napus/metabolism/microbiology ; Soil/chemistry ; Plant Roots/metabolism/microbiology ; Metagenomics ; },
abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.},
}

*Selenium/metabolism
*Cadmium/metabolism
Rhizosphere
*Microbiota/physiology/genetics
Soil Microbiology
*Brassica napus/metabolism/microbiology
Soil/chemistry
Plant Roots/metabolism/microbiology
Metagenomics

@article {pmid40329496,
year = {2025},
author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B},
title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.},
journal = {Journal of forensic sciences},
volume = {70},
number = {4},
pages = {1261-1273},
pmid = {40329496},
issn = {1556-4029},
mesh = {Animals ; *Postmortem Changes ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Swine ; *Specimen Handling/methods ; *Immersion ; DNA, Bacterial ; *Water Microbiology ; Models, Animal ; *Bone and Bones/microbiology ; },
abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).},
}

Animals
*Postmortem Changes
RNA, Ribosomal, 16S/genetics
*Microbiota
Swine
*Specimen Handling/methods
*Immersion
DNA, Bacterial
*Water Microbiology
Models, Animal
*Bone and Bones/microbiology

@article {pmid40170447,
year = {2025},
author = {Veríssimo, J and Lopes-Lima, M and Amaral, F and Chaves, C and Fernandes, V and Kemanja, M and Teixeira, A and Martins, FMS and Beja, P},
title = {Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14082},
pmid = {40170447},
issn = {1755-0998},
support = {2020.03608.CEECIND//Fundação para a Ciência e a Tecnologia/ ; COVID/BD/152600/2022//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/133159/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund (ERDF)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; *Metagenomics/methods ; Mediterranean Region ; *Vertebrates/classification/genetics ; *Environmental Monitoring/methods ; },
abstract = {Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high- versus low-capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high-capacity filtration and sampling across multiple sites. Site-level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site-level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade-offs in different study systems.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
*Metagenomics/methods
Mediterranean Region
*Vertebrates/classification/genetics
*Environmental Monitoring/methods

@article {pmid40079420,
year = {2025},
author = {Jurburg, SD},
title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14102},
pmid = {40079420},
issn = {1755-0998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Metagenomics/methods
Microbiota
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid40071381,
year = {2025},
author = {da Silva, LP and Porto, M and Amorim, F and Beja, P and Mata, VA},
title = {Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14100},
doi = {10.1111/1755-0998.14100},
pmid = {40071381},
issn = {1755-0998},
support = {CEECIND/02064/2017//Fundação para a Ciência e a Tecnologia/ ; CEECIND/02547/2020//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1440/CP1646/CT0018//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund/ ; SR20/1575//British Ecological Society/ ; },
mesh = {*Chiroptera/physiology ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics/isolation & purification ; Feces/chemistry ; *Plants/genetics/classification ; *Diet ; *Metagenomics/methods ; Arthropods ; },
abstract = {DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.},
}

*Chiroptera/physiology
Animals
*DNA Barcoding, Taxonomic/methods
*DNA, Plant/genetics/isolation & purification
Feces/chemistry
*Plants/genetics/classification
*Diet
*Metagenomics/methods
Arthropods

@article {pmid40013331,
year = {2025},
author = {Standley, JM and Marcelino, J and Yu, F and Ellis, JD},
title = {A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14090},
doi = {10.1111/1755-0998.14090},
pmid = {40013331},
issn = {1755-0998},
support = {//University of Florida Entomology and Nematology Gahan Endowment/ ; //Clay County Beekeepers Association/ ; 1019945//USDA/NIFA Multi-State Project/ ; AP22PPQS&T00C189//USDA/APHIS Cooperative Agreement/ ; },
mesh = {Animals ; Bees/microbiology/virology/metabolism ; *Metagenomics/methods ; *Fatty Acids/metabolism ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Virome ; High-Throughput Nucleotide Sequencing ; },
abstract = {Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.},
}

Animals
Bees/microbiology/virology/metabolism
*Metagenomics/methods
*Fatty Acids/metabolism
*Microbiota
Bacteria/classification/genetics/isolation & purification
Virome
High-Throughput Nucleotide Sequencing

@article {pmid40603374,
year = {2025},
author = {Guta, M and Van Eenooghe, B and Bacha, K and Cools, P},
title = {Bacterial community profile of three Ethiopian hot springs based on 16S rRNA gene nanopore sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23491},
pmid = {40603374},
issn = {2045-2322},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; Ethiopia ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Nanopore Sequencing/methods ; Biodiversity ; },
abstract = {Ethiopia harbors a number of hot springs not yet well explored or studied using a metagenomic approach to reveal their bacterial diversity. Understanding the bacterial diversity of these ecosystems is valuable for uncovering their ecological roles and potential for biotechnological applications. The aim of this study was, therefore, to perform the first full-length 16S rRNA gene nanopore sequencing on the three Ethiopian hot springs, namely Shalla, Woliso and Wondo Genet. The bacterial community composition of the three hot springs, whose temperatures ranged from 45 to 96 °C, was effectively assessed using the ONT MinION sequencer. It was found that Shalla hot spring had the highest species richness and accounted for 323 species, followed by 116 species from Woliso and 54 species from Wondo Genet hot springs. Pseudomonadota and Bacillota were the most dominant phyla recovered from the three hot springs, whereas Acinetobacter and Paracoccus were the most abundant bacterial genera. The most abundant species were Alkalihalobacterium elongatum from Shalla hot spring, and Acinetobacter junii and Acinetobacter johnsonii from Wondo Genet hot spring. Our study provided the first insight into the bacterial diversity of three Ethiopian hot springs and may serve as a basis for further functional analysis of these hot springs.},
}

*RNA, Ribosomal, 16S/genetics
*Hot Springs/microbiology
Ethiopia
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Nanopore Sequencing/methods
Biodiversity

@article {pmid40603287,
year = {2025},
author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC},
title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6099},
pmid = {40603287},
issn = {2041-1723},
support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; },
abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.},
}

Humans
*Breast Feeding
*Bifidobacterium/physiology/genetics
*Gastrointestinal Microbiome/genetics/drug effects
Infant
Female
Infant, Newborn
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Cesarean Section
Metagenome
Adult
Male
Milk, Human/microbiology
Feces/microbiology

@article {pmid40602621,
year = {2025},
author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X},
title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70139},
doi = {10.1111/1758-2229.70139},
pmid = {40602621},
issn = {1758-2229},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.},
}

*Geologic Sediments/microbiology/chemistry
*Salinity
*Bacteria/classification/genetics/isolation & purification/metabolism
Estuaries
China
Biodiversity
Microbiota
Ecosystem
Metagenome
Phylogeny

@article {pmid40601719,
year = {2025},
author = {Wanjiru, T and Bulimo, W and Langat, S and Kinyua, J and Odemba, N and Yalwala, S and Oullo, D and Ochieng, R and Ngere, F and Kerich, G and Ambale, J and Achieng, E and Abuom, D and Egbo, T and Johnson, J and Ojwang, E and Eads, J and Garges, E and Eyase, F},
title = {Vertical transmission of Dengue virus type-3 and metagenomic virome profiles of Aedes aegypti mosquitoes collected in Kisumu, Kenya.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0315492},
doi = {10.1371/journal.pone.0315492},
pmid = {40601719},
issn = {1932-6203},
mesh = {Animals ; *Aedes/virology ; Kenya ; *Dengue Virus/genetics/isolation & purification/classification ; *Virome/genetics ; *Mosquito Vectors/virology ; *Infectious Disease Transmission, Vertical ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Dengue/transmission/virology ; Metagenome ; Female ; },
abstract = {Aedes aegypti is the main vector of several arboviruses including chikungunya, dengue, yellow fever and Zika. Beyond arboviruses, Aedes aegypti harbours insect-specific viruses (ISVs), which can modulate mosquito's ability to transmit diseases by interfering with viral processes and triggering immune responses. Both arboviruses and ISVs can be transmitted vertically, where viruses are passed from parent to offspring. The lack of systematic molecular and entomological surveillance, has left the diversity of viruses in local Aedes aegypti populations largely unexplored. This study aimed to characterize the viromes of Aedes aegypti mosquitoes from Kisumu, Kenya, focusing on viral diversity. Immature larvae and pupae were collected from Jua Kali area in Kisumu, reared into adults, and subjected to viral isolation by cell culture and metagenomic next-generation sequencing. RNA extraction, library preparation, and Illumina MiSeq sequencing were performed on CPE positive pools and metagenomic superpools. Initial data analysis was conducted using the CZ-ID platform, with quality control applied using PrinseqLite v0.20.4 to filter low-quality reads and remove adapters. De novo sequence assembly was performed with MEGAHIT v1.2.9, followed by BLAST analysis. Phylogenetic relationships were analyzed using the Maximum Likelihood method. A total of 2,142 female Aedes aegypti, grouped into 86 pools and 4 superpools, were analyzed using cell culture and metagenomic next-generation sequencing respectively. Dengue virus type-3 was detected in one of the 86 pool. Additionally, a variety of ISVs were identified, including Iflaviruses related to Tesano Aedes Iflavirus (TeAV), Armigeres Iflavirus, and Negeviruses related to Rabai Virus. An unclassified virus closely related to Korle-Bu Aedes virus was also detected. Our study provides insights into the viral diversity within Aedes aegypti mosquitoes in Kisumu and evidence of natural vertical transmission, specifically transovarial transmission of dengue virus type-3. Ongoing research is imperative to unravel vertical transmission mechanisms and subtleties governing ISV-arbovirus interactions across diverse environmental settings.},
}

Animals
*Aedes/virology
Kenya
*Dengue Virus/genetics/isolation & purification/classification
*Virome/genetics
*Mosquito Vectors/virology
*Infectious Disease Transmission, Vertical
Metagenomics
High-Throughput Nucleotide Sequencing
Phylogeny
Dengue/transmission/virology
Metagenome
Female

@article {pmid40601568,
year = {2025},
author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS},
title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325380},
doi = {10.1371/journal.pone.0325380},
pmid = {40601568},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; },
abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.

METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.

RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.

CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.},
}

Humans
*Microbiota/genetics
Male
*Skin/microbiology
*Elephantiasis, Filarial/microbiology
Adult
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Case-Control Studies
*Lymphedema/microbiology
Pilot Projects
Skin Microbiome

@article {pmid40599650,
year = {2025},
author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA},
title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1522970},
pmid = {40599650},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.

OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.

METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.

RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.

CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.

CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.},
}

Humans
*Dental Caries/diagnosis/microbiology
Child
*Biomarkers/analysis
*Metagenomics/methods
Saliva/microbiology
Female
Male
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid40598608,
year = {2025},
author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW},
title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {133},
pmid = {40598608},
issn = {1297-9716},
support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.},
}

Animals
*Sheep Diseases/parasitology/microbiology/immunology
Sheep
*Trichostrongylosis/veterinary/parasitology/immunology
*Trichostrongylus/physiology
*Escherichia coli/physiology
*Gastrointestinal Microbiome
Disease Susceptibility/veterinary/parasitology/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid40598319,
year = {2025},
author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C},
title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {155},
pmid = {40598319},
issn = {2049-2618},
support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; },
mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.},
}

Phylogeny
*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
Metagenomics/methods
*Data Mining/methods
Metagenome
Biodiversity
RNA, Ribosomal, 16S/genetics
Ecosystem
Sequence Analysis, DNA

@article {pmid40597620,
year = {2025},
author = {Yang, L and Yan, Y and Shen, J and Xia, Y and Lang, F and Chen, C and Zou, W},
title = {Metagenomic insights into microbial community succession and its functional changes during the stage of acetic acid fermentation of shanxi aged vinegar.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {374},
pmid = {40597620},
issn = {1471-2180},
support = {20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; },
mesh = {*Acetic Acid/metabolism ; Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Acetobacter/metabolism/genetics ; Metabolic Networks and Pathways ; *Microbiota/genetics ; Food Microbiology ; Metagenome ; },
abstract = {Traditional fermentation of Shanxi aged vinegar involves complex microbial interactions driving flavor synthesis, but the mechanisms underpinning metabolic adaptation and community succession remain poorly characterized. This study aimed to unravel stage-specific microbial dynamics and their functional contributions to flavor formation during Cupei fermentation. Metagenomic sequencing analyzed microbial communities and metabolic pathways at three fermentation stages (D3, D6, D9). Functional annotation (KEGG, CAZy) and species-level contribution assessments identified key taxa and genes linked to flavor biosynthesis. Microbial succession shifted from Lactobacillus dominance (64.68% at D3) to Acetobacter prevalence (48.04% at D9), with Lactobacillus acetotolerans persisting throughout (17.15-26.23%). Early-stage carbohydrate metabolism (GHs-driven: 60.38% at D3) transitioned to late-stage amino acid (15.62%) and cofactor synthesis (12.17%), activating valine, leucine, and histidine pathways critical for flavor compounds. Acetobacter oryzoeni and Acetobacter pomorum drove acetate (ALDH: 27.07-41.52%), valine (ilvE: 53.21-20.22%), and histidine (hisD: 41.83-33.30%) metabolism at D9. Low abundance species (Weissella confusa, 0.51%) and uncultured Limosilactobacillus sp. contributed via multi-gene networks (e.g., dat, ldh), which revealed an important functional contribution by overlooked low-abundance species. The study uncovers ecological coupling between microbial succession and metabolic adaptation, where dominant taxa and rare species synergistically govern flavor formation. These insights enable targeted microbial community design for flavor optimization in traditional fermented foods.},
}

*Acetic Acid/metabolism
Fermentation
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
Acetobacter/metabolism/genetics
Metabolic Networks and Pathways
*Microbiota/genetics
Food Microbiology
Metagenome

@article {pmid40597414,
year = {2025},
author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R},
title = {Microbiome-based therapeutics towards healthier aging and longevity.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {75},
pmid = {40597414},
issn = {1756-994X},
mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; },
abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.},
}

Humans
*Longevity
*Gastrointestinal Microbiome
*Healthy Aging
*Aging
*Microbiota
Animals

@article {pmid40597307,
year = {2025},
author = {Wang, Z and Wang, W and Wang, Y and Hu, H and Wang, B and Zhu, W and Li, X and Hou, X and Sun, W and Liu, Z and Lu, S and Chen, X},
title = {Mapping gut microbiota and metabolite alterations in patients with postmenopausal osteoporosis in the Beijing Community of China.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {539},
pmid = {40597307},
issn = {2047-783X},
support = {No.2020YFC2004900//National Key Research and Development Program of China/ ; H0608//National Natural Science Foundation of China/ ; No.81672201, 81871794//Natural Science Foundation of China/ ; No.7242065//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology ; Middle Aged ; Aged ; Bone Density ; Beijing ; China ; Feces/microbiology ; },
abstract = {INTRODUCTION: Postmenopausal osteoporosis (PMO) is a chronic disease in the elderly women, which has been shown to be related to the gut microbiota (GM) alternation in recent studies. Few studies have investigated which specific bacterial species and metabolites have an impact on postmenopausal osteoporosis patients, especially in urban communities.

METHODS: With the aim of comprehending GM features and metabolite variation in women suffering from PMO in the Beijing Community of China, we divided the 76 eligible participants into osteoporosis (OP) and health control (HC) groups taking into account the bone mineral density (BMD), and adopted 16 S rRNA gene sequencing and metagenomic sequencing to examine the GM compositions in the respective groups. Besides, the study adopted liquid chromatography and mass spectrometry (LC-MS) for the fecal metabolite analysis.

RESULTS: The OP group presented obviously changed bacterial α-diversity and β-diversity versus the HC group. GM at the genus level was differentially enriched in the OP or HC groups. Megamonas genus exhibited the strongest positive relevance to BMD and OC. Bacteroides genus had the strongest negative relevance to BMD and positive relevance to β-CTX. GM at the species level was also differentially enriched in OP or HC groups. After multiple linear regression analysis, Roseburia_intestinalis and Glycoursodeoxycholic acid were positively associated with BMD, hinting their beneficial effect in BMD. Corresponding signaling pathways also exhibited an obvious change, particularly in up-regulation Glycerol Phosphate Shuttle and down-regulation Malate-Aspartate Shuttle pathways.

CONCLUSIONS: According to the results of this study, GM and metabolites in women with PMO in the Beijing Community changed dramatically, which were significantly associated with BMD and bone turnover markers. Roseburia_intestinalis and Glycoursodeoxycholic acid levels were the most positively associated with BMD. All these assist in understanding the development mechanism of PMO from new perspectives and in developing novel therapeutic methods for improving bone health.},
}

Humans
Female
*Gastrointestinal Microbiome
*Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology
Middle Aged
Aged
Bone Density
Beijing
China
Feces/microbiology

@article {pmid40596882,
year = {2025},
author = {Hekker, MD and Platteel, TN and Venekamp, RP and Top, J and Geerlings, SE and Schultsz, C and de Vos, MGJ and van de Wijgert, JHHM},
title = {Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {822},
pmid = {40596882},
issn = {1471-2334},
support = {OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; },
mesh = {Humans ; Female ; *Urinary Tract Infections/microbiology/epidemiology ; *Postmenopause ; Prospective Studies ; Middle Aged ; Recurrence ; Vagina/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recurrent urinary tract infections (RUTI) are prevalent, particularly among postmenopausal women, and place a significant burden on the affected individuals and the healthcare system. While Escherichia coli is the primary cause of most UTIs in premenopausal women, this may not hold true for postmenopausal women. To facilitate development of novel diagnostics, preventive interventions, and clinical management of RUTI in postmenopausal women, it is essential to strengthen the biological evidence base.

METHODS: This observational prospective cohort study will enrol 20 postmenopausal women without RUTI (controls) and approximately 30 with RUTI (cases), aiming to sample at least 50 UTI episodes. Questionnaires are completed, samples (urine, vulvoperineal and vaginal swabs, and faeces) are collected by participants or study staff at five scheduled time points over one year of follow-up, as well as during and after each UTI episode. All samples will undergo 16S rRNA amplicon sequencing, with selected urine samples also subjected to bacterial culturing, metagenomic sequencing, and metabolomics. Various urobiome comparisons will be conducted, such as between women with and without RUTI in the absence of a UTI, and over time during UTIs. Urobiomes will also be compared to vaginal, vulvoperineal, and gut microbiomes in the same women at the same time points. Finally, urine samples will be cultured to obtain bacterial isolates, which will be characterised and used for co-culture and urothelium organoid experiments.

DISCUSSION: The UTIr cohort study is an exploratory, hypothesis-generating study designed to improve understanding of the ecological mechanisms driving UTI onset, response to antibiotic treatment, and UTI recurrence in postmenopausal women. The data collected from each individual woman is longitudinal and comprehensive, which is instrumental for advancing the field. The study population consists of women over the age of 50 and the study procedures are demanding. Flexibility with protocol procedures has proven to be essential to maximise retention and minimise missing data. We recommend employing a sufficiently large recruitment team and/or planning for a sufficiently long recruitment period to accommodate the demanding nature of these types of in-depth studies with vulnerable populations.

TRIAL REGISTRATION: Not applicable.},
}

Humans
Female
*Urinary Tract Infections/microbiology/epidemiology
*Postmenopause
Prospective Studies
Middle Aged
Recurrence
Vagina/microbiology
*Microbiota
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid40596159,
year = {2025},
author = {Bayatian, M and Pourbabaee, AA and Amoozegar, MA},
title = {Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22016},
pmid = {40596159},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Petroleum/metabolism ; Soil/chemistry ; *Microbiota ; Petroleum Pollution ; Iran ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {This study explores prokaryotic diversity and oil biodegradation potential in soils from three evaporation ponds in the Ahvaz and Maroon oil fields, Iran. Despite prior studies on prokaryotic diversity in contaminated soils, systematic comparisons within the same region remain limited. The analysis identified distinct physicochemical differences across sites. Ahvaz 1 soil, with a loamy silty clay texture, had the highest salinity (15.4%) and total petroleum hydrocarbons (TPH, 3.5%). Ahvaz 4 soil, loamy silty in texture, showed 7.49% salinity and 1% TPH, while Maroon 3 soil exhibited the lowest salinity (5.06%) and TPH (0.5%). Prokaryotic diversity and biodegradation traits were assessed using 16S rRNA next-generation sequencing (NGS) and qPCR, respectively. NGS revealed reduced prokaryotic diversity in all contaminated soils, with Bacillota dominating, whereas Pseudomonadota prevailed in all control samples. Maroon 3 soils had higher diversity, but Cyanobacteria and Actinomycetota, dominant in controls, were replaced by Chloroflexota, Gemmatimonadota, and Acidobacteriota in polluted soils. At the genus level, Bacillus, Lysinibacillus, Virgibacillus, Brevibacillus, and Paenibacillus showed increased abundance in contaminated soils. Real-time PCR of alkB and C23DO genes indicated enhanced hydrocarbon degradation potential. FAPROTAX and PICRUSt2 analyses revealed enhanced microbial capacity for hydrocarbon degradation in polluted soils, with enriched functions related to chemoheterotrophy, aromatic compound degradation, and increased levels of alkane 1-monooxygenase, alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase subunits. The findings highlight crude oil's impact on microbial community structure, reducing archaea and emphasizing bacterial dominance while underscoring shifts in microbial responses and functional gene expression in hydrocarbon degradation.},
}

*Soil Microbiology
*Hydrocarbons/metabolism
Biodegradation, Environmental
*Bacteria/genetics/classification/metabolism
*Soil Pollutants/metabolism
RNA, Ribosomal, 16S/genetics
*Petroleum/metabolism
Soil/chemistry
*Microbiota
Petroleum Pollution
Iran
High-Throughput Nucleotide Sequencing
Phylogeny

@article {pmid40595658,
year = {2025},
author = {Zhang, Z and Liu, Y and Zhao, W and Liu, K and Chen, Y and Wang, F and Mao, G and Ji, M},
title = {Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5926},
pmid = {40595658},
issn = {2041-1723},
support = {42421001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42330410//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20176//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Tibet ; *Nitrogen Cycle/genetics ; *Ice Cover/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Metagenome/genetics ; Climate Change ; Bacteria/genetics/metabolism/classification ; Temperature ; Nitrous Oxide/metabolism ; Nitrogen Fixation/genetics ; Transcriptome ; },
abstract = {The Tibetan Plateau (TP) glaciers are influenced by monsoon and westerlies. They are highly sensitive to climate change, with atmospheric nitrogen deposition significantly impacting microbial communities and functions. However, key uncertainties persist regarding biogeography and drivers of genes and microbial communities involved in nitrogen cycling. Here, we investigate the diversity and transcriptional activity of microbial communities and nitrogen-cycling genes using 85 metagenomes and 28 metatranscriptomes from the ablation zone of 21 TP glaciers. Our results show that over 90% of the glacial taxa possess the potential for nitrogen metabolism, with ~33% exhibiting transcriptional activity. Moreover, monsoon-dominated glaciers present greater microbial diversity and higher prevalence of nitrogen-fixing genes than westerlies-dominated glaciers, linked to higher temperatures. Comparatively, the latter show elevated genomic potential for nitrous oxide emissions, likely due to higher nitrate concentrations. These findings establish temperature-nitrogen co-regulation of microbial nitrogen transformations, critical for predicting climate feedback in the extreme environment.},
}

Tibet
*Nitrogen Cycle/genetics
*Ice Cover/microbiology
*Microbiota/genetics
Nitrogen/metabolism
Metagenome/genetics
Climate Change
Bacteria/genetics/metabolism/classification
Temperature
Nitrous Oxide/metabolism
Nitrogen Fixation/genetics
Transcriptome

@article {pmid40595444,
year = {2025},
author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B},
title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {970},
pmid = {40595444},
issn = {2399-3642},
support = {1R35GM155208-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; },
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.},
}

*Gastrointestinal Microbiome
Humans
*Sweetening Agents/metabolism
*Fructose/metabolism
Adult
*Clostridium/genetics/enzymology/metabolism

@article {pmid40595004,
year = {2025},
author = {Raina, TK and Gupta, M and Salgotra, RK},
title = {Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22864},
pmid = {40595004},
issn = {2045-2322},
mesh = {*Oryza/microbiology/genetics ; *Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Odorants/analysis ; Microbiota ; },
abstract = {The captivating aroma of basmati rice is highly favoured by consumers across the globe. Unfortunately, the aroma of basmati rice has been gradually diminishing over time due to the excessive use of inorganic fertilizers and the impact of climate change. To understand the microbial community that plays a significant role in aroma enhancement in basmati rice accessions, a systematic study is required. A unique rhizobacteria of basmati rice associated with basmati rice were Actinobacteria, Bacillus subtilis, Burkholderia, Enterobacter, Klebsiella, Lactobacillus, Micrococcus, Pseudomonas, and Sinomonas. The biosynthesis of potential precursors (ornithine, putrescine, proline, and polyamines) of aroma in basmati rice involved various enzymes such as acetylornithine aminotransferase, acetylornithine deacetylase, N-acetylornithine carbomyltransferase, acetylornithine/succinyldiaminopimelate aminotransferase, and ornithine cyclodeaminase. These findings significantly contribute to the existing understanding of the rhizobacteria associated with basmati rice that play a crucial role in enhancing the aroma. The introduction of these cultures into the basmati rice growing areas has the potential to augment the plant growth and enhances the aroma. The present study explored the functional potential of the microbial community associated with aroma improvement in basmati rice. This will also enhance the export potential of the basmati rice in the region on sustainable basis.},
}

*Oryza/microbiology/genetics
*Rhizosphere
*Metagenomics/methods
Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
Odorants/analysis
Microbiota

@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}

*Solanum lycopersicum/microbiology/genetics
*Microbiota/genetics
Soil Microbiology
Rhizosphere
Ecuador
Plant Roots/microbiology
Biodiversity
*Adaptation, Physiological
Phylogeny

@article {pmid40594317,
year = {2025},
author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D},
title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20549},
pmid = {40594317},
issn = {2045-2322},
support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Pancreatitis/microbiology
Male
Female
Middle Aged
Adult
Aged
Acute Disease
Bacteria/genetics/classification

@article {pmid40593979,
year = {2025},
author = {Chen, L and Chen, H and Lv, T and Guo, X and Wu, W and Zhao, D and Liu, F},
title = {Differences of the respiratory microbiota between children suffering from community acquired pneumonia with presence or absence of asthma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20458},
pmid = {40593979},
issn = {2045-2322},
mesh = {Humans ; *Asthma/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia/microbiology/complications ; Infant ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Adolescent ; Community-Acquired Pneumonia ; },
abstract = {Recent advancements in respiratory microbiota research have progressively elucidated their pivotal role in pediatric respiratory pathologies. Alterations in airway microbial communities are intricately associated with diverse respiratory conditions and distinct disease states. This study conducted a comparative analysis of respiratory microecological profiles in pediatric cohorts diagnosed with community-acquired pneumonia (CAP), stratified by the presence or absence of comorbid bronchial asthma, from whom nasopharyngeal aspirates were obtained for metagenomic next-generation sequencing (mNGS). Analyses revealed comparable alpha-diversity indices between groups; however, beta-diversity metrics demonstrated marked compositional divergence. In the asthma-CAP cohort, Streptococcus pneumoniae and Rothia mucilaginosa emerged as predominant taxa, whereas Mycoplasmoides pneumoniae and Trichoderma citrinoviride dominated microbial profiles in uncomplicated CAP patients.},
}

Humans
*Asthma/microbiology/complications
*Community-Acquired Infections/microbiology/complications
*Microbiota
Male
Female
Child
Child, Preschool
*Pneumonia/microbiology/complications
Infant
High-Throughput Nucleotide Sequencing
Metagenomics
Adolescent
Community-Acquired Pneumonia

@article {pmid40593735,
year = {2025},
author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC},
title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {121},
pmid = {40593735},
issn = {2055-5008},
support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; },
abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.},
}

Female
Humans
Infant
Infant, Newborn
Pregnancy
*Bifidobacteriales Infections/transmission/microbiology
*Bifidobacterium/classification/genetics/isolation & purification
Gastrointestinal Microbiome
*Infectious Disease Transmission, Vertical
Metagenomics
Mothers
Vagina/microbiology

@article {pmid40593262,
year = {2025},
author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C},
title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21436},
pmid = {40593262},
issn = {2045-2322},
support = {81903340//National Natural Science Foundation of China/ ; },
mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; },
abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).},
}

Child
Female
Humans
Male
*Blood Proteins/metabolism
Feces/microbiology
*Gastrointestinal Microbiome
*Insulin Resistance
Metagenomics/methods
*Pediatric Obesity/microbiology/blood/metabolism
Proteomics/methods

@article {pmid40593012,
year = {2025},
author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S},
title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21245},
pmid = {40593012},
issn = {2045-2322},
support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; },
mesh = {*Benzoquinones/administration & dosage/pharmacology ; *Lactams, Macrocyclic/administration & dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; },
abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.},
}

*Benzoquinones/administration & dosage/pharmacology
*Lactams, Macrocyclic/administration & dosage/pharmacology
Animals
*Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism
*HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism
Mice
Humans
Disease Models, Animal
Administration, Topical
*Skin/drug effects/pathology/microbiology
Female
Cytokines/metabolism
Eosinophils/drug effects/metabolism
Gastrointestinal Microbiome/drug effects
Staphylococcus aureus/drug effects
Inflammation/drug therapy
Keratinocytes/drug effects/metabolism

@article {pmid40592825,
year = {2025},
author = {Mali, N and Mali, S and Zhang, L and Fu, P},
title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522976},
pmid = {40592825},
issn = {1525-6049},
mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; },
abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.},
}

Humans
*Acute Kidney Injury/microbiology/immunology/physiopathology
*Gastrointestinal Microbiome/immunology/physiology
Kidney/physiopathology/microbiology
Animals

@article {pmid40497681,
year = {2025},
author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J},
title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0057325},
pmid = {40497681},
issn = {2165-0497},
support = {OPP1019093//Bill and Melinda Gates Foundation/ ; },
mesh = {Humans ; *Feces/microbiology ; *Shigella/genetics/isolation & purification/pathogenicity/classification ; *Dysentery, Bacillary/microbiology/diagnosis ; Child, Preschool ; *Diarrhea/microbiology ; Infant ; Virulence Factors/genetics ; Female ; Male ; *Gastrointestinal Microbiome ; Child ; Developing Countries ; },
abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.},
}

Humans
*Feces/microbiology
*Shigella/genetics/isolation & purification/pathogenicity/classification
*Dysentery, Bacillary/microbiology/diagnosis
Child, Preschool
*Diarrhea/microbiology
Infant
Virulence Factors/genetics
Female
Male
*Gastrointestinal Microbiome
Child
Developing Countries

@article {pmid40494644,
year = {2025},
author = {Ma, R and Shi, Y and Wu, W and Huang, C and Xue, F and Hou, R and Zhou, Y and Gu, J and Feng, F and Yu, X and Liu, J and Li, Z and Zhang, L and Lan, G and Chen, C and Bi, W and Song, X and Fu, M and Yang, H and Gu, H and Yang, J and Qi, D},
title = {The bacterial diversity and potential pathogenic risks of giant panda-infesting ticks.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0219724},
pmid = {40494644},
issn = {2165-0497},
support = {U21A20193//National Natural Science Foundation of China/ ; 32400405//National Natural Science Foundation of China/ ; 2023NSFSC1156//Sichuan Science and Technology Program/ ; 2024NSFSC0023//Sichuan Science and Technology Program/ ; 2023-YF09-00017-SN//Chengdu Science and Technology Bureau/ ; 2024CPB-A23, 2024CPB-Y05, CAZG2025C13//Chengdu Giant Panda Breeding Research Foundation/ ; },
mesh = {Animals ; *Ursidae/parasitology/microbiology ; Female ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; RNA, Ribosomal, 16S/genetics ; Male ; *Ticks/microbiology ; *Tick Infestations/veterinary/parasitology/microbiology ; Seasons ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Microbiota ; },
abstract = {UNLABELLED: As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations.

IMPORTANCE: Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.},
}

Animals
*Ursidae/parasitology/microbiology
Female
*Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects
RNA, Ribosomal, 16S/genetics
Male
*Ticks/microbiology
*Tick Infestations/veterinary/parasitology/microbiology
Seasons
Metagenomics
Anti-Bacterial Agents/pharmacology
Microbiota

@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0145924},
pmid = {40488467},
issn = {2165-0497},
support = {2024YFC3506300, 2024YFC3506303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Prediabetic State/microbiology/metabolism ; *Metabolomics/methods ; *Gastrointestinal Microbiome/genetics ; Male ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Blood Glucose ; Multiomics ; },
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}

Humans
*Prediabetic State/microbiology/metabolism
*Metabolomics/methods
*Gastrointestinal Microbiome/genetics
Male
Diabetes Mellitus, Type 2/microbiology/metabolism
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenome
Blood Glucose
Multiomics

@article {pmid40488405,
year = {2025},
author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H},
title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40488405},
issn = {1751-7370},
mesh = {*Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Carbon Cycle ; *Lakes/microbiology ; Photosynthesis ; Oxidation-Reduction ; Hydrogen/metabolism ; *Microbiota ; Phototrophic Processes ; *Nutrients/metabolism ; },
abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolism found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.},
}

*Archaea/metabolism/genetics/classification
*Bacteria/metabolism/genetics/classification
Carbon Cycle
*Lakes/microbiology
Photosynthesis
Oxidation-Reduction
Hydrogen/metabolism
*Microbiota
Phototrophic Processes
*Nutrients/metabolism

@article {pmid40407311,
year = {2025},
author = {Li, H and Wang, Z and He, S and Zhao, X and Wu, Q and Sun, Y and Fan, Y and Hu, X and Tian, Z and Zhang, S},
title = {Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0230224},
pmid = {40407311},
issn = {2165-0497},
support = {20220484031//Beijing Nova Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Male ; Female ; Middle Aged ; *Amyloid Neuropathies, Familial/microbiology/metabolism ; Aged ; *Metabolome ; Taurine/blood/metabolism ; gamma-Aminobutyric Acid/blood ; Bacteria/classification/genetics/metabolism/isolation & purification ; Glutamic Acid/metabolism ; Adult ; Metagenomics ; },
abstract = {UNLABELLED: Hereditary transthyretin amyloidosis (hATTR) is a rare, often fatal disease characterized by the abnormal aggregation of atypical transthyretin fibrils. Given the variability in the penetrance and clinical manifestations of hATTR, the role of nongenetic factors, particularly those related to the gut microbiota, warrants investigation. We conducted a cross-sectional study, examining the untargeted serum metabolome and gut metagenome in 13 patients with hATTR and 22 healthy controls. Significant disparities were observed in both the serum metabolome and gut microbiome of individuals with hATTR when compared to healthy controls. Notably, the serum levels of gamma-aminobutyric acid (GABA) and taurine were markedly decreased in the hATTR group, with the most pronounced reduction in those exhibiting hATTR-related cardiac amyloidosis. Additionally, commensals such as Bifidobacterium pseudocatenulatum, Lactobacillus rogosae, and Hungatella hathewayi were significantly diminished in hATTR patients and were positively correlated with the metabolite module containing GABA and taurine. Metagenomic and metabolomic pathway enrichment analyses collectively revealed disruptions in glutamate and taurine metabolism in hATTR. Our findings imply that patients with hATTR may exhibit metabolic irregularities in glutamate and taurine, potentially associated with an imbalance in the gut microbiota.

IMPORTANCE: Hereditary transthyretin amyloidosis (hATTR) is influenced not only by genetic factors but also by environmental or host factors during its onset and progression. Previous studies have independently examined the metabolome or gut microbiome in hATTR, but the interplay between the microbiota and metabolism under this condition remains largely unknown. Our cross-sectional study represents the first comprehensive integration of gut metagenome and serum metabolome analyses in hATTR patients. We observed disturbances in glutamate and taurine metabolism among these patients, which correlated with distinctive shifts in the gut microbiota. This study offers insights into the intricate dynamics among gut dysbiosis, metabolic imbalances, and the progression of hATTR, suggesting directions for future research into the underlying mechanisms and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome
Cross-Sectional Studies
Male
Female
Middle Aged
*Amyloid Neuropathies, Familial/microbiology/metabolism
Aged
*Metabolome
Taurine/blood/metabolism
gamma-Aminobutyric Acid/blood
Bacteria/classification/genetics/metabolism/isolation & purification
Glutamic Acid/metabolism
Adult
Metagenomics

@article {pmid40151093,
year = {2025},
author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J},
title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.},
journal = {Journal of basic microbiology},
volume = {65},
number = {7},
pages = {e70024},
doi = {10.1002/jobm.70024},
pmid = {40151093},
issn = {1521-4028},
support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; },
mesh = {*Quorum Sensing/physiology ; *Homoserine/analogs & derivatives/metabolism ; *Lactones/metabolism ; Humans ; *Signal Transduction ; Bacterial Proteins/metabolism/genetics ; *Bacteria/metabolism/genetics/classification ; Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.},
}

*Quorum Sensing/physiology
*Homoserine/analogs & derivatives/metabolism
*Lactones/metabolism
Humans
*Signal Transduction
Bacterial Proteins/metabolism/genetics
*Bacteria/metabolism/genetics/classification
Gastrointestinal Microbiome
Metagenomics

@article {pmid40015361,
year = {2025},
author = {Liu, W and Geng, Y and Wang, Y and Zhao, J and Fan, Y and Zhang, X and Xie, W and Zhang, L and Zhang, Z},
title = {Evolution of gut microbiota in psoriatic arthritis treated with IL-17 inhibitor revealed by metagenomics.},
journal = {Joint bone spine},
volume = {92},
number = {4},
pages = {105868},
doi = {10.1016/j.jbspin.2025.105868},
pmid = {40015361},
issn = {1778-7254},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; *Arthritis, Psoriatic/drug therapy/microbiology/diagnosis ; *Interleukin-17/antagonists & inhibitors ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Feces/microbiology ; Treatment Outcome ; Adult ; Aged ; },
abstract = {OBJECTIVES: To explore the evolution of gut microbiota in taxonomy and function in PsA patients during IL-17i treatment.

METHODS: Twenty PsA patients treated with secukizumab were included. Fecal samples were collected before treatment (0 mo.), first month (1 mo.) and third month (3 mo.) after treatment, and a total of 60 samples were collected. Shotgun metagenomic sequencing was used to detect all fecal samples.

RESULTS: In the 1 mo. and 3 mo. after IL-17i treatment, the disease activity in PsA patients decreased significantly. Compared with 0 mo., α-diversity calculated by Shannon index and Pielou index increased significantly at 1 mo. and 3 mo. after treatment. Microbial genes encoding Carbohydrate-Active enZymes (CAZymes) tended to be upregulated after treatment. After treatment, Bacteroidota phylum expanded, especially the abundance of Phocaeicola genus increased gradually with the treatment time (P<0.05). The abundance of Phocaeicola genus was positively correlated with the α-diversity. The Polysaccharide Lyases and Carbohydrate Esterases in CAZymes were significantly positively correlated with most of species in Phocaeicola genus.

CONCLUSIONS: Treatment with IL-17i induces gut microbiota evolution in PsA patients. The key features of this evolution include increased α-diversity, expansion of the Phocaeicola genus, and upregulation of CAZymes. Species within the Phocaeicola genus may be the critical bacteria driving this evolution.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Male
*Metagenomics/methods
Female
Middle Aged
*Arthritis, Psoriatic/drug therapy/microbiology/diagnosis
*Interleukin-17/antagonists & inhibitors
*Antibodies, Monoclonal, Humanized/therapeutic use
Feces/microbiology
Treatment Outcome
Adult
Aged

@article {pmid40591379,
year = {2025},
author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG},
title = {[Microbiota of the ocular surface in children with myopia].},
journal = {Vestnik oftalmologii},
volume = {141},
number = {3},
pages = {5-12},
doi = {10.17116/oftalma20251410315},
pmid = {40591379},
issn = {0042-465X},
mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; },
abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.

PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.

MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.

RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.

CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.},
}

Humans
Child
*Myopia/diagnosis/microbiology/physiopathology
Male
Female
Adolescent
*Microbiota
*Conjunctiva/microbiology
*Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Disease Progression

@article {pmid40589860,
year = {2025},
author = {Nimnoi, P and Pongsilp, N},
title = {Insights into the metagenomic and metabolomic compositions of the bacterial communities in Thai traditional fermented foods as well as the relationships between food nutrition and food microbiomes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19606},
pmid = {40589860},
issn = {2167-8359},
mesh = {*Fermented Foods/microbiology ; Thailand ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenomics ; Metabolomics ; Fermentation ; },
abstract = {Five Thai traditional fermented foods, including khao-mak (sweet fermented sticky rice), pak-kard-dong (sour salt-fermented mustard greens), nor-mai-dong (sour salt-fermented bamboo sprouts), moo-som (sour salt-fermented pork), and pla-som (sour salt-fermented fish), were analyzed for their food nutrition and bacterial community structures. Sour salt-fermented bamboo sprouts possessed the highest unique amplicon sequence variables (ASVs), which were 3,476, as well as the highest bacterial diversity and richness, while in contrast, sweet fermented sticky rice possessed the lowest such indices. The phylum Firmicutes accounted for the largest proportions in both sour salt-fermented meats and sweet fermented sticky rice whereas the Proteobacteria occupied the largest proportions in both sour salt-fermented vegetables. The bacterial community structures of both sour salt-fermented meats were similar in terms of composition at class level, while the dominant genera compositions were totally different among all foods. Gene functions, enzymes, and metabolic pathways annotated from the bacterial communities in all foods were those involved in growth metabolisms, genetic information processing, environmental information processing, and cellular signaling. Sour salt-fermented bamboo sprouts had the highest numbers of unique annotated genes, enzymes, and metabolic pathways.},
}

*Fermented Foods/microbiology
Thailand
*Food Microbiology
*Bacteria/genetics/classification/metabolism
*Microbiota
Metagenomics
Metabolomics
Fermentation

@article {pmid40586794,
year = {2025},
author = {Chadd, EF and Ergunay, K and Kumsa, B and Bourke, BP and Broomfield, BS and Long, LS and Linton, YM},
title = {Nanopore sequencing reveals a diversity of microorganisms in ticks from Ethiopia.},
journal = {Parasitology research},
volume = {124},
number = {7},
pages = {73},
pmid = {40586794},
issn = {1432-1955},
support = {FY23 Award # 23-101//Deployed Warfighter Protection (DWFP) Program/ ; Award # P0031_21_WR//Armed Forces Health Surveillance Division/ ; },
mesh = {Animals ; Ethiopia ; *Nanopore Sequencing ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Ticks/microbiology ; Rickettsia/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; *Biodiversity ; },
abstract = {Ethiopia is home to a diverse group of ixodid ticks that are known to transmit disease to both animals and humans. Recent advances in metagenome sequencing show there is more microorganism diversity found in ticks than previously known. Compared to amplicon-based gene identification methods, agnostic metagenomic sequencing provides broader insights into the diversity of microorganisms in ticks, providing knowledge that will better enable public health measures in preventing the spread of zoonotic disease. In the present study, metagenomic sequencing was used to look at the microbial diversity of ticks collected from livestock in Ethiopia. This study identified six bacterial genera (Coxiella, Francisella, spotted-fever group (SFG) Rickettsia, Spiroplasma, Ehrlichia, and Borrelia), one genus of eukaryotic parasite (Babesia sp.), and one virus species (Parapoxvirus bovinestomatitis) from 154 tick pools representing 22 species of ticks among four genera (Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus). We were able to differentiate between pathogenic and nonpathogenic microorganisms, highlighting concerns among traditional gene-targeted screening methods. Among all pooled samples, the predominant microorganisms included Coxiella-like endosymbionts (55.2%), SFG Rickettsia (38.3%), and nonpathogenic Francisella spp. (26.0%). Rickettsia africae was the predominant pathogenic agent detected, and phylogenetic analysis of two samples from A. gemma and A. variegatum confirmed the presence of R. africae. This study highlights the power of metagenomics applied to potential vectors of zoonotic disease, and it expands the knowledge on tick-pathogen associations in Ethiopia.},
}

Animals
Ethiopia
*Nanopore Sequencing
Metagenomics
*Bacteria/genetics/classification/isolation & purification
*Ticks/microbiology
Rickettsia/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
Metagenome
Phylogeny
*Biodiversity

@article {pmid40523415,
year = {2025},
author = {Xu, Y and Ontita, NC and Zeng, W and Huang, J and Jiang, L and Huang, X and Li, Q and Hu, P},
title = {High-efficiency nitrogen removal by cold-tolerant bacteria consortium at low temperatures.},
journal = {Bioresource technology},
volume = {434},
number = {},
pages = {132816},
doi = {10.1016/j.biortech.2025.132816},
pmid = {40523415},
issn = {1873-2976},
mesh = {*Nitrogen/isolation & purification/metabolism ; *Cold Temperature ; Wastewater/chemistry ; *Bacteria/metabolism/genetics ; *Microbial Consortia/physiology ; Water Purification/methods ; },
abstract = {A cold-tolerant bacteria consortium (M2) was developed to enhance nitrogen removal efficiency in wastewater treatment processes operating at low temperatures (below 15 ℃). Bacteria consortium M2 demonstrated high removal efficiencies for nitrogen (NH4[+]-N, 97.34 %; NO3[-]-N, 97.13 %; NO2[-]-N, 59.92 %). Dominated by genera including Comamonas, Pseudomonas, and Acinetobacter, M2 produced substantial extracellular polymeric substances (EPS) and unsaturated fatty acids, which mitigated cold-induced stress. Metagenomic analysis revealed the presence of cold-shock responsive genes, including unsaturated fatty acid synthase, and cpsA, which contribute to its resilience under low-temperature conditions. Moreover, M2 enhanced both nitrogen assimilation and nitrate reduction under cold stress. These findings highlight the potential of M2 as an effective and practical strategy for improving nitrogen removal in wastewater treatment facilities during winter, thereby addressing a critical operational limitation in cold-climate regions.},
}

*Nitrogen/isolation & purification/metabolism
*Cold Temperature
Wastewater/chemistry
*Bacteria/metabolism/genetics
*Microbial Consortia/physiology
Water Purification/methods

@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
mesh = {Humans ; *Appendicitis/microbiology/pathology ; Child ; Male ; Female ; Child, Preschool ; Adolescent ; *Bacteria/classification/isolation & purification/genetics ; Acute Disease ; Severity of Illness Index ; C-Reactive Protein/analysis ; *Microbiota ; Appendectomy ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.

RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.

CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.},
}

Humans
*Appendicitis/microbiology/pathology
Child
Male
Female
Child, Preschool
Adolescent
*Bacteria/classification/isolation & purification/genetics
Acute Disease
Severity of Illness Index
C-Reactive Protein/analysis
*Microbiota
Appendectomy
Metagenomics
Dysbiosis/microbiology

@article {pmid40403370,
year = {2025},
author = {Liang, X and Li, B and Dong, X and Zhao, X and Li, H and Ye, Y and Ma, H and Ran, S and Li, J},
title = {Impact of microplastics exposure on the reconfiguration of viral community structure and disruption of ecological functions in the digestive gland of Mytilus coruscus.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138692},
doi = {10.1016/j.jhazmat.2025.138692},
pmid = {40403370},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; *Mytilus/virology/drug effects ; Animals ; Biofilms/drug effects ; *Water Pollutants, Chemical/toxicity ; Digestive System/virology/drug effects ; *Virome/drug effects ; *Viruses/genetics/drug effects ; },
abstract = {Microplastics (MPs) pose ecological risks by serving as viral vectors and disrupting host microbiomes. This study investigated the impact of MPs on the digestive gland virome of Mytilus coruscus through an in situ exposure experiment on Xixuan Island, Zhoushan, China, using polyethylene MPs and metagenomic sequencing. MPs biofilms were dominated by lytic viruses (> 99 %) with low diversity (Shannon index = 4.10 ± 0.39), whereas digestive glands harbored a more diverse virome (Shannon index = 7.26 ± 1.26). MPs ingestion significantly reduced virome diversity and altered viral community composition. Functional analysis showed that MPs biofilms were enriched in genes related to genetic processing, carbohydrate metabolism and membrane biogenesis, while transcription- and replication-related genes declined (P < 0.05) in digestive glands post-ingestion. MPs biofilms carried abundant antibiotic resistance genes (ARGs) and virulence factors, selectively enriching multidrug resistance genes (efrA, patB) while reducing functional viral gene abundance. Metal (Zn, Hg, As) and biocide resistance genes were prevalent in MPs biofilms but declined post-ingestion. Additionally, MPs ingestion weakened microbial network stability, potentially impairing immune regulation and metabolic homeostasis. These findings underscore MPs' role in shaping viral communities and spreading resistance genes, heightening ecological risks in marine environments.},
}

*Microplastics/toxicity
*Mytilus/virology/drug effects
Animals
Biofilms/drug effects
*Water Pollutants, Chemical/toxicity
Digestive System/virology/drug effects
*Virome/drug effects
*Viruses/genetics/drug effects

@article {pmid40378749,
year = {2025},
author = {Yu, YL and Lin, WH and Surampalli, RY and Chen, SC and Kao, CM},
title = {Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138628},
doi = {10.1016/j.jhazmat.2025.138628},
pmid = {40378749},
issn = {1873-3336},
mesh = {*Calcium Sulfate/chemistry ; *Fluorides/chemistry ; *Phosphates/metabolism/chemistry ; *Nitrogen/metabolism/chemistry ; *Water Pollutants, Chemical/chemistry/metabolism ; Groundwater/chemistry ; Microbiota ; Bacteria/metabolism/genetics ; },
abstract = {Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.},
}

*Calcium Sulfate/chemistry
*Fluorides/chemistry
*Phosphates/metabolism/chemistry
*Nitrogen/metabolism/chemistry
*Water Pollutants, Chemical/chemistry/metabolism
Groundwater/chemistry
Microbiota
Bacteria/metabolism/genetics

@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
mesh = {*Lakes/microbiology ; *Planktothrix ; Biomarkers ; Microbiota ; Nitrogen/metabolism ; Cyanobacteria ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S ; },
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}

*Lakes/microbiology
*Planktothrix
Biomarkers
Microbiota
Nitrogen/metabolism
Cyanobacteria
*Harmful Algal Bloom
RNA, Ribosomal, 16S

@article {pmid40339368,
year = {2025},
author = {Zhang, X and Liu, T and Sun, W and Zhang, C and Jiang, X and You, X and Wang, X},
title = {The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138440},
doi = {10.1016/j.jhazmat.2025.138440},
pmid = {40339368},
issn = {1873-3336},
mesh = {*Insecticides/toxicity ; *Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; *ortho-Aminobenzoates/toxicity ; Ecosystem ; Soil/chemistry ; Nitrogen/metabolism ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; },
abstract = {Diamide insecticides are the third most widely used class of pesticides worldwide. However, the long-term impacts of repeated diamide applications on soil ecosystems remain unclear. This study investigated chlorantraniliprole (CLP) and cyantraniliprole (CYP) effects on soil ecosystems through simulated repeated exposures. Results showed both exhibited slow degradation in the soil, with repeated applications extending their persistence, particularly for CLP. Both significantly inhibited soil alkaline nitrogen and organic matter accumulation, while reducing urease and sucrase activities, with CLP exerting stronger inhibitory effects. Metagenomic analysis indicated that CLP and CYP notably reduced soil microbial diversity. Additionally, the two insecticides altered the soil microbial community structure and inhibited carbon-nitrogen metabolic pathways. Further analysis revealed that CLP treatment significantly decreased the relative abundances of Mesorhizobium and Marmoricola, whereas CYP treatment primarily reduced Clostridium_sensu_stricto_1. All of these genera exhibited significant positive correlations with key metabolic pathways in soil carbon and nitrogen cycling. Notably, the relative abundance of Sphingomonas increased significantly following CLP and CYP treatments, demonstrating potential degradation capabilities. Overall, both CLP and CYP posed ecological risks to soil ecosystems, with CLP exhibiting more severe impacts. These findings revealed the need for strengthened scientific management in actual production.},
}

*Insecticides/toxicity
*Soil Microbiology
*Soil Pollutants/toxicity/analysis
*ortho-Aminobenzoates/toxicity
Ecosystem
Soil/chemistry
Nitrogen/metabolism
Bacteria/drug effects/genetics
Microbiota/drug effects

@article {pmid40304704,
year = {2025},
author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J},
title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.},
journal = {Molecular oral microbiology},
volume = {40},
number = {4},
pages = {137-146},
pmid = {40304704},
issn = {2041-1014},
support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; },
mesh = {*Biofilms ; *In Situ Hybridization, Fluorescence/methods ; *Mouth/microbiology ; Humans ; Microbiota/genetics ; Streptococcus/genetics/classification ; Species Specificity ; *Bacteria/classification/genetics ; },
abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.},
}

*Biofilms
*In Situ Hybridization, Fluorescence/methods
*Mouth/microbiology
Humans
Microbiota/genetics
Streptococcus/genetics/classification
Species Specificity
*Bacteria/classification/genetics

@article {pmid40156536,
year = {2025},
author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ},
title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.},
journal = {Australian veterinary journal},
volume = {103},
number = {7},
pages = {416-421},
doi = {10.1111/avj.13442},
pmid = {40156536},
issn = {1751-0813},
support = {DE200100367//Australian Research Council/ ; },
mesh = {Animals ; *Circovirus/genetics/isolation & purification ; *Genome, Viral ; *Bird Diseases/virology ; Phylogeny ; *Circoviridae Infections/veterinary/virology ; *Parakeets/virology ; *Parvovirus/genetics/isolation & purification ; Endangered Species ; Feces/virology ; *Parvoviridae Infections/veterinary/virology ; },
abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.},
}

Animals
*Circovirus/genetics/isolation & purification
*Genome, Viral
*Bird Diseases/virology
Phylogeny
*Circoviridae Infections/veterinary/virology
*Parakeets/virology
*Parvovirus/genetics/isolation & purification
Endangered Species
Feces/virology
*Parvoviridae Infections/veterinary/virology

@article {pmid40585302,
year = {2025},
author = {Louca, S},
title = {Machine learning models for delineating marine microbial taxa.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf090},
doi = {10.1093/nargab/lqaf090},
pmid = {40585302},
issn = {2631-9268},
mesh = {*Machine Learning ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Metagenome ; Phylogeny ; Genome, Bacterial ; *Aquatic Organisms/genetics/classification ; },
abstract = {The relationship between gene content differences and microbial taxonomic divergence remains poorly understood, and algorithms for delineating novel microbial taxa above genus level based on multiple genome similarity metrics are lacking. Addressing these gaps is important for macroevolutionary theory, biodiversity assessments, and discovery of novel taxa in metagenomes. Here, I develop machine learning classifier models, based on multiple genome similarity metrics, to determine whether any two marine bacterial and archaeal (prokaryotic) metagenome-assembled genomes (MAGs) belong to the same taxon, from the genus up to the phylum levels. Metrics include average amino acid and nucleotide identities, and fractions of shared genes within various categories, applied to 14 390 previously published non-redundant MAGs. At all taxonomic levels, the balanced accuracy (average of the true-positive and true-negative rate) of classifiers exceeded 92%, suggesting that simple genome similarity metrics serve as good taxon differentiators. Predictor selection and sensitivity analyses revealed gene categories, e.g. those involved in metabolism of cofactors and vitamins, particularly correlated to taxon divergence. Predicted taxon delineations were further used to de novo enumerate marine prokaryotic taxa. Statistical analyses of those enumerations suggest that over half of extant marine prokaryotic phyla, classes, and orders have already been recovered by genome-resolved metagenomic surveys.},
}

*Machine Learning
*Archaea/genetics/classification
*Bacteria/genetics/classification
Metagenome
Phylogeny
Genome, Bacterial
*Aquatic Organisms/genetics/classification

@article {pmid40580323,
year = {2025},
author = {Callejas, C and Guerrero, L and Erijman, L and López, I and Borzacconi, L},
title = {Microbiota and methanogenic activities in an anaerobic internal circulation reactor: insights into biogas production from brewery wastewater.},
journal = {Biodegradation},
volume = {36},
number = {4},
pages = {56},
pmid = {40580323},
issn = {1572-9729},
support = {2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; },
mesh = {*Bioreactors/microbiology ; *Methane/metabolism ; *Microbiota ; *Biofuels/microbiology ; *Wastewater/microbiology ; Anaerobiosis ; Archaea/metabolism/genetics/classification ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; },
abstract = {In this study, we analyzed the prokaryotic community and methanogenic activities in sludge samples collected from a full-scale internal circulation (IC) reactor used to treat brewery wastewater. The reactor performance was monitored over 15 months, and specific methanogenic activities were periodically measured in fresh sludge samples using CO2/H2 or acetate as substrates. The maximum hydrogenotrophic activities were consistently higher than maximum acetoclastic activities, suggesting the relevance of hydrogenotrophic methanogens in the sludge. Over six months, the prokaryotic community present in four sludge samples was analyzed using amplicon libraries and metagenomics. V4-16S rRNA amplicon libraries revealed the presence of a diverse microbial community dominated by Firmicutes and Bacteroidetes among bacterial phyla, and Halobacterota and Euryarchaeota among archaea. Furthermore, the 16S libraries constructed with cDNA were consistent with the methanogenic activity assays. A genome-centric metagenomics approach was used to assemble 42 high-quality metagenome-assembled genomes (MAGs), among which Methanothrix and Methanobacterium were the dominant archaeal members, and Acidobacteriota, Synergistota, Krumholzibacteriota, and Nitrospirota phyla were among the bacteria. Potential acetogenic members were explored via the fths gene; 15 MAGs contained this marker gene. A combination of methanogenic activity tests, amplicon libraries, and MAG analysis was used to gain insights into the prokaryotic structure and functional potential of the microbial community driving methane production in the reactor.},
}

*Bioreactors/microbiology
*Methane/metabolism
*Microbiota
*Biofuels/microbiology
*Wastewater/microbiology
Anaerobiosis
Archaea/metabolism/genetics/classification
Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
Sewage/microbiology

@article {pmid40580234,
year = {2025},
author = {Biessy, L and Sissons, J and Kihika, JK and Wood, SA and Pearman, JK},
title = {Microbial adaptations to acidic, nutrient- and metal-rich lakes in Aotearoa New Zealand.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {24},
pmid = {40580234},
issn = {1433-4909},
mesh = {*Lakes/microbiology/chemistry ; New Zealand ; *Microbiota ; *Adaptation, Physiological ; Geologic Sediments/microbiology ; *Metals/analysis ; Nutrients/analysis ; Bacteria/genetics/metabolism ; },
abstract = {Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.},
}

*Lakes/microbiology/chemistry
New Zealand
*Microbiota
*Adaptation, Physiological
Geologic Sediments/microbiology
*Metals/analysis
Nutrients/analysis
Bacteria/genetics/metabolism

@article {pmid40575481,
year = {2025},
author = {Chen, L and Li, Z and Yuan, D and Chen, Y and Xu, Y and Tang, W and Liu, C},
title = {Microorganism changes in the gut of Apis mellifera surviving for the long term in Camellia oleifera forests.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1608835},
pmid = {40575481},
issn = {2235-2988},
mesh = {Animals ; Bees/microbiology ; *Camellia ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Forests ; Metabolomics ; Metagenomics ; *Gastrointestinal Tract/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Alpha-galactosides (oligosaccharides) in C. oleifera nectar and pollen cause honey bee larval rot and worker bloats. Honey bee colonies surviving in C. oleifera forests for a long period have low rates of larval rot and worker bloats; however, the mechanism of oligosaccharide metabolism is unclear. In this study, we used metagenomics and metabolomics to investigate the structure and function of the gut flora and the digestion characteristics of oligosaccharides in the gut of A. mellifera foragers (CN group) that had been in the C. oleifera forest for a long period (continuously for 14 years), and those that had not been pollinated with C. oleifera (N group) after 24 h of consumption of C. oleifera honey. The results revealed that the abundance of Gilliamella apicola up to 24.08%, which can metabolize α-galactoside (α-Gal), was significantly higher (P < 0.05) in the gut of foragers in the CN group than in the N group. Additionally, the gut flora of foragers in the CN group carried a significantly higher (P < 0.05) abundance of genes encoding α-galactosidase (Glycoside hydrolase family 4, GH4) than the N group. Similarly, metabolomic results indicated that the three toxic oligosaccharides in C. oleifera honey were lower in the gut of CN group foragers. These results suggest that the gut flora of A. mellifera, which inhabits oil tea forests for long periods of time, changes and adapts to the predominant ecological niche, enhancing the host's ability to metabolize toxic oligosaccharides. This important discovery provides positive guidance for the subsequent directions for breeding of A. mellifera (G. apicola enrichment and GH4 upregulation), specialized in pollinating C. oleifera.},
}

Animals
Bees/microbiology
*Camellia
*Gastrointestinal Microbiome
Oligosaccharides/metabolism
Forests
Metabolomics
Metagenomics
*Gastrointestinal Tract/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40573768,
year = {2025},
author = {Giménez-Valero, C and Maciá-Vázquez, AA and Núñez-Gómez, D and Conesa, A and Lidón, V and Melgarejo, P},
title = {Evolution of the Soil Bacterial Community as a Function of Crop Management: A Metagenomic Study in Orange Tree (Citrus sinensis) Plantations.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121781},
pmid = {40573768},
issn = {2223-7747},
support = {AGROALNEXT program (AGROALNEXT 2022/013, SIRIS Project)//European Union/ ; },
abstract = {Soil management significantly influences the structure and diversity of soil bacterial communities, affecting biodiversity and ecosystem functions. In semi-arid regions, water efficiency strategies like anti-weed netting are implemented, but their impact on soil microbial communities remains underexplored. This study evaluates the temporal evolution of soil bacterial communities in orange tree (Citrus sinensis (L.) Osbeck) plantations under two conditions: with and without anti-weed netting. Soil samples were collected at three time points over a period of 18 months since the establishment of the crop and analyzed using high-throughput 16S rRNA sequencing, assessing alpha and beta diversity, taxonomic composition, and functional pathways via KEGG analysis. The results indicate that weed control netting contributes to stabilizing bacterial diversity over time and increases the relative abundance of dominant phyla such as Planctomycetota, Proteobacteria, Bacteroidota, and Acidobacteriota. Functional predictions revealed significant differences in metabolic pathways, including those associated with nitrogen fixation and organic matter degradation. These findings suggest that anti-weed netting not only influences the taxonomic composition of soil bacterial communities but also modulates their functional potential, with implications for sustainable agriculture in semi-arid environments. This study provides new insights into the interaction between soil management and soil bacterial communities, offering valuable information for optimizing agricultural practices and soil conservation strategies.},
}

@article {pmid40573403,
year = {2025},
author = {Zhang, X and Fan, IX and Xu, Y and Rule, J and Tse, LPV and Pourkarim, MR and Lee, WM and Di Bisceglie, AM and Fan, X},
title = {Novel Viral Sequences in a Patient with Cryptogenic Liver Cirrhosis Revealed by Serum Virome Sequencing.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060812},
pmid = {40573403},
issn = {1999-4915},
support = {1R21AI175438-24/NH/NIH HHS/United States ; },
mesh = {Humans ; *Liver Cirrhosis/virology ; *Virome/genetics ; Male ; Middle Aged ; Female ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Metagenomics ; Aged ; Sequence Analysis, DNA ; Adult ; *Serum/virology ; },
abstract = {Clinical studies indicate the etiology of liver disease to be unknown in 5% to 30% of patients. A long-standing hypothesis is the existence of unknown viruses beyond hepatitis A through E virus. We conducted serum virome sequencing in nine patients with cryptogenic liver disease and identified eight contigs that could not be annotated. One was determined to be a contaminant, while two of seven contigs from an individual (Patient 3) were validated by reverse transcription and polymerase chain reaction (RT-PCR) and Sanger sequencing. The possibility of contamination was completely excluded through PCR, with templates extracted using different methods from samples taken at different time points. One of the contigs, Seq260, was characterized as negative-sense single-stranded DNA via enzymatic digestion and genome walking. Digital-droplet PCR revealed the copy number of Seq260 to be low: 343 copies/mL. Seq260-based nested PCR screening was negative in 200 blood donors and 225 patients with liver disease with/without known etiologies. None of the seven contigs from Patient 3 was mapped onto 118,713 viral metagenomic data. Conclusively, we discovered seven unknown contigs from a patient with cryptogenic liver cirrhosis. These sequences are likely from a novel human virus with a negative-sense, linear single-stranded DNA genome.},
}

Humans
*Liver Cirrhosis/virology
*Virome/genetics
Male
Middle Aged
Female
*Viruses/genetics/classification/isolation & purification
Genome, Viral
Metagenomics
Aged
Sequence Analysis, DNA
Adult
*Serum/virology

@article {pmid40573349,
year = {2025},
author = {Hernández-Villegas, EN and Castelán-Sánchez, HG and Moreira-Soto, A and Vigueras-Galván, AL and Jiménez-Rico, MA and Rico-Chávez, O and Rodríguez-González, S and Tolsá-García, MJ and Roiz, D and Martínez-Duque, P and Arana-Guardía, R and García-Súarez, O and Jiménez, MZ and Falcón, LI and Roche, B and Sarmiento-Silva, RE and Arnal, A and Drexler, JF and Suzán, G},
title = {Characterization of the Virome in Mosquitoes Across Distinct Habitats in the Yucatán Peninsula, Mexico.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060758},
pmid = {40573349},
issn = {1999-4915},
mesh = {Animals ; Mexico ; *Culicidae/virology ; *Ecosystem ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Genome, Viral ; Biodiversity ; },
abstract = {Human activities and land use changes have a major impact on the distribution and diversity of mosquito vectors and their associated viruses. This study describes the diversity and differential abundance of viruses associated with mosquito species from four habitats of the Yucatan Peninsula, Mexico. Using next-generation sequencing (NGS), we analyzed 61 genomic libraries belonging to 20 mosquito species to characterize the viral community. A total of 16 viral species were identified, representing 14 different viral families. Most identified viruses were associated with insects, plants, and fungi. Additionally, vertebrate associated viral families, including Herpesviridae, Peribunyaviridae, Nairoviridae, and Arenaviridae, were detected in mosquitoes from urban habitats. Notably, insect-associated viruses like Hubei mosquito virus 4 and Hubei virga-like virus 2 were identified, along with the first report of Mercadeo virus in Mexico. Variations in viral community composition were primarily driven by mosquito species, with species of the same genus maintaining similar viromes despite occupying different habitats. These findings reinforce that intrinsic traits of mosquito species play a key role in shaping viral community composition. To our knowledge, this is the first study that describes the viral community in mosquitoes in Yucatan Peninsula, Mexico. This study provides essential baseline data for the surveillance of mosquitoes and associated viruses from a biodiverse tropical region that faces strong land use modifications.},
}

Animals
Mexico
*Culicidae/virology
*Ecosystem
*Virome
*Mosquito Vectors/virology
*Viruses/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Phylogeny
Genome, Viral
Biodiversity

@article {pmid40572043,
year = {2025},
author = {Yang, C and Sun, J and Li, L and Zheng, J and Wang, C and Zhao, Y and Yun, D and Jia, M and Wu, Z and Liang, H and Li, W and Hu, T and Guo, R and Xiao, L and Zou, Y and Liu, Z},
title = {Synbiotics of Lactobacillus suilingensis and inulin alleviates cognitive impairment via regulating gut microbiota indole-3-lactic acid metabolism in female AD mice.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70406},
doi = {10.1002/alz.70406},
pmid = {40572043},
issn = {1552-5279},
support = {2022ZD0208100//National Science and Technology Innovation 2030-Major Program of Brain Science and Brain-Like Research/ ; 32241012//National Natural Science Foundation of China/ ; 32472351//National Natural Science Foundation of China/ ; JCYJ20220818102810022//Shenzhen Science and Technology Program/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; 2022A1515110717//Regional Consolidated Fund-Youth Fund Project in Guangdong Province/ ; BGIRSZ20220009//open project of BGI-shenzhen/ ; //China Biotechnology Development Center/ ; //Shenzhen Science and Technology Innovation Commission/ ; //Shenzhen Municipal Government/ ; //Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Inulin/pharmacology/administration & dosage ; Female ; *Cognitive Dysfunction/metabolism ; Mice ; *Synbiotics/administration & dosage ; *Indoles/metabolism ; *Alzheimer Disease/metabolism ; Humans ; Tryptophan/metabolism ; Disease Models, Animal ; Receptors, Aryl Hydrocarbon/metabolism ; Probiotics ; },
abstract = {INTRODUCTION: Recent studies have found that gut microbial tryptophan metabolism is altered in Alzheimer's disease (AD) patients. However, the functional consequences of these changes and their therapeutic potential remain unclear.

METHODS: The metagenomic data of 49 preclinical AD patients and 115 healthy controls were analyzed. A synbiotic with targeted metabolic functions was formulated based on in vitro testing, and its effect on AD was evaluated using female 5×FAD mice.

RESULTS: Indole lactic acid (ILA) synthesis was downregulated in AD patients. Synbiotic treatment combining Lactobacillus suilingensis and inulin outperformed probiotic treatment alone in enhancing tryptophan metabolism, and increasing ILA biosynthesis. Increased ILA could reduce Aβ accumulation and significantly alleviate cognitive impairment in female AD mice by inhibiting neuroinflammation through activation of the aryl hydrocarbon receptor (AhR) signaling pathway.

DISCUSSION: This study highlights the therapeutic potential of targeting gut microbial tryptophan metabolism in AD and provides a rationale for future precision strategies aimed at modulating microbiota-derived metabolic pathways.

HIGHLIGHTS: Gut metagenomic analysis reveals reduced indole lactic acid (ILA) biosynthesis genes in preclinical AD patients. Screening and formulating ILA-producing synbiotic by using whole-genome analysis. Synbiotic treatment alleviates cognitive impairment and promotes ILA synthesis in female 5×FAD mice. ILA alleviates neuroinflammation in female 5×FAD mice by activating aryl hydrocarbon receptor (AhR) in the brain. Synbiotic targeting tryptophan metabolism provides a novel approach for Alzheimer's intervention.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Inulin/pharmacology/administration & dosage
Female
*Cognitive Dysfunction/metabolism
Mice
*Synbiotics/administration & dosage
*Indoles/metabolism
*Alzheimer Disease/metabolism
Humans
Tryptophan/metabolism
Disease Models, Animal
Receptors, Aryl Hydrocarbon/metabolism
Probiotics