@article {pmid40449445,
year = {2025},
author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F},
title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125972},
doi = {10.1016/j.jenvman.2025.125972},
pmid = {40449445},
issn = {1095-8630},
abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.},
}

@article {pmid40449443,
year = {2025},
author = {Hou, M and Gu, X and Lai, W and Fan, Y and Sun, S and Yan, P and Zhang, Y and Zheng, X and He, S},
title = {Sulfur-iron interactions forming activated FexSy pool in-situ to synergistically improve nitrogen removal in denitrification system.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126047},
doi = {10.1016/j.jenvman.2025.126047},
pmid = {40449443},
issn = {1095-8630},
abstract = {Sulfur-iron coupling has received increasing attention for improving nitrogen removal. However, the boosting mechanisms of denitrification in sulfur-iron coupling biological system are still ambiguous, and no reasonable explanation has been given for the mismatch between the amount of S[0] loss and the amount of SO4[2-] produced in the coupling system. Therefore, this study established sulfur-iron coupling denitrification systems, and investigated the nitrogen removal performances and coupling mechanisms of the systems. The research results showed that the TN removal efficiencies of the sulfur-iron coupling systems were 122.73-149.27 % higher than those of the single electron donor systems. In the process of nitrogen removal, about 26.03-35.32 % of the more leached S[0] and Fe[0] in the coupling systems co-precipitated to form activated FexSy pool in-situ, contributing about 25.41 % of the nitrogen removal and allowing the systems to remove 76.32-100 % of TN without external electron donors; moreover, the oxidation process of S[2-] provided electrons for the reduction of Fe (Ⅲ) to Fe (Ⅱ), generating more electron donors. Metagenomic sequencing results showed significant increases in the richness and diversity of functional microorganisms associated with sulfur and iron autotrophic denitrification in the coupling systems, and their contributions to the key genes in the denitrification, sulfur transformation and iron cycle processes increased substantially. In general, this study offered deeper understanding for assessing the nitrogen removal potential of the sulfur-iron coupling system, as well as investigating the interactions between S[0] and Fe[0] and elucidating nitrogen removal pathways within the system.},
}

@article {pmid40449312,
year = {2025},
author = {Xia, Z and Ng, HY and Bae, S},
title = {Synergistic microalgal-bacterial interactions enhance nitrogen removal in membrane-aerated biofilm photoreactors treating aquaculture wastewater under salt stress: Insights from metagenomic analysis.},
journal = {Water research},
volume = {283},
number = {},
pages = {123878},
doi = {10.1016/j.watres.2025.123878},
pmid = {40449312},
issn = {1879-2448},
abstract = {This study investigates the membrane-aerated biofilm photoreactor (MABPR) for treating aquaculture effluents with low C/N ratio and elevated salinity (0.5%-3.2%). The MABPR integrated biofilm reactors with microalgal-bacterial consortia, achieving superior total inorganic nitrogen (TIN) removal by leveraging counter-diffusional biofilm properties, bubbleless aeration, and enhanced microalgal productivity. The system consistently outperformed conventional reactors, achieving 84.7 ± 1.9% TIN removal at 3.2% salinity with TIN removal flux increasing from 0.82 ± 0.04 to 1.22 ± 0.07 g/m[2] d. The MABPR promoted microalgal proliferation (Chl-a/VSS: 8.08-15.04 mg/g) and higher biomass productivity (1.83 g/m[2] d) compared to SBBPR and MABR. Elevated salinity stimulated extracellular polymeric substance (EPS) production, reinforcing biofilm stability and microbial resilience. The MABPR demonstrated 22%-65% higher nitrogen removal efficiency than controls at the highest salinity. Canonical nitrification-denitrification remained the primary nitrogen removal pathway, with short-cut nitrification-denitrification contributing under salt stress. Metagenomic analysis revealed bidirectional adaptation between microalgae and bacteria, with enriched nitrogen assimilation (GS/GOGAT pathway) compensating for bacterial deficits. Microalgae facilitated pollutant removal through ammonia uptake and dissolved organic matter release, supporting denitrification. At 3.2% salinity, Nitrosomonas and Nitrobacter abundance increased by 42.6% and 35.8%, while denitrifiers Denitromonas and Hoeflea dominated, comprising 59.4% and 35.9% of the population. The MABPR further promoted the synthesis of growth cofactors (vitamins, phytohormones), enhancing microalgal productivity and stress resilience. These synergistic microalgal-bacterial interactions supported pollutant removal, showcasing the MABPR as a robust, sustainable solution for aquaculture wastewater treatment and resource recovery under salt stress.},
}

@article {pmid40449097,
year = {2025},
author = {Cañete-Reyes, Á and González, JG and Alteio, LV and Rodríguez-Lázaro, D and Hernández, M},
title = {Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs.},
journal = {Veterinary microbiology},
volume = {306},
number = {},
pages = {110542},
doi = {10.1016/j.vetmic.2025.110542},
pmid = {40449097},
issn = {1873-2542},
abstract = {Watery Mouth Disease is the main disease in neonatal lambs, causing great economic losses. Despite this, the cause of the condition remains poorly understood. Therefore, we have analysed the main bacteria found in sick animals, their intestinal and temporal distribution, as well as the main sources of contamination. Twelve different farms were sampled, from which 331 samples were taken in total. From these samples, 184 environments were analyzed using 16S rRNA amplicon sequencing, 164 isolates were identified by whole genome sequencing and 35 bacterial counts were performed. The dominant bacterial groups at the rectal level were Escherichia-Shigella (36 %) and Clostridium (29 %), with a homogeneous distribution along the digestive tract and a maximum abundance ranging between 12 and 24 hours of lamb life. Within Escherichia-Shigella: Escherichia coli and Escherichia fergusonii and within Clostridium: Clostridium perfringens, Clostridium cadaveris, Clostridium tertium and Clostridium paraputricum were identified as the main isolates present in sick animals. The high presence of Clostridium strains, especially potentially pathogenic species like C. perfringens in sick animals, point out Clostridium as a new important protagonist of watery mouth disease and the need of their inclusion in future studies. In particular, bedding was established as the main microbial contaminating factor, reaching the highest increase 48 hours after removal and cleaning of the lambing area (i.e. 8.03 ×10[8], 1.88 ×10[6], 3.88 ×10[6], 4.85 ×10[7] and 4.00 ×10[5] CFU/g for mesophilic aerobes, coliforms, E. coli, mesophilic anaerobes and sporulates, respectively). These results highlight the need to increase cleanliness in bedding to reduce the presence of these bacteria.},
}

@article {pmid40448586,
year = {2025},
author = {Jones, LM and El Aidy, S},
title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf112},
pmid = {40448586},
issn = {1751-7370},
abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.},
}

@article {pmid40448221,
year = {2025},
author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF},
title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {122},
pmid = {40448221},
issn = {1758-9193},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.

METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.

RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.

CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology/pathology/metabolism
*Alzheimer Disease/microbiology/pathology/metabolism
Male
Female
Aged
Feces/microbiology
Biomarkers
Brain/pathology/metabolism
Aged, 80 and over
Dysbiosis
tau Proteins
Middle Aged

@article {pmid40447717,
year = {2025},
author = {Lai, LM and Dai, QB and Cao, ML and Liu, Y and Zhao, R and Yuan, L},
title = {Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19039},
pmid = {40447717},
issn = {2045-2322},
support = {2024B1362//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; },
abstract = {Identifying pathogens in patients with lower respiratory tract infections (LRTIs) has always been a major challenge. Metagenomic next-generation sequencing (mNGS) technology is a new diagnostic tool that can assist clinicians in the etiological diagnosis of LRTIs. This study focuses on the clinical value of mNGS in the diagnosis of suspected LRTIs. A total of 400 patients with suspected LRTIs admitted at the First Affiliated Hospital of Nanchang University from July 2020 to February 2023 were enrolled in this retrospective study. Bronchoalveolar lavage fluid (BALF) samples were analyzed using both mNGS and culture methods. The diagnostic accuracy of two approaches was systematically compared against the final clinical diagnosis, which served as the gold-standard reference. Of the 400 enrolled cases, 82.3% (329/400) were diagnosed with LRTIs. From these cases, mNGS identified 76.8% (307/400) truepositive cases, 8.0% (32/400) falsepositive cases, 9.8% (39/400) truenegative cases, and 5.5% (22/400) falsenegative cases. mNGS demonstrated significantly higher sensitivity [93.3% (307/329) vs. 55.6(183/329)%] alongside greater negative predictive values [63.9% (39/61) vs.25.9%(51/197)], whereas culture offered higher specificity [54.9%(39/71) vs. 71.8%(51/71)]. The area under the receiver-operating curve (AUC) of mNGS[0.744(95%CI: 0.67-0.82)]was significantly higher than that of cultures[0.636(95%CI: 0.57-0.71)]. Specifically, mNGS detected more Streptococcus pneumoniae (7.0% vs. 0%), Haemophilus influenzae (6.7% vs. 0%), Aspergillus (9.4% vs. 3.5%), Pneumocystis jirovecii (11.9% vs. 0%) and other intracellular pathogens. Of the 329 patients with LRTIs, antibiotic treatment was modified based on the mNGS results in more than half of the patients(50.5%,166/329), including 20 cases of adjusted antimicrobial regimens, 70 cases de-escalated the empirical antibiotic treatment, and 76 patients escalated the treatment by increasing dosage or medication. 60.8%(101/166) of patients responded to modified antibiotic treatment. Significant benefits of mNGS have been shown in pathogen identification and antimicrobial treatment stewardship in patients with LRTIs. For those with suboptimal therapeutic responses, physicians should be alert to some emerging intracellular pathogens, including Chlamydia psittaci, Mycobacterium tuberculosis, and Pneumocystis jirovecii.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Female
Male
*Metagenomics/methods
Middle Aged
Retrospective Studies
Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity

@article {pmid40447596,
year = {2025},
author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W},
title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {92},
pmid = {40447596},
issn = {2055-5008},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Metagenomics/methods ; China ; *Lactobacillus/genetics/isolation & purification/classification/physiology ; Adult ; Gardnerella vaginalis/growth & development ; Microbiota ; Vaginosis, Bacterial/microbiology ; Biofilms/growth & development ; Asian People ; Pregnant People ; Young Adult ; },
abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Metagenomics/methods
China
*Lactobacillus/genetics/isolation & purification/classification/physiology
Adult
Gardnerella vaginalis/growth & development
Microbiota
Vaginosis, Bacterial/microbiology
Biofilms/growth & development
Asian People
Pregnant People
Young Adult

@article {pmid40447587,
year = {2025},
author = {Paluoja, P and Vaher, M and Teder, H and Krjutškov, K and Salumets, A and Raime, K},
title = {Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {91},
pmid = {40447587},
issn = {2396-8370},
support = {616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; },
abstract = {Honey's DNA mixture originates from various organisms like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey's biological composition. We conducted a honey bulk DNA metagenomic analysis to characterize the honey's taxonomic composition and identify honey bee-related pathogens and parasites based on 266 Estonian and 103 foreign honey samples. 70.4% of the DNA in Estonian honey was derived from green plant families like Brassicaceae, Rosaceae, Fabaceae, and Pinaceae. Geographical distribution analysis revealed distinct botanical compositions between Estonian mainland and island samples. The bacterial family Lactobacillaceae was prevalent overall, reflecting the honey bee microbiota in honey. We detected 12 honey bee pathogens and parasites, including Paenibacillus larvae, Nosema ceranae, Varroa destructor, and Aethina tumida. In conclusion, the study underscores the potential of bulk DNA-based non-targeted metagenomic approaches for monitoring honey bee health, environment, and honey composition, origin, and authenticity.},
}

@article {pmid40447574,
year = {2025},
author = {Rodríguez Del Río, Á and Scheu, S and Rillig, MC},
title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5058},
pmid = {40447574},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; },
abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.},
}

*Soil Microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects
Metagenome
Soil/chemistry
Droughts
Microbiota/genetics
Salinity
*Climate Change
Global Warming

@article {pmid40446767,
year = {2025},
author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A},
title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.},
journal = {Water research},
volume = {284},
number = {},
pages = {123887},
doi = {10.1016/j.watres.2025.123887},
pmid = {40446767},
issn = {1879-2448},
abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.},
}

@article {pmid40446617,
year = {2025},
author = {Rono, JK and Zhang, Q and He, Y and Zhao, L and Wang, S and Lyu, Y and Li, C and Ngigi, AN and Yang, ZM and Feng, Z},
title = {Identification and characterization of halotolerant multifunctional GH6 endoglucanases ZFEG1605 and ZFEG1663 from Mt. Everest soil metagenome.},
journal = {Carbohydrate research},
volume = {554},
number = {},
pages = {109549},
doi = {10.1016/j.carres.2025.109549},
pmid = {40446617},
issn = {1873-426X},
abstract = {Environmental microorganisms express enzymes with unique hydrolytic activity, stability, and kinetic parameters, which are of great interest for biotechnological applications. In this study, two novel endoglucanases, ZFEG1605 and ZFEG1663, were cloned from Mt. Everest soil metagenomic library, heterologously expressed in E. coli BL21(DE3), and characterized. Both enzymes exhibited high activity on konjac glucommanan (KG) and sodium carboxymethylcellulose (CMC), while ZFEG1605 also exhibited activity towards guar gum (GG). The optimal pH for both enzymes was slightly shifted toward acidic range (pH 5/6). The optimal reaction temperatures for ZFEG1605 and ZFEG1663 were 50 and 40 °C, respectively. ZFEG1605 was more thermostable than ZFEG1663 as it remained stable up to 50 °C, compared to 40 °C for ZFEG1663. Both enzymes showed broad pH stability, although they retained more mannanase activity than CMCase activity within the same pH range. The endoglucanases exhibited remarkable salt tolerance, retaining over 70 % of their enzymatic activity in the presence of 2.5 M NaCl. The purified enzymes hydrolyzed alkali-pretreated rice straw to release reducing sugars, demonstrating their potential usage for biomass saccharification.},
}

@article {pmid40445840,
year = {2025},
author = {Ricci, L and Selma-Royo, M and Golzato, D and Servais, C and Nabinejad, A and Marchi, P and Punčochář, M and Trenti, F and Garcia-Aloy, M and Armanini, F and Marconi, R and Asnicar, F and Pinto, F and Guella, G and Tamburini, S and Segata, N},
title = {Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.006798},
pmid = {40445840},
issn = {1466-5034},
mesh = {*Phylogeny ; *Feces/microbiology ; Humans ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Genome, Bacterial ; Adult ; Fatty Acids/analysis ; Phospholipids/analysis ; },
abstract = {A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ones. We isolated and characterized a strain of this clade from the stool of a healthy adult volunteer. Strain CMD8551[T] is strictly anaerobic, appears as long chains of Gram-positive rods and produces acetate in the presence of glucose. The lipidomic profile showed a higher proportion of saturated lipid species amongst the detected phospholipids. The whole genome is 2,320,430 bp long and has a G+C content of 33.7 mol% with 2,239 CDSs. A phylogenetic analysis comparing the sequences of the strain CMD8551[T] with publicly available reference genomes from the Catenibacterium genus revealed that the CMD8551[T] isolate, together with other isolate genomes, forms a distinct subspecies of C. mitsuokai and has an average nucleotide identity lower than 94% with respect to the previously described C. mitsuokai subsp. mitsuokai. Given the phenotypic, chemotaxonomic and phylogenetic characteristics of the newly isolated CMD8551[T] (=DSM 118469[T]=LMG 33725[T]=CIP 112509[T]) that clearly differ from those of the C. mitsuokai subsp. mitsuokai type strain RCA14-39[T], we propose it as the type strain of a novel subspecies of C. mitsuokai, with the name C. mitsuokai subsp. tridentinum subsp. nov.},
}

*Phylogeny
*Feces/microbiology
Humans
Base Composition
DNA, Bacterial/genetics
Bacterial Typing Techniques
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Genome, Bacterial
Adult
Fatty Acids/analysis
Phospholipids/analysis

@article {pmid40445833,
year = {2025},
author = {Li, W and Huang, B and Guo, M and Zeng, Z and Cai, T and Feng, L and Zhang, X and Guo, L and Jiang, X and Yin, Y and Wang, E and Huang, X and Zheng, J},
title = {Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115773},
doi = {10.1016/j.celrep.2025.115773},
pmid = {40445833},
issn = {2211-1247},
abstract = {Antimicrobial resistance poses a major threat to public health, prompting the development of alternative therapies such as antimicrobial peptides (AMPs). Protein language models (PLMs) have advanced protein structure and function predictions, facilitating AMP discovery. We developed antimicrobial peptide structural evolution miner (AMP-SEMiner), an AI-driven framework that integrates PLMs, structural clustering, and evolutionary analysis to systematically identify AMPs encoded by small open reading frames and AMP-containing proteins in metagenome-assembled genomes. AMP-SEMiner identified over 1.6 million AMP candidates across diverse environments. Experimental validation showed antimicrobial activity in 9 of the 20 tested candidates, with 5 surpassing antibiotic effectiveness; variant peptides derived from these candidates similarly demonstrated strong antimicrobial efficacy. AMPs from human gut microbiomes revealed both conserved and adaptive evolutionary strategies, reflecting their dynamic ecological roles. AMP-SEMiner thus represents a valuable tool for expanding AMP discovery and has significant potential to inform the development of alternative antimicrobial treatments.},
}

@article {pmid40445752,
year = {2025},
author = {Xing, Y and Hernandez Santos, HJ and Qiu, L and Ritter, SR and Zulk, JJ and Lahowetz, R and Patras, KA and Terwilliger, AL and Maresso, AW},
title = {Phage-induced protection against lethal bacterial reinfection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {22},
pages = {e2423286122},
doi = {10.1073/pnas.2423286122},
pmid = {40445752},
issn = {1091-6490},
support = {U19AI157981//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI144297//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5F31DK136201//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; 5359//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation (Kleberg Foundation)/ ; },
mesh = {*Phage Therapy/methods ; Animals ; *Bacteriophages/physiology ; *Reinfection/prevention & control/therapy/microbiology ; Mice ; *Bacterial Infections/therapy/prevention & control ; },
abstract = {Bacteriophages, or phages, are viruses that target and infect bacteria. Due to a worldwide rise in antimicrobial resistance (AMR), phages have been proposed as a promising alternative to antibiotics for the treatment of resistant bacterial infections. Up to this point in history, phage use in preclinical animal studies, clinical trials, and emergency-use compassionate care cases has centered around the original observation from 1915 showing phage as lytic agent, and thus a treatment that kills bacteria. Here, we describe an activity associated with phage therapy that extends beyond lytic activity that results in long-term protection against reinfection. This activity is potent, providing almost complete protection against a second lethal infection for animals treated with phage therapy. The activity also reduced infection burden an astounding billion-fold over the control. Reinfection protection requires phage lytic killing of its target bacterium but is independent of additional phage therapy. The effect is not driven by phage alone, lingering phage resistors, or a sublethal inoculum. In vitro phage-lysed bacteria provide partial protection, suggesting a combination of phage-induced lytic activity and immune stimulation by phage treatment is responsible for the effect. These observations imply certain phages may induce host adaptive responses following the lysis of the infecting bacteria. This work suggests phage therapy may contain a dual-action effect, an initial treatment efficacy followed by a long-term protection against reoccurring infection, a therapeutic-vaccination mechanism of action.},
}

*Phage Therapy/methods
Animals
*Bacteriophages/physiology
*Reinfection/prevention & control/therapy/microbiology
Mice
*Bacterial Infections/therapy/prevention & control

@article {pmid40445195,
year = {2025},
author = {Schuele, L and Masirika, LM and Cassidy, H and Clausen, PTLC and Zaeck, LM and Boter, M and Ndishimye, P and Udahemuka, JC and de Vries, RD and Otani, S and Molenkamp, R and Nieuwenhuijse, DF and Mbiribindi, JB and Siangoli, FB and Koopmans, M and Aarestrup, FM and Oude Munnink, BB},
title = {Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051225},
doi = {10.1128/spectrum.00512-25},
pmid = {40445195},
issn = {2165-0497},
abstract = {Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalized patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV), and viral co-infections. High-quality MPXV whole-genome sequences were obtained until a Ct value of 27. Furthermore, co-infections with other clinically relevant viruses, such as varicella zoster virus and herpes simplex virus-2, were detected and confirmed by real-time PCR. In addition, metagenomic sequence analysis of the bacterial content showed the presence of bacteria associated with skin and soft tissue infection in 10 of the 19 samples analyzed. These bacteria had a high abundance of resistance genes, with possible implications for antimicrobial treatment based on the predicted antimicrobial resistance. In conclusion, we report the presence of bacterial and viral pathogens in mpox lesions and detection of widespread resistance genes to the standard antibiotic treatment. The possibility of a co-infection, including antimicrobial resistance, should be considered when discussing treatment options, along with the determination of the case-fatality ratio.IMPORTANCEThe mpox virus clade Ib lineage emerged in the eastern Democratic Republic of the Congo owing to continuous human-to-human transmission in a vulnerable patient population. A major challenge of this ongoing outbreak is its occurrence in regions with severely limited healthcare infrastructure. As a result, less is known about co-infections in affected patients. Identifying and characterizing pathogens, including their antimicrobial resistance, is crucial for reducing infection-related complications and improving antimicrobial stewardship. In this study, we applied a unified metagenomics approach to detect and characterize bacterial and viral co-infections in mpox lesions of hospitalized mpox patients in the eastern DRC.},
}

@article {pmid40445192,
year = {2025},
author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL},
title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40445192},
issn = {2050-084X},
support = {AI139154/NH/NIH HHS/United States ; 2330095//National Science Foundation/ ; CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; },
mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; },
abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.},
}

Animals
*Alleles
Female
Male
*Drosophila Proteins/genetics/immunology
*Selection, Genetic
Providencia/immunology
*Drosophila/genetics/immunology/microbiology
Gastrointestinal Microbiome
*Drosophila melanogaster/genetics/immunology/microbiology
*Antimicrobial Peptides/genetics/immunology

@article {pmid40445060,
year = {2025},
author = {Gao, H and Guo, Z and Xu, R and He, X and Fernio, JU and Li, S and Liu, X and Liu, H and Xue, W},
title = {Chemolithoautotrophic Antimonite Oxidation Coupled Nitrogen Fixation in the Rhizosphere of Local Plant in Antimony Tailing Area.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03872},
pmid = {40445060},
issn = {1520-5851},
abstract = {Antimony (Sb) tailings pose a significant environmental challenge. N-fixing microorganisms are essential for nutrient accumulation and plant colonization in degraded habitats. However, the oligotrophic conditions of tailings often inhibit the energy-intensive N-fixing process. This study identified a chemolithoautotrophic Sb(III) oxidation-coupled nitrogen fixation (SbNF) pathway in the rhizosphere of local plants. SbNF integrates biological detoxification and nutrient accumulation, enabling plant colonization and ecological restoration of degraded habitats. Multi-omic analyses reveal that Sb content strongly shapes the composition of Sb-oxidizing and N-fixing bacterial communities in the rhizosphere. Abundant marker genes for carbon fixation (cbbL), Sb(III) oxidase (aioAB/anoA), and nitrogenase (nifH) were consistently detected in SbNF metagenome-assembled genomes. Positive correlations between gene abundances associated with autotrophic potential (aioA-cbbL) and coupling potential (aioA-nifH) were observed in the rhizoplane but not in the endosphere. In addition to genetic potentials, high-throughput cultivation of native SbNF-isolates (e.g., Pseudomonas, Arthrobacter, and Sphingomonas) confirmed their rapid Sb(III) oxidation coupling autotrophic growth and nitrogen fixation. Isolates also exhibited plant growth-promoting traits, including indole-3-acetic acid production, phosphate solubilization, and siderophore secretion, providing multiple benefits to host plants. Co-cultivation of these isolates revealed minimal antagonism, suggesting the potential for designing synthetic microbial communities for sustainable phytoremediation. Cross-validation further suggests that SbNF is widespread in the rhizosphere of various local plants. These findings uncover a novel biogeochemical process in the rhizosphere, linking mineral oxidation, autotrophic growth, and nitrogen fixation, highlighting its importance for the ecological restoration of degraded tailing area.},
}

@article {pmid40445001,
year = {2025},
author = {Andréani, J and Smiljkovic, M and Lametery, E and Khedimallah, S and Court, N and Jardin, H and Arata-Bardet, J and Truffot, A and Germi, R and Morand, P and Cappy, P and Rodriguez, C and Lupo, J and Larrat, S},
title = {Metagenomics Diagnosis of a Parvovirus B19-Associated Encephalomyelitis in an Epidemic Context.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004780},
pmid = {40445001},
issn = {1532-0987},
abstract = {In the context of increasing parvovirus B19 (B19V) infections, we describe a case of B19V encephalomyelitis without any usually associated clinical features. Etiology was identified by metagenomics and confirmed by PCR and whole-genome sequencing. This case highlights the need to consider the diagnosis of B19V infection in patients presenting with neurological symptoms.},
}

@article {pmid40444981,
year = {2025},
author = {Harrison, K and Rapp, JZ and Jaffe, AL and Deming, JW and Young, J},
title = {Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0060425},
doi = {10.1128/aem.00604-25},
pmid = {40444981},
issn = {1098-5336},
abstract = {The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of autotrophic pathways and chemolithoautotrophic Rubiscos from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. The Calvin-Benson-Bassham (CBB) cycle was widely found in both environments, although with different predominant Rubisco forms. From cryopeg brine, reconstructions of metagenome-assembled genomes (MAGs) uncovered four MAGs with the potential for chemolithoautotrophy, of which the CBB-containing genus Thiomicrorhabdus was most abundant. A broader survey of Thiomicrorhabdus genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with a complex pattern of gain and loss, with form II constitutively present in genomes from subzero environments. Using representative kinetic data, we modeled carboxylation rates of Rubisco forms II, IAc, and IAq across CO2, O2, and temperature conditions. We found that form II outcompetes form I at low O2, but cold temperatures minimize this advantage. Inspection of form II from genomes from cold environments identified signals of potential thermal adaptation due to key amino acid substitutions, which resulted in a more exposed active site. We argue that subzero form II from Thiomicrorhabdus warrants further study as it may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies.IMPORTANCEAutotrophy, or the fixation of inorganic carbon to biomass, is a key factor in life's ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found evidence for potential cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.},
}

@article {pmid40444423,
year = {2025},
author = {Yi, H and Zhang, S and Wang, J and Xu, C and Yang, D and Lin, Q and Wang, X and Feng, S},
title = {CT Features for Prognostic Assessment of Pulmonary Mucormycosis in Patients With Hematological Diseases.},
journal = {Journal of thoracic imaging},
volume = {},
number = {},
pages = {},
doi = {10.1097/RTI.0000000000000832},
pmid = {40444423},
issn = {1536-0237},
support = {2021-I2M-1-017 and 2023-I2M-2-007//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; },
abstract = {PURPOSE: To explore the CT features in prognostic evaluations for pulmonary mucormycosis in patients with hematological diseases.

MATERIALS AND METHODS: A retrospective analysis of clinical data and chest CT features of 53 HD patients with PM was conducted. Univariate and multivariate logistic regression analyses were used to determine the risk factors for death. The Cox regression model was used to analyze the factors affecting the survival rate.

RESULTS: A total of 30 patients with proven PM and 23 with probable PM were included. All 30 patients with proven PM underwent bronchoscopy-guided biopsy, among which 9 cases underwent surgical resection. Of the 23 patients with probable PM, 5 cases had positive results in sputum smear microscopy, 4 cases in sputum culture, 13 cases in bronchoalveolar lavage fluid (BALF) microscopy, and 1 case in BALF culture. All identification of pathogen genera and partial species was conducted by metagenomic next-generation sequencing (mNGS) testing. In the multivariate regression analysis, the CT feature of multiple lesions (≥2) on the initial CT scan was an independent risk factor for mortality (P=0.019). Cox survival analysis demonstrated a significantly lower survival rate (P=0.043) in patients exhibiting the CT feature of multiple lesions on the initial CT scan.

CONCLUSIONS: The CT feature of multiple lesions (≥2) on the initial CT may serve as an independent risk factor for mortality in patients with hematologic disorders with pulmonary mucormycosis.},
}

@article {pmid40444400,
year = {2025},
author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ},
title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {e23617},
doi = {10.1002/alr.23617},
pmid = {40444400},
issn = {2042-6984},
support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; },
}

@article {pmid40444000,
year = {2025},
author = {Pacheco-Dorantes, C and Tovar-Pedraza, JM and Ochoa-Martínez, DL and González-Garza, R and Diaz-Lara, A},
title = {Unleashing the potential of high-throughput sequencing for plant virus and viroid detection in Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1603010},
pmid = {40444000},
issn = {1664-302X},
abstract = {High-throughput sequencing (HTS) has revolutionized plant virology in Mexico by enhancing the detection and characterization of plant viruses and viroids. This technology has contributed to identifying previously neglected pathogens affecting key crops such as corn, beans, and tomato. The use of HTS has also revealed the presence of mixed viral infections, highlighting the complexity of plant viromes within agricultural ecosystems. Furthermore, metagenomic studies have demonstrated the role of water sources as reservoirs for plant viruses, underscoring the urgent need for improved management strategies. Despite its advantages, the widespread adoption of HTS faces challenges, including high costs, the need for bioinformatics expertise, and infrastructure limitations. Supporting collaborations between research institutions and regulatory agencies is crucial to integrating HTS into routine phytosanitary programs. Future research should aim to expand HTS applications to include epidemiological monitoring, resistance breeding, and the development of sustainable management strategies to mitigate the impact of emerging plant viruses in Mexico.},
}

@article {pmid40443674,
year = {2025},
author = {Wang, Y and Ma, X and Ma, C and Sun, T and Zhao, D and Li, H and Yan, Y and Guo, J},
title = {Case Report: Anti-NMDAR encephalitis associated with neurobrucellosis: causality or coexistence?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1536740},
pmid = {40443674},
issn = {1664-3224},
mesh = {Humans ; Male ; *Brucellosis/complications/diagnosis/immunology/drug therapy/microbiology ; Adult ; *Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis/etiology/immunology/drug therapy ; *Brucella melitensis/immunology ; Autoantibodies/immunology ; },
abstract = {Human brucellosis, caused by Brucella, is an infectious disease with specific endemic regions, especially in pastoral areas, and may affect multiple organ systems. Neurological involvement, namely neurobrucellosis, occurs in very few of these patients. Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most frequent type of autoimmune encephalitis and is usually associated with tumors or herpes simplex virus infections. However, the link between the two disease entities is unknown. In this report, we present a rare case of a 29-year-old Chinese man with anti-NMDAR encephalitis associated with neurobrucellosis, with the detection of anti-NMDAR antibodies by cell-based assay and Brucella melitensis by metagenomic next-generation sequencing in his cerebrospinal fluid sample. The patient improved after antimicrobial treatment and immunotherapies, including steroids and intravenous immunoglobulin. This case implicates Brucella infection as a possible trigger for the production of anti-NMDAR antibodies, and prospective studies should reveal whether there is a casual relationship between brucellosis and anti-NMDAR antibodies.},
}

Humans
Male
*Brucellosis/complications/diagnosis/immunology/drug therapy/microbiology
Adult
*Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis/etiology/immunology/drug therapy
*Brucella melitensis/immunology
Autoantibodies/immunology

@article {pmid40443669,
year = {2025},
author = {Zhang, C and Xu, Y and Zhang, M and Li, J and Sun, Z and Wang, Y and Lin, P},
title = {An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1500866},
pmid = {40443669},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/immunology/microbiology/metabolism ; Adult ; Proteomics/methods ; *Th2 Cells/immunology/metabolism ; *Th1 Cells/immunology/metabolism ; Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; *Pregnancy Complications/immunology/metabolism/microbiology ; *Proteome ; Cytokines/metabolism ; },
abstract = {OBJECTIVE: To explore the gut microbiota and proteomic characteristics of hypothyroidism in the first half of pregnancy (referred to as hypothyroidism in the first half of pregnancy) and its association with Th (T helper cells, Th)1/Th2 balance using metagenomics combined with proteomics.

METHODS: Stool and blood samples were collected from 20 hypothyroid (hypothyroidism group) and normal pregnant women (normal group) in the first half of pregnancy. Flora and proteomic characteristics were analyzed using metagenomics sequencing and 4D-DIA proteomics. Th1 and Th2 cells were quantified, and cytokine levels were measured using cellular micro-bead arra. The enzyme-linked immunosorbent test (ELISA) was utilized to assess differential proteins.

RESULTS: (1) Metagenomic sequencing revealed distinct microbial profiles: The β-diversity of gut microbiota was diminished in the hypothyroidism group (p < 0.05). LEfSe analysis identified Phocaeicola vulgatus and Bacteroides fragilis enriched in the hypothyroidism group (p<0.05), and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed significant enrichment in pathways related to peptidoglycan biosynthesis and glycerol ester metabolism.(2) Proteomic analysis demonstrated downregulation of Diacylglycerol Kinase Kappa (DGKK) and P05109|S10A8(S10A8) proteins in the hypothyroidism group, with marked enrichment in the KEGG pathways for vascular smooth muscle contraction and phosphatidylinositol signaling. (3) ELISA validation confirmed that the proteins DGKK and S10A8 were downregulated in pregnant women in the hypothyroidism group.

CONCLUSION: Increased P. vulgatus and B. fragilis, decreased DGKK and S10A8 proteins, and a left shift in the Th1/Th2 balance in patients with hypothyroidism in the first half of pregnancy may be associated with the development of the disease.},
}

Humans
Female
Pregnancy
*Hypothyroidism/immunology/microbiology/metabolism
Adult
Proteomics/methods
*Th2 Cells/immunology/metabolism
*Th1 Cells/immunology/metabolism
Metagenomics/methods
*Gastrointestinal Microbiome/immunology
*Pregnancy Complications/immunology/metabolism/microbiology
*Proteome
Cytokines/metabolism

@article {pmid40442718,
year = {2025},
author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P},
title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.},
journal = {International breastfeeding journal},
volume = {20},
number = {1},
pages = {44},
pmid = {40442718},
issn = {1746-4358},
support = {LM2023069//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 857560//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation & purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs & derivatives ; },
abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.},
}

Humans
*Milk, Human/microbiology
Female
*Bacteria/isolation & purification/genetics/classification
*Food Storage/methods
Adult
RNA, Ribosomal, 16S
*Microbiota
Freezing
Refrigeration
Azides
Propidium/analogs & derivatives

@article {pmid40442502,
year = {2025},
author = {Tzlil, G and Marín, MDC and Matsuzaki, Y and Nag, P and Itakura, S and Mizuno, Y and Murakoshi, S and Tanaka, T and Larom, S and Konno, M and Abe-Yoshizumi, R and Molina-Márquez, A and Bárcenas-Pérez, D and Cheel, J and Koblížek, M and León, R and Katayama, K and Kandori, H and Schapiro, I and Shihoya, W and Nureki, O and Inoue, K and Rozenberg, A and Chazan, A and Béjà, O},
title = {Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40442502},
issn = {2058-5276},
support = {3131/20//Israel Science Foundation (ISF)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.},
}

@article {pmid40442233,
year = {2025},
author = {Li, X and Tang, C and Zhou, M and Mi, J and Liu, J and Han, L and Yu, X and Zhang, X},
title = {Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18923},
pmid = {40442233},
issn = {2045-2322},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; 23DX1900300//Shanghai Targeted Biomedical Emergency Project/ ; },
mesh = {Humans ; *COVID-19/virology/epidemiology ; *SARS-CoV-2/genetics/isolation & purification/classification ; Aged ; Female ; Male ; *Coinfection/virology/microbiology/epidemiology ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Phylogeny ; Retrospective Studies ; Hospitalization ; Adult ; Aged, 80 and over ; },
abstract = {Metagenomic next-generation sequencing (mNGS) is widely used to diagnose complex infections in hospitalized patients, particularly those associated with COVID-19 which has garnered significant concern over the past five years. To investigate the molecular epidemic of the viral variant and the potential co-infection pathogens, we conducted retrospective mNGS analysis of 254 SARS-CoV-2-positive specimens collected from 200 hospitalized patients between March and September 2023. Phylogenetic analysis of the identified Omicron subvariants showed minimal evolutionary divergence, with no association between sub-lineages and pneumonia severity. Notably, mNGS demonstrated enhanced detection of polymicrobial coinfections, identifying bacterial, fungal, and viral co-pathogens in 92.5% (185/200) of cases. Pneumonia severity was associated with advanced age (proportion of elderly patients: 61.1 vs 78.3%; p = 0.032) and comorbid conditions, particularly diabetes mellitus (OR 2.03, 95% CI 1.03-4.02, p = 0.041), but showed no correlation with SARS-CoV-2 sub-lineages or coinfecting pathogens. While mNGS enhances coinfection diagnosis, COVID-19 outcomes are predominantly driven by host factors rather than Omicron subvariant evolution. Prioritized monitoring of elderly and comorbid individuals remained critical for severe pneumonia management.},
}

Humans
*COVID-19/virology/epidemiology
*SARS-CoV-2/genetics/isolation & purification/classification
Aged
Female
Male
*Coinfection/virology/microbiology/epidemiology
Middle Aged
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Phylogeny
Retrospective Studies
Hospitalization
Adult
Aged, 80 and over

@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}

Humans
*Dermatitis, Atopic/microbiology
*Gastrointestinal Microbiome
Infant
*Bifidobacterium longum/genetics/isolation & purification/classification/metabolism
Female
Male
Metabolomics
Metagenomics/methods
Feces/microbiology
*Host Microbial Interactions
Clostridium/genetics/isolation & purification
Transcriptome
Multiomics

@article {pmid40441146,
year = {2025},
author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B},
title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.003},
pmid = {40441146},
issn = {1934-6069},
abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.},
}

@article {pmid40440847,
year = {2025},
author = {Shirai, T and Motooka, D and Ushikai, Y and Komano, J and Shioda, T and Iida, T and Sakon, N},
title = {Molecular epidemiology of human sapovirus based on the surveillance of wastewater and patients with acute gastroenteritis in Osaka, Japan.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179622},
doi = {10.1016/j.scitotenv.2025.179622},
pmid = {40440847},
issn = {1879-1026},
abstract = {Wastewater-based epidemiology has recently emerged as a promising tool for determining the prevalence of infectious diseases in a community. In the present study, human sapoviruses (HuSaVs) detected in wastewater collected weekly from January 2023 to March 2024 were analyzed using qPCR and next-generation sequencing (NGS), and the results were compared with those from clinical surveillance samples obtained from patients with acute gastroenteritis (AGE) in Osaka Prefecture, Japan. The detection trend of HuSaV in wastewater agreed with the clinical surveillance data in that HuSaV genomes increased in the cold season. In wastewater surveillance, five genotypes were detected, including GI.1, GI.2, GII.3, GII.5, and GV.1. GI.2 was not detected in the clinical surveillance. In the phylogenetic analysis, VP1 gene sequences obtained from wastewater were positioned in close proximity to those obtained from clinical samples. It is suggested that the results of wastewater surveillance reflect the status of ongoing HuSaV infection in a community. Interestingly, GV.1 was detected less frequently than GI.1 in clinical surveillance samples, but was predominantly detected in wastewater at nearly all time points, accounting for up to 94.5 % of all reads in November 2023. In particular, in November 2023, most gastroenteritis outbreaks and pediatric AGE cases were attributable to GI.1, but GV.1 was present at a higher proportion in the wastewater surveillance than GI.1. Wastewater surveillance was shown to complement clinical surveillance in that the former might be able to cover asymptomatic carriers. Our results demonstrate the importance of systematic clinical and wastewater surveillance in epidemiological analyses of HuSaV.},
}

@article {pmid40440727,
year = {2025},
author = {Ning, J and Du, Y and Wang, J and Liu, W and Deng, Y and Gan, Y and Wang, Y},
title = {Contribution of Microbial Metabolism to Geogenic Phosphorus Enrichment in Groundwater: Insights from Metagenomic Sequencing and Organic Molecular Characterization.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02169},
pmid = {40440727},
issn = {1520-5851},
abstract = {Microbial mediation in the enrichment of geogenic phosphorus (P) is often mentioned but rarely explored, especially in P enrichment processes through the mineralization of dissolved organic matter (DOM) containing natural P. To bridge the theoretical gap, this study investigated the mechanisms of P enrichment through microbially mediated mineralization of natural P-containing DOM by adopting an approach combining comprehensive field investigation with hydrochemical and molecular biological analyses. The co-analysis of the dominant microbial community compositions and genomics revealed that the microbial metabolism pathways involved in the biodegradation of P-containing DOM were associated with the enrichment level of dissolved inorganic phosphorus (DIP). Specifically, dephosphorylation was more pronounced under conditions of limited DIP, while C-P bond cleavage was the primary metabolic pathway under sufficient DIP. Co-occurrence network analysis further indicated that the substrates for DIP enrichment differed between dephosphorylation and C-P bond cleavage, namely CHONSP1 compounds in the region of highly unsaturated-low O compounds (AI ≤ 0.5, H/C < 1.5, and O/C < 0.4) and CHOP1 compounds in the region of highly unsaturated-high O compounds (AI ≤ 0.5, H/C < 1.5, and O/C ≥ 0.4), respectively. These findings provide new insights into geogenic P enrichment in groundwater from the perspective of microbial metabolism and have potential implications for the bioremediation of P-contaminated groundwater at different contamination levels.},
}

@article {pmid40440710,
year = {2025},
author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X},
title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004845},
pmid = {40440710},
issn = {1532-0987},
support = {No. 2021GG0209//Science and Technology Project of the Inner Mongolia Department of Science and Technology/ ; },
abstract = {OBJECTIVE: To explore the clinical characteristics of neurobrucellosis in children and the diagnostic value of metagenomics next-generation sequencing (mNGS) of cerebrospinal fluid and traditional microbial detection methods.

METHODS: Three patients in the pediatrics department from April 2022 to October 2023 were diagnosed with brucellosis, and 5 mL of cerebrospinal fluid was taken and sent for routine biochemical, bacterial Gram-stained smear, antacid-stained smear, ink staining, bacterial culture and second-generation sequencing of the microgeneration of the cerebrospinal fluid, respectively (Beijing AJiAn Genetics Medical Laboratory). Cranial magnetic resonance imaging, blood culture and blood Brucella antibody test were also performed to summarize the clinical features and pathogenic analysis.

RESULTS: The chief presentations were fever, headache, vomiting, somnolence and positive signs of meningeal irritation in all patients. Case 3: persistent hemiparesis of the left limb and cerebral infarction. Brucella was detected by cerebrospinal fluid mNGS in all cases, with sequence numbers of 5252, 162 and 59 Brucella and relative abundances of 80.26%, 6.14% and 1.06%, respectively. Cerebrospinal fluid cultures were negative, and blood cultures were positive in case 3.

CONCLUSIONS: The clinical characteristics of neurobrucellosis in children are variable, and meningoencephalitis is common. Traditional microbiological tests are difficult to detect Brucella, whereas cerebrospinal fluid mNGS can provide a precise diagnosis.},
}

@article {pmid40440092,
year = {2025},
author = {Lawniczak, MKN and Kocot, KM and Astrin, JJ and Blaxter, M and Sotero-Caio, CG and Barker, KB and Childers, AK and Coddington, J and Davis, P and Howe, K and Johnson, WE and McKenna, DD and Wideman, JG and Pettersson, OV and Ras, V and Santos, BF and , },
title = {Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40440092},
issn = {2047-217X},
support = {//Science for Life Laboratory/ ; //Swedish Research Council/ ; 1846174//National Science Foundation/ ; 2138994//National Science Foundation/ ; 2321308//National Science Foundation/ ; 2001303//National Science Foundation/ ; 2110053//National Science Foundation/ ; 1937815//National Science Foundation/ ; DBI-2119963//National Science Foundation/ ; U24HG006941/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; //Agricultural Research Service/ ; },
mesh = {*Genome ; *Genomics/standards/methods ; *Metagenomics/standards/methods ; Earth, Planet ; *Specimen Handling/standards/methods ; },
abstract = {The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.},
}

*Genome
*Genomics/standards/methods
*Metagenomics/standards/methods
Earth, Planet
*Specimen Handling/standards/methods

@article {pmid40439988,
year = {2025},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ},
title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {40439988},
issn = {1573-7330},
abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.

METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.

RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.

CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.},
}

@article {pmid40439829,
year = {2025},
author = {Wu, C and Han, X and Yang, F and Zhang, G and Zhao, C},
title = {Misdiagnosis of autoimmune glial fibrillary acidic protein astrocytopathy as infectious meningitis: a case report.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {},
number = {},
pages = {},
pmid = {40439829},
issn = {1590-3478},
abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein astrocytopathy (A-GFAP-A) is a rare autoimmune central nervous system disorder associated with anti-GFAP IgG, presenting with meningoencephalitis or myelitis. Differential diagnosis from infectious causes, such as tuberculous meningitis (TBM), is challenging due to overlapping clinical and radiological features.

CASE PRESENTATION: A 24-year-old Chinese female presented with acute headache, fever, and vomiting. The cerebrospinal fluid (CSF) analysis showed lymphocytic pleocytosis, elevated protein and decreased glucose level. Brain magnetic resonance imaging (MRI) showed diffuse leptomeningeal enhancement. She was initially diagnosed with infectious meningitis and emperically treated with antibiotics and anti-tuberculosis therapy. However, her symptoms progressed with seizures, urinary retention, and tremor. Subsequent MRI revealed the involvement of the whole spinal cord. CSF analysis identified anti-GFAP IgG (titer 1:32). Bacterial, viral and tuberculous infection were excluded through bacterial culturing, metagenomic next-generation sequencing and Xpert MTB/RIF assay. The patient responded well to intravenous immunoglobulin and corticosteroids, achieving full remission. Finally, the diagnosis of A-GFAP-A was confirmed.

CONCLUSION: A-GFAP-A mimics infectious meningitis such as TBM due to similar CSF abnormalities and neuroimaging findings. This case underscores the importance of GFAP-IgG testing in differential diagnosis of patients with meningitis who have negative microbiological studies and atypical symptoms such as urinary retention and tremor.},
}

@article {pmid40439813,
year = {2025},
author = {Biktasheva, L and Galitskaya, P and Kuryntseva, P and Shipaeva, M and Selivanovskaya, S},
title = {Challenges and distortions in microbial community analysis of oil reservoirs: a case study with heavy crude oil from the Romashkino field.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40439813},
issn = {1618-1905},
support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The study of the microbial community of wells is a methodologically complex, but urgent problem. In the course of our work, five samples of oil wells were selected from one deposit of the Romashkino field. The samples were subjected to nucleic acid extraction using three methods-direct DNA extraction, and after enrichment using aerobic and anaerobic cultivation methods. In three samples from wells W1-W3, extraction after anaerobic enrichment was successful. Effective aerobic cultivation was possible in all five samples. All three of these samples represented the aqueous part of the produced fluid; samples from wells W4 and W5, where extraction was difficult, represented the oil part. During the analysis of the microbial community in enrichment cultures from wells W1-W3, exogenous microorganisms such as Desulfovibrio, Acetobacterium, Bacillus, and Georgenia were discovered, which can be explained by the long-term exploitation of this section of the field. In one sample from well W1, community information was obtained using direct extraction and anaerobic enrichment. It was found that the microbial community changed significantly after enrichment, and its diversity decreased. At the same time, however, the functional profile of microorganisms has not changed, and sulfate-reducing microorganisms dominate in both samples. Thus, the results of the work allow us to make an assumption about the physicochemical parameters of samples in which the study of the microbial community is possible. In addition, it became known that well W1 needs to control the process of biological acidification and has a high risk of equipment corrosion.},
}

@article {pmid40439791,
year = {2025},
author = {Gigliucci, F and Barbieri, G and Veyrunes, M and Chiani, P and Marra, M and Carollo, M and Knijn, A and Brambilla, G and Morabito, S},
title = {Characterization of the resistome and antibiotic-resistant bacteria in top soil improvers and irrigation waters devoted to food production: a case study from Italy.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40439791},
issn = {1614-7499},
support = {RF-2019-12369714//Ministero della Salute/ ; },
abstract = {Biosolids and reclaimed waters are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive agricultural food system. While the circular economy is a sustainable practice, it may introduce vulnerabilities in the food chain, by exposing crops to zoonotic agents and antimicrobial resistance determinants. This option is far from being a speculation and evidence start to accumulate indicating that the risk is tangible. This study provides further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antibiotic resistance genes (ARGs) targeting molecules used to treat human bacterial infections. We screened biosolid and water samples for ARGs presence using shotgun metagenomic sequencing. We demonstrated that the identified ARGs are present in live bacterial organisms, harbouring multidrug-resistant gene clusters, confirmed through phenotypic testing and whole-genome sequencing of isolated bacteria. Additionally, we observed that most of the antibiotic-resistant bacteria identified belonged to environmentally widespread species, which were not expected to be exposed to the antimicrobials, suggesting that inter-species transfer of resistance genes.},
}

@article {pmid40439580,
year = {2025},
author = {Bondeelle, L and Cheng, GS and Bergeron, A},
title = {What's new in the management of pulmonary complications in allogeneic stem cell transplantation?.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2513519},
pmid = {40439580},
issn = {1747-6356},
abstract = {INTRODUCTION: As survival increases after allogeneic hematopoietic stem cell transplantation (allo-HCT), several organ complications have emerged, including those involving the lung, which require a multidisciplinary management approach. The constant evolution of allo-HCT procedures, advances in diagnostic tools for infections and pulmonary disease, as well as new treatment approaches, require frequent updating of knowledge in this field.

AREAS COVERED: We review the multiple infectious and noninfectious lung complications that occur both early and late after allo-HCT. This includes an updated description of these complications, risk factors, diagnostic approach and outcome. A literature search was performed using PubMed-indexed journals.

EXPERT OPINION: The diagnosis of pulmonary complications after allo-HCT remains challenging, further complicated by the frequent association of co-infections and/or links between infection and noninfectious complications. The development of metagenomic next-generation sequencing (mNGS) should enhance the diagnostic yield of bronchoalveolar lavage but its clinical relevance remains to be evaluated. A better understanding of the pathophysiology of the lung chronic graft-versus-host disease (GVHD) and improved phenotyping are essential for advancing its diagnostic and therapeutic management. This requires a revision of diagnostic criteria and the identification of new biomarkers of early disease.},
}

@article {pmid40439559,
year = {2025},
author = {Rouse, N and Buttler, J and Pabilonia, K and Weller, C and Respicio-Kingry, L and Dietrich, E and Petersen, J and Kovalenko, G and Bortz, E and Huntington, KB},
title = {Francisella tularensis Subspecies holarctica in Stranded Beluga Whales, Cook Inlet, Alaska, USA.},
journal = {Emerging infectious diseases},
volume = {31},
number = {6},
pages = {1247-1250},
doi = {10.3201/eid3106.250033},
pmid = {40439559},
issn = {1080-6059},
mesh = {Animals ; *Francisella tularensis/genetics/classification/isolation & purification ; Alaska/epidemiology ; *Tularemia/veterinary/microbiology/epidemiology/diagnosis ; *Beluga Whale/microbiology ; Multilocus Sequence Typing ; Phylogeny ; },
abstract = {We report fatal tularemia in stranded beluga whales in Cook Inlet, Alaska, USA. Francisella tularensis was detected by nanopore metagenomics, confirmed by quantitative PCR and immunohistochemistry, and characterized as F. tularensis subspecies holarctica by multilocus sequence typing. Our findings should be considered when assessing biosecurity and marine mammal health in the North Pacific.},
}

Animals
*Francisella tularensis/genetics/classification/isolation & purification
Alaska/epidemiology
*Tularemia/veterinary/microbiology/epidemiology/diagnosis
*Beluga Whale/microbiology
Multilocus Sequence Typing
Phylogeny

@article {pmid40439405,
year = {2025},
author = {Scribano, FJ and Gebert, JT and Engevik, KA and Hayes, NM and Villanueva, J and Pham, S and Kaundal, S and Dave, JJ and Prasad, BVV and Estes, MK and Ramani, S and Hyser, JM},
title = {BTP2 restricts Tulane virus and human norovirus replication independent of store-operated calcium entry.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0044425},
doi = {10.1128/jvi.00444-25},
pmid = {40439405},
issn = {1098-5514},
abstract = {Human norovirus is the leading cause of viral gastroenteritis across all age groups. While there is a need for human norovirus antivirals, therapeutic development has been hindered by a lack of cell culture systems and animal models of infection. Surrogate viruses, such as Tulane virus (TV), have provided tractable systems to screen potential antiviral compounds. Our previous work demonstrated that TV encodes a viral ion channel, which dysregulates cytosolic calcium signaling. We set out to investigate whether host pathways triggered by viral ion channel activity, including store-operated calcium entry (SOCE), play a role in virus replication. Using pharmacologic inhibitors and genetically engineered cell lines, we establish that the SOCE inhibitor, BTP2, reduces TV replication in an SOCE-independent manner. We observed a significant reduction in TV replication, protein expression, and RNA synthesis in cells with both pre- and post-infection BTP2 treatment. By serial passage and plaque isolation, we demonstrate that TV quasi-species have mixed susceptibility and resistance to BTP2. Sequence comparison of the quasi-species revealed that amino acid changes in the structural proteins were associated with drug resistance. We utilized reverse genetics to generate TV with the resistance-associated VP1 and VP2 amino acid changes and found that amino acid changes in both proteins conferred BTP2 resistance. Together, this supports that TV structural proteins are the targets of BTP2. Finally, using human intestinal organoids, we demonstrate that BTP2 significantly reduces human norovirus replication.IMPORTANCEOur work identifies BTP2 as a potential human norovirus antiviral pharmacophore and highlights the utility of targeting calicivirus structural proteins to restrict viral replication. Furthermore, we establish a system whereby Tulane virus (TV) can be used to screen novel antiviral candidates and establish their mechanism of action. Together, this will facilitate rapid preclinical validation of other novel human norovirus therapeutics.},
}

@article {pmid40439403,
year = {2025},
author = {Pang, Y and Qiu, J and Yang, H and Zhang, J and Mo, J and Huang, W and Zeng, C and Xu, P},
title = {Application value of metagenomic next-generation sequencing based on protective bronchoalveolar lavage in nonresponding pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0313824},
doi = {10.1128/spectrum.03138-24},
pmid = {40439403},
issn = {2165-0497},
abstract = {This study aims to explore the application value of metagenomic next-generation sequencing (mNGS) of protective bronchoalveolar lavage fluid in the differential diagnosis and pathogenetic identification of nonresponding pneumonia. This study analyzed patient symptoms, auxiliary examinations including pathogen detection, and treatment response to identify the reasons for the lack of response to initial treatment and the pathogenetic diagnosis of pulmonary infections. The diagnostic efficacy of pathogen culture and mNGS was statistically analyzed and compared based on the clinical diagnosis criteria. (1) The two most common reasons for the ineffectiveness of initial treatment in nonresponding pneumonia cases are that (i) the initial treatment did not cover the pathogenic bacteria in pulmonary infection cases and that (ii) non-infectious pulmonary diseases were responsible. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are Mycobacterium tuberculosis (MTB), Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa. (2) In pulmonary infectious cases, mNGS demonstrated a higher detection sensitivity for pathogenic bacteria than pathogen cultures. mNGS combined with protective bronchoalveolar lavage has good clinical application value in the accurate diagnosis of pathogens and identification of non-infectious diseases.IMPORTANCEThe combination of mNGS and the protective BAL technique demonstrates significant utility in accurately diagnosing pathogens and identifying non-infectious diseases. Misdiagnosis of non-infectious lung diseases as infectious lung diseases is a common factor contributing to the lack of response to initial treatment in nonresponding pneumonia patients. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are MTB, Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa.},
}

@article {pmid40439232,
year = {2025},
author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC},
title = {Polyphenol rewiring of the microbiome reduces methane emissions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf108},
pmid = {40439232},
issn = {1751-7370},
abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.},
}

@article {pmid40438915,
year = {2025},
author = {Rivas-Santisteban, J and Martínez, JM and Escudero, C and Hernández-Antolín, R and Cid-Barrio, L and Ellis, GJ and Domingo, E and Sánchez, C and Sobrino, F and Amils, R},
title = {Metagenomic analysis of heavy water-adapted bacterial communities.},
journal = {Microbial genomics},
volume = {11},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001414},
pmid = {40438915},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Water Microbiology ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome ; DNA Transposable Elements ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Micro-organisms can survive and thrive in unusual and extreme environments. Here, we present a metagenomic analysis of living bacteria found in highly pure, deleterious heavy water (>99% D2O), stored in sealed plastic containers for more than 30 years, without any external supply. Deep DNA sequencing analyses have revealed that the most abundant genetic signatures were primarily associated with Pseudomonadota and Bacteroidota. These bacteria exhibited shorter gene lengths and depletion of polar and metabolically costly amino acids compared to the related species from light water environments. Genes related to DNA transposition, repair and modification were notably abundant, particularly mutant forms of the IS3 transposable elements family. We also explore potential carbon and energy sources and discuss the evolutionary implications of bacteria capable of surviving in such an extreme human-made environment.},
}

*Metagenomics/methods
*Water Microbiology
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Metagenome
DNA Transposable Elements
Phylogeny
Sequence Analysis, DNA

@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}

@article {pmid40438301,
year = {2025},
author = {Marra, PS and Marra, AR and Chen, E and Kobayashi, T and Celeghini, PD and Gutfreund, MC and Pardo, I and Lopes, GOV and Hsieh, MK and Boodhoo, NA and Fu, D and Torres-Espinosa, MA and Li, Y and Deliberato, RO and Algain, SMA and Salinas, JL and Edmond, MB and Amgarten, DE and de Mello Malta, F and Dos Santos, NV and Pinho, JRR and Louine, M and Wilson, MR},
title = {Metagenomic Next-generation Sequencing in Patients With Infectious Meningoencephalitis: A Comprehensive Systematic Literature Review and Meta-analysis.},
journal = {Open forum infectious diseases},
volume = {12},
number = {5},
pages = {ofaf274},
pmid = {40438301},
issn = {2328-8957},
abstract = {BACKGROUND: We aimed to assess the accuracy, clinical efficacy, and limitations of metagenomic next-generation sequencing (mNGS) for diagnosing infectious meningoencephalitis.

METHODS: We performed a systematic literature review and meta-analysis of studies that evaluated the performance of mNGS to determine the cause of infectious meningoencephalitis. We explored PubMed, Cumulative Index to Nursing and Allied Health, Embase, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, and Web of Science up to 12 November 2024. To perform a meta-analysis, we calculated the pooled diagnostic odds ratio (DOR) for mNGS and for conventional microbiological tests (CMTs) compared to the clinical diagnosis.

RESULTS: Thirty-four studies met the inclusion criteria, with mNGS-positive rates ranging from 43.5% to 93.5% for infectious meningoencephalitis. The meta-analysis included 23 studies with 1660 patients. The pooled sensitivity was 0.70 (95% confidence interval [CI], .67-.72), and its specificity was 0.93 (95% CI, .92-.94). The DOR for mNGS was 26.7 (95% CI, 10.4-68.8), compared to 12.2 (95% CI, 3.2-47.0) for CMTs. For tuberculosis meningoencephalitis, mNGS demonstrated a pooled sensitivity of 0.67 (95% CI, .61-.72) and specificity of 0.97 (95% CI, .95-.99), with a DOR of 43.5 (95% CI, 7.4-256.6).

CONCLUSIONS: Our review indicates that mNGS can be a valuable diagnostic tool for infectious meningoencephalitis, offering high sensitivity and specificity. mNGS's superior DOR compared to that of CMTs highlights its potential for more accurate diagnoses and targeted interventions. Further research is needed to optimize which patients and at what point in the diagnostic process mNGS should be used.},
}

@article {pmid40438215,
year = {2025},
author = {Hanna, A and Abbas, H and Yassine, F and AlBush, A and Bilen, M},
title = {Systematic review of gut microbiota composition, metabolic alterations, and the effects of treatments on PCOS and gut microbiota across human and animal studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549499},
pmid = {40438215},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting around 12% of women globally, associated with infertility and various comorbidities. Emerging evidence suggests a crucial role of gut microbiota in PCOS pathophysiology, prompting research to investigate alterations in gut microbial composition in patients with PCOS.

METHODS: This systematic review aims to analyze human and animal studies that compare gut microbiota composition, gut-derived metabolites, and treatment interventions in PCOS patients versus healthy controls. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science, yielding studies examining gut microbiota, metabolomic shifts, and treatment responses in PCOS models and human populations.

RESULTS: Our analysis revealed decreases in alpha diversity in PCOS patients, with more pronounced changes in beta diversity in animal models. Specific bacterial taxa, such as Bacteroides vulgatus, Escherichia-Shigella and Lactobacillus, showed implication in PCOS pathogenesis, suggesting potential microbial markers. Furthermore, discrepancies between human and animal studies show the need for humanized mouse models to bridge this gap. Interventions like probiotics and fecal microbiota transplantation (FMT) showed varying levels of efficacy, with FMT emerging as a more promising but invasive option, offering live bacteriotherapy as a potential therapeutic alternative. Alterations in gut-derived metabolites, including short-chain fatty acids and bile acids, highlighted the multifaceted nature of PCOS, with implications extending to metabolic, hormonal, and gut-brain axis disruptions.

DISCUSSION: In conclusion, PCOS exhibits complex interactions between gut microbiota and metabolic pathways, necessitating further research with standardized methods and larger sample sizes to elucidate the microbiome's role in PCOS.},
}

@article {pmid40438118,
year = {2025},
author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M},
title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561459},
pmid = {40438118},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; },
abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.

METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.

FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.

CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Adult
Mali
*Dysbiosis/chemically induced/immunology
Middle Aged
*Tuberculosis/drug therapy/microbiology/immunology/metabolism
Cytokines/blood
Longitudinal Studies
*Antitubercular Agents/therapeutic use/adverse effects
Young Adult
Metabolomics

@article {pmid40437943,
year = {2025},
author = {Franzin, M and Lagatolla, C and Forgiarini, SS and Haag, M and Neef, SK and Comar, M and Schaeffeler, E and Bellich, B and Bramuzzo, M and Decorti, G and Lucafò, M and Hofmann, U and Schwab, M and Stocco, G},
title = {Klebsiella pneumoniae contributes to altered cytotoxicity of thiopurines in vitro: Possible implications of biotransformation and bacterial metabolism.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70089},
pmid = {40437943},
issn = {1476-5381},
support = {RC 07/22//Italian Ministry of Health, through the contribution given to the Institute for Maternal and Child Health IRCCS Burlo Garofolo/ ; //Robert Bosch Stiftung/ ; },
abstract = {BACKGROUND AND PURPOSE: Thiopurines are used in paediatric inflammatory bowel disease (IBD), but some patients do not respond. Because the gut microbiota influences drug efficacy and IBD-patient microbiota presents increased bacterial abundance, we investigated the impact of candidate Enterobacteriaceae on drug cytotoxicity, metabolism and efficacy.

EXPERIMENTAL APPROACH: Thiopurines were exposed in vitro to bacteria for 4 h at 37°C and drug concentrations measured by UV spectrophotometry. Cytotoxic effects and drug metabolite concentrations on NALM6 and JURKAT cells were determined after treatment with thiopurines exposed or not to bacteria. Drugs were measured in Klebsiella pneumoniae lysates and bacterial conditioned media were used for metabolomic analyses. Shotgun metagenomic sequencing was performed on eight IBD-patient faecal stools.

KEY RESULTS: Incubation of thiopurines with K. pneumoniae, but not Escherichia coli and Salmonella enterica, reduced thiopurine concentrations and cytotoxicity on NALM6 and JURKAT cells. Thiopurine metabolites were lower in cells treated with drugs previously exposed to K. pneumoniae. Internalisation of drugs was demonstrated by their detection in lysates after bacterial incubation. Untargeted metabolomics revealed biotransformation of thiopurines by K. pneumoniae, as reactions of deconjugation, reduction, glycosylation, acetylation or conjugation with propionic acid. Incubation with thiopurines led to changes in the secretion of endogenous bacterial metabolites. K. pneumoniae faecal abundance was associated with lower thiopurine metabolite concentrations in erythrocytes of paediatric IBD-patients.

CONCLUSIONS AND IMPLICATIONS: K. pneumoniae decreases the cytotoxicity of thiopurines through internalisation of MP and TG. We revealed potential bacterial drug biotransformation, as well as negative correlations between bacterial abundance and drug metabolites.},
}

@article {pmid40437611,
year = {2025},
author = {Zhang, P and Tuo, X and Jiang, J and Zhang, Y and Zhao, J and Deng, C and Zhao, G and Cheng, Y and Song, L and Yang, Y and Guo, R and Zhang, H and Zhao, H and Ma, S and Li, L and Shi, H},
title = {Characteristics of the gut virome in patients with premalignant colorectal adenoma.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {597},
pmid = {40437611},
issn = {1479-5876},
support = {No.S2024-JC-QN-1554//Natural Science Basic Research Program of Shaanxi Province/ ; },
mesh = {Humans ; *Virome ; *Colorectal Neoplasms/virology/microbiology ; *Adenoma/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Precancerous Conditions/virology/microbiology ; Case-Control Studies ; Aged ; Reproducibility of Results ; },
abstract = {BACKGROUND: The multi-kingdom gut microbiota (e.g., bacteriome, mycobiome, and virome) characteristics of colorectal cancer have been extensively studied, yet there is still an insufficient description of the microbiota features in its early-stage, colorectal adenoma, particularly in the gut virome aspect.

METHODS: Based on the Metagenomic Gut Virus catalogue (MGV) containing 54,118 non-redundant gut viral genomes, this study characterized the virome composition and diversity using publicly available metagenomic sequencing data from 419 individuals with premalignant colorectal adenoma and 552 healthy controls. Furthermore, we identified and assessed the reliability and classification performance of adenoma-associated microbial signatures through comparative analysis and the random forest model.

RESULTS: Our results revealed a notable shift in the gut virome structure of patients compared to healthy controls, characterized by a significant increase in viral families such as Microviridae, Podoviridae_crAss-like, and Quimbyviridae. At the viral operational taxonomic unit (vOTU) level, we identified 479 vOTU signatures showing significant differences in relative abundances between patients and controls, including some patient-enriched vOTUs tending to infect Bacteroidaceae and Lachnospiraceae. Correlation network analysis revealed specific bacterial species correlated with adenoma-associated viruses, suggesting frequent interactions between them. Moreover, random forest models trained on gut viral and bacterial signatures demonstrated area under the curve (AUC) scores of 0.68, 0.82, and 0.76 for classifying healthy individuals versus patients with tubular adenomas, patients with sessile serrated adenomas, and patients with both conditions, respectively. In three independent validation cohorts, the classification performance achieved AUC scores ranging from 0.61 to 0.65.

CONCLUSIONS: Our study provides insights into the gut virome in premalignant colorectal adenoma, highlighting its potential role in disease development and diagnosis. Further investigations are warranted to elucidate the underlying mechanisms of gut virus-bacteria interactions and validate diagnostic models in larger populations.},
}

Humans
*Virome
*Colorectal Neoplasms/virology/microbiology
*Adenoma/virology/microbiology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Precancerous Conditions/virology/microbiology
Case-Control Studies
Aged
Reproducibility of Results

@article {pmid40437401,
year = {2025},
author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Pyśniak, K and Piątkowska, M and Czarnowski, P and Goryca, K and Mróz, A and Żeber-Lubecka, N and Wójcik-Trechcińska, U and Bałabas, A and Dąbrowska, M and Surynt, P and Radkiewicz, M and Mikula, M and Ostrowski, J},
title = {Western Diet and fecal microbiota transplantation alter phenotypic, liver fatty acids, and gut metagenomics and metabolomics in Mtarc2 knockout mice.},
journal = {Genes & nutrition},
volume = {20},
number = {1},
pages = {13},
pmid = {40437401},
issn = {1555-8932},
support = {2018/29/B/NZ7/00809//Narodowe Centrum Nauki/ ; },
}

@article {pmid40436871,
year = {2025},
author = {Zeng, L and Yu, B and Zeng, P and Duoji, Z and Zuo, H and Lian, J and Yang, T and Dai, Y and Feng, Y and Yu, P and Yang, J and Yang, S and Dou, Q},
title = {Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {90},
pmid = {40436871},
issn = {2055-5008},
support = {723B2017//National Natural Science Foundation of China/ ; XZ202201ZD0001G//Science and Technology Major Project of Tibetan Autonomous Region of China/ ; XZ202303ZY0007G//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CQFYJB01005//Chongqing Maternal and Child Health Hospital/ ; 2023YFC3604702//National Key Research and Development Program of China/ ; 2023YFC3604701; 2020YFC2008005; 2018YFC2002405//National Key Research and Development Program of China/ ; 2023YFS0251//Key R&D Project of Sichuan Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dyslipidemias/microbiology/epidemiology ; Male ; Cross-Sectional Studies ; Female ; *Life Style ; Middle Aged ; Adult ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; China ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Metabolomics ; Triglycerides/blood ; Aged ; },
abstract = {Whether the role of gut microbial features lies in the pathways from lifestyles to dyslipidemia remains unclear. In this cross-sectional study, we conducted a metagenome-wide association analysis and fecal metabolomic profiling in 994 adults from the China Multi-Ethnic cohort. A total of 26 microbial species were identified as mediators between lifestyle factors and risk for dyslipidemia. Specifically, the abundance of [Ruminococcus] gnavus mediated the associations between lifestyles and risks for dyslipidemia, elevated low-density lipoprotein cholesterol, elevated total cholesterol, and elevated triglycerides. [Ruminococcus] gnavus, Alistipes shahii, and Lachnospira eligens were replicated to be associated with dyslipidemia in an external validation cohort. The potential metabolic pathways included arachidonic acid, bile acid, and aromatic amino-acid metabolism.},
}

Humans
*Gastrointestinal Microbiome
*Dyslipidemias/microbiology/epidemiology
Male
Cross-Sectional Studies
Female
*Life Style
Middle Aged
Adult
*Metabolic Networks and Pathways
Feces/microbiology/chemistry
China
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenome
Metabolomics
Triglycerides/blood
Aged

@article {pmid40436643,
year = {2025},
author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y},
title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {5},
pages = {477-492},
doi = {10.1631/jzus.B2400341},
pmid = {40436643},
issn = {1862-1783},
support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; },
abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.},
}

Aged
Aged, 80 and over
Female
Humans
Male
Middle Aged
Bacteroides
China
Diabetes Mellitus, Type 2/microbiology
*Escherichia coli/genetics/isolation & purification/classification
*Gastrointestinal Microbiome/genetics
*Metagenomics
East Asian People

@article {pmid40436596,
year = {2025},
author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z},
title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {213},
number = {},
pages = {116577},
doi = {10.1016/j.foodres.2025.116577},
pmid = {40436596},
issn = {1873-7145},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; },
abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.},
}

*Fermented Foods/microbiology
*Food Microbiology
*Fast Foods/microbiology
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Metagenomics
Dairy Products/microbiology
Vegetables/microbiology

@article {pmid40436373,
year = {2025},
author = {Vosough, M and Drees, F and Sieber, G and Stach, TL and Beisser, D and Probst, AJ and Boenigk, J and Schmidt, TC},
title = {Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00539},
pmid = {40436373},
issn = {1520-6882},
abstract = {Significant progress in high-throughput analytical techniques has paved the way for novel approaches to integrating data sets from different compartments. This study leverages nontarget screening (NTS) via liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a crucial technique for analyzing organic micropollutants and their transformation products, in combination with biological indicators. We propose a combined multivariate data processing framework that integrates LC-HRMS-based NTS data with other high-throughput data sets, exemplified here by 18S V9 rRNA and full-length 16S rRNA gene metabarcoding data sets. The power of data fusion is demonstrated by systematically evaluating the impact of treated wastewater (TWW) over time on an aquatic ecosystem through a controlled mesocosm experiment. Highly compressed NTS data were compiled through the implementation of the region of interest-multivariate curve resolution-alternating least-squares (MCR-ALS) method, known as ROIMCR. By integrating ANOVA-simultaneous component analysis with structural learning and integrative decomposition (SLIDE), the innovative SLIDE-ASCA approach enables the decomposition of global and partial common, as well as distinct variation sources arising from experimental factors and their possible interactions. SLIDE-ASCA results indicate that temporal variability explains a much larger portion of the variance (74.6%) than the treatment effect, with both contributing to global shared space variation (41%). Design structure benefits include enhanced interpretability, improved detection of key features, and a more accurate representation of complex interactions between chemical and biological data. This approach offers a greater understanding of the natural and wastewater-influenced temporal patterns for each data source, as well as reveals associations between chemical and biological markers in an exemplified perturbed aquatic ecosystem.},
}

@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

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

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

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

@article {pmid40435848,
year = {2025},
author = {Jung, H and Park, S and Park, SA and Kim, H and Lee, M and Park, CH and Jegal, J and Shin, G and Kim, HJ},
title = {FDA-hydrolysis activity: A pre-screening tool for optimizing compost selection in standardized plastic biodegradation testing.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114907},
doi = {10.1016/j.wasman.2025.114907},
pmid = {40435848},
issn = {1879-2456},
abstract = {Current ISO 14855-1 standards for assessing plastic biodegradability under composting conditions rely on physicochemical parameters, such as pH and volatile solids, to select compost inocula. However, these indicators do not directly reflect microbial activity, which is central to biodegradation processes. This study proposes fluorescein diacetate hydrolase (FDA-H) activity as a rapid, integrative biological indicator to pre-screen composts before standardized biodegradation testing. FDA-H activity was measured in five composts and showed a strong correlation with early CO2 evolution (r = 0.93), reflecting initial microbial metabolic potential. Moderate correlations were also observed with final biodegradation rates of cellulose and polybutylene succinate (PBS), suggesting that microbial community shifts and substrate-specific adaptation influence long-term outcomes. Metagenomic analysis supported this by revealing distinct microbial succession patterns during degradation, especially for synthetic polymers. We also compared FDA-H with standardized microbial activity assays, including respiration and dehydrogenase activity. Unlike these methods, FDA-H captures extracellular hydrolytic enzyme activity relevant to polymer breakdown and offers advantages in speed and operational simplicity. While FDA-H does not replace ISO/OECD biodegradation standards, it complements them by providing early-stage insight into compost suitability. Integrating FDA-H into existing testing frameworks could enhance the reliability, efficiency, and biological relevance of compost selection, ultimately improving standardized biodegradation assessments.},
}

@article {pmid40435563,
year = {2025},
author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V},
title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128226},
doi = {10.1016/j.micres.2025.128226},
pmid = {40435563},
issn = {1618-0623},
abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.},
}

@article {pmid40434915,
year = {2025},
author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M},
title = {Comparing the metagenomic performance of stools collected from custom cards and 95% ethanol in epidemiologic studies.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-25-0157},
pmid = {40434915},
issn = {1538-7755},
abstract = {Background Stool cards have been used for microbiome assessment in epidemiological studies. Methods We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card vs. a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa. Results Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in alpha diversity and only ~1% of variation in beta diversity was explained by the collection method. At the species level, while the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (out of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, 4 showed differential abundances between collection methods; however, this number was consistent with what would be expected by chance. Conclusions Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results, although differential abundances were observed for a small number of individual species. Impact Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.},
}

@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
doi = {10.1099/mic.0.001564},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}

*High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Sequence Analysis, DNA/methods
*DNA, Environmental/genetics/analysis/isolation & purification
Humans
Environmental Monitoring/methods
Computational Biology/methods
Biodiversity

@article {pmid40434093,
year = {2025},
author = {Koldaş, SS and Sezerman, OU and Timuçin, E},
title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019625},
doi = {10.1128/msystems.00196-25},
pmid = {40434093},
issn = {2379-5077},
abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.

IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.},
}

@article {pmid40434086,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rodriguez-Carrio, SM and Melendez Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and García-Arrarás, JE and Rios-Velazquez, C},
title = {Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029325},
doi = {10.1128/mra.00293-25},
pmid = {40434086},
issn = {2576-098X},
abstract = {Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.},
}

@article {pmid40434078,
year = {2025},
author = {Weisse, L and Martin, L and Moumen, B and Héchard, Y and Delafont, V},
title = {Environmental diversity of Candidatus Babelota and their relationships with protists.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0026125},
doi = {10.1128/msystems.00261-25},
pmid = {40434078},
issn = {2379-5077},
abstract = {Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.},
}

@article {pmid40434009,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and Zhang, M and He, LY and Liu, YS and Ying, GG},
title = {Key Contribution and Risk of Airborne Antibiotic Resistance: Total Suspended Particles or Settled Dust?.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11038},
pmid = {40434009},
issn = {1520-5851},
abstract = {The atmosphere is an important environmental medium in spreading antimicrobial resistance (AMR) in animal farming systems, yet the exposure risks associated with airborne pathways remain underexplored. This study employed metagenomic sequencing to investigate the airborne transmission of AMR in chicken farms (i.e., chicken feces, total suspended particles (TSP), and dust) and its exposure risks on the gut and nasal cavities of workers, office staff, and nearby villagers. Results revealed that TSP exhibited greater abundance, diversity, and transfer potential of antibiotic resistance genes (ARGs) compared to dust. The abundance of airborne resistome decreased with distance from the chicken house, and ARGs were estimated to spread up to 9.48 km within 1 h. While the gut resistome of workers and villagers showed limited differences, emerging tet(X) variants and high-risk dfrA remain future concerns. More nasal resistome was attributable to TSP compared to dust. Workers faced significantly higher inhalable exposures to antibiotic-resistant bacteria (ARB) and human pathogenic antibiotic-resistant bacteria (HPARB), exceeding those of office staff and villagers by an order of magnitude. We also compiled lists of high-risk and potential-risk airborne ARGs to inform monitoring. These findings highlight the need for regular air disinfection in animal farms and better protective measures for workers.},
}

@article {pmid40433987,
year = {2025},
author = {Zhou, Z and Yang, M and Fang, H and Zhang, B and Ma, Y and Li, Y and Liu, Y and Cheng, Z and Zhao, Y and Si, Z and Zhu, H and Chen, P},
title = {Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14232},
doi = {10.1002/advs.202414232},
pmid = {40433987},
issn = {2198-3844},
support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//Lanzhou Municipal Science and Technology Program/ ; 2024-8-30//Lanzhou Municipal Science and Technology Program/ ; 2024-4-2//Lanzhou Municipal Science and Technology Program/ ; 20250260006//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260016//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260020//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; },
abstract = {Polymorphic microbiomes play important roles in colorectal cancer (CRC) occurrence and development. In particular, Fusobacterium nucleatum (F. nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial for treatment. Here, multiple metagenomic sequencing cohorts are combined with multiomics to analyze the microbiome and related functional alterations. Furthermore, local human metagenome and metabolomics are used to discover commensal consortia. A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing result shows that F. nucleatum is more abundant in both the feces and tumor tissues of CRC patients. It causes alterations through various pathways, including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile acid metabolism disorders. The designed SynCom contains seven species with low competition interrelationship. Furthermore, the SynCom successfully inhibits F. nucleatum growth in vitro and achieves colonization in vivo. Additionally, it promotes F. nucleatum decolonization, and enhances tryptophan metabolism and secondary bile acid conversion, leading to reduced lipid accumulation, decreased inflammatory reaction, and enhanced tumor inhibition effect. Overall, the bottom-up designed SynCom is a controllable and promising approach for treating F. nucleatum-positive CRC.},
}

@article {pmid40433668,
year = {2025},
author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF},
title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1531084},
pmid = {40433668},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Adult ; Biomarkers ; Aged ; },
abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.},
}

Humans
*COVID-19/microbiology/pathology/virology
Cross-Sectional Studies
Disease Susceptibility
*Microbiota
SARS-CoV-2
Female
Male
Severity of Illness Index
Middle Aged
*Respiratory System/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Adult
Biomarkers
Aged

@article {pmid40433443,
year = {2025},
author = {Dahal, U and Bansal, A},
title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.},
journal = {Current genomics},
volume = {26},
number = {2},
pages = {81-94},
pmid = {40433443},
issn = {1389-2029},
abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.},
}

@article {pmid40432811,
year = {2025},
author = {Wang, H and Zhao, J and Wang, X and Li, M and Hu, T and Xu, H and Dong, M and He, W and Che, Z},
title = {Diagnostic Performance of Clinical Metagenomic Next-Generation Sequencing for Suspected Central Nervous System Infections in a Municipal Hospital: A Retrospective Study in China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2637-2652},
pmid = {40432811},
issn = {1178-6973},
abstract = {PURPOSE: Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) has the potential to identify the majority of pathogens in a single test. Accurate pathogen identification is vital for central nervous system infection (CNSi). However, there are few related studies investigating in a municipal hospital.

PATIENTS AND METHODS: A total of 52 suspected CNSi patients were retrospectively recruited in Xinxiang central hospital between July 2019 and April 2023. The diagnostic performance of CSF mNGS, conventional microbiological tests (CMT), and the combination of CSF mNGS and CMT were evaluated by comparing to the final diagnosis.

RESULTS: Among 52 suspected CNSi patients, 35 were diagnosed as CNSi. In comparison to the final diagnosis, the area under curves (AUC) for CSF CMT, CSF mNGS, and the combination of CMT and mNGS for the diagnosis of CNSi were 0.56 (95% CI 0.4-0.72), 0.74 (95% CI 0.61-0.84), and 0.76 (95% CI 0.63-0.88), respectively. The sensitivities were 11.43% (95% CI 4.54%-25.95%), 48.57% (95% CI 32.99%-64.43%), and 51.43% (95% CI 35.57%-67.01%), respectively. The accuracy was 40.38 (95% CI 27.01%-54.90%), 65.38% (95% CI 50.91%-78.03%), and 67.31% (95% CI 52.89%-79.67%), respectively. Furthermore, based on CSF mNGS results, seven patients confirmed initial treatment, two escalated, and one de-escalated. Additionally, we identified the optimal cutoff values as 1.75 U/L for CSF adenosine deaminase (ADA), 75.44 U/L for CSF protein, and 185 mmH2O for CSF pressure, when these values were exceeded, CSF mNGS tended to yield positive results.

CONCLUSION: CSF mNGS showed superior diagnostic performance in CNSi and hence could serve as a complementary tool to CMT and conjunctively guide the precision therapy. Additionally, the values for CSF ADA, protein and pressure could assist in predicting mNGS positive result. With technical improvements for mNGS sample processing to increase throughput and reduce costs, clinicians may use mNGS more widely in municipal hospital laboratories.},
}

@article {pmid40431707,
year = {2025},
author = {Fougere, GC and Xu, D and Gaiero, JR and McCreary, C and Marchand, G and Despres, C and Wang, A and Fall, ML and Griffiths, JS},
title = {Genomic Diversity of Tomato Brown Rugose Fruit Virus in Canadian Greenhouse Production Systems.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/v17050696},
pmid = {40431707},
issn = {1999-4915},
support = {J-003395//Agriculture and Agri-Food Canada/ ; J-002497//Agriculture and Agri-Food Canada/ ; },
mesh = {*Solanum lycopersicum/virology ; *Plant Diseases/virology ; Phylogeny ; *Genome, Viral ; Canada ; *Genetic Variation ; *Tobamovirus/genetics/classification ; Genomics ; },
abstract = {Tomato brown rugose fruit virus (ToBRFV) is a recently emerged viral pathogen in the Tobamovirus genus first observed in 2014 in the Middle East that has since spread worldwide, causing significant losses in greenhouse tomato production. ToBRFV is easily mechanically transmitted and can escape the durable Tm-2[2] resistance gene, facilitating its global spread. Seed companies have identified novel sources of resistance and introduced these resistance traits into commercial cultivars. The identity, number, and mechanisms of these putative novel resistance genes are largely unknown but could be exerting selective pressures on ToBRFV. Here, we report 15 new ToBRFV genomic sequences from Canadian greenhouse production systems in susceptible and novel resistant or tolerant cultivars collected since 2023. We combined these sequences with five other Canadian ToBRFV genomes previously deposited in Genbank and a further five consensus sequences derived from metagenomic-based wastewater monitoring sequence data and conducted phylogenetic analysis. Most Canadian sequences grouped together when compared with 332 publicly available international sequences, but several isolates appeared distantly related, suggesting multiple introductions to Canadian production systems. High sequence identity between samples suggest movement of ToBRFV between independent greenhouses, highlighting areas where biosecurity can be improved. Several novel non-synonymous polymorphisms identified in the p126 and movement protein (MP) open reading frames (ORFs) were unique to Canadian sequences and associated with infection of novel resistant tomato cultivars. Many polymorphisms in the p126 ORF are located in a region of the protein associated with Tm-1 resistance-breaking isolates of tomato mosaic virus and ToBRFV, but have not been previously reported. Four novel polymorphisms in MP were also identified and do not appear to be associated with sites previously identified as interacting with Tm-2[2] and could be related to other unknown resistance genes. Together, these results confirm the difficulties in preventing the transmission of ToBRFV, identify putative adaptations to novel and existing resistance genes, and emphasize the urgent need for the cloning and characterization of these new sources of resistance to ToBRFV.},
}

*Solanum lycopersicum/virology
*Plant Diseases/virology
Phylogeny
*Genome, Viral
Canada
*Genetic Variation
*Tobamovirus/genetics/classification
Genomics

@article {pmid40431691,
year = {2025},
author = {Penzes, JJ and Kaelber, JT},
title = {Capsid Structure of the Fish Pathogen Syngnathus Scovelli Chapparvovirus Offers a New Perspective on Parvovirus Structural Biology.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/v17050679},
pmid = {40431691},
issn = {1999-4915},
mesh = {Animals ; *Capsid/chemistry/ultrastructure ; *Capsid Proteins/chemistry/genetics ; *Parvovirus/ultrastructure/genetics/chemistry ; *Parvoviridae Infections/veterinary/virology ; *Fish Diseases/virology ; Models, Molecular ; Cryoelectron Microscopy ; Phylogeny ; },
abstract = {Chapparvoviruses (ChPVs) comprise a divergent lineage of the Parvoviridae ssDNA virus family and evolved to infect vertebrate animals independently from the Parvovirinae subfamily. Despite being pathogenic and widespread in environmental samples and metagenomic assemblies, their structural characterization has proven challenging. Here, we report the first structural analysis of a ChPV, represented by the fish pathogen, Syngnathus scovelli chapparvovirus (SsChPV). We show through the SsChPV structure that the lineage harbors a surface morphology, subunit structure, and multimer interactions that are unique among parvoviruses. The SsChPV capsid evolved a threefold-related depression of α-helices that is analogous to the β-annulus pore of denso- and hamaparvoviruses and may play a role in monomer oligomerization during assembly. As interacting β-strands are absent from the twofold symmetry axis, the viral particle lacks the typical stability and resilience of parvovirus capsids. Although all parvoviruses thus far rely on the threading of large, flexible N-terminal domains to the capsid surface for their intracellular trafficking, our results show that ChPVs completely lack any such N-terminal sequences. This led to the subsequent degradation of their fivefold channel, the site of N-terminus externalization. These findings suggest that ChPVs harbor an infectious pathway that significantly deviates from the rest of the Parvoviridae.},
}

Animals
*Capsid/chemistry/ultrastructure
*Capsid Proteins/chemistry/genetics
*Parvovirus/ultrastructure/genetics/chemistry
*Parvoviridae Infections/veterinary/virology
*Fish Diseases/virology
Models, Molecular
Cryoelectron Microscopy
Phylogeny

@article {pmid40431505,
year = {2025},
author = {Zhang, R and Hu, W and Zhong, S and Chen, W and Chen, M and Yu, Q},
title = {Impact of Enterococcus faecium Kimate-X on Reducing Stress in Dogs Through Gut Microbiota Modulation.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050412},
pmid = {40431505},
issn = {2306-7381},
abstract = {Stress in dog breeding leads to significant physiological and psychological burdens, including anxiety, reduced appetite, weakened immune function, gut microbiota imbalance, and even death. Currently, there are various pharmacological interventions for stress management, but few focus on gut health. This study evaluates the potential of a novel strain, Enterococcus faecium Kimate-X, in alleviating transport stress and improving gut health in dogs, providing an alternative to traditional pharmacological treatments. In vitro experiments showed that Kimate-X significantly enhanced the activities of superoxide dismutase (SOD) and catalase (CAT) while reducing the levels of malondialdehyde (MDA) and tumor necrosis factor-α (TNF-α) in RAW 264.7 macrophage cells. In vivo, dogs supplemented with Kimate-X exhibited significantly lower cortisol levels after transport, indicating reduced stress. Metagenomic analysis revealed increased gut microbiota diversity and higher concentrations of short-chain fatty acids (acetate, propionate, and butyrate) in fecal samples. This study systematically uncovers the mechanism by which Enterococcus faecium Kimate-X alleviates transport stress through modulation of the gut microbiota. These findings provide new scientific evidence supporting the use of probiotics as a novel approach to stress management in animals.},
}

@article {pmid40431358,
year = {2025},
author = {Yue, Y and Yang, HJ and Li, C and Ryu, MS and Seo, JW and Jeong, DY and Park, S},
title = {Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/nu17101617},
pmid = {40431358},
issn = {2072-6643},
support = {2023-3//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats, Sprague-Dawley ; *Soy Foods/microbiology ; Rats ; *Memory/drug effects ; *Neuroinflammatory Diseases ; *Glucose/metabolism ; Scopolamine ; *Fermented Foods ; Water/metabolism ; Neuroprotective Agents/pharmacology ; *Glycine max ; Fermentation ; },
abstract = {Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Male
Rats, Sprague-Dawley
*Soy Foods/microbiology
Rats
*Memory/drug effects
*Neuroinflammatory Diseases
*Glucose/metabolism
Scopolamine
*Fermented Foods
Water/metabolism
Neuroprotective Agents/pharmacology
*Glycine max
Fermentation

@article {pmid40431314,
year = {2025},
author = {Li, B and Gesang, Q and Sun, Y and Wang, Y and Nan, J and Xu, J},
title = {Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai-Tibetan Plateau.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051142},
pmid = {40431314},
issn = {2076-2607},
support = {XZ202401YD0026//Science and Technology Projects of Xizang Autonomous Region, China/ ; },
abstract = {Alpine meadows on the Qinghai-Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows.},
}

@article {pmid40431310,
year = {2025},
author = {Castaño-Jiménez, PA and Baltazar-Díaz, TA and González-Hernández, LA and García-Salcido, R and Klimov-Kravtchenko, K and Andrade-Villanueva, JF and Arellano-Arteaga, KJ and Padilla-Sánchez, MP and Del Toro-Arreola, S and Bueno-Topete, MR},
title = {Deciphering the Language of Intestinal Microbiota Associated with Sepsis, Organ Failure, and Mortality in Patients with Alcohol-Related Acute-on-Chronic Liver Failure (ACLF): A Pioneer Study in Latin America.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051138},
pmid = {40431310},
issn = {2076-2607},
support = {P3E 277752-2024//Universidad de Guadalajara/ ; },
abstract = {ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico.},
}

@article {pmid40431283,
year = {2025},
author = {Huang, J and Sheng, Y and Jia, X and Qian, W and Li, Z},
title = {Comparative Analysis of Microbial-Short-Chain Fatty Acids-Epithelial Transport Axis in the Rumen Ecosystem Between Tarim Wapiti (Cervus elaphus yarkandensis) and Karakul Sheep (Ovis aries).},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051111},
pmid = {40431283},
issn = {2076-2607},
abstract = {Under long-term ecological stress, the Tarim wapiti (Cervus elaphus yarkandensis) has evolved unique adaptations in digestive physiology and energy metabolism. A multi-omics comparison of three Tarim wapiti and five Karakul sheep was used to examine the synergistic mechanism between rumen bacteria, short-chain fatty acids, and host epithelial regulation in order to clarify the mechanism of high roughage digestion efficiency in Tarim wapiti. Metagenomic sequencing (Illumina NovaSeq 6000) and gas chromatography revealed that Tarim wapiti exhibited significantly higher acetate and total VFA (TVFA) concentrations compared to Karakul sheep (p < 0.01), accompanied by lower ruminal pH and propionate levels. Core microbiota analysis identified Bacteroidetes (relative abundance: 52.3% vs. 48.1%), Prevotellaceae (22.7% vs. 19.4%), and Prevotella (18.9% vs. 15.6%) as dominant taxa in both species, with significant enrichment of Bacteroidetes in wapiti (p < 0.01). Functional annotation (PICRUSt2) demonstrated enhanced glycan biosynthesis (KEGG ko00511), DNA replication/repair (ko03430), and glycoside hydrolases (GH20, GH33, GH92, GH97) in wapiti (FDR < 0.05). Transcriptomic profiling (RNA-Seq) of rumen epithelium showed upregulated expression of SCFA transporters (PAT1: 2.1-fold, DRA: 1.8-fold, AE2: 2.3-fold; p < 0.01) and pH regulators (Na[+]/K[+] ATPase: 1.7-fold; p < 0.05) in wapiti. Integrated analysis revealed coordinated microbial-host interactions through three key modules: (1) Bacteroidetes-driven polysaccharide degradation, (2) GHs-mediated fiber fermentation, and (3) epithelial transporters facilitating short-chain fatty acids absorption. These evolutionary adaptations, particularly the Bacteroidetes-short-chain fatty acids-transporter axis, likely underpin the wapiti's superior roughage utilization efficiency, providing molecular insights for improving ruminant feeding strategies in an arid environment.},
}

@article {pmid40431261,
year = {2025},
author = {Mendes Silva Cruz, A and Cardoso, JF and Pinheiro, KC and Ferreira, JA and Barbagelata, LS and Silva, SP and Chagas Junior, WD and Lobo, PS and Teixeira, DM and André Junior, W and Ordenes Silva, I and Santos, MC and Soares Farias, LS and Sousa, MS and Neto Tavares, F},
title = {Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051088},
pmid = {40431261},
issn = {2076-2607},
support = {4648 MPT/IEC/FADESP//Public Ministry of Labor through the Research Support and Development Foudation/ ; 159996/2021-0//National Council for Scientific and Technological Development/ ; NU2GGH002174/CC/CDC HHS/United States ; NU2GGH002174//Fundação Oswaldo Cruz/ ; },
abstract = {It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas-Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (p < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as Klebsiella pneumoniae, Staphylococcus spp, and Shigella sonnei, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria.},
}

@article {pmid40431220,
year = {2025},
author = {Goldiș, A and Dragomir, R and Mercioni, MA and Goldiș, C and Sirca, D and Enătescu, I and Olariu, L and Belei, O},
title = {Personalized Microbiome Modulation to Improve Clinical Outcomes in Pediatric Inflammatory Bowel Disease: A Multi-Omics and Interventional Approach.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051047},
pmid = {40431220},
issn = {2076-2607},
support = {Without a Grant Number//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; without a Grant Number/ ; },
abstract = {Inflammatory bowel disease (IBD) is a complex disorder influenced by genetic, environmental, and microbial factors, with emerging evidence highlighting the gut microbiome's role in disease pathogenesis. This study investigates the impact of microbiome-targeted interventions in pediatric IBD by integrating multi-omics analysis, including metagenomics, metabolomics, transcriptomics, and clinical biomarkers, to identify microbial dysbiosis patterns and potential therapeutic targets. A cohort of pediatric IBD patients underwent a personalized intervention involving dietary modifications, probiotic supplementation, and selective antibiotic therapy. Microbiome composition, inflammatory markers (fecal calprotectin, CRP), and disease activity scores (PCDAI/PUCAI) were assessed before and after treatment. At the 3-month follow-up, patients showed significant clinical improvement, with reduced stool frequency (p = 0.004) and improved stool consistency (p < 0.001). Symptoms such as bloating and abdominal pain decreased, while energy levels increased (p < 0.001). Dietary changes included higher fruit, meat, and dairy intake, and lower fast-food and sweets consumption (p < 0.001). Physician assessments classified 90% as "improved", reinforcing the effectiveness of personalized microbiome interventions. Microbiome-targeted interventions (diet, probiotics, and selective antibiotics) improved pediatric IBD outcomes by reducing pathogenic bacteria and increasing short-chain fatty acid (SCFA)-producing species, lowering inflammation and symptoms. Early-life factors (cesarean birth, and formula feeding) influence IBD risk. Personalized diets enhanced microbial balance. Integrating multi-omics supports precision medicine, offering microbiome-based biomarkers and reducing immunosuppressive reliance.},
}

@article {pmid40431204,
year = {2025},
author = {Han, H and Chen, P and Zhao, W and Li, S and Zhang, K},
title = {Acclimation Time Enhances Adaptation of Heterotrophic Nitrifying-Aerobic Denitrifying Microflora to Linear Anionic Surfactant Stress.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051031},
pmid = {40431204},
issn = {2076-2607},
support = {22YFZCSN00170//Tianjin Science and technology planning project fund/ ; 2022YFD1601104//the National Key R&D Program of China during the 14th Five-Year Plan period/ ; CAAS-ZDRW202306//the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences, and the Major Scientific Research Task of the Agricultural Science and Technology Innovation Program of CAAS/ ; },
abstract = {Linear anionic surfactants (LAS) pose significant stress to microbial denitrification in wastewater treatment. This study investigated the performance and adaptation mechanisms of heterotrophic nitrification-aerobic denitrification (HN-AD) microbial consortia under LAS exposure after short-term (SCM, 2 months) and long-term (LCM, 6 months) acclimation. Results showed a dose-dependent inhibition of total nitrogen (TN) removal, with LCM achieving 97.40% TN removal under 300 mg/L LAS, which was 16.89% higher than SCM. Biochemical assays indicated that LCM exhibited lower reactive oxygen species (ROS) levels, a higher ATP content, and reduced LDH release, suggesting enhanced oxidative stress resistance and membrane stability. EPS secretion also increased in LCM, contributing to environmental tolerance. Metagenomic analysis revealed that long-term acclimation enriched key genera including Pseudomonas, Aeromonas, and Stutzerimonas, which maintained higher expression of denitrification (e.g., nosZ, nirS) and ammonium assimilation genes (glnA, gltB). Although high LAS concentrations reduced overall community diversity and led to convergence between SCM and LCM structures, LCM retained greater functional capacity and stress resistance. These findings underscore the importance of acclimation in sustaining denitrification performance under surfactant pressure and offer valuable insights for engineering robust microbial consortia in complex wastewater environments.},
}

@article {pmid40431180,
year = {2025},
author = {Wang, R and Yang, S and Zhao, W},
title = {Microbial Community Responses and Nitrogen Cycling in the Nitrogen-Polluted Urban Shi River Revealed by Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051007},
pmid = {40431180},
issn = {2076-2607},
support = {LH2022C098//Research Grants of Nature Scientific Foundation of Heilongjiang Province/ ; ES202217//the 2022 Open Fund of National Key Laboratory of Urban Water Resources and Water Environ-ment/ ; 2023-KYYWF-1495//Basic Research Business Fees for Provincial Higher Education Institutions in Heilongjiang Prov-ince/ ; },
abstract = {Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021-2023) water quality monitoring with metagenomic sequencing to investigate microbial community dynamics, nitrogen cycling processes, and their responses to nitrogen pollution in the Shi River, Qinhuangdao, China. Nitrogen pollution was predominantly derived from industrial discharges from enterprises in the Shi River Reservoir upstream (e.g., coolant and chemical effluents), agricultural runoff, untreated domestic sewage (particularly from catering and waste in Pantao Valley), and livestock farming effluents. Total nitrogen (TN) concentrations ranged from 2.22 to 6.44 mg/L, exceeding China's Class V water standard (2.0 mg/L, GB 3838-2002), with the highest level at the urbanized W4 site (6.44 mg/L). Nitrate nitrogen (NO3-N) accounted for 60-80% of TN. Metagenomic analysis revealed Fragilaria, Microcystis, and Flavobacterium thriving (up to 15% relative abundance) under nitrogen stress, with nitrogen metabolism genes (narG, nifH, nirK) enriched at polluted sites (W2, W4), narG reaching 26% at W1. Dissolved oxygen positively correlated with nitrate reductase gene abundance, while ammonia nitrogen inhibited it. Burkholderiales and Limnohabitans dominated denitrification, offering insights into sustainable urban river management.},
}

@article {pmid40431168,
year = {2025},
author = {Mameda, R and Bono, H},
title = {Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050995},
pmid = {40431168},
issn = {2076-2607},
support = {JPMJPF2010//Japan Science and Technology Agency/ ; },
abstract = {For gene expression analysis in complex microbiomes, utilizing both metagenomic and metatranscriptomic reads from the same sample enables advanced functional analysis. Due to their diversity, metagenomic contigs are often used as reference sequences instead of complete genomes. However, studies optimizing mapping strategies for both read types remain limited. In addition, although transcripts per million (TPM) is commonly used for normalization, few studies have evaluated the influence of ribosomal RNA (rRNA) in metatranscriptomic reads. This study compared Burrows-Wheeler Aligner-Maximal Exact Match (BWA-MEM) and Bowtie2 as mapping tools for metagenomic contigs. Even after optimizing Bowtie2 parameters, BWA-MEM showed higher efficiency in mapping both metagenomic and metatranscriptomic reads. Further analysis revealed that rRNA sequences contaminate predicted protein-coding regions in metagenomic contigs. When comparing TPM values across samples, contamination by rRNA led to an overestimation of TPM changes. This effect was more pronounced when the difference in rRNA content between samples was larger. These findings suggest that metatranscriptomic reads mapped to rRNA should be excluded before TPM calculations. This study highlights key factors influencing read mapping and quantification in gene expression analysis of complex microbiomes. The findings provide insights for improving analytical accuracy and advancing functional studies using both metagenomic and metatranscriptomic data.},
}

@article {pmid40431158,
year = {2025},
author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE},
title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050985},
pmid = {40431158},
issn = {2076-2607},
support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; },
abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.},
}

@article {pmid40431157,
year = {2025},
author = {Coates, N and John, DA and Jordan, S and Storey, M and Thornton, CA and Garaiova, I and Wang, D and Allen, SJ and Michael, DR and Plummer, SF and Facey, PD},
title = {The Impact of Probiotic Supplementation on the Development of the Infant Gut Microbiota: An Exploratory Follow-Up of a Randomised Controlled Trial.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050984},
pmid = {40431157},
issn = {2076-2607},
support = {Collaborative Industrial Research (Project No. HE09 COL 1002)//Knowledge Exploitation Fund/ ; Accelerate Programme (Project code: PR-0228)//European Regional Development Fund (ERDF)/ ; N/A//Cultech Ltd/ ; },
abstract = {Early-life establishment of the gut microbiota plays a role in lifelong health, with disruptions linked to heightened risks of metabolic and immune disorders. Probiotic supplementation may be used to modulate the infant gut microbiome to promote favourable development. Here, we evaluate how Lab4B probiotic supplementation shapes the development of the infant gut microbiome over the first 6 months. Faecal samples collected from infants enrolled in PROBAT (ISRCTN26287422), a randomised, double-blind, placebo-controlled trial, were analysed using culture-dependent and -independent (16S rDNA and metagenomic shotgun sequencing) techniques to examine the composition, diversity, and metabolic capabilities of the microbiome, as well as the abundance of antimicrobial resistance genes (ARGs). Probiotic supplementation encouraged the development of a microbiome with a distinct composition characterised by elevated abundances of Bifidobacteriaceae in the first 6 weeks (p = 0.006) and Lactobacillaceae throughout the first 6 months (p < 0.05 at every 6-week time point), accelerated microbial diversification, reduced abundance of beta-lactam- and cephalosporin-resistance genes, and differences in predicted metabolic capabilities at the start and end points. Supplementation of this neonatal population, which is at high risk of atopy, with the Lab4B probiotic significantly influenced the development of the infant gut microbiota during the first 6 months.},
}

@article {pmid40431145,
year = {2025},
author = {Jiang, K and Ye, L and Cao, C and Che, G and Wang, Y and Hong, Y},
title = {Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050972},
pmid = {40431145},
issn = {2076-2607},
support = {32360005//National Natural Science Foundation of China/ ; 2022JBQN091//Fundamental Research Funds for the Inner Mongolia Normal University/ ; 2022JBTD010//Fundamental Research Funds for the Inner Mongolia Normal University/ ; },
abstract = {Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.},
}

@article {pmid40431076,
year = {2025},
author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D},
title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/plants14101511},
pmid = {40431076},
issn = {2223-7747},
support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.},
}

@article {pmid40430824,
year = {2025},
author = {Mwendwa, K and Mutuku, F and Wambua, S and Nzaro, M and Ndenga, BA and Agoi, K and LaBeaud, AD and Bosire, C},
title = {Temporal Variation and Human Host Predominance in Aedes aegypti from Coastal and Western Kenya: Insights from Pooled Blood Meal Metagenomics.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/pathogens14050505},
pmid = {40430824},
issn = {2076-0817},
support = {NIH R01 AI102918/NH/NIH HHS/United States ; },
mesh = {Animals ; *Aedes/physiology/genetics/virology ; Kenya ; Humans ; *Mosquito Vectors/virology/physiology/genetics ; *Metagenomics/methods ; Feeding Behavior ; Seasons ; Cattle ; },
abstract = {Aedes aegypti is the primary vector of arboviral diseases such as dengue, chikungunya, yellow fever, and Zika, posing significant global health and economic challenges. The effective control of this mosquito species requires understanding its seasonality, feeding behavior, and ecological dynamics. Modern molecular techniques, such as amplicon metagenomic sequencing, provide insights into vector-host interactions and feeding patterns. This study investigated the temporal variation of Ae. aegypti abundance and its blood meal sources in coastal and western Kenya over 16 months. A total of 64,360 mosquitoes were collected, with Ae. aegypti comprising 10.9% (7035/64,360). Coastal sites had a higher proportion (64.7%) of Ae. aegypti than western Kenya. Seasonal variation in abundance was observed, with peaks during the long rainy season and decline during the dry season. Blood meal analysis identified 15 vertebrate hosts, with humans being the primary source (86.6-95.9%). Other hosts included domestic animals such as turkey, sheep, cow, goat, and chicken. These findings highlight the role of rainfall in arboviral disease transmission and Ae. aegypti's strong preference for human hosts. Additionally, this study demonstrates the cost-effectiveness of group testing for identifying blood meal sources, with implications for public health interventions.},
}

Animals
*Aedes/physiology/genetics/virology
Kenya
Humans
*Mosquito Vectors/virology/physiology/genetics
*Metagenomics/methods
Feeding Behavior
Seasons
Cattle

@article {pmid40430785,
year = {2025},
author = {Tóth, AG and Solymosi, N and Tenk, M and Káldy, Z and Németh, T},
title = {First Animal Source Metagenome Assembly of Lawsonella clevelandensis from Canine External Otitis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/pathogens14050465},
pmid = {40430785},
issn = {2076-0817},
support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020 research and innovation program/ ; MILAB//European Union project RRF-2.3.1-21-2022-00004/ ; },
mesh = {Animals ; Dogs ; *Dog Diseases/microbiology ; Female ; *Otitis Externa/microbiology/veterinary ; *Metagenome ; Genome, Bacterial ; Nanopore Sequencing ; High-Throughput Nucleotide Sequencing ; },
abstract = {External otitis is one of the most common conditions in dogs to be presented to the veterinarian. Moreover, the disorder is often challenging to manage. The range and role of microorganisms involved in the pathogenesis are currently not fully understood. Therefore, the condition has been studied using third-generation sequencing (Oxford Nanopore Technology) to gain a more complete picture of the pathogens involved. Throughout the metagenome assembly of a sample from the ear canal of an 11-year-old female Yorkshire terrier suffering from chronic external otitis, a genome of Lawsonella clevelandensis was compiled. To our knowledge, this result is the first of its type of animal origin. The outcome of the assembly is a single circular chromosome with a length of 1,909,339 bp and 1727 predicted genes. One open reading frame associated with antimicrobial resistance could have been identified. Comparing all available genomes, the species can be associated with three main genome clusters. The finding contributes to the extending knowledge bank about this often-overlooked pathogen and raises attention to the role of nanopore sequencing by the identification and characterization of microorganisms that are difficult to culture.},
}

Animals
Dogs
*Dog Diseases/microbiology
Female
*Otitis Externa/microbiology/veterinary
*Metagenome
Genome, Bacterial
Nanopore Sequencing
High-Throughput Nucleotide Sequencing

@article {pmid40430233,
year = {2025},
author = {Rivera-Martínez, A and Laredo-Tiscareño, SV and Adame-Gallegos, JR and Luna-Santillana, EJ and Rodríguez-Alarcón, CA and García-Rejón, JE and Casas-Martínez, M and Garza-Hernández, JA},
title = {Viruses in Simuliidae: An Updated Systematic Review of Arboviral Diversity and Vector Potential.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/life15050807},
pmid = {40430233},
issn = {2075-1729},
support = {419-24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (Secihti) of Mexico/ ; 740742, 769056, and 842817//The Secretaría de Ciencia, Humanidades, Tecnología e Innovación (Secihti) of Mexico/ ; RIPI2019ICB45//RIPI2019ICB45/ ; 4034275//The Secretaría de Ciencia, Humanidades, Tecnología e Innovación (Secihti) of Mexico/ ; },
abstract = {Black flies (Diptera: Simuliidae) are important vectors of pathogens, including filarial nematodes, protozoans, and arboviruses, which significantly impact human and animal health. Although their role in arbovirus transmission has not been as thoroughly studied as that of mosquitoes and ticks, advances in molecular tools, particularly metagenomics, have enabled the identification of non-cultivable viruses, significantly enhancing our understanding of black-fly-borne viral diversity and their public and veterinary health implications. However, these methods can also detect insect-specific viruses (i.e., viruses that are unable to replicate in vertebrate hosts), which may lead to the incorrect classification of black flies as potential vectors. This underscores the need for further research into their ecological and epidemiological roles. This systematic review, conducted following the PRISMA protocol, compiled and analyzed evidence on arbovirus detection in Simuliidae from scientific databases. Several arboviruses were identified in these insects, including vesicular stomatitis virus New Jersey serotype (VSVNJ), Venezuelan equine encephalitis virus (VEEV), and Rift Valley fever virus. Additionally, in vitro studies evaluating the vector competence of Simuliidae for arboviruses such as dengue virus, Murray Valley encephalitis virus, and Sindbis virus were reviewed. These findings provide critical insights into the potential role of black flies in arbovirus transmission cycles, emphasizing their importance as vectors in both public and veterinary health contexts.},
}

@article {pmid40430189,
year = {2025},
author = {Escorcia Mora, P and Valbuena, D and Diez-Juan, A},
title = {The Role of the Gut Microbiota in Female Reproductive and Gynecological Health: Insights into Endometrial Signaling Pathways.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/life15050762},
pmid = {40430189},
issn = {2075-1729},
abstract = {Fertility is a dynamic, multifactorial process governed by hormonal, immune, metabolic, and environmental factors. Recent evidence highlights the gut microbiota as a key systemic regulator of reproductive health, with notable impacts on endometrial function, implantation, pregnancy maintenance, and the timing of birth. This review examines the gut-endometrial axis, focusing on how gut microbial communities influence reproductive biology through molecular signaling pathways. We discuss the modulatory roles of microbial-derived metabolites-including short-chain fatty acids, bile acids, and tryptophan catabolites-in shaping immune tolerance, estrogen metabolism, and epithelial integrity at the uterine interface. Emphasis is placed on shared mechanisms such as β-glucuronidase-mediated estrogen recycling, Toll-like receptor (TLR)-driven inflammation, Th17/Treg cell imbalance, and microbial translocation, which collectively implicate dysbiosis in the etiology of gynecological disorders including endometriosis, polycystic ovary syndrome (PCOS), recurrent implantation failure (RIF), preeclampsia (PE), and preterm birth (PTB). Although most current evidence remains correlational, emerging insights from metagenomic and metabolomic profiling, along with microbiota-depletion models and Mendelian randomization studies, underscore the biological significance of gut-reproductive crosstalk. By integrating concepts from microbiology, immunology, and reproductive molecular biology, this review offers a systems-level perspective on host-microbiota interactions in female fertility.},
}

@article {pmid40429958,
year = {2025},
author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, Á and Ferrero, MÁ and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N},
title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104818},
pmid = {40429958},
issn = {1422-0067},
mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; },
abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.},
}

Humans
*Celiac Disease/microbiology/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
Biomarkers/metabolism
*Colorectal Neoplasms/microbiology/metabolism
Animals
Metagenomics/methods

@article {pmid40429402,
year = {2025},
author = {Tar, I and Krisztina, S and Martos, R and Kiss, C and Márton, I},
title = {Effects of Comorbid Disease Improvement on Oral Lichen Planus (OLP) and Oral Leukoplakia (OL) Lesions: A Retrospective Longitudinal Study.},
journal = {Journal of clinical medicine},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jcm14103408},
pmid = {40429402},
issn = {2077-0383},
abstract = {Background: Previous attempts to treat oral potentially malignant disorders OPMDs) effectively have failed. Longitudinal studies investigating the effects of comorbid diseases improvement on OPMDs are not yet available. Therefore, the current study examined the effects of comorbid disease improvement on OPMDs healing, both in oral lichen planus (OLP) and oral leukoplakia (OL) patients. Methods: The data from 197 consecutive patients (144 females and 53 males, age ± SD: 55.19 ± 12.37 years, with ages ranging from 23 to 91 years), with oral lesions considered OLP and OL, were processed and evaluated. The frequency of comorbid diseases and the presence of HPV (here, subtypes were not evaluated) in the lesions in OLP and OL patient groups were evaluated and compared to the results of controls (n = 139). Risk models for OLP and OL lesions were established. High-risk models for erosive-atrophic OLP and non-homogeneous OLP were also described. The influence of comorbid disease improvement was also evaluated. Lesions were scored at the first and last visit (full recovery = 0, improvement = 1, and no improvement = 2). Results: One hundred and ninety-seven patients (144 OLP + 53 OL) were followed up for an average of 47.66 months (min-max: 1-203 months, SD: 54.19). Based on the established models, HPV infection, iron deficiency, diabetes, and thyroid function disorders seem to act as risk factors for OLP and may also affect OL formation. The improvement in comorbid diseases can cause significant improvement in OLP and OL lesions. Conclusions: By meticulous follow-up of comorbid diseases, improvement in OLP and OL lesions can be achieved.},
}

@article {pmid40429337,
year = {2025},
author = {Brożek-Mądry, E and Ziuzia-Januszewska, L and Misztal, O and Burska, Z and Sosnowska-Turek, E and Sierdziński, J},
title = {Nasal Rinsing with Probiotics-Microbiome Evaluation in Patients with Inflammatory Diseases of the Nasal Mucosa.},
journal = {Journal of clinical medicine},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jcm14103341},
pmid = {40429337},
issn = {2077-0383},
support = {RPWM.01.02.01-28-0027/18-00//European Regional Development Fund, European Social Fund, Regional Operational Program of the Warmian-Masurian Voivodeship - Research at Probios/ ; },
abstract = {Background/Objectives: The evidence regarding the efficacy of probiotics in chronic rhinosinusitis (CRS) is very limited, prompting the EPOS2020 steering group to advise against their use in CRS treatment. Therefore, further research to evaluate the impact of probiotics on microbial communities is particularly important. This study aimed to assess the influence of probiotic nasal rinses on nasal microbiota profiles in patients with primary CRS, granulomatosis with polyangiitis (GPA), and nasal septal perforation (NSP) using 16S rRNA sequencing. Methods: Thirty-six patients with nasal mucosal diseases, including sixteen with primary CRS, eleven with GPA, and nine with NSP, were randomly assigned to either a study group receiving nasal rinses with probiotics containing Lactobacillus plantarum and Bifidobacterium animalis, or a control group using nasal rinses with saline. Metagenomic analysis targeting the V3-V4 hypervariable region of the 16S rRNA gene was performed to characterize bacterial and archaeal populations. Results: At the genus level, the most abundant co-colonizers included Staphylococcus, Streptococcus, and Haemophilus. After one month of probiotic rinsing, a decrease in abundance of the genera Finegoldia (p = 0.010), Haemophilus (p = 0.020), Streptococcus (p = 0.027), Staphylococcus (p = 0.033), Micrococcus (p = 0.035), Corynebacterium (p = 0.049), Gemella (p = 0.055), Rubrobacter (p = 0.055), and Pseudonocardia (p = 0.058) was observed. Conversely, the abundance of probiotic species Lactobacillus plantarum and Bifidobacterium animalis increased. Moreover, increases in the genera Dolosigranulum and Stenotrophomonas were observed, although they did not reach statistical significance. Conclusions: Probiotic nasal rinses may contribute to restoring microbial homeostasis by reducing genera associated with inflammatory dysbiosis in nasal inflammatory diseases, warranting further research on their clinical benefits.},
}

@article {pmid40429183,
year = {2025},
author = {Zhou, J and Qin, W and Zeng, Y and Huang, X and Yuan, J and Yin, Y and Xu, P and Fan, X and Zhang, R and Li, G and Zhang, Y},
title = {Effects of Colony Breeding System and Nest Architecture on Soil Microbiome and Fertility in the Fungus-Growing Termite Macrotermes barneyi Light.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050470},
pmid = {40429183},
issn = {2075-4450},
support = {31601891//National Natural Science Foundation of China/ ; 2023AFB1005//Natural Science Foundation of Hubei Province of China/ ; IWHR-2024TE003//Open Research Fund of Key Laboratory of Termite Control of Ministry of Water Resources, China Institute of Water Resources and Hydropower Research/ ; EWPL202408//Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization/ ; },
abstract = {Macrotermes barneyi is a typical fungus-growing termite that forms both monogynous (single queen) and polygynous (multiple queen) colonies in nature. This species influences the local soil fertility in part by redistributing nutrients across the landscape in its habitats. However, how the colony structure of M. barneyi affects nutrient cycling and microbial communities within the nest is not well understood. In this study, we compared the physicochemical properties and microbial communities across nest parts between monogynous and polygynous colonies of M. barneyi. Our results showed that the fungus garden is the most nutrient-rich part of the nest, with higher soil moisture, organic matter, ammonium nitrogen, nitrate nitrogen, available sulfur, available potassium, available silicon, and available boron than other nest parts. Notably, the fungus garden in monogynous colonies had higher nitrate nitrogen, available sulfur, and available silicon than those in the polygynous colonies. The microbial α-diversity in the fungus garden was lower than that in other parts of the nest. β-diversity analysis revealed a clear separation of microbial communities between monogynous and polygynous colonies across nest parts. Furthermore, the relative abundance of functional genes associated with "cell cycle control, cell division, and chromosome partitioning" was higher in the fungus garden of polygynous colonies compared to monogynous colonies. Our results suggest that the fungus garden plays a crucial role in maintaining colony stability in M. barneyi colonies. The rapid depletion of nutrients in the fungus garden to sustain the larger population in polygynous colonies likely influences microbial community dynamics and nutrient cycling.},
}

@article {pmid40428846,
year = {2025},
author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R},
title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
doi = {10.3390/medicina61050888},
pmid = {40428846},
issn = {1648-9144},
support = {SRA-882725/CCF/CCF/United States ; },
mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; },
abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.},
}

Humans
Female
*Endometriosis/microbiology/physiopathology
*Feces/microbiology
*Vagina/microbiology
*RNA, Ribosomal, 16S/analysis/genetics
Dysbiosis/microbiology
Adult
Gastrointestinal Microbiome
Metagenomics/methods

@article {pmid40428471,
year = {2025},
author = {Detcharoen, M and Khrueakaew, P and Benjakul, S and Romyasamit, C and Suyapoh, W and Saetang, J},
title = {Surveillance of Antimicrobial Resistance in the Asian Seabass (Lates calcarifer) Supply Chain Using Nanopore Sequencing.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/foods14101691},
pmid = {40428471},
issn = {2304-8158},
support = {SEAOHUN/2024-SC218-0105-3009//the United States Agency for International Development (USAID) through SEAOHUN 2024 One Health Research & Training (OHRT) Awards/ ; },
abstract = {Intensive fish farming worldwide has increased reliance on antibiotics to control bacterial pathogens, raising concerns about antimicrobial resistance (AMR) in aquaculture. These resistant bacteria can persist and pass through the food supply chain, from farms to consumers. Despite this risk, antimicrobial resistance genes (ARGs) in aquaculture environments and fish products have not been elucidated. This study aimed to detect ARGs found in the Asian seabass (Lates calcarifer), an economically important fish in Thailand, collected from farms, fish container vehicles, and markets, using Nanopore metagenomic sequencing. We detected multiple ARGs in all sample types. Water samples harbored the rpsL gene conferring streptomycin resistance. Container samples exhibited the highest diversity of ARGs, including multiple beta-lactamases and the rsmA gene, conferring resistance to fluoroquinolones, diaminopyrimidines, and phenicol antibiotics. Fish samples generally lacked ARGs, except for one sample harboring rsmA. Non-metric multidimensional scaling revealed distinct microbial communities in water, compared with those found in container and fish samples, indicating potential cross-contamination during handling or storage. Our findings emphasize that containers could be critical control points for minimizing AMR spread. Overall, this study highlights the interconnection between environmental, fish, and human health, highlighting the importance of integrated AMR surveillance and management in aquaculture systems.},
}

@article {pmid40428372,
year = {2025},
author = {Dimitrova, L and Ilieva, Y and Gouliamova, D and Kussovski, V and Hubenov, V and Georgiev, Y and Bratanova, T and Kaleva, M and Zaharieva, MM and Najdenski, H},
title = {Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/genes16050551},
pmid = {40428372},
issn = {2073-4425},
support = {КP-06-N71/8 from 08.12.2023//National Fund for Scientific Research, Republic of Bulgaria/ ; },
mesh = {*Cellulose/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Microbial Consortia/genetics ; Biodegradation, Environmental ; Bacteria/genetics/isolation & purification/metabolism ; Aerobiosis ; *Bacteria, Anaerobic/genetics/isolation & purification/metabolism ; Methane/metabolism ; Biofuels ; },
abstract = {Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.},
}

*Cellulose/metabolism
*Bioreactors/microbiology
Anaerobiosis
*Microbial Consortia/genetics
Biodegradation, Environmental
Bacteria/genetics/isolation & purification/metabolism
Aerobiosis
*Bacteria, Anaerobic/genetics/isolation & purification/metabolism
Methane/metabolism
Biofuels

@article {pmid40428326,
year = {2025},
author = {Sun, YF and Han, ZX and Yao, XK and Meng, J and Ren, WL and Wang, CK and Yuan, XX and Zeng, YQ and Wang, YF and Sun, ZW and Wang, JW},
title = {Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/genes16050504},
pmid = {40428326},
issn = {2073-4425},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Physical Conditioning, Animal ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Feces/microbiology
*Physical Conditioning, Animal
*Bacteria/genetics/classification/isolation & purification

@article {pmid40428305,
year = {2025},
author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J},
title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/genes16050483},
pmid = {40428305},
issn = {2073-4425},
support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.},
}

Animals
*Elephants/microbiology/genetics
*Gastrointestinal Microbiome/genetics
*Diet
China
Metagenomics/methods
Bacteria/genetics/classification

@article {pmid40427823,
year = {2025},
author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG},
title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {5},
pages = {},
doi = {10.3390/ijerph22050707},
pmid = {40427823},
issn = {1660-4601},
support = {PTDC/CTA AMB/29586/2017//Fundação para a Ciência e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; },
mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation & purification/genetics ; },
abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.},
}

*Wastewater/virology
*Computational Biology/methods
*Virome
Portugal
*Metagenomics/methods
*Viruses/classification/isolation & purification/genetics

@article {pmid40427639,
year = {2025},
author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR},
title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050746},
pmid = {40427639},
issn = {2218-273X},
support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; },
mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.},
}

Humans
Child
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Metagenomics/methods
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Metabolomics/methods
Adolescent
*Colitis, Ulcerative/microbiology/genetics/metabolism
*Crohn Disease/microbiology/genetics/metabolism
Biomarkers/metabolism
Transcriptome
Multiomics

@article {pmid40427376,
year = {2025},
author = {Tang, J and Dong, L and Tang, M and Arif, A and Zhang, H and Zhang, G and Zhang, T and Xie, K and Su, S and Zhao, Z and Dai, G},
title = {Metagenomic Analysis Reveals the Characteristics of Cecal Microbiota in Chickens with Different Levels of Resistance During Recovery from Eimeria tenella Infection.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101500},
pmid = {40427376},
issn = {2076-2615},
support = {(JATS [2023]447)//Jiangsu Agricultural Industry Technology System/ ; },
abstract = {Coccidiosis, caused by Eimeria protozoa, is a severe intestinal parasitic disease that results in substantial economic losses to the global poultry industry annually. The gut microbiota plays a crucial role in host health, metabolism, immune function, and nutrient absorption in chickens. Recent studies have focused on the effects of Eimeria tenella's (E. tenella) acute infection period on host health. However, recovery conditions, cecal microbiota composition, and functional differences in the ceca of chickens with varying resistance to E. tenella remain poorly understood during the recovery period after infection. This study aimed to compare growth performance, cecal histopathology, and the cecal microbiota characteristics in control (R_JC), resistant (R_JR), and susceptible (R_JS) chickens during recovery, using metagenomic sequencing. The results revealed significant differences in both cecal tissue structure and growth performance between the different groups during recovery. Although no significant differences were observed in microbial alpha diversity among the groups, sequencing analysis highlighted notable changes in microbial composition and abundance. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant phyla in chicken cecal contents; however, Firmicutes abundance was lower in the R_JS group than in the R_JC and R_JR groups. Further analysis, combining linear discriminant analysis effect size (LEfSe) and differential heatmap analysis, identified Bacteroides_fluxus, Ruminococcus_flavefaciens, and Bacteroides_sp_CACC_737 as dominant microorganisms in the R_JR group (p < 0.05) compared to both the R_JC and R_JS groups. In contrast, Sutterella_sp_AM11-39, Bacteroides_sp_43_108, Mycobacterium, Mycoplasma_arginini, and Chlamydia dominated in the R_JS group, while Butyricimonas, Butyricimonas_sp_Marseille-P3923, and Flavonifractor_plautii were significantly reduced in the R_JS group (p < 0.05). Additionally, beneficial cecal microorganisms such as Flavonifractor_sp__An10, Pseudoflavonifractor, and Faecalicoccus were significantly decreased in both the R_JR and R_JS groups (p < 0.05) compared to the R_JC group. Predictive functional analysis using the KEGG and CAZy databases further indicated that the cecal microbiota in the R_JR group exhibited enhanced metabolism-related pathways, whereas these pathways were significantly diminished in the R_JS group, potentially influencing the recovery process from coccidial infection. These findings provide valuable insights into the cecal microbiota's role during recovery from E. tenella infection and deepen our understanding of the impact of coccidial infections on host health.},
}