@article {pmid40611965,
year = {2025},
author = {Ivanova, M and Aarestrup, FM and Otani, S},
title = {Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597804},
pmid = {40611965},
issn = {1664-302X},
abstract = {The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. Here, we evaluate how different multiplexing levels (four and eight samples per flowcell) on two ONT platforms, GridION and PromethION, influence the detection of ARGs, bacterial taxa and pathogens. While overall resistome and bacterial community profiles remained comparable across multiplexing levels, ARG detection was more comprehensive in the four-plex setting with low-abundance genes. Similarly, pathogen detection was more sensitive in the four-plex, identifying a broader range of low abundant bacterial taxa compared to the eight-plex. However, triplicate sequencing of the same microbiomes revealed that these differences were primarily due to sequencing variability rather than multiplexing itself, as similar inconsistencies were observed across replicates. Given that eight-plex sequencing is more cost-effective while still capturing the overall resistome and bacterial community composition, it may be the preferred option for general surveillance. Lower multiplexing levels may be advantageous for applications requiring enhanced sensitivity, such as detailed pathogen research. These findings highlight the trade-off between multiplexing efficiency, sequencing depth, and cost in metagenomic studies.},
}

@article {pmid40611959,
year = {2025},
author = {Qi, S and Qian, J and Li, Y and Li, Y and Li, W and Gao, X},
title = {Effect of acupuncture at Back-Shu points on gut microbiota in insomnia model rats based on metagenomic sequencing technology.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541958},
pmid = {40611959},
issn = {1664-302X},
abstract = {BACKGROUND: Increasing evidence indicates a bidirectional interaction between the gut microbiota and sleep regulation via the microbiota-gut-brain axis. Acupuncture is widely used to treat insomnia, and its efficacy may be mediated in part by modulation of the gut microbiota and its metabolic pathways.

METHODS: A rat model of insomnia was established by intraperitoneal injection of para-chlorophenylalanine (PCPA). Rats received acupuncture at Back-Shu points for 2 weeks. Sleep behavior was assessed using the pentobarbital-induced sleep test, and fecal samples were collected for metagenomic sequencing to analyze changes in gut microbial composition and function before and after acupuncture.

RESULTS: Compared with the model group, acupuncture significantly shortened sleep latency and prolonged sleep duration. Metagenomic analysis revealed that acupuncture partially restored the PCPA-induced decline in α-diversity and markedly altered β-diversity. Functionally, acupuncture enriched beneficial taxa such as Lactobacillus johnsonii and Ligilactobacillus murinus, and promoted pathways involved in tryptophan and glutamate metabolism as well as short-chain fatty acid (SCFA) synthesis. These changes may act by restoring neurotransmitter balance, strengthening gut barrier integrity, and modulating immune responses. Notably, SCFAs can activate G-protein-coupled receptors to suppress overactivation of the hypothalamic-pituitary-adrenal (HPA) axis, counteracting insomnia-related pathophysiology.

CONCLUSION: Acupuncture at Back-Shu points ameliorates PCPA-induced insomnia-like behavior in rats and beneficially remodels gut microbiota structure and metabolic function. These findings support a key role for the microbiota-gut-brain axis in acupuncture's regulation of sleep and provide a theoretical basis for developing microbiota-targeted adjunctive therapies for insomnia.},
}

@article {pmid40611899,
year = {2025},
author = {Pokharel, SK and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.19.660557},
pmid = {40611899},
issn = {2692-8205},
abstract = {A surge in sequenced myxobacteria catalyzed by advancements in long read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze eleven genera and 195 sequenced genomes including ten newly reported myxobacterial isolate, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient, sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium ; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.},
}

@article {pmid40611207,
year = {2025},
author = {Wang, Q and Zhang, M and Meng, M and Luo, Z and Pan, Z and Deng, L and Qin, J and Guo, B and Zhu, D and Zhang, Y and Guo, H and Liang, Y and Su, Z},
title = {Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {106},
pmid = {40611207},
issn = {1749-8546},
support = {82060763//National Natural Science Foundation of China/ ; GXFCDP-PS-2022//Guangxi First-class Discipline Project for Pharmaceutical Sciences/ ; GXQH202409//Guangxi Youth Qihuang Scholars Training Project/ ; },
abstract = {BACKGROUND: Bile acids and gut microbiota participate in the pathogenesis of liver fibrosis (LF). The total alkaloids of Corydalis saxicola Bunting (TACS) is a traditional Chinese medicine extract that has been used to treat LF, but the underlying mechanisms are not clear. This study performed integrated metabolomics and gut microbiome analysis to study the anti-LF mechanism of TACS using a rat model.

METHODS: Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to identify the chemical compounds in TACS. Biochemical and histopathological analysis were performed to determine the efficacy of TACS. Bile acid-targeted metabolomics was used to assess changes in the bile acid (BA) profiles in TACS-treated LF rats. 16S rRNA gene sequencing and metagenomics were used to assess changes in the gut microbiota of the TACS-treated LF rats. Antibiotic cocktail treatment and fecal microbiota transplantation (FMT) were used to determine the relationship between the gut microbiota and the anti-LF effects of TACS. Metagenomics was used to identify significantly enriched gut microbiota after TACS treatment and its correlation with the anti-LF effects was verified by in vivo experiments.

RESULTS: TACS treatment significantly reduced the levels of serum liver enzymes, fibrosis and pro-inflammatory cytokines in the liver. TACS significantly increased the levels of chenodeoxycholic acid (CDCA) and taurochenodeoxycholic acid (TCDCA) in the cecum and decreased the levels of cholic acid (CA) and deoxycholic acid (DCA) in the liver of the LF rats. TACS significantly increased the abundances of Lactobacillus and Akkermansia in the LF rats. Antibiotic cocktail treatment and FMT have shown that the effect of TACS cure liver fibrosis depends on the gut microbiota. The abundance of Lactobacillus reuteri was significantly increased by TACS. Administration of Lactobacillus reuteri via gavage ameliorated LF.

CONCLUSIONS: TACS exerted anti-LF effects in rats by modulating bile acid metabolism and gut microbiome.},
}

@article {pmid40610423,
year = {2025},
author = {Fuhrmeister, ER and Kim, S and Mairal, SA and McCormack, C and Chieng, B and Swarthout, JM and Paulos, AH and Njenga, SM and Pickering, AJ},
title = {Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5898},
pmid = {40610423},
issn = {2041-1723},
support = {OPP1129535//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; UL1TR002544//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1906957//National Science Foundation (NSF)/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; Animals ; Humans ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; Kenya ; Anti-Bacterial Agents/pharmacology ; Dogs ; *Bacteria/genetics/drug effects ; Klebsiella pneumoniae/genetics/drug effects ; Child ; Adult ; Escherichia coli/genetics/drug effects ; Poultry/microbiology ; beta-Lactamases/genetics ; Genome, Bacterial ; Haemophilus influenzae/genetics/drug effects ; },
abstract = {Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing blaTEM and blaCTX-M that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumoniae, and Haemophilus influenzae in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.},
}

*CRISPR-Cas Systems/genetics
Animals
Humans
*Nanopore Sequencing/methods
*Drug Resistance, Bacterial/genetics
Kenya
Anti-Bacterial Agents/pharmacology
Dogs
*Bacteria/genetics/drug effects
Klebsiella pneumoniae/genetics/drug effects
Child
Adult
Escherichia coli/genetics/drug effects
Poultry/microbiology
beta-Lactamases/genetics
Genome, Bacterial
Haemophilus influenzae/genetics/drug effects

@article {pmid40609888,
year = {2025},
author = {Maki, T and Takami, H and Pointing, S and Kurosaki, Y and Fukui, H and Bin, C and Kai, K},
title = {Bacterial stress adaptation and antibiotic resistance in dust-transportable bioaerosols originating from the Gobi Desert.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126759},
doi = {10.1016/j.envpol.2025.126759},
pmid = {40609888},
issn = {1873-6424},
abstract = {Airborne microorganisms which dispersed from the Gobi Desert throughout East Asia via long-range dust transports, are believed to maintain their viability against atmospheric stressors that influence ecosystem dynamics and human health during deposition in downwind environments. However, the adaptative mechanisms that facilitate microbial tolerance to environmental stressor, and the persistence of factors such as antibiotic resistance relevant to human health have not been determined. Here, we described the metagenomic and physiological interrogation of airborne bacteria collected from aerosols at an altitude of 500 m using a balloon-mounted sampler and at a parallel site 3 m above the ground in the dust-source region of Gobi Desert. The shotgun metagenomic DNA sequencing which determine was performed for characterizing the taxonomic compositions of airborne bacteria and their potential functions. The communities were dominated by species in the phyla Actinobacteria, Bacillota, Bacteroidota, and Pseudomonadota (Alpha). Metabolic-pathway analysis revealed that Gobi Desert bioaerosols were enriched in functions associated with antibiotic resistance, cell-membrane transporters, and/or environmental adaptation. The antibiotic and osmotic-change resistances were confirmed among viable bacteria isolates showing higher level of resistances in the aerosols collected at 500 m than those of 3 m. These findings suggest that elevated altitudes result in environmental filtering that allows bacterial taxa to survive long-term transport to distant locations during dust events and transfer antibiotic resistance.},
}

@article {pmid40609443,
year = {2025},
author = {Lu, B and Wang, P and Hu, J and Qian, J and Liu, F and He, Y and Tang, S and Shen, J and Liu, Y},
title = {PFOS-induced alterations in phosphorus dynamics and soil microbial functions in wetlands.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126445},
doi = {10.1016/j.jenvman.2025.126445},
pmid = {40609443},
issn = {1095-8630},
abstract = {Perfluorooctanesulfonate (PFOS), a widely persistent pollutant, poses significant ecological risks, yet its impact on critical nutrient cycles, such as phosphorus (P), in wetland ecosystems remains poorly understood. Phosphorus is essential for plant growth and microbial functions, and disruptions in its cycling can have profound effects on ecosystem stability. This study investigates the influence of PFOS on P dynamics and soil microbial functions in the rhizosphere of Phragmites communis. We examined how varying PFOS concentrations affect inorganic and organic P forms and microbial gene expression associated with P transformations. High PFOS concentrations significantly reduced shoot and root P content, corresponding to declines in labile phosphorus (NaHCO3-Pi). Additionally, shifts in microbial community diversity and composition were observed, particularly under high PFOS exposure, where key phosphorus-cycling genes, such as phoD in rhizosphere soils, showed significantly reduced transcriptional levels (as quantified by qRT-PCR), despite increased gene abundance as revealed by metagenomic sequencing. These findings offer new insights into how emerging contaminants like PFOS disrupt phosphorus cycling and microbial functions in wetland ecosystems, with broader implications for ecological risk assessments.},
}

@article {pmid40609272,
year = {2025},
author = {Ji, B and Chen, Q and Song, Y and Dong, Z and Ding, J and Wang, G and Liu, G and Gao, P and Zhao, J},
title = {Distributions of pathogenic bacteria, antibiotic resistance genes, and virulence factors in pig farms in China.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118607},
doi = {10.1016/j.ecoenv.2025.118607},
pmid = {40609272},
issn = {1090-2414},
abstract = {The abundance of antibiotic resistance genes (ARGs) in pig feces can lead to their dissemination in the pig farm environment, posing a serious risk to human health through potential exposure and transmission. However, the extent of microbial contamination in pig farms, including ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and human bacterial pathogens (HBPs), is still largely unknown. In this study, metagenomics was employed to identify the composition and characteristics of microorganism communities, ARGs, VFGs, MGEs and HBPs in pig farm environments from seven different regions of China. The results showed that there were significant differences in the composition of microorganisms and Firmicutes, Bacteroides, Proteobacteriahe Spirochaetes were the dominant phyla in the pig farm environment. The abundance and composition of ARGs, VFGs, MGEs and HBPs varied significantly in pig farm environments in different regions, with the abundance in Fujian being significantly higher than that in other regions. In total, 216 ARGs, 479 VFGs, 143 MGEs and 78 HBPs were identified across all pig feces, soil, and wastewater samples. The most prominent ARGs were those related to tetracycline, aminoglycoside, and MLS resistance. Escherichia coli, Arcobacter cryaerophilus, Corynebacterium xerosis, Aerococcus viridans, and Collinsella aerofaciens were the most commonly found HBPs in the pig farm environment. Procrustes analysis and Mantel test results showed a strong correlation between ARGs and HBPs, VFGs and HBPs, and ARGs and VFGs. ARGs were mainly harbored by E. coli, Klebsiella pneumoniae, and Enterococcus faecalis in the pig farm environments. The random forest model indicated that the presence of MGEs (intI1, IS91, and tnpA) was significantly correlated with the total abundance of resistance genes, which can be utilized as an important indicator for measuring resistance genes. The study establishes a foundational understanding of the prevalence and diversity of ARGs, VFGs, and HBPs in pig farm environments, aiding in the development of effective management strategies to mitigate ecological and public health risks.},
}

@article {pmid40609120,
year = {2025},
author = {Jiang, M and Xie, Z and Fan, Q and Tang, G and Pan, N and Zeng, H and Xu, Y and Zhang, C and Luo, M and Li, F},
title = {Epidemiological characteristics of Circovirus Human infection in hospitalized patients in a representative infectious disease hospital in Guangzhou, China, from Feb 2023 to Dec 2024.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {116962},
doi = {10.1016/j.diagmicrobio.2025.116962},
pmid = {40609120},
issn = {1879-0070},
abstract = {Circovirus Human reported in recent years have drawn attention as potential human pathogens in susceptible patients. However, its epidemiological characteristics are less investigated. We found 3 infected cases in 1330 hospitalized patients with suspected unidentified infections in a designated hospital for treating infectious diseases by retrospectively analyzing their metagenomic sequencing data. All three patients were HIV-positive and immunosuppressed. Liver function tests were normal at admission but showed transient acute injury during antimicrobial therapy, without hepatitis virus coinfection.},
}

@article {pmid40608709,
year = {2025},
author = {Jiang, L and Zhou, L and Huang, S and Ao, Z and Han, X},
title = {Venovenous extracorporeal membrane oxygenation in severe community-acquired Acinetobacter baumannii pneumonia.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {6},
pages = {971-976},
doi = {10.3855/jidc.19761},
pmid = {40608709},
issn = {1972-2680},
mesh = {Humans ; Male ; *Extracorporeal Membrane Oxygenation/methods ; Middle Aged ; *Acinetobacter baumannii/isolation & purification ; *Community-Acquired Infections/therapy/microbiology/diagnosis ; *Acinetobacter Infections/therapy/diagnosis/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/therapy/diagnosis/microbiology ; Treatment Outcome ; Respiratory Distress Syndrome/therapy ; Meropenem/therapeutic use ; Tigecycline ; },
abstract = {INTRODUCTION: Globally, Acinetobacter baumannii (A. baumannii) is a significant nosocomial pathogen. Community-acquired pneumonia (CAP) caused by A. baumannii is rare, but often associated with severe outcomes.

CASE PRESENTATION: A 48-year-old man was admitted to a local hospital, presenting a 14-hour history of acute fever, cough, expectoration, chest pain, and dyspnea. Owing to the development of severe acute respiratory distress syndrome (ARDS) and septic shock, the patient was promptly transferred to our institution for veno-venous extracorporeal membrane oxygenation (VV-ECMO) following intubation and mechanical ventilation. Sputum culture, digital polymerase chain reaction (dPCR) assay of blood, and metagenomic next-generation sequencing (mNGS) assay of bronchoalveolar lavage fluid (BALF) all indicated A. baumannii. The patient responded favorably to treatment with meropenem and tigecycline. The amelioration of his respiratory function allowed for the cessation of ECMO after 7 days; and subsequently, the patient was successfully weaned from ventilatory support.

CONCLUSIONS: A. baumannii should be considered as a possible causative organism of CAP based on presentation in the tropical or subtropical wet season, a very aggressive clinical course, typical chest imaging features, and the presence of A. baumannii in sputum. ECMO represents an efficacious treatment alternative for severe ARDS and septic shock complications associated with A. baumannii when conventional mechanical ventilation proves inadequate, particularly when initiated early in the clinical course.},
}

Humans
Male
*Extracorporeal Membrane Oxygenation/methods
Middle Aged
*Acinetobacter baumannii/isolation & purification
*Community-Acquired Infections/therapy/microbiology/diagnosis
*Acinetobacter Infections/therapy/diagnosis/microbiology
Anti-Bacterial Agents/therapeutic use
*Pneumonia, Bacterial/therapy/diagnosis/microbiology
Treatment Outcome
Respiratory Distress Syndrome/therapy
Meropenem/therapeutic use
Tigecycline

@article {pmid40608623,
year = {2025},
author = {Nascimento, GMD and Romano, CM and Rozanski, A and de Moura Coletti, T and Urbinatti, PR and Natal, D and Marrelli, MT and de Araújo, AB and Nardi, MS and da Costa, AC and Natal Fernandes, L},
title = {Detection of Furrundu phlebovirus in Aedes scapularis (Diptera: Culicidae) collected in urban parks, in a highly urbanized city.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {67},
number = {},
pages = {e38},
pmid = {40608623},
issn = {1678-9946},
mesh = {Animals ; *Aedes/virology ; Phylogeny ; Brazil ; *Phlebovirus/isolation & purification/genetics/classification ; Female ; *Mosquito Vectors/virology ; Parks, Recreational ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; },
abstract = {Mosquitoes (Diptera: Culicidae) are arthropods of medical importance because they can carry arboviruses. High-throughput sequencing (HTS) technology and metagenomic approaches conducted in mosquitoes have contributed to the discovery of many insect-specific viruses (ISVs), which have the potential to affect their vector competence. Mosquitoes were collected in urban parks in Sao Paulo city, Brazil and 20 pools with female mosquitoes were subjected to HTS by HiSeq 2500 sequencing system (Illumina). Long viral sequences (1,585-6,701 base pairs) were recovered from two pools of Aedes scapularis. BLASTx analyses revealed they had greater identity with segment L and S of Salarivirus and segment M of Furrundu phlebovirus, which encode, respectively, the RNA-dependent RNA polymerase (RdRd), the nucleocapsid protein, and a polyprotein. Phylogenetic tree of the segment L and S of the Phenuiviridae Family showed our sequences grouped with unverified sequences of Furrundu phlebovirus, an unclassified ISV that belongs to the Hareavirales Order and was first reported in mosquitoes in the Brazilian Pantanal, the largest natural tropical wetland worldwide. We report the second detection of Furrundu phlebovirus in mosquitoes collected in urban parks, showing it could be in mosquitoes from natural places and in green areas in urban cities. We conclude that Furrundu phlebovirus possibly occurs in Aedes scapularis in green areas, in Sao Paulo. Further studies should elucidate the role of this virus in the vector competence of Aedes scapularis and its interaction with different arboviruses.},
}

Animals
*Aedes/virology
Phylogeny
Brazil
*Phlebovirus/isolation & purification/genetics/classification
Female
*Mosquito Vectors/virology
Parks, Recreational
High-Throughput Nucleotide Sequencing
RNA, Viral/genetics

@article {pmid40608492,
year = {2025},
author = {Ozuru, R and Yamagishi, J and Takeuchi, A and Date, Y and Fujii, T and Sugimoto, C and Nakajima, C and Suzuki, Y and Aoki, K and Fujii, J and Matsuba, T},
title = {Unification of Symbiotic Bacteria During Larva-to-Adult Transition in Culicoides circumscriptus (Diptera: Ceratopogonidae).},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf069},
pmid = {40608492},
issn = {1574-6968},
abstract = {Blood-sucking midges such as Leptoconops and Culicoides are of medical importance due to their role in causing skin irritation and potentially transmitting pathogens. Investigating their bacterial communities, including possible endosymbionts, may help clarify ecological adaptations and interactions with hosts. Leptoconops nipponensis Tokunaga (Lnt) and Culicoides circumscriptus (Cc), blood-sucking midges, cause severe itching and inflammation in humans. Cc was collected from a small sample of an outbreak swarm of Lnt in the peninsula area of Yonago City, Tottori Prefecture, Japan. This study compared the bacterial flora of Lnt and Cc, revealing distinct bacterial diversity shifts in these insect species between life stages. We analyzed the bacterial communities of adult and larval females of Cc and Lnt using MiSeq sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Notably, alpha diversity in Cc adults was significantly reduced to 1.5 (n = 43), indicating that Cc adults were dominated by a single bacterial genus, compared to 14.9 in Cc larvae (n = 19). BLAST analysis identified this dominant genus in adult Cc as Rickettsia (Candidatus Tisiphisa), which is known for transovarial transmission in arthropod vectors. In contrast, the bacterial diversity of Lnt showed no significant difference between adults (18.1, n = 32) and larvae (n = 15). These findings suggest that the dominance of Rickettsia in Cc (Candidatus Tisiphisa) adults is linked to their emergence, potentially reflecting differences in reproductive biology and ecological adaptations between these two insect species. Further research is needed to elucidate the functional role of Rickettsia in the life cycle and physiology of Cc.},
}

@article {pmid40607849,
year = {2025},
author = {Zhang, H and Zhao, D and Wu, QL and Zeng, J},
title = {Environment selected microbial function rather than taxonomic species in a plateau saline-alkaline wetland.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0220624},
doi = {10.1128/aem.02206-24},
pmid = {40607849},
issn = {1098-5336},
abstract = {UNLABELLED: Comprehending the microbial community in plateau saline-alkaline wetlands, an understudied and vulnerable ecosystem, is vital for predicting ecosystem functions within the context of global climate change. Despite the rapid shrinkage and potential drying up of some of these wetlands, our knowledge of the microbial community in this ecosystem remains fragmented. Here, we utilized metagenomic sequencing to investigate the distribution of methane, nitrogen, and sulfur cycling genes/pathways and formation mechanism of microbial communities across sediment, surface rhizosphere soils (Rsurface), subsurface rhizosphere soils (Rsubsurface), surface bulk soils (Bsurface), and subsurface bulk soils (Bsubsurface) in Cuochuolong Wetland, a typical saline-alkaline wetland located in the Tibetan Plateau. The results showed that sediment exhibited relatively higher functional potentials for methanogenesis but lower potentials for methane oxidation. Denitrification and dissimilatory sulfate reduction potentials increased with decreasing salinity across the five habitats, following the trend: sediment
IMPORTANCE: Understanding the formation mechanism of microbial communities is a central goal in ecology. However, our understanding of microbial community remains fragmented in plateau saline-alkaline wetlands, despite their unique status as a vulnerable ecosystem characterized by high altitude, low disturbance, high salinity, sensitivity to global climate change, and localized shrinkage in some areas. Furthermore, previous studies on community formation mechanism have predominantly focused on microbial taxonomic structure, neglecting their functional compositions. Beyond providing a comprehensive understanding of the distribution patterns of methane, nitrogen, and sulfur cycling microbial communities within plateau saline-alkaline wetland, this study offers a novel perspective on formation mechanism of microbial community by emphasizing the deterministic selection of extreme environment on microbial function. This study also expands our comprehension of the diversity of microbes containing the nod gene, which may substantially contribute to global methane and nitrogen budgets.},
}

@article {pmid40607829,
year = {2025},
author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB},
title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0038025},
doi = {10.1128/msystems.00380-25},
pmid = {40607829},
issn = {2379-5077},
abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.},
}

@article {pmid40607500,
year = {2025},
author = {Luo, Y and Cheng, W and Ma, L and Wang, T and Shi, W},
title = {Diagnostic value of nanopore-based metagenomic third-generation sequencing in the diagnosis of Pneumocystis jirovecii infection in patients with lung cancer.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
pmid = {40607500},
issn = {1473-5644},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Pneumonia, Pneumocystis/diagnosis/microbiology/complications ; *Pneumocystis carinii/genetics/isolation & purification ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Prospective Studies ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Nanopore Sequencing/methods ; Adult ; Aged, 80 and over ; China ; },
abstract = {Introduction. Pneumocystis jirovecii pneumonia (PJP, formerly known as Pneumocystis carinii pneumonia), an opportunistic fungal infection caused by the fungus P. jirovecii, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.Gap Statement. Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.Aim. This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing P. jirovecii infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.Methodology. A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary P. jirovecii infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.Results. Metagenomics showed a significantly higher detection rate of P. jirovecii (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as Cytomegalovirus and Epstein-Barr virus.Conclusion. Metagenomics technology demonstrates high sensitivity and specificity in diagnosing P. jirovecii infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Pneumonia, Pneumocystis/diagnosis/microbiology/complications
*Pneumocystis carinii/genetics/isolation & purification
Male
Female
Middle Aged
*Metagenomics/methods
Aged
Prospective Studies
Sensitivity and Specificity
Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing
*Nanopore Sequencing/methods
Adult
Aged, 80 and over
China

@article {pmid40607081,
year = {2025},
author = {Zhang, Q and Teng, Z and Gong, P},
title = {A case of acute renal dysfunction and multiorgan dysfunction caused by Rickettsia japonica infection.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02283},
pmid = {40607081},
issn = {2214-2509},
abstract = {This article reports a case of acute renal dysfunction and multi-organ dysfunction syndrome caused by Rickettsia japonica infection. The patient, a 79-year-old male, presented with unexplained fever, fatigue, anorexia, vomiting, and chest tightness, followed by oliguria and a decline in mental status. Laboratory tests revealed significant abnormalities, including elevated white blood cells, thrombocytopenia, hepatic and renal dysfunction, and coagulopathy. Imaging studies showed pulmonary infection and bilateral pleural effusion. Based on the history of tick bite, clinical manifestations, and metagenomic next-generation sequencing (mNGS) results, which detected R. japonica, the patient was diagnosed with Japanese spotted fever (JSF). He received multidisciplinary comprehensive treatment, including mechanical ventilation, continuous renal replacement therapy (CRRT), antimicrobial therapy, blood transfusions, and supportive care. After 15 days of treatment, the patient's fever resolved, inflammatory markers decreased significantly, and organ functions improved gradually, leading to eventual recovery and discharge. This case highlights the importance of early recognition and treatment of R. japonica infection, especially in endemic areas, to prevent rapid deterioration and multi-organ failure.},
}

@article {pmid40606566,
year = {2025},
author = {Wang, L and Wang, L and Chen, L},
title = {NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {208-211},
pmid = {40606566},
issn = {2730-5848},
abstract = {UNLABELLED: Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00168-8.},
}

@article {pmid40606560,
year = {2025},
author = {Wang, H and Zhuang, Y and Hua, R and Yao, T and Lin, K and Zhang, Y and Huang, R and Wang, R and Guo, S and Shen, Q and Shao, Y and Wu, W and Fan, L and Feng, Y and Yao, Q and Ye, H and Kong, X and Zhang, Q and Wang, R and Liu, T},
title = {Multi-Omics Exploration of Obesity Biomarkers in Sedentary and Weight Loss Cohorts.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {137-153},
pmid = {40606560},
issn = {2730-5848},
abstract = {UNLABELLED: Sedentary behavior for two years during the coronavirus disease 2019 (COVID-19) pandemic contributes to weight gain. Gut microbiota and blood metabolome are related to body mass index (BMI) and indicate individual metabolic changes. Surgery and exercise are effective weight-loss methods. The precise plasma metabolites and gut microbiota biomarkers involved and the underlying mechanisms are still largely unclear. To address this issue, we analyzed weight gain and weight loss cohorts to identify biomarkers associated with obesity. In the sedentary cohort, 49 subjects were recruited in year 2019. After two years of sedentary behavior during the COVID-19 pandemic, the BMI of 24 subjects significantly increased (Weight gain group), while that of the remnant 25 subjects remained constant (Maintaining weight group). At baseline and two years post baseline, the gut microbiota and blood metabolome, as well as body composition and clinical indicators, were all collected. In weight loss studies, we analyze the plasma metabolome of the two cohorts, including individuals who underwent laparoscopic sleeve gastrectomy (LSG) surgery and exercise intervention. Weight gain through sedentary behavior contributed to the variation of the gut microbiota and plasma metabolites composition. Creatine, phenylalanine and tyrosine exhibited significant positive associations with BMI and fat mass. We further confirmed the association between BMI and plasma metabolites in two weight loss cohorts. By utilizing a linear regression model, we found that 10 metabolites including creatine were correlated with BMI in weight loss individuals. Based on receiver operating characteristic (ROC) curves, creatine exhibited a satisfactory classification performance in regard to predicting weight reduction (AUCLSG = 0.890, AUCS ports = 0.840). Moreover, some gut microbiota, including Bifidobacterium angulatum DSM 20098 = JCM 7096 and Rothia dentocariosa M567I could affect BMI through the mediating factor of creatine.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00165-x.},
}

@article {pmid40606175,
year = {2025},
author = {Wang, J and Zhu, Y and Li, D and Zheng, X and Chai, C and Zhang, J and Wu, J and Hu, Q and Zhao, S},
title = {The diversity of viral community in Sogatella furcifera revealed by meta-transcriptomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617239},
pmid = {40606175},
issn = {1664-302X},
abstract = {INTRODUCTION: Metagenomic analyses has significantly advanced our understanding of viral evolution and their functions within organismal biology. In particular, exploring the virome of agricultural pests like the white-backed planthopper (WBPH) is essential for understanding their role as potential virus vectors and developing effective pest management strategies.

METHODS: To explore viral diversity, we collected white-backed planthoppers (WBPHs) from nine sites spanning four Chinese provinces (Liaoning, Fujian, Guangxi, and Yunnan) and performed metagenomic sequencing.

RESULTS: Our analysis identified 11 novel viruses belonging to 7 viral families, encompassing positive-sense single-stranded RNA (+ssRNA), negative-sense single-stranded RNA (-ssRNA), and double-stranded RNA (dsRNA) viruses. Remarkably, eight of the southern Chinese sites, excluding one in Liaoning province, contained a previously undiscovered Sobelivirales virus. Using rapid-amplification of cDNA ends (RACE), we determined the complete genome sequence of this novel Sobelivirales virus. Subsequent analyses of its encoded proteins, potential structural domains, and phylogenetic relationships suggested that it may belong to a new genus within the Sobelivirales. Small RNA sequencing confirmed viral replication in WBPH by revealing that virus-derived small interfering RNAs (vsiRNAs) were primarily 21 and 22 nucleotides long.

DISCUSSION: Our results have important implications for understanding virus carriage in WBPHs, evaluating their role as virus vectors, and informing the development of improved pest management strategies. Furthermore, this study highlights the power of metagenomics in uncovering novel viruses and expanding our knowledge of viral diversity.},
}

@article {pmid40606163,
year = {2025},
author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Lee, SW and Ueno, T},
title = {Gastrectomy-induced alterations in gut microbiota linked to changes in oral and gastric microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599503},
pmid = {40606163},
issn = {1664-302X},
abstract = {INTRODUCTION: Gastrectomy serves as a primary treatment for gastric cancer, a leading global malignancy, and affects significant physiological and anatomical changes in the digestive tract. Recent studies highlight the critical role of gastrointestinal microbiota in postoperative health following digestive tract surgeries, including gastrectomy. These alterations possibly impact the gut microbiota and affect patient health by influencing the bacterial environment in the gastrointestinal tract. However, the relationships between the gastrointestinal tract and the oral, gastric, and gut microbiota after gastrectomy are not clear. In this study, we aimed to characterize alterations in the gut microbiota due to gastrectomy and evaluate whether these alterations are associated with the oral and gastric microbiota.

METHODS: Saliva, gastric fluid, and stool samples were collected from patients diagnosed with primary gastric cancer who underwent gastrectomy at two time points, before and 6 months after gastrectomy. Next, 16S rRNA metagenomic analysis was performed. Diversity and linear discriminant analysis effect size (LEfSe) analyses of each microbiota were conducted before and after gastrectomy to compare alterations in the gut, oral, and gastric microbiota.

RESULTS: The diversity of gut microbiota increased after gastrectomy compared to that before gastrectomy (Shannon index, p = 0.044), with LEfSe analysis showing increased abundance of Rothia and Lactobacillus in the gut microbiota. Additionally, the proportion of participants with Rothia in their gut microbiota increased, and this genus was present in the oral and gastric microbiota of almost all participants. Furthermore, a significant rise in Lactobacillus was observed in the gut, oral, and gastric microbiota of paired participants.

DISCUSSION: We characterized gut microbiota alterations caused by gastrectomy and demonstrated their relationship with changes in oral and gastric microbiota, thereby elucidating interactions between the gastrointestinal tract microbiota in response to changes in the gastric environment.},
}

@article {pmid40606158,
year = {2025},
author = {Tang, MLY and Lau, SCK},
title = {Varying effects of chlorination on microbial functional repertoire and gene expression in contrasting effluents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593147},
pmid = {40606158},
issn = {1664-302X},
abstract = {Effluents produced from different influent sources and sewage treatment processes carry distinct microbial community compositions. These microbiomes exhibit varying degrees of resistance and resilience under chlorination; however, their survival strategies and potential risks to the public health and ecosystem have yet to be fully characterized. In view of this, we subjected microbiomes from two contrasting types of effluents with distinct influent properties (seawater/freshwater-based) and prior treatment processes (primary/secondary) to metagenomics and metatranscriptomics analyses for comparing the alterations in their functional genes and activities under chlorination. The effluents presented highly dissimilar genomic and transcriptomic profiles. The variations in these profiles were significantly correlated to physicochemical factors including salinity, DO, BOD5, TSS, and TN. We recovered novel metagenome-assembled genomes (MAGs) from each type of effluent, revealing that those recovered from the same effluent tended to share similar functional properties which aligned with the physicochemical parameters of the effluent. Notably, the type and extent of alterations in genomic and transcriptomic profiles under chlorination varied greatly between effluents. Most of the genes and transcripts with significant changes in relative abundances were exclusive to their respective effluents. Also, the number of genes and transcripts with significant increase in relative abundances after chlorination were much higher than those with reduction. These enriched genes and transcripts were responsible for a wide range of functions, including energy generation, repair of damaged components and stress responses. Furthermore, the remanent microbiomes in chlorinated effluents still harbored numerous genes related to waterborne diseases and antimicrobial resistance, suggesting the potential risks of discharging these effluents into the environment. This study revealed the diverse effects of chlorination on different types of effluent microbiomes. It suggested that the remanent microbiomes in chlorinated effluents would have great variance in genetic potential and activities, providing insights into the evaluation and regulation of chlorine disinfection in sewage treatment.},
}

@article {pmid40605980,
year = {2025},
author = {Xu, Z and Zhang, Y and Wang, D and Xuan, C and Li, Z and Xu, H},
title = {Impact of cytomegalovirus DNAemia detected by next-generation sequencing on short-term prognosis after lung transplantation.},
journal = {Infectious medicine},
volume = {4},
number = {2},
pages = {100185},
pmid = {40605980},
issn = {2772-431X},
abstract = {BACKGROUND: Cytomegalovirus (CMV) is a common opportunistic pathogen following lung transplantation, associated with post-transplant complications and adverse outcomes. This study aims to evaluate the incidence of CMV DNAemia identified through metagenomic next-generation sequencing (mNGS) during the early postoperative phase of lung transplantation and assess its effects on the short-term outcomes for recipients.

METHODS: We conducted a retrospective analysis of clinical data from 115 patients who received lung transplants at the Affiliated Wuxi People's Hospital of Nanjing Medical University between May 2020 and November 2023. Based on mNGS-detected CMV DNAemia status, patients were stratified into DNAemia group and normal group. Nonparametric tests (Mann-Whitney U/Wilcoxon signed-rank) and mixed-effects models for intergroup comparisons. Kaplan-Meier survival analysis with log-rank testing for overall survival differences. Univariate logistic regression to identify risk factors for ICU mortality and 90-day mortality. Multivariate logistic regression adjusting for confounders. Propensity score matching (1∶1 optimal nearest neighbor, caliper = 0.25) was implemented to address covariate imbalance, followed by univariate logistic regression analyses in the matched cohort.

RESULTS: In the early postoperative period following lung transplantation, CMV DNAemia was detected via mNGS with an incidence rate of 15.7%. The CMV DNAemia group demonstrated a significantly lower 90-day overall survival rate compared to the normal group, with the Log-rank test revealing statistically significant survival differences between groups (p < 0.001). Univariate and multivariate logistic regression analyses identified CMV DNAemia as an independent risk factor for ICU all-cause mortality (OR = 5.00, 95% CI: 1.37-18.27, p = 0.015), while with other pathogens infections independently predicted 90-day all-cause mortality (OR = 3.40, 95% CI: 1.10-10.44, p = 0.033). After propensity score matching, baseline characteristics were well-balanced between the CMV DNAemia and normal groups. In the matched cohort, univariate logistic regression further confirmed CMV DNAemia as an independent risk factor for ICU mortality (OR = 7.43, 95% CI: 1.23-45.00, p = 0.029). Mediation analysis demonstrated that co-pathogen infections mediated the relationship between CMV DNAemia and 90-day all-cause mortality, with a proportion mediated of 20.6% (95% CI: 1.7%-138.5%, p < 0.001).

CONCLUSIONS: mNGS revealed a higher incidence of early CMV DNAemia post-lung transplantation than previously reported. CMV DNAemia significantly correlates with poor prognosis. Despite limitations in sample size and retrospective design, this study provides novel insights into CMV monitoring and management post-transplantation. Future research should determine optimal timing for preemptive antiviral strategies guided by mNGS.},
}

@article {pmid40605848,
year = {2025},
author = {Grevskott, DH and Victor, MP and Lima, TE and Radisic, V and Nimje, PS and Marathe, NP},
title = {High-throughput sequencing data of the microbiota and antibiotic resistance genes from biofilms on polystyrene and nylon rope incubated in Bergen harbor.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111718},
pmid = {40605848},
issn = {2352-3409},
abstract = {Plastics can provide a hydrophobic surface for microorganisms to attach, colonize and form microbial biofilms, referred to as 'plastisphere.' The aim of this study was to determine the microbiota of biofilms on plastic, using field trials in Bergen harbour, Norway using metagenomics. Polystyrene (PS) and nylon ropes (PA) were submerged in sea for four weeks, biofilm communities were collected, and the extracted DNA was subjected to metagenomic sequencing (n=12). The average salinity and temperature during the experiment were 9.02 °C (8.2-10.7) and 28.85 ‰ (26.1 ‰ - 33.1 ‰). We obtained a total of ∼460 Gigabases of sequence data from our samples. Gammaproteobacteria and Alpha proteobacteria were the most prominent on these polymers with β-lactamases as the most abundant resistance gene class. The datasets will be useful for the scientific community working on plastic-associated biofilms.},
}

@article {pmid40605092,
year = {2025},
author = {Han, Y and Deng, Z and Peng, Y and Peng, J and Cao, L and Xu, Y and Yang, Y and Zhou, H and Zhang, C and Zhang, D and Wang, M and Zhang, C and Greening, C and Dong, X},
title = {Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {156},
pmid = {40605092},
issn = {2049-2618},
support = {42406109//National Natural Science Foundation of China/ ; 42406131//National Natural Science Foundation of China/ ; 42376084//National Natural Science Foundation of China/ ; 42276150//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 20250131//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2023M734096//China Postdoctoral Science Foundation/ ; 2024M762799//China Postdoctoral Science Foundation/ ; GZC20241467//Postdoctoral Fellowship Program of CPSF/ ; 2023B0303000015//Guangdong Major Project of Basic and Applied Basic Research/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification/enzymology ; Phylogeny ; *Halogenation ; *Archaea/genetics/classification/metabolism/isolation & purification/enzymology ; *Seawater/microbiology ; Metagenomics/methods ; Bacterial Proteins/genetics/metabolism ; Metagenome ; Oxidation-Reduction ; },
abstract = {BACKGROUND: Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is not completely understood, especially in deep-sea environments. To address this gap, we investigated the diversity and expression of genes encoding reductive dehalogenase catalytic subunits (RdhAs), and ecophysiology of potential organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds.

RESULTS: Through genome-resolved metagenomic analysis of 165 global cold seep sediment samples, 4 types of RdhA-like sequences were identified based on their features and phylogenetic relationships: prototypical respiratory, transmembrane respiratory, cytosolic, and a novel clade. Cold seeps were found to harbor a higher abundance of these rdhA-like genes compared to other marine sediments, highlighting their potential as microbial reductive dehalogenation hotspots. These rdhA-like genes are encoded by a wide range of microorganisms across 4 archaeal and 36 bacterial phyla, significantly expanding the known diversity of organohalide reducers. Halogen geochemistry, laboratory incubations, metatranscriptomic data, and metabolomic profiling confirmed the presence of organohalides at concentrations of up to 18 mg/g in these sediments and suggested the potential for microbial reductive dehalogenation. Our findings suggest that organohalide reducers in cold seep sediments may participate in diverse biogeochemical processes, as inferred from the presence of genes related to carbon, hydrogen, nitrogen, sulfur, and trace element cycling. Additionally, RdhA-like proteins from cold seeps have diverse N-terminal structures across different gene groups.

CONCLUSIONS: These findings collectively suggest that reductive dehalogenation is an important process in deep-sea environments, mediated by a diverse array of microbes and novel enzymes. The discovery of diverse and abundant rdhA-like genes, along with their genomic context and potential metabolic linkages, highlights the role of cold seeps as reservoirs of microbial diversity with possible implications for environmental remediation. Video Abstract.},
}

*Geologic Sediments/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification/enzymology
Phylogeny
*Halogenation
*Archaea/genetics/classification/metabolism/isolation & purification/enzymology
*Seawater/microbiology
Metagenomics/methods
Bacterial Proteins/genetics/metabolism
Metagenome
Oxidation-Reduction

@article {pmid40605035,
year = {2025},
author = {Liu, J and Zhang, Y and Xu, L and Gu, G and Dong, Z},
title = {Parabacteroides johnsonii inhibits the onset and progression of colorectal cancer by modulating the gut microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {734},
pmid = {40605035},
issn = {1479-5876},
support = {School Science [2022] No.7//Clinical Program of Air Force Medical University/ ; 22BJQN004//Fourth Military Medical University/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most prevalent malignant tumor and the second leading cause of cancer-related deaths globally. The genus Parabacteroides is an important component of the gut microbiota. P. distasonis and P. goldsteinii are reported probiotics, and their roles in CRC have been investigated in related studies. However, the association between P. johnsonii and CRC remains unknown.

METHODS: P. johnsonii (10–42) and Lactococcus formosensis (22–2) were isolated from healthy human feces. 29 mice that demonstrated normal feeding and activity were randomly assigned to four groups: normal control (NC group), CRC model (IC group), P. johnsonii (PJ group), and L. formosensis (LO group). Colonic tumor tissues from the IC, PJ, and LO groups and normal colon tissues from the NC group were then collected for HE staining and immunohistochemical staining. Fecal samples from mice during the hyperproliferative and adenoma phases were collected for Metagenomic sequencing and metabolite analysis.

RESULTS: P. johnsonii intervention reduced the number and slowed the growth of colonic tumors, improved tumor histological scores, and decreased microenvironmental inflammation levels. P. johnsonii improved the composition of intestinal flora in mice with colon cancer, increased gut microbial species diversity, and maintained gut microbiota stability. Furthermore, P. johnsonii intervention increased the abundance of Bifidobacterium pseudolongum and Lactobacillus, which play a role in ameliorating AOM/DSS-induced gut microbiota dysbiosis. P. johnsonii intervention affected the metabolic pathways, including amino sugar degradation and galactose metabolism, sphingolipid synthesis, amino acid synthesis, and polyphenol synthesis pathways, with the tryptophan metabolism pathway as the primary pathway being affected.

CONCLUSION: Our study profiled the P. johnsonii administration reduces the number of tumors and lower tumor staging in AOM/DSS-induced colon cancer mice by modulating gut microbiota and its metabolites at early stages.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-06675-0.},
}

@article {pmid40605027,
year = {2025},
author = {Yun, CS and Kim, JK and Kwon, H and Kim, Y and Her, M and Moon, JS},
title = {Conventional diagnosis and metagenomic analysis of a novel co-infection case involving Escherichia coli and immunosuppressive conditions with petechial hepatitis of broilers in South Korea: a case report.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {432},
pmid = {40605027},
issn = {1746-6148},
support = {N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; },
mesh = {Animals ; *Chickens ; *Poultry Diseases/diagnosis/microbiology/virology ; *Escherichia coli Infections/veterinary/diagnosis/microbiology/complications ; *Coinfection/veterinary/diagnosis/microbiology ; Metagenomics ; Escherichia coli/isolation & purification/genetics ; Republic of Korea ; *Hepatitis, Animal/diagnosis/microbiology/virology ; *Purpura/veterinary/diagnosis/microbiology ; Liver/pathology/microbiology ; },
abstract = {BACKGROUND: The conventional diagnosis in poultry disease enhances accuracy by combining clinical and necropsy observation with various molecular biological analysis. However, if the causative agents of a disease are not isolated and detected, accurate diagnosis and future disease management become challenging. The purpose of the present study aimed to diagnose and identify the causes of disease in broilers with novel petechial hepatitis by applying metagenomic analysis.

CASE PRESENTATION: Through the necropsy, tracheal and pericardial congestion, and severe petechia and perihepatitis in the livers were observed. Histopathological examination revealed infiltration of lymphocytes and bacterial colonies in various organs, as well as severe sinusoidal congestion, hemorrhages and hepatocyte necrosis in the livers. E. coli was isolated and identified in the liver samples. Although FAdV, CkChpV, CAstV, IBV and IBDV were detected, no viral agents were detected in the livers. Metagenomic analysis of the livers showed a predominance of bacterial composition, followed by fungal and viral agents, with E. coli being the most abundant. Analysis of virulence factors in E. coli revealed the presence of those associated with APEC, as well as other IPEC and ExPEC pathotypes.

CONCLUSION: The present study identified a novel petechial hepatitis in broilers, associated with co-infections of antigenic variant IBDV, multiple pathotypes of E. coli, and possibly various causative. The application of metagenomic analysis proved valuable in identifying diverse potential pathogens when conventional methods were limited. These findings highlight the utility of metagenomic approaches as a complementary diagnostic tool and support their continued use in advancing poultry disease management.},
}

Animals
*Chickens
*Poultry Diseases/diagnosis/microbiology/virology
*Escherichia coli Infections/veterinary/diagnosis/microbiology/complications
*Coinfection/veterinary/diagnosis/microbiology
Metagenomics
Escherichia coli/isolation & purification/genetics
Republic of Korea
*Hepatitis, Animal/diagnosis/microbiology/virology
*Purpura/veterinary/diagnosis/microbiology
Liver/pathology/microbiology

@article {pmid40604425,
year = {2025},
author = {Wang, C and Song, W and Li, C and Cao, Y and Li, X and Zhao, J and Yang, F and Yu, H and Liang, Q and Yang, KQ and Liu, JN and Fang, H},
title = {Metagenomic analysis reveals Bacillus cereus OTU8977 as a potential probiotic in promoting walnut growth.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {839},
pmid = {40604425},
issn = {1471-2229},
support = {2024LZGC025//Improved Variety Program of Shandong Province of China/ ; },
mesh = {*Bacillus cereus/genetics/physiology ; *Juglans/growth & development/microbiology ; Rhizosphere ; Metagenomics ; Soil Microbiology ; *Probiotics ; Plant Roots/microbiology/growth & development ; },
abstract = {BACKGROUND: Rhizosphere microorganisms can improve soil quality, promote plant growth, and enhance plant health. Despite the isolation of numerous plant growth-promoting rhizobacteria (PGPR) strains, research on how PGPR enhances walnut growth remains limited.

RESULTS: In this study, the metagenomic sequencing of the rhizosphere soil in 8 major walnut-producing areas in China was conducted to identify 150 shared core amplicon sequence variants. Then, we isolated a strain of Bacillus cereus OTU8977 from the walnut rhizosphere soil and evaluated its potential plant growth-promoting functions. B. cereus OTU8977 can optimize the walnut rhizosphere microecology and promote its growth through its considerable potential in nitrogen fixation, phosphorus solubilization, and potassium dissolution. Transcriptomic analysis of walnut roots revealed that B. cereus OTU8977 promotes the growth of walnuts by enhancing phenylpropanoid biosynthesis and carbohydrate metabolic processes.

CONCLUSIONS: This study identified a strain of Bacillus cereus with multiple plant growth-promoting functions, which significantly enhanced walnut growth. Moreover, the study further elucidated the mechanisms underlying its growth-promoting effects, providing a theoretical foundation for the development of walnut-specific microbial fertilizers.},
}

*Bacillus cereus/genetics/physiology
*Juglans/growth & development/microbiology
Rhizosphere
Metagenomics
Soil Microbiology
*Probiotics
Plant Roots/microbiology/growth & development

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@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 {pmid40604305,
year = {2025},
author = {Li, Y and Shi, Z and Zhang, X and Ren, H and Ji, H and Yang, F and Fu, Z and Kong, X and Cheng, X and Li, J and Wu, K and Zhong, Y and Zhong, H and Ji, L},
title = {Metagenomic analysis revealing links between age, gut microbiota and bone loss in Chinese adults.},
journal = {npj metabolic health and disease..},
volume = {3},
number = {1},
pages = {18},
pmid = {40604305},
issn = {2948-2828},
support = {7222238//Beijing Natural Science Founding/ ; },
abstract = {Accumulating evidence has linked gut microbiota to bone health. However, investigations into the impacts of aging, gut microbiota, and their interactions in the development of osteoporosis remain inconclusive. We employed quantitative computed tomography to measure lumbar bone mass density (BMD) and analyzed shotgun metagenomic data in 684 Chinese adults. Our analyses revealed significant positive associations between BMD and abundances of multiple Lachnospiraceae species, including Lachnospira eligens, Blautia wexlerae, and Roseburia hominis, as well as pathways involved in L-arginine biosynthesis and butyrate production-independent of age, diet habits, and lifestyles. Moreover, we demonstrated that individuals with enterotype Bacteroides exhibited a more pronounced age-related decline in BMD compared to those with enterotype Prevotella, a pattern we validated in an independent cohort. Our findings offer valuable insights into BMD-related gut microbial features and interactions between aging, gut microbiota, and bone loss, opening potential avenues for microbiota-based prevention and treatment strategies for osteoporosis.},
}

@article {pmid40604156,
year = {2025},
author = {Kim, H and Nelson, P and Nzabarushimana, E and Shen, J and Jensen, J and Bhosle, A and Li, C and Lee, N and Everett, C and Berdy, B and Frongillo, G and Livny, J and Hu, FB and Simon, TG and McIver, L and Franzosa, EA and Chan, AT and Hayete, B and Thompson, KN and Huttenhower, C and Nguyen, LH},
title = {Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40604156},
issn = {2522-5812},
support = {K23DK125838//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32CA009001//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35CA253185//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; Research Professorship//American Cancer Society (American Cancer Society, Inc.)/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common condition linked to obesity and the metabolic syndrome, yet its transkingdom connections have been under-investigated. We performed high-resolution multi-omic profiling-including stool metagenomes, metatranscriptomes and metabolomes-in 211 MASLD cases and 502 controls from a cohort of female nurses. Here we show that MASLD is associated with shifts in 66 gut bacterial species, including widespread enrichment of oral-typical microbes, and transkingdom dysbiosis involving not only bacterial but also viral taxa. Streptococcus spp. are more abundant in non-lean versus lean MASLD, the latter being a paradoxical subtype of a disease typically associated with increased adiposity. These microbial changes correspond with shifts in transcripts and metabolites, including increases in polyamines and acylcarnitines and reductions in secondary bile acids. We highlight gut viral perturbations in MASLD, showing that expansions of bacteriophage targeting oral-typical bacteria correspond to expansions of their bacterial hosts in the gut. We provide a comprehensive resource for understanding MASLD and highlight transkingdom multi-omic microbial shifts as potential contributors to its aetiopathogenesis.},
}

@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 {pmid40603748,
year = {2025},
author = {Zhou, W and Kang, L and Qiao, S and Duan, H and Yin, C and Liu, C and Liao, Z and Tang, M and Zhang, R and Li, L and Shi, L and Du, M and Wang, Y and Yue, W and Xiao, Y and Di, L and Zhang, X and Pang, Y and Li, M and Ren, L and Wang, J and Chen, Z and Huang, Y},
title = {A fuzzy sequencer for rapid DNA fragment counting and genotyping.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {40603748},
issn = {2157-846X},
support = {T2225005//National Natural Science Foundation of China (National Science Foundation of China)/ ; Z201100005320016//Beijing Municipal Science and Technology Commission/ ; Z211100003321006//Beijing Municipal Science and Technology Commission/ ; Z221100007022003//Beijing Municipal Science and Technology Commission/ ; },
abstract = {High-throughput sequencing technologies generate a vast number of DNA sequence reads simultaneously, which are subsequently analysed using the information contained within these fragmented reads. The assessment of sequencing technology relies on information efficiency, which measures the amount of information entropy produced per sequencing reaction cycle. Here we propose a fuzzy sequencing strategy that exhibits information efficiency more than twice that of currently prevailing cyclic reversible terminator sequencing methods. To validate our approach, we develop a fully functional and high-throughput fuzzy sequencer. This sequencer implements an efficient fluorogenic sequencing-by-synthesis chemistry and we test it across various application scenarios, including copy-number variation detection, non-invasive prenatal testing, transcriptome profiling, mutation genotyping and metagenomic profiling. Our findings demonstrate that the fuzzy sequencing strategy outperforms existing methods in terms of information efficiency and delivers accurate resequencing results with faster turnaround times.},
}

@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 {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 {pmid40602565,
year = {2025},
author = {Rajeswari, G and Kumar, V and Jacob, S},
title = {Advanced lignocellulose bioprocessing for Aloe vera leaf rind through novel termite gut microbiome consortia for acetone butanol ethanol (ABE) production: Metagenomics insights and process economic analysis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145691},
doi = {10.1016/j.ijbiomac.2025.145691},
pmid = {40602565},
issn = {1879-0003},
abstract = {Consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) using microbes simplifies the process, eliminates enzyme cost and reduces the overall processing expenses. In this regard, termite gut, a potent reservoir of microbial symbionts produces various lignocellulolytic enzymes which acts synergistically to degrade LCB. However, the effectiveness of adapting the microbes with LCB for improved lignocellulolytic enzyme secretion and substrate degradation has been overlooked. Hence, in this study adaptive laboratory (ALE) of termite gut isolates was performed with various substrates such as saw dust (SD) and Aloe vera leaf rind (AVLR) under different conditions. Among the consortia, enriched termite consortium (ETC-3) showed the highest degradation of lignin (51.86 ± 2.03 %, w/w), hemicellulose (29.27 ± 1.29 %, w/w) and cellulose (41.97 ± 2.99 %, w/w) with maximum specific enzyme activities. High throughput sequencing revealed the significant enrichment of Proteobacteria (88.95 %) and Ascomycota (99.94 %) groups in ETC-3. Further, the efficiency of ETC-3 in consolidated pretreatment and bioprocessing (CPBP) and CBP of AVLR towards acetone, butanol and ethanol (ABE) production was studied. Compared to the CPBP, CBP resulted in 1.6-fold higher glucose yield which subsequently enhanced the butanol yield (7.97 ± 0.40 g/L). Finally, cost benefit analysis ensured the economic feasibility of process strategies for AVLR valorization.},
}

@article {pmid40602513,
year = {2025},
author = {Zhang, Z and Wang, X and Yang, L and Cui, Y and Zhang, Z},
title = {Soil redox-adaptive anode potentials enhance microbial electroactivity through targeted enrichment of exoelectrogenic consortia in paddy soil.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122265},
doi = {10.1016/j.envres.2025.122265},
pmid = {40602513},
issn = {1096-0953},
abstract = {Exoelectrogenic bacteria (EEB) act as critical drivers in terrestrial and aquatic ecosystems, mediating pivotal biogeochemical processes. However, their low abundance in natural environments poses significant challenges for accurate identification and enrichment. Bioelectrochemical systems (BESs) have emerged as a promising tool for enriching EEB from environmental samples, yet the influence of applied potentials on shaping specific EEB populations remains poorly understood. Here, we developed an effective strategy to selectively enrich targeted exoelectrogenic consortia by adapting anode potentials to the redox conditions of paddy soil. Notably, in BESs inoculated with flooded soil, an applied potential of -0.28 V (simulating the redox conditions dominated by iron oxide-hydroxide reduction) preferentially enriched Geobacter-dominated EEB consortia. Metagenomic functional analysis indicated these EEB were primarily engaged in iron respiration. In contrast, drained soil-inoculated BESs required a higher potential (0.33 V, mimicking nitrate-reducing conditions) for optimal enrichment, resulting in Aeromonas as the predominant genus. The enriched community in this scenario exhibited chemoheterotrophic metabolism and nitrate reduction capabilities. The enrichment dynamics underscore how applied potentials modulate both taxonomic composition and functional specialization of EEB along soil redox gradients, with implications for targeted manipulation of microbial communities for environmental biotechnology applications.},
}

@article {pmid40602191,
year = {2025},
author = {de Sant'Anna, FM and Chakrawarti, A and Haley, BJ and Barlow, J},
title = {The resistome of pasteurized and raw milk cheeses from the state of Vermont.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111333},
doi = {10.1016/j.ijfoodmicro.2025.111333},
pmid = {40602191},
issn = {1879-3460},
abstract = {This study investigates the resistome dynamics in cheese production, focusing on both raw milk and pasteurized varieties comparing a standard and lytic method of DNA extraction. Metagenomic analysis revealed the presence of single nucleotide polymorphism (SNP) confirmed antimicrobial resistance genes (ARGs) in core and rind samples of cheeses at different stages of ripening. No statistical significance was found between the extraction methods for antimicrobial resistance gene (ARG) classes. In pasteurized cheese, the resistome was influenced by the initial microbial composition and ripening period, with limited ARGs detected due to pasteurization. Nonetheless, detection of class B β-lactamase and Fosfomycin B resistance genes was observed in the pasteurized cheese core, possibly harbored by Bacillus cereus. Raw milk cheese exhibited a distinct resistome profile, with fluctuations in macrolide and oxazolidinone resistance genes associated with changes in microbial populations during ripening. Notably, the likely presence of multi-drug resistance genes in Lactococcus lactis highlights the importance of understanding resistance mechanisms in starter cultures. The study emphasizes the need for antimicrobial stewardship and hygiene practices in dairy production to mitigate the spread of resistance genes. Despite sequencing biases, this research contributes valuable insights into the cheese resistome, advocating for future studies to employ enhanced sequencing methods for comprehensive analysis and to develop practical strategies for resistance management in dairy products.},
}

@article {pmid40602179,
year = {2025},
author = {Tang, X and Zheng, W and Chen, L and Liu, H and Li, M and Chen, M and Yang, Y},
title = {Enhanced neonicotinoid removal in constructed wetlands using Fungus-Fe/Mn biochar.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126430},
doi = {10.1016/j.jenvman.2025.126430},
pmid = {40602179},
issn = {1095-8630},
abstract = {The environmental persistence and toxicity of neonicotinoids, such as imidacloprid (IMI) and thiamethoxam (THX), pose substantial threats to aquatic ecosystems. This study evaluated the performance of constructed wetlands (CWs) amended with a novel Fungus-Fe/Mn biochar substrate (synthesized by immobilizing the white-rot fungus Phanerochaete chrysosporium onto Fe/Mn-modified biochar) for enhanced removal of IMI and THX from simulated agricultural wastewater. CWs integrated with Fungus-Fe/Mn biochar demonstrated significantly improved removal efficiencies of 73.3 % for IMI and 66.7 % for THX, surpassing those of Fe/Mn biochar alone (66.4 % IMI, 58.1 % THX) and control systems (55.1 % IMI, 37.3 % THX). Mechanistic analysis indicated that removal was facilitated by both substrate adsorption (32.3-37.5 %) and microbial degradation (32.4-35.1 %), with enhanced production of degradation metabolites in the amended systems. Metagenomic analysis revealed increased microbial diversity and the enrichment of biodegradation and pesticide degradation genes, including key genes such as p450 and mnp. Additionally, potential microbial hosts for these genes, such as Rhodococcus and Pseudomonas, were identified. Redox-active Fe[3+]/Fe[2+] and Mn[4+]/Mn[2+] species additionally promoted electron transfer and rhizosphere iron plaque formation, improving pollutant sequestration and on-situ degradation. These findings highlight the potential of fungus-biochar synergism to overcome the limitations of conventional substrates, offering a scalable and sustainable approach for pesticide remediation in CWs.},
}

@article {pmid40601836,
year = {2025},
author = {Tarek, S and ElMaghloob, Y and Smith, H and Smith, TJ and ElRakaiby, MT and Habib, MH},
title = {A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00323},
pmid = {40601836},
issn = {1554-8937},
abstract = {Dye-decolorizing peroxidase (DyP)-type peroxidases are heme-containing enzymes that play a role in lignin synthesis and degradation and dye decolorization. Despite numerous studies about this class of enzymes, the enzyme remains under-explored. We used 1000 DyP sequences retrieved from the NCBI database to forge a phylogenetic tree. Nodes in the tree, where sequences displayed a degree of conservation, were used to design degenerate primers to locate DyP-peroxidase sequences from the DNA extract of a tannery wastewater sample. After PCR amplification and visualization using agarose electrophoresis, a band at the expected size of a DyP peroxidase (500-700 bp) was seen. TA cloning followed by blue-white colony selection validated our finding after amplicon sequencing of the PCR product to confirm the presence of an Acinetobacter species DyP-peroxidase. Our metagenomic DyP displayed 99% similarity to the DyP-peroxidase sequence found in the Acinetobacter baumannii ATCC 19606 strain. As a result, and due to the minute differences between our found DyP and the ATCC 19606 strain DyP, we expressed the latter cloned in a pET28b(+) vector and purified it from culture medium using Escherichia coli SoluBl21 as a host strain. A crude oxidation assay using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) deemed the enzyme active as shown by the formation of a green color. The crystal structure of the enzyme was solved at 2.6 Å resolution (PDB ID 9OBR) using X-ray crystallography and presented as a hexamer in solution.},
}

@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},
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},
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 {pmid40601244,
year = {2025},
author = {Posthumus, AM and Knobbe, TJ and Kremer, D and Gomes-Neto, AW and Dielwart, IJC and Jonker, J and Doorenbos, CSE and Eisenga, MF and van Londen, M and Douwes, RM and Nieuwenhuis, LM and Annema, C and de Boer, MT and de Borst, MH and Damman, K and Pol, RA and Gan, CT and Verschuuren, EAM and Blokzijl, H and de Meijer, VE and Bakker, SJL and , },
title = {TransplantLines, a biobank and cohort study of solid organ transplant recipients and donors.},
journal = {European journal of epidemiology},
volume = {},
number = {},
pages = {},
pmid = {40601244},
issn = {1573-7284},
support = {TransplantLines Biobank//Astellas Pharma, Netherlands/ ; Cohort study//Astellas Pharma, Netherlands/ ; PA-SP/PRJ-2020-9136//Chiesi Pharmaceuticals BV/ ; project code: 14939//DSM, Animal Nutrition and Health/ ; project code: PPP-2019-032//Ministerie van Economische Zaken en Klimaat/ ; PPP-2022-015//Ministerie van Economische Zaken en Klimaat/ ; },
abstract = {The TransplantLines Biobank and Cohort Study (NCT03272841) is an ongoing prospective study conducted at the University Medical Centre Groningen, The Netherlands. TransplantLines aims to identify risk factors and biomarkers associated with health problems following solid organ transplantation and donation. Additionally, the study seeks to develop new interventions to reduce symptom burden and improve long-term outcomes, including health-related quality of life, cardiovascular complications, graft failure, and mortality. It includes recipients of (combined) heart, liver, lung, kidney, pancreas, and small bowel transplants, as well as living liver and kidney donors, and deceased (multi-)organ donors. The biobank contains a wide range of biomaterials including whole blood, serum, EDTA-plasma, buffy coat, 24-h urine samples, faeces, hair, nails, and tissues. Data collection includes physical and cognitive assessments, extensive laboratory analysis, metagenomic sequencing, and questionnaires. TransplantLines, initiated in 2015, consists of 5143 participants as of October 2024, among 2312 (45%) females. The mean age was 50 (± 16) years at transplantation, 55 (± 11) years at living donation and 56 (± 15) years at deceased donation. Both cross-sectional and longitudinal biomaterials and data are included. For recipients, longitudinal biomaterials and data were collected at: pre-transplantation, at transplantation, and at 3, 6, 12, 24, and 60 months post-transplantation. For living donors, data were collected at pre-donation, donation, 3 months post-donation, and/or 5 or 10 years post-donation.},
}

@article {pmid40600930,
year = {2025},
author = {Gómez-Gómez, A and Aterido, A and Li, T and Guillén, Y and Martínez, S and Julià, A and Marsal, S and Andreu, JL},
title = {Understanding the molecular basis of Sjögren's disease using omic technologies.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf360},
pmid = {40600930},
issn = {1462-0332},
abstract = {Primary Sjögren's Disease (SjD) is a chronic autoimmune disease (AD) that primarily affects the exocrine glands, particularly lacrimal and salivary glands, presenting extra glandular manifestations in a significant number of patients. Although it is a prevalent and globally widespread disease, its pathogenesis has not been fully elucidated. Recently, high-throughput omics technologies are providing unprecedented insights into the molecular landscape of various ADs, including SjD. These technical advances are prepared to decipher new aspects of its pathogenesis and to eventually enable the development of more effective treatment strategies. This review explores recent developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics in SjD, highlighting the potential of integrating multiple omics datasets to identify better drug targets and useful biomarkers for precision medicine.},
}

@article {pmid40600714,
year = {2025},
author = {Li, Y and Sun, C and Zhu, J and Geng, M and Li, M and Zhao, X-M and Chen, W-H},
title = {Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0001325},
doi = {10.1128/spectrum.00013-25},
pmid = {40600714},
issn = {2165-0497},
abstract = {UNLABELLED: Due to varying sequencing strategies, current gut virome findings show significant variability. Specifically, bulk- and virus-like particle (VLP)-enriched metagenomic sequencing (termed bulk and VLP, respectively) present unique advantages and limitations, affecting viral genome discovery, taxonomic annotation, and community structure analysis. A comprehensive comparison of these strategies is crucial for thoroughly understanding the gut virome. This study comprehensively compared gut viromes identified from paired bulk and VLP data from 151 adult and 141 infant fecal samples. The VLP method showed superior performance to bulk in viral genome discovery in both data sets by recovering longer and more complete viral genomes, with higher sensitivity for low-abundant ones, resulting in a higher taxonomic annotation rate. However, we observed no correlations in the viral community structure (i.e., Shannon diversities) between bulk- and VLP-derived viromes, implying biases introduced during VLP enrichment. Such biases could be caused by the bacterial host features, such as the structural differences in cell walls and the prevalence and abundance of the viruses. Viruses that are of low prevalence, low abundance, or have Gram-positive bacteria as their hosts were enriched in VLP-derived viromes, in both the adult and infant data sets. Significant complementarity was observed between bulk and VLP viromes, with only about a quarter (26.7% in infants; 29.3% in adults) of VLP-viral genomes overlapping with bulk viruses. Together, our study identifies causal factors underlying the biases of bulk and VLP strategies in human gut virome studies and advocates the use of both strategies to enhance a comprehensive understanding of gut viromes.

IMPORTANCE: The two mainstream gut phageome profiling strategies, namely bulk and virus-like particle (VLP), generated significantly overlapped results and have their own merits and drawbacks. Particularly, VLP exhibits higher efficiency in obtaining more, longer, and more complete viral genomes. However, VLP sequencing has the potential to alter the natural structure of viral communities, often resulting in the identification of viruses with lower prevalence and those specifically associated with Gram-positive bacterial hosts. While bulk metagenome features a more stable and diverse community, which can well reveal the interactions between viruses and bacteria. Nevertheless, bulk sequencing can suffer from lower coverage, leading to fragmented sequences and potentially missing some viral species. Therefore, it is essential to recognize that these methods are complementary rather than competitive in the comprehensive characterization of the gut phageome.},
}

@article {pmid40600712,
year = {2025},
author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR},
title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002725},
doi = {10.1128/msystems.00027-25},
pmid = {40600712},
issn = {2379-5077},
abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.},
}

@article {pmid40600350,
year = {2025},
author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M},
title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70135},
pmid = {40600350},
issn = {1536-4801},
support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.

METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n = 41), 3 months (n = 19), and 12 months (n = 12) and in healthy controls (HC; n = 34). Evaluation for diabetes (DM) or prediabetes (pre-DM) was performed. At 12-month follow-up gastrointestinal (GI) symptom surveys were completed and AP recurrence-acute recurrent pancreatitis (ARP) recorded. Shotgun metagenomic sequencing was performed on extracted microbial DNA.

RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p < 0.008). Bray-Curtis ordinations showed the AP cohort did not cluster by time point, highlighting similarity in microbial composition over time. Within 12-month follow-up: 7/44 participants developed pre-DM/DM, 7/42 developed ARP, 16 had zero or one while 15 had multiple GI symptoms. Distinct clustering of samples was observed in the baseline samples of the group that developed ARP (p = 0.023) and in follow-up samples with multiple GI symptoms, p < 0.05. Relative abundance of most species was lower in AP samples when compared to HC at all time points with enrichment in Ruminococcus gnavus and Clostridium innocuum (AQ) (False Discovery Rate p < 0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.

CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.},
}

@article {pmid40600142,
year = {2025},
author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W},
title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1516393},
pmid = {40600142},
issn = {1664-302X},
abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.

METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.

RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.

CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.},
}

@article {pmid40600141,
year = {2025},
author = {Elbehery, AHA and Becker, K and Mishra, A and Ahmad, R},
title = {Editorial: Metagenomic approach for exploration of antimicrobial resistance in uncultivated microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633252},
pmid = {40600141},
issn = {1664-302X},
}

@article {pmid40585104,
year = {2025},
author = {Madi, N and Sayeed, MA and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ},
title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40585104},
abstract = {Phage predation is inversely associated with severe cholera yet its importance as a determinant of dehydration severity is unknown relative to other factors. Here we used machine learning to assess and rank potential host, microbial, and environmental factors as determinants of severe dehydration among a cohort of cholera patients enrolled at hospital admission across Bangladesh. We found the phage to pathogen ratio ranked among the top classifying features, placing just behind patient age and admission location. We advocate that phage predation is a key factor to include in the characterization of cholera for scientific, clinical and epidemiological applications.},
}

@article {pmid40571179,
year = {2025},
author = {Perrin, A and Clément, L and Szentiványi, T and Théou, P and López-Baucells, A and Bonny, L and Scaravelli, D and Glaizot, O and Christe, P},
title = {Bat phylogeny and geographic location, rather than bat individual characteristics, explains the pattern of trypanosome infection in Europe.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.06.008},
pmid = {40571179},
issn = {1879-0135},
abstract = {Understanding the drivers of parasite susceptibility provides valuable information, such as how parasites spread, what conditions favour their transmission, and what host characteristics make infections more likely. It can also reveal co-evolutionary dynamics and adaptation strategies between hosts and parasites. In this study, we investigated the infection patterns of several bat species across Europe by trypanosome parasites. We used phylogenetic generalised linear mixed models to investigate whether geographic location, individual characteristics (sex, body mass and body size) or species affect trypanosome infection. Additionally, we examined whether infection patterns were influenced by host phylogeny (similar prevalence among genetically close species) and tested for a cophylogenetic signal between bats and trypanosomes. Our results show that individual characteristics were poor predictors of trypanosome infection, whereas host phylogeny and geographic location significantly explained variation in infection. We also found a cophylogenetic congruence between bat species and trypanosome lineages, but this was primarily driven by the association between the bent-winged bat (Miniopterus schreibersii) and its trypanosome lineages. Overall, host phylogeny emerges as the main determinant of trypanosome infection in bats. These findings suggest that the probability of infection is governed by deterministic factors rather than random encounters between bats and their trypanosome parasites. However, the high host specificity and absence of a strong cophylogenetic signal indicate that random host switching, rather than co-speciation, is the dominant mechanism shaping bat-trypanosome associations.},
}

@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 {pmid40600049,
year = {2025},
author = {Xu, H and Zhang, R and Zhang, X and Zhang, Z and Feng, Y and Lin, L},
title = {Pulmonary microbial spectrum of Burkholderia multivorans infection identified by metagenomic sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1577363},
pmid = {40600049},
issn = {2296-858X},
abstract = {PURPOSE: Burkholderia multivorans, a Gram-negative bacterium, often infect patients with severe immunocompromised and cystic fibrosis. B. multivorans infection is challenging to treat due to its ability to disrupt the action of multiple antimicrobial agents through intrinsic and acquired resistance mechanisms. A better understanding of the pulmonary microbial spectrum of B. multivorans infection is crucial for the prevention and treatment of B. multivorans.

CASE PRESENTATION: This case series reviewed the respiratory microbiome structure and alternations during the treatment of B. multivorans infection through metagenomic next-generation sequencing (mNGS). Analysis of mNGS data of 19 pharyngeal secretion samples collected from the 3 COVID-19 patients at different time points showed that the relative abundance of B. multivorans was fluctuated and eventually increased, indicating the possible development of drug resistance. A total of 40 antibiotic-resistant genes (ARGs) were detected. Significantly, the levels of CEOA, CEOB, and OPCM were consistent with the trends in the relative abundance of B. multivorans. Besides, we described nine previously uncharacterized non-synonymous mutations in PenA of B. multivorans. These mutations lead to amino acid changes Thr32Ala, Ala43Ser, Gln105Arg, Asn202Ser, Gln219Arg, Gly241Ala, Val259Ala, Thr279Ala, and Ser298Ile that may associate with resistance to β-lactam antibiotics.

CONCLUSION: This report shed light on the importance of rapidly diagnosis and treatment of B. multivorans infection. mNGS serve as a powerful microbial detection tool that provides a comprehensive, sensitive, and rapid method for pathogen detection and drug resistance analysis.},
}

@article {pmid40599704,
year = {2025},
author = {Klimczuk, A and Chattoo, S and Izugbara, C and Klimczuk-Kochańska, M and Toczyski, P and Kumar, A and Kanozia, R and Gawron, GP and Ozair, A},
title = {Editorial: Towards 2030: sustainable development goal 3: good health and wellbeing. A sociological perspective.},
journal = {Frontiers in sociology},
volume = {10},
number = {},
pages = {1616878},
pmid = {40599704},
issn = {2297-7775},
}

@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 {pmid40599424,
year = {2025},
author = {Pérez-Valera, E and Elhottová, D},
title = {Dataset of 111 metagenome-assembled genomes from cattle manure, soil and manured soil samples.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111748},
pmid = {40599424},
issn = {2352-3409},
abstract = {This data report presents 111 metagenome-assembled genomes (MAGs) reconstructed from manure, soil and manured soil samples from microcosms after enriching for non-fermenting Gram-negative bacteria (NFGNB). Two independent microcosm experiments were conducted to investigate the spread of NFGNB from the fresh manure of dairy cows under antibiotic prophylaxis to the pasture soil of two organic farms. After sampling the microcosms on days 2, 14 and 28, the manure and soil samples were plated in duplicate on CHROMagar Acinetobacter medium for NFGNB enrichment and incubated at 28°C for 24 h. DNA was extracted from the cultures and sequenced using the Illumina NovaSeq 6000 platform with 150-bp paired-end reads. Reads were assembled with metaSPAdes both individually and by co-assembly. MAGs were reconstructed using MetaBAT, MaxBin, SemiBin2, COMEbin, and AVAMB, and then de-replicated at >95 % ANI (pairwise comparisons) using dRep. A total of 111 MAGs of at least medium quality (MIMAG standard) were obtained. These included 10 high-quality MAGs (>90 % completeness, <5 % contamination, rRNA genes and tRNA for at least 18 amino acids), 47 putative high-quality MAGs (>90 % completeness, <5 % contamination) and 54 medium-quality MAGs (>50 % completeness, <10 % contamination). The FASTA files of the MAGs as well as their taxonomic identifications, completeness and contamination, origin, genomic statistics and rRNA sequences are publicly available in a Zenodo dataset and the genomes in the NCBI database. The majority of MAGs (99) were assigned to Pseudomonadota, mainly Pseudomonas (28 MAGs), Stenotrophomonas (20 MAGs) and Acinetobacter (18 MAGs), while the remaining 12 MAGs belonged to Bacteroidota. Most MAGs (44) were of manure origin, followed by manured soil (38 MAGs) and soil (29 MAGs). High-quality MAGs were predominantly obtained from manure (6 high-quality, 21 putative high-quality), compared to manured soil (3 high-quality, 12 putative high-quality) and soil (1 high-quality, 14 putative high-quality). By providing their MAGs, this dataset offers a valuable resource for researchers investigating the genomic characteristics associated with the survival, environmental dispersal and ecological role of potentially hazardous NFGNB species in soil, particularly following the application of antibiotic-treated animal manure, and for comparative genomics studies in related environments.},
}

@article {pmid40598913,
year = {2025},
author = {Ni, N and Qiu, J and Ge, W and Guo, X and Zhu, D and Wang, N and Luo, Y},
title = {Fibrous and Fragmented Microplastics Discharged from Sewage Amplify Health Risks Associated with Antibiotic Resistance Genes in Aquatic Environments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01335},
pmid = {40598913},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are key sources of antibiotic resistance genes (ARGs) and microplastics (MPs) in aquatic environments. However, field data on ARG-MP copollution remain scarce, hindering environmental risk assessment of ARGs. This study used metagenomic sequencing and high-throughput qPCR to examine the composition and association of ARGs and MPs in sewage discharge-receiving waters. The results indicated that sewage discharge significantly increased the abundance of ARG-MP complexes in receiving waters, with fibrous and fragmented MPs exhibiting enhanced ARG enrichment and thereby serving as selective vectors for pathogens. Effluents promoted plasmid-mediated gene transfer and microbial functional shifts, driving intracellular ARG proliferation in the plastisphere. Fibrous and fragmented MPs showed strong co-occurrence patterns with ARGs, virulence factor genes, and mobile genetic elements, suggesting their role in antimicrobial resistance dissemination. A projection pursuit regression model indicated effluent-induced MP risk escalation at the estuary and downstream areas, which was associated with fragmented and polyamide MPs. Notably, WWTPs released substantial extracellular ARGs, with MPs potentially serving as a protective niche and a proliferative microenvironment. Here, we determined the role of WWTPs in shaping the aquatic resistome via MPs, which provides critical data for risk assessment and control strategies.},
}

@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 {pmid40598447,
year = {2025},
author = {Bulzu, PA and Henriques Vieira, H and Ghai, R},
title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {154},
pmid = {40598447},
issn = {2049-2618},
support = {25-15920S//Grantová Agentura České Republiky/ ; 24-11998S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; },
mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; },
abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.

RESULTS: We leveraged long-read sequencing to recover large (200-600 Mb), high-quality, and highly repetitive (> 60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.

CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.},
}

*Cryptophyta/virology/genetics
Metagenomics
Phylogeny
Genome, Viral
Photosynthesis
*Giant Viruses/genetics/classification
*DNA Viruses/genetics/classification

@article {pmid40598440,
year = {2025},
author = {Lin, Z and Zhou, X and Lu, T and An, W and Chen, S and Li, S and Miao, H and Han, X},
title = {Co-cultivation of Lactobacillus acidophilus and Bacillus subtilis mediates the gut-muscle axis affecting pork quality and flavor.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {93},
pmid = {40598440},
issn = {1674-9782},
abstract = {BACKGROUND: Pork quality and flavor are critical determinants of consumer preference, yet the role of gut microbiota in shaping meat characteristics remains underexplored. In this study, we investigated how a probiotic consortium (FAM: Lactobacillus acidophilus and Bacillus subtilis) modulates the gut-muscle axis to enhance pork flavor.

RESULTS: In finishing pigs, FAM supplementation significantly increased flavor-associated nucleotides and umami-enhancing amino acids in longissimus dorsi muscle. Metagenomic analysis revealed FAM-driven enrichment of glycan-degrading Prevotella and short-chain fatty acid-producing Phascolarctobacterium, accompanied by reduced antibiotic resistance genes and virulence factors. Spearman correlation linked Prevotella copri abundance with elevated muscle amino acids, suggesting microbial-encoded CAZymes as key mediators.

CONCLUSIONS: This study provides the first evidence that probiotic-induced gut microbiota remodeling enhances pork flavor through metabolic cross-talk along the gut-muscle axis. The findings suggest a novel strategy for improving pork quality via dietary interventions targeting gut microbiota.},
}

@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 {pmid40597897,
year = {2025},
author = {Wang, X and Xie, Y and Chen, M and Zhu, H and He, G and Yu, W and Qiao, D and Shen, Y and Song, L and Deng, Q},
title = {The complex diagnosis of post-dialysis fever: a case report and literature review of infective endocarditis in a dialysis patient.},
journal = {BMC nephrology},
volume = {26},
number = {1},
pages = {331},
pmid = {40597897},
issn = {1471-2369},
support = {2024-KHRCBZ-B15 and 2024-KHRCBZ-B08//Science and Technology plan project of the First People' s Hospital of Yunnan Province/ ; 82460150//National Natural Science Foundation of China/ ; 202401AU070048//Yunnan Fundamental Research Projects/ ; },
mesh = {Humans ; Male ; Aged ; *Renal Dialysis/adverse effects ; *Kidney Failure, Chronic/therapy ; *Fever/etiology/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *Endocarditis/diagnosis ; },
abstract = {BACKGROUND: Post-dialysis fever is a common but diagnostically challenging issue in hemodialysis patients, with potential causes including dialysis-related infections, pulmonary infections, and cardiovascular complications.

CASE PRESENTATION: We report a 76-year-old male with end-stage renal disease (ESRD) on maintenance hemodialysis, coronary artery disease, and prior cardiac stent implantation, who presented with recurrent post-dialysis fever. Despite persistently negative conventional cultures, metagenomic next-generation sequencing (NGS) of pre-dialysis blood samples identified Pseudomonas aeruginosa (P. aeruginosa), Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes), Staphylococcus epidermidis (S. epidermidis), and Corynebacterium accolens (C. accolens) and Epstein-Barr virus (EBV), while post-dialysis samples revealed only C. acnes and EBV. Given the temporal association with fever, these two pathogens were considered the primary causative agents. Subsequent transesophageal echocardiography (TEE) confirmed aortic valve vegetations, establishing the diagnosis of infective endocarditis (IE). Following targeted antimicrobial and antiviral adjustments based on NGS findings, the patient exhibited complete resolution of post-dialysis fever and was discharged. However, as the vegetation was not surgically removed, he was hospitalized multiple times over the following five months for recurrent infections and ultimately died of septic shock and multi-organ failure due to carbapenem-resistant Klebsiella pneumoniae.

CONCLUSIONS: This case underscores the complementary role of TEE and NGS in diagnosing IE in high-risk patients, enabling the detection of uncommon pathogens and informing targeted therapy to improve clinical outcomes.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
Aged
*Renal Dialysis/adverse effects
*Kidney Failure, Chronic/therapy
*Fever/etiology/diagnosis/microbiology
*Endocarditis, Bacterial/diagnosis/microbiology
*Endocarditis/diagnosis

@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 {pmid40597432,
year = {2025},
author = {Ehau-Taumaunu, H and Bell, TH and Sadeghi, J and Hockett, KL},
title = {Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {77},
pmid = {40597432},
issn = {2524-6372},
support = {492F//PA Vegetable Growers Association/ ; 1016871//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.

RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.

CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.},
}

@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 {pmid40597335,
year = {2025},
author = {Drake, MJ and Pierdon, M and DeMers, G and Daniel, SG and Bittinger, K and Redding, LE},
title = {The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {71},
pmid = {40597335},
issn = {2524-4671},
abstract = {Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.},
}

@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 {pmid40596444,
year = {2025},
author = {Li, YC and Liu, YX and Li, L and Wang, H and Zhao, ZR and Yao, ZY},
title = {Metagenomic next-generation sequencing (mNGS) versus tissue culture technique (TCT) in diagnosis of spinal infection: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20926},
pmid = {40596444},
issn = {2045-2322},
support = {2022K57//Quzhou Science and Technology Tackling Project/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Spinal Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; },
abstract = {Spinal infections pose a significant clinical challenge due to the difficulty of early diagnosis. Traditional Tissue Culture Technique (TCT) has limitations, while Metagenomic Next-Generation Sequencing (mNGS) has emerged as a promising diagnostic tool. However, reports on the diagnostic performance of mNGS and TCT for spinal infections are inconsistent, and there has been a lack of systematic analysis of the evidence. This systematic review and meta-analysis included 10 studies involving a total of 770 patients to compare the diagnostic accuracy of mNGS and TCT. A comprehensive literature search was conducted using PubMed, Embase, Web of Science, Cochrane Library, and SinoMed to identify studies evaluating the diagnostic accuracy of mNGS and TCT for spinal infections. Data were analyzed using Review Manager 5.3 and Stata 16.0 to compute the sensitivity, specificity, and Area Under the Summary Receiver Operating Characteristic Curve (AUC). The meta-analysis revealed pooled estimates for mNGS with a sensitivity of 0.81 (95% CI, 0.74-0.87), specificity of 0.75 (95% CI, 0.48-0.91), and an AUC of 0.85 (95% CI, 0.82-0.88). In contrast, pooled estimates for TCT showed a sensitivity of 0.34 (95% CI, 0.27-0.43), specificity of 0.93 (95% CI, 0.79-0.98), and an AUC of 0.59 (95% CI, 0.55-0.63). While mNGS demonstrates higher sensitivity and overall diagnostic accuracy than TCT, its lower specificity suggests that it may be most effective when used alongside conventional methods to enhance diagnostic reliability in spinal infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Spinal Diseases/diagnosis/microbiology
Sensitivity and Specificity

@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 {pmid40595289,
year = {2025},
author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT},
title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20953},
pmid = {40595289},
issn = {2045-2322},
support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; },
abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.},
}

Animals
*Chickens/microbiology
*Interspersed Repetitive Sequences/genetics
Aquaculture
Fishes
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/pathogenicity/drug effects
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Virulence/genetics
Bangladesh

@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 {pmid40594802,
year = {2025},
author = {Deka, NC and Kumari, G and Nath, T},
title = {Microbial dynamics in rice ecosystem under supplementation of organic sources of nitrogen with inorganics and their concomitant impact on yield.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20473},
pmid = {40594802},
issn = {2045-2322},
abstract = {Microorganisms play crucial role in the ecosystem building. Their presence or absence in a particular environment are indicative of the web of interactions they undergo to impact the life of other components of the system. The current experiment was undertaken in rice-rice cropping sequence, for two years, to understand the changes in composition of microorganism as a result of interaction of herbicide and different nutrient sources added to soil under lowland area and a resultant grain yield obtained in rice. The experiment was divided into two simultaneous studies, i.e., field experiment and metagenomic study, to obtain the rice yield and soil microbial dynamics, respectively. Pooled soil samples were collected from rice field with constant herbicide application, i.e. Pyraszosulfuron (pre-emergent) @25 g/ha + 2, 4-D (post-emergent @0.5 kg/ha), but with 5 different sources of nutrients, viz., T0—absolute control, T1—100% N-P2O5-K2O through inorganic fertilizers (recommended dose of 40-20-20 kg/ha)), T2—75% N through inorganic + 25% N through FYM (P2O5 and K2O recommended doses), T3—75% N through inorganic + 25% N through vermicompost (P2O5 and K2O recommended doses) and T4—75% N through inorganic + 25% N through crop residues and bio-fertilizer (P2O5 and K2O recommended doses). Based on the amplicon DNA sequencing approach, it was observed that though there was an overall increase in bacterial phyla, viz., Chloroflexi, Actinomycetes, Euryarchaeota, Firmicutes in all the treatments from 0 days after transplanting (DAT) to physiological maturity of plant, however, soil treated with vermicompost (TH3) showed a dramatic increase in the population of one particular microbe viz., Firmicutes. Amongst fungal populations, Actinomycetes increased in soils of all the treatments from 0 DAS to physiological maturity, however, the increase was lowest in soil treated with vermicompost while it was highest in soil having crop residues (T4). The result obtained in microbial dynamics in case of vermicompost supplementation are concomitant to the biological yield of rice that was observed to be the highest in the same. The findings highlighted that the soil with vermicompost supplementation outperformed in terms of beneficial microbial changes and highest grain yield which, again, could be attributed to the favourable niche provided by vermicompost. Hence, supplementing vermicompost along with inorganic N sources can surpass the other organic sources in preventing deleterious effects of the chemical build-up in soil, due to herbicides and inorganic fertilizers, while synthesizing and releasing plant hormones, metabolites and antibiotics to suitably allow the growth and dominance of beneficial bacterial population.},
}

@article {pmid40594590,
year = {2025},
author = {Lan, N and Mao, C and Chen, M and Wang, X and Bai, S and Ren, J},
title = {Metagenomic insights into resistance trends related to microbial VB12 synthesis in eutrophic urban lakes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20599},
pmid = {40594590},
issn = {2045-2322},
support = {2023-YBSF-666//Scientific and Technological Research Foundation of Shaan'xi Province, Key Research and Development Project/ ; 2021A011//Shaanxi Provincial Key Research and Development Plan Project/ ; YXJLRH2022006//Basic and Clinical Integration Innovation Project of Xi' an Jiao tong University/ ; TQ202205//Nanjing Tianqing Scientific Research Fund of First Affliated Hospital of Xi'an Jiaotong University/ ; },
mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Metagenome ; *Vitamin B 12/biosynthesis/genetics ; Eutrophication ; Humans ; *Bacteria/genetics/metabolism ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Vitamin B12 (VB12) is essential for human health, and its deficiency can lead to various health issues, including anemia and neurological problems. Additionally, the presence of antibiotic resistance genes in various environments raises concerns about the spread of antibiotic resistance. This study aims to explore potential connections between these two functional gene categories in freshwater environments, which are closely intertwined with human health. We conducted a comprehensive metagenomic sequencing analysis across 23 sampling points from five different eutrophic urban lakes. The results highlight the dominance of the precorrin-2 synthesis pathway in the microbial synthesis of VB12 within urban lakes. Eutrophication may potentially enhance the precorrin-2 synthesis pathway while inhibiting others. The risk of antibiotic resistance is reduced in the anaerobic pathway of VB12 synthesis, while the abundance of metal resistance genes is increased. Binning analysis reveals that 26 metagenome-assembled genomes (MAGs) actively participate in VB12 synthesis, with at least 4 MAGs showing resistance during the VB12 synthesis process and demonstrating pathogenicity. These findings provide critical insights into the VB12 synthesis process and its implications for human health in terms of resistance risks.},
}

*Lakes/microbiology
*Metagenomics/methods
*Metagenome
*Vitamin B 12/biosynthesis/genetics
Eutrophication
Humans
*Bacteria/genetics/metabolism
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@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 {pmid40594045,
year = {2025},
author = {Bhamidipati, SV and Surathu, A and Chao, H and Agustinho, DP and Xiang, Q and Kottapalli, K and Santhanam, A and Momin, Z and Walker, K and Menon, VK and Weissenberger, G and Emerick, N and Mahjabeen, F and Meng, Q and Hu, J and Sucgang, R and Henke, D and Sedlazeck, FJ and Khan, ZM and Metcalf, GA and Avadhanula, V and Piedra, PA and Ramani, S and Atmar, RL and Estes, MK and Petrosino, JF and Gibbs, RA and Muzny, DM and Javornik, SC and Doddapaneni, H},
title = {Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20526},
pmid = {40594045},
issn = {2045-2322},
mesh = {Humans ; *Norovirus/genetics/isolation & purification ; *Genome, Viral ; *Respiratory Syncytial Virus, Human/genetics ; *Caliciviridae Infections/virology ; Genomics/methods ; *Respiratory Syncytial Virus Infections/virology ; Genotype ; Phylogeny ; Gastroenteritis/virology ; Oligonucleotide Probes/genetics ; },
abstract = {Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. Samples with Ct values 17.0-29.9 for RSV, and 20.2-34.8 for HuNoV, with some HuNoV below the detection limit were sequenced. The percentage of reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries. Full-length genomes were obtained for all RSV positive samples and in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data.},
}

Humans
*Norovirus/genetics/isolation & purification
*Genome, Viral
*Respiratory Syncytial Virus, Human/genetics
*Caliciviridae Infections/virology
Genomics/methods
*Respiratory Syncytial Virus Infections/virology
Genotype
Phylogeny
Gastroenteritis/virology
Oligonucleotide Probes/genetics

@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 {pmid40593605,
year = {2025},
author = {Butcher, J and Villette, C and Zumsteg, J and Maurer, L and Barchietto, T and Rigo, R and Floch, K and Cseh, A and Buchet, S and Stintzi, A and Heintz, D},
title = {Microbial bioremediation of persistent organic pollutants in plant tissues provides crop growth promoting liquid fertilizer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5768},
pmid = {40593605},
issn = {2041-1723},
support = {251174 and 199015//Agence de l'Eau Seine-Normandie/ ; 251174 and 199015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; OGI-149//Genome Canada (Génome Canada)/ ; OGI-149//Ontario Genomics Institute (OGI)/ ; },
mesh = {*Fertilizers ; Biodegradation, Environmental ; Wetlands ; *Persistent Organic Pollutants/metabolism ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; *Crops, Agricultural/growth & development/microbiology ; Wastewater ; Metagenomics ; },
abstract = {Constructed wetlands are used to clean domestic wastewater via phytoremediation, commonly involving the use of reeds. The process results in the production of large amounts of polluted plant tissues, which are then considered unusable waste products. In this study, the reusability of reeds and nettle-polluted tissues is investigated. Fermenting contaminated plant tissues to produce liquid fertilizer is a sustainable means to remove 87-95% of persistent organic pollutants. A multiomics approach combining metabolomics and amplicon metagenomics is used to analyze the mechanisms that occur during fertilizer production from polluted plant tissues and identify the microbes that are likely key for this transformation. A consortium of bacteria and fungi with cellulolytic activity is identified. In addition, the obtained liquid fertilizer positively impacts plant growth in the presence of pathogens and therefore exhibits potential application in farming. This approach may be a simple, commercially attractive solution for the management of contaminated plant tissues originating from constructed wetlands, which are currently considered problematic, useless waste products.},
}

*Fertilizers
Biodegradation, Environmental
Wetlands
*Persistent Organic Pollutants/metabolism
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
*Crops, Agricultural/growth & development/microbiology
Wastewater
Metagenomics

@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 {pmid40593191,
year = {2025},
author = {Park, K and Lee, J and Kim, J and Kim, SG and Song, DH and Gu, SH and Lee, SH and Lee, D and Kim, WK and Song, JW},
title = {Discovery and genomic characterization of Ulleung virus harbored by Crocidura utsuryoensis on Ulleung Island in Republic of Korea.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21748},
pmid = {40593191},
issn = {2045-2322},
support = {UE242006TD and 411FF5-912A01201//Agency for Defense Development/ ; },
mesh = {Animals ; Phylogeny ; *Shrews/virology ; Republic of Korea ; *Genome, Viral ; *Orthohantavirus/genetics/classification ; Genomics ; Haplotypes ; Islands ; },
abstract = {Hantaviruses are zoonotic RNA viruses that cause hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, posing significant public health risks. This study reports the identification and genomic characterization of Ulleung virus (ULLEV), a newly discovered genetic lineage of Orthohantavirus jejuense harbored by Crocidura utsuryoensis, a shrew species endemic to Ulleung Island, Republic of Korea. In 2009, a surveillance effort involving 62 shrews revealed a molecular prevalence of 64.5%. Metagenomic next-generation sequencing identified four viral variants, with ULLEV Cu09-33 fully characterized. Comparative genomic and phylogenetic analyses confirmed ULLEV as a distinct subtype within O. jejuense and suggested that ULLEV and Jeju virus (JJUV) share a common ancestor, with divergence shaped by long-term co-evolution with their hosts and geographic isolation. Haplotype network analysis of mitochondrial DNA detected eight unique haplotypes in C. utsuryoensis, distinct from C. shantungensis populations, indicating genetic isolation. While incongruences among the tripartite genomes of ULLEV and JJUV suggested independent evolutionary trajectories, evidence for reassortment remains insufficient. These findings highlight the ecological significance of geographically isolated environments as reservoirs for unique hantavirus lineages and underscore the need for expanded genomic surveillance and phylogenetic studies to assess the zoonotic potential and public health implications of ULLEV.},
}

Animals
Phylogeny
*Shrews/virology
Republic of Korea
*Genome, Viral
*Orthohantavirus/genetics/classification
Genomics
Haplotypes
Islands

@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 {pmid40592271,
year = {2025},
author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F},
title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139054},
doi = {10.1016/j.jhazmat.2025.139054},
pmid = {40592271},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.},
}

@article {pmid40592243,
year = {2025},
author = {Gao, Z and Liu, X and Yu, J and Li, Z and Shi, H and Zhang, G and Ling, J},
title = {Structural basis of immunomodulation by edible fungal polysaccharides: From molecular characteristics to action mechanisms.},
journal = {Carbohydrate research},
volume = {555},
number = {},
pages = {109591},
doi = {10.1016/j.carres.2025.109591},
pmid = {40592243},
issn = {1873-426X},
abstract = {Edible Fungal polysaccharides as Immunomodulators: A Systematic Review at the Crossroads of Immunology, Natural Products Chemistry, and Microbiology. The chemical structure-specifically molecular weight, branching degree, and functional group modifications-directly dictates immunological activity. For instance, high-molecular-weight β-glucans activate macrophage surface receptors through triple-helix conformations, whereas sulfation enhances electrostatic interactions with immune cells. Mechanistically, polysaccharides regulate macrophage polarization, dendritic cell maturation, and T/B cell activation, therebyengaging core signaling pathways such as TLR4/MyD88/NF-κB, NLRP3 inflammasome, and MAPK, This orchestrates synergistic enhancement of innate and adaptive immunity. Recent research further demonstrate that polysaccharides can also reshape the gut microbiota-immune metabolic axis by promoting the production of short-chain fatty acids (SCFAs) and activating receptors (e.g., GPR43), indirectly modulating systemic immune responses. Clinically, polysaccharides from Ganoderma lucidum and Lentinus edodes demonstrate efficacy in cancer adjuvant therapy by enhancing immune function and reducing radiotherapy/chemotherapy side effects. However, species-specific receptor recognition heterogeneity and lack of standardized preparation protocols impede clinical translation. Therefore,the implementing an integrated strategy of "polysaccharide structure-immunometabolic reprogramming-precision delivery" to overcome the existing bottlenecks. Combining multi-omics approaches (e.g., gut metagenomics and metabolomics) will advance therapeutics targeting microbiota-immune crosstalk. Such strategies aim to address chronic inflammatory inflammation", malignancies, and related pathologies with enhanced mechanistic specificity.},
}

@article {pmid40592211,
year = {2025},
author = {Zhioua, S and Khan, I and Gonzalez, D and Junier, P and Sieber, S},
title = {Genomic and chemical characterization of cytotoxic Ahp-cyclodepsipeptides from Phormidium using Thamnocephalus platyurus bioassay.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {179750},
doi = {10.1016/j.scitotenv.2025.179750},
pmid = {40592211},
issn = {1879-1026},
abstract = {Toxic benthic cyanobacterial mats have been identified globally as a potential health hazard since they can produce potent cyanotoxins. Such mats have been connected to the death of mammals worldwide, with a significant fraction of recent cases associated to benthic cyanobacterial blooms producing anatoxin-a or its derivatives. A recent event involving the death of a dog led to monitoring of mats in the area and to the discovery of the first cyanopeptolin producer among the genus Phormidium. Using metagenomics, the genome of the dominant species in the cyanobacterial mats collected was reconstructed, but no evidence for the production of anatoxin-a or other congeners was obtained. In contrast, the biosynthetic gene cluster for cyanopeptolin was detected in the genome. Further chemical analysis of metabolites extracted from the same mats enabled the isolation and characterization of two novel cyanopeptolins with their truncated products. Toxicity was confirmed using the cytotoxic reporting organism Thamnocephalus platyurus. The untruncated cyanopeptolins had an LC50 as low as 6.4 μM while the truncated products did not exhibit cytotoxicity in the same assay. The presence of truncated analogues lacking cytotoxicity might suggest that other mat-associated microorganisms could degrade those compounds. While Phormidium may not be the direct cause of dog's death, our study provides the first evidence that Phormidium can produce cyanopeptolins. This highlights the underexplored variety of neglected cyanotoxin classes. These findings not only expand the known chemical diversity of cyanotoxins but also raise concerns regarding the potential ecological impact of toxic Ahp-cyclodepsipeptides in freshwater environments.},
}

@article {pmid40591894,
year = {2025},
author = {Fu, S and Du, X and Xu, Z and Li, H and Yao, H and Tang, S and Zhao, W and Hao, M and Qiu, Z and Wang, Z},
title = {The potential of wastewater monitoring as a novel surveillance tool for early warning of Bordetella pertussis outbreaks.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2528537},
doi = {10.1080/22221751.2025.2528537},
pmid = {40591894},
issn = {2222-1751},
abstract = {The prolonged latency period and delayed reporting of clinical surveillance data have led to a sluggish response to Bordetella pertussis outbreaks in China. Wastewater-based surveillance (WBS) provides real-time, cost-effective monitoring of various viruses. To confirm whether this approach can be applied to B. pertussis, 271 patients infected with B. pertussis were enrolled to evaluate the fecal shedding patterns of the bacterium. Concurrently, we collected wastewater samples in a typical northern (Xi'an) and southern city (Nanchang) in China, from September 2023 to July 2024. The concentrations of B. pertussis in the sewage were detected using quantitative polymerase chain reaction (qPCR). Additionally, metagenomic sequencing with pre-enrichment was employed to trace genotypes of B. pertussis. We report that 40.2% of cases tested positive for B. pertussis in fecal samples. Sewage surveillance identified two waves of B. pertussis infection in Xi'an and one wave of B. pertussis outbreak in Nanchang. The concentration of B. pertussis in sewage showed a strong correlation with the dynamics of diagnosed cases. Notably, each peak of sewage B. pertussis concentration occurred 10 days prior to clinical surveillance, underscoring the value of WBS in early warning. Additionally, both clinical and wastewater surveillance demonstrated consistency in the prevalence estimation of B. pertussis infection cases. Finally, relative to clinical surveillance, wastewater sequencing also revealed the same genotypes of B. pertussis. This study presents the first comprehensive analysis of the fecal shedding of B. pertussis, thereby establishing the potential for early detection of B. pertussis outbreaks through WBS.},
}

@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 {pmid40590722,
year = {2025},
author = {Jin, H and Li, X and Wang, J and Cui, Y and Huang, S and Shi, K and Zhou, T and Yan, J},
title = {Draft genomes of Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2 from a tetrachloroethene-dechlorinating consortium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048525},
doi = {10.1128/mra.00485-25},
pmid = {40590722},
issn = {2576-098X},
abstract = {Two metagenome-assembled genomes were recovered from an anaerobic consortium capable of complete reductive dechlorination of tetrachloroethene to ethene. The draft genomes, assigned to Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2, are 1.37 and 3.84 Mb in size and encode 1,448 and 3,630 genes, respectively.},
}

@article {pmid40590427,
year = {2025},
author = {Nalla, S and Ganta, S and Bukke, SPN and Bandaru, N and Onohuean, H and Alagbonsi, AI},
title = {Kaempferide and Norbergenin avert aluminium chloride-induced amyloid β accumulation and neurocognitive shutdown via oxidative and apoptotic mechanisms.},
journal = {International journal of immunopathology and pharmacology},
volume = {39},
number = {},
pages = {3946320251343687},
pmid = {40590427},
issn = {2058-7384},
mesh = {Animals ; Aluminum Chloride ; Male ; *Apoptosis/drug effects ; Rats, Wistar ; *Oxidative Stress/drug effects ; *Neuroprotective Agents/pharmacology ; *Amyloid beta-Peptides/metabolism ; Rats ; *Cognition/drug effects ; Antioxidants/pharmacology ; Chlorides/toxicity ; Disease Models, Animal ; Aluminum Compounds ; },
abstract = {OBJECTIVE: To investigate the involvement of oxidative and apoptotic mechanisms in the possible neuroprotective effect of Kaempferide (KPD) and Norbergenin (NRG) against AlCl3-induced cognitive shutdown in rats.

INTRODUCTION: Aluminium chloride (AlCl3) is widely known as a neurotoxic agent that induces memory and cognitive shutdown via induction of oxidative stress and apoptosis. KPD is an O-methylated flavonol that possesses anti-oxidant, anti-inflammatory, anti-dementia and anti-depression properties, whereas NRG, a demethylated compound derived from bergenin, possesses an anti-oxidant property and has neuroprotective effects. Both alleviate D-galactose-induced neurotoxicity in rats.

METHODS: Eighty-four male Wistar rats were randomly divided into two experimental models: prophylactic (pre-treatment with donepezil, KPD or NRG; n = 42) and curative (post-treatment with donepezil, KPD, or NRG; n = 42). In each of these models, the animals were divided into seven groups (n = 6 per group): group 1 (normal saline), group 2 (200 mg/kg AlCl3), group 3 (donepezil + AlCl3), group 4 (5 mg/kg KPD + AlCl3), group 5 (10 mg/kg KPD + AlCl3), group 6 (5 mg/kg NRG + AlCl3) and group 7 (10 mg/kg NRG + AlCl3)Results:Kaempferide and Norbergenin averted the increase in TBARS, NO and AChE, and decrease in the number of crossings, time spent and distance moved in the target quadrant, latency of fall, speed, paw withdrawal threshold (PWT), SOD, CAT, GPx, GR and GSH induced by AlCl3. These agents also averted the upregulation of Aβ1-41, p-Tau, caspase-3, Bax and downregulation of Akt, p-CREB, SOD1 and BCl-2 induced by AlCl3Conclusion:The neuroprotective effects of KPD and NRG against AlCl3-induced Aβ accumulation and cognitive shutdown are mediated via suppression of oxidative stress and apoptosis.},
}

Animals
Aluminum Chloride
Male
*Apoptosis/drug effects
Rats, Wistar
*Oxidative Stress/drug effects
*Neuroprotective Agents/pharmacology
*Amyloid beta-Peptides/metabolism
Rats
*Cognition/drug effects
Antioxidants/pharmacology
Chlorides/toxicity
Disease Models, Animal
Aluminum Compounds

@article {pmid40590044,
year = {2025},
author = {Zhang, L and Rao, Y and Li, Z and Fan, M and Xiang, Z and Wang, J},
title = {The Advance and Clinical Practice on Lung Disease Caused by Mycobacterium abscessus.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3103-3115},
pmid = {40590044},
issn = {1178-6973},
abstract = {Mycobacterium abscessus (M. abscessus) lung disease has gradually become a common clinical condition, with its incidence rate continuously rising, especially among patients with weakened immune function or those with chronic lung diseases. Given the high resistance of M. abscessus to antibiotics, the options for antibiotics are very limited. Additionally, long treatment times and poor patient compliance lead to low cure rates and high recurrence rates, making it one of the significant public health challenges threatening global health. This article presents two cases of patients diagnosed with M. abscessus lung disease using next-generation metagenomic sequencing technology. It reviews and analyzes the current research on M. abscessus along with details from these cases. Furthermore, this article emphasizes the necessity of timely, regular, and comprehensive treatment for M. abscessus lung disease. Meanwhile, we call for the formulation of robust prevention strategies, the optimization and innovation of treatment regimens, and the enhancement of follow-up management after cure to improve the understanding and handling capabilities of M. abscessus lung disease, thereby addressing the increasing clinical challenges.},
}

@article {pmid40589867,
year = {2025},
author = {Xu, W and Han, D and Chen, T and Wang, Q},
title = {Infected pericardial effusion caused by Prevotella intermedia: a rare diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1612282},
pmid = {40589867},
issn = {2235-2988},
mesh = {Humans ; *Pericardial Effusion/microbiology/diagnosis ; *Prevotella intermedia/isolation & purification/genetics ; *Bacteroidaceae Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; China ; Male ; Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Female ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Prevotella intermedia is a Gram-negative bacterium that thrives in anaerobic environments. It presents challenges in detection through routine laboratory assays, and hitherto, there has been no documented instance of detecting this bacterium in pericardial effusion in China. Metagenomic Next-Generation Sequencing (mNGS) can boost the detection rate of this pathogen and furnish early guidance for clinical management.},
}

Humans
*Pericardial Effusion/microbiology/diagnosis
*Prevotella intermedia/isolation & purification/genetics
*Bacteroidaceae Infections/diagnosis/microbiology
High-Throughput Nucleotide Sequencing
China
Male
Metagenomics
Anti-Bacterial Agents/therapeutic use
Female
RNA, Ribosomal, 16S/genetics