@article {pmid41091222,
year = {2025},
author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY},
title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {49},
pmid = {41091222},
issn = {1432-1831},
support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.},
}

Animals
*Dysbiosis/chemically induced/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
*Anti-Bacterial Agents/adverse effects/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
*Klebsiella Infections/microbiology/therapy
*Bacterial Translocation/drug effects
Carbapenems/pharmacology
Humans
Mice, Inbred C57BL
Feces/microbiology

@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.

METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.

RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.

DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects

@article {pmid41088296,
year = {2025},
author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J},
title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1083},
pmid = {41088296},
issn = {1479-5876},
support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; },
abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.

METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.

RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC = 91.12%) and predict the treatment effect (AUC = 91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.

CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
Adolescent
*Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology
Male
Female
*Emotions
Quetiapine Fumarate/therapeutic use/pharmacology
Magnetic Resonance Imaging
Case-Control Studies
Brain/physiopathology/diagnostic imaging
Neuroimaging

@article {pmid41087898,
year = {2025},
author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C},
title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {660},
pmid = {41087898},
issn = {1471-2180},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism ; *Mycobiome ; *Gastrointestinal Microbiome ; *Metabolome ; Male ; Female ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Feces/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; },
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.

METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.

RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.

CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism
*Mycobiome
*Gastrointestinal Microbiome
*Metabolome
Male
Female
Middle Aged
*Fungi/classification/genetics/isolation & purification
Feces/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics

@article {pmid41087864,
year = {2025},
author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X},
title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {663},
pmid = {41087864},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China,China/ ; },
mesh = {Animals ; *Helicobacter Infections/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Helicobacter pylori/physiology ; Mice ; Humans ; Mice, Inbred C57BL ; *Homeostasis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; Male ; Retrospective Studies ; *Glucose/metabolism ; Glucagon-Like Peptide 1/metabolism ; Female ; Middle Aged ; Colon/microbiology/metabolism ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; Insulin Resistance ; Diabetes Mellitus, Experimental/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.

METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.

RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.

CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).},
}

Animals
*Helicobacter Infections/microbiology/metabolism/complications
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Helicobacter pylori/physiology
Mice
Humans
Mice, Inbred C57BL
*Homeostasis
*Diabetes Mellitus, Type 2/microbiology/metabolism
Male
Retrospective Studies
*Glucose/metabolism
Glucagon-Like Peptide 1/metabolism
Female
Middle Aged
Colon/microbiology/metabolism
Fecal Microbiota Transplantation
Anti-Bacterial Agents
Insulin Resistance
Diabetes Mellitus, Experimental/microbiology
Feces/microbiology

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
mesh = {Animals ; Swine ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Enterotoxigenic Escherichia coli/physiology ; Gastrointestinal Microbiome/drug effects ; Liver/drug effects ; *Metabolome/drug effects ; *Metagenome/drug effects ; *Escherichia coli Infections/veterinary/drug therapy ; Inflammation ; Weaning ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

Animals
Swine
Oxidative Stress/drug effects
Apoptosis/drug effects
Enterotoxigenic Escherichia coli/physiology
Gastrointestinal Microbiome/drug effects
Liver/drug effects
*Metabolome/drug effects
*Metagenome/drug effects
*Escherichia coli Infections/veterinary/drug therapy
Inflammation
Weaning

@article {pmid41015306,
year = {2026},
author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC},
title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133395},
doi = {10.1016/j.biortech.2025.133395},
pmid = {41015306},
issn = {1873-2976},
mesh = {*Ionic Liquids/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonium Compounds/metabolism ; Wastewater/microbiology ; Oxidation-Reduction ; Anaerobiosis ; *Gene Expression Regulation, Bacterial/drug effects ; Bacteria/metabolism/genetics/drug effects ; Molecular Docking Simulation ; },
abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.},
}

*Ionic Liquids/pharmacology
*Microbiota/drug effects/genetics
*Ammonium Compounds/metabolism
Wastewater/microbiology
Oxidation-Reduction
Anaerobiosis
*Gene Expression Regulation, Bacterial/drug effects
Bacteria/metabolism/genetics/drug effects
Molecular Docking Simulation

@article {pmid40914221,
year = {2025},
author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y},
title = {Succession-driven potential functional shifts in microbial communities in the tire-plastisphere: Comparison of pristine and scrap tire.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {385},
number = {},
pages = {127074},
doi = {10.1016/j.envpol.2025.127074},
pmid = {40914221},
issn = {1873-6424},
mesh = {*Microbiota ; *Microplastics/analysis ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Bacteria ; Lakes/microbiology ; },
abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.},
}

*Microbiota
*Microplastics/analysis
Environmental Monitoring
*Water Pollutants, Chemical/analysis
Ecosystem
Bacteria
Lakes/microbiology

@article {pmid40896895,
year = {2025},
author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P},
title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127129},
doi = {10.1016/j.jenvman.2025.127129},
pmid = {40896895},
issn = {1095-8630},
mesh = {*Greenhouse Gases ; Fertilizers ; *Agricultural Irrigation ; *Soil Microbiology ; Soil/chemistry ; *Microbiota ; China ; Agriculture ; Oryza ; Methane ; },
abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.},
}

*Greenhouse Gases
Fertilizers
*Agricultural Irrigation
*Soil Microbiology
Soil/chemistry
*Microbiota
China
Agriculture
Oryza
Methane

@article {pmid40882272,
year = {2025},
author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M},
title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127108},
doi = {10.1016/j.jenvman.2025.127108},
pmid = {40882272},
issn = {1095-8630},
mesh = {*Denitrification ; *Wastewater/chemistry ; *Microalgae/metabolism ; Carbon ; Nitrates ; Bacteria/metabolism ; Nitrogen ; Microbial Consortia ; },
abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.},
}

*Denitrification
*Wastewater/chemistry
*Microalgae/metabolism
Carbon
Nitrates
Bacteria/metabolism
Nitrogen
Microbial Consortia

@article {pmid40882267,
year = {2025},
author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A},
title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126986},
doi = {10.1016/j.jenvman.2025.126986},
pmid = {40882267},
issn = {1095-8630},
mesh = {*Wetlands ; Wastewater/microbiology ; Bacteria/genetics ; Microbiota ; Anti-Bacterial Agents ; },
abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.},
}

*Wetlands
Wastewater/microbiology
Bacteria/genetics
Microbiota
Anti-Bacterial Agents

@article {pmid40834570,
year = {2025},
author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L},
title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127000},
doi = {10.1016/j.jenvman.2025.127000},
pmid = {40834570},
issn = {1095-8630},
mesh = {*Waste Management/methods ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Engineering ; Fermentation ; },
abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.},
}

*Waste Management/methods
Biodegradation, Environmental
*Microbial Consortia
Metabolic Engineering
Fermentation

@article {pmid40796326,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the Upper Respiratory Microbiome Among Children Living With HIV Infection in Botswana.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {815-825},
doi = {10.1093/infdis/jiaf429},
pmid = {40796326},
issn = {1537-6613},
support = {T32 HL 007538//Institutional Training Grant in Pulmonary and Critical Care Medicine/ ; D43 TW009337/TW/FIC NIH HHS/United States ; K23-HL166022//NIH Career Development Award/ ; //Duke University Center for AIDS Research/ ; 5P30-AI064518//NIH-funded program/ ; K23-AI135090//NIH-funded program/ ; //NIH/ ; P30-AI045008//Penn Center for AIDS Research/ ; },
mesh = {Humans ; *HIV Infections/microbiology/complications ; Botswana/epidemiology ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; *Nasopharynx/microbiology ; Child, Preschool ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; },
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected and HIV-unexposed, uninfected children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.},
}

Humans
*HIV Infections/microbiology/complications
Botswana/epidemiology
Female
Male
Cross-Sectional Studies
*Microbiota
*Nasopharynx/microbiology
Child, Preschool
*Respiratory Tract Infections/microbiology/epidemiology
Infant

@article {pmid40795737,
year = {2025},
author = {Zhao, J and Kou, X and Liu, H and Wu, T and Li, J and Wang, Y and Xie, H and Wang, M and Wu, L and Wen, L and Wang, L},
title = {Microbial community responses and functional shifts in carbon degradation driven by water-salt gradients in lakeshore wetlands of semi-arid lakes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126893},
doi = {10.1016/j.jenvman.2025.126893},
pmid = {40795737},
issn = {1095-8630},
mesh = {*Wetlands ; *Lakes ; *Carbon/metabolism ; Soil/chemistry ; Salinity ; Soil Microbiology ; Microbiota ; Ecosystem ; },
abstract = {Wetlands, especially lakeshore ecosystems, play an essential role in global carbon (C) cycling and are strongly influenced by dynamic water-salt gradients. However, the mechanisms by which these gradients shape microbial communities and affect soil organic C (SOC) degradation remain incompletely understood. Here, we aimed to elucidate microbial mechanisms driving C degradation shifts along water-salt gradients. We investigated microbially mediated SOC degradation potential in Daihai Lake wetlands by metagenomic profiling of carbohydrate-active enzyme (CAZyme) genes. Our results demonstrated a significant shift in CAZyme gene abundances across the gradients. Genes involved in plant-derived C (cellulose, hemicellulose, lignin) degradation decreased with increasing soil salinity and moisture, while those related to microbial-derived C (chitin, peptidoglycan, glucans) decomposition were significantly enriched. Concurrently, the microbial community composition shifted toward greater abundance of salt-tolerant taxa, notably Proteobacteria and Bacteroidetes, while Actinobacteria and Firmicutes declined under higher water-salt conditions. Statistical analyses revealed strong correlations between key environmental factors (soil salinity (EC), soil moisture (SM), and pH) and both microbial community structure and CAZyme gene abundances (p < 0.001). Random Forest analysis further identified EC and SM as primary factors influencing C-degrading microbial functions. This study highlights the importance of water-salt gradients in regulating microbial-mediated C cycling in wetlands, providing critical insights into microbial adaptation strategies and their implications for wetland C dynamics under environmental change.},
}

*Wetlands
*Lakes
*Carbon/metabolism
Soil/chemistry
Salinity
Soil Microbiology
Microbiota
Ecosystem

@article {pmid40581627,
year = {2025},
author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H},
title = {The Gut Microbiome and Its Resistome as Predictors of Clinical Infections and Phenotypic Antibiotic Resistance in Hematopoietic Stem Cell Transplant Recipients.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {806-814},
doi = {10.1093/infdis/jiaf330},
pmid = {40581627},
issn = {1537-6613},
support = {DNRF126//Danish National Research Foundation/ ; R167-A108665-17-S2//Danish Cancer Society/ ; R218-2016-1482//Lundbeck Foundation/ ; NNF15OC0014158//Novo Nordisk Foundation/ ; //Svend Anderson Foundation/ ; RD16/0025/0041//RED de SIDA/ ; //European Regional Development Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects/isolation & purification ; Enterococcus faecalis/drug effects/isolation & purification ; Metagenomics ; *Drug Resistance, Bacterial ; Young Adult ; Escherichia coli/drug effects/isolation & purification ; Aged ; Gram-Positive Bacterial Infections/microbiology ; Transplant Recipients ; },
abstract = {A relationship among the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here by using 663 shotgun-sequenced fecal samples from 276 stem cell transplants. Enterococcus faecium, Escherichia coli, and Enterococcus faecalis were the 3 most prevalent causes of clinical infection, with vancomycin resistance in E faecium as the most common antibiotic resistance feature. Associations among the gut microbiome, resistome, and clinical infections were tested, with significant findings (false discovery rate <0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E faecium was positively associated with subsequent clinical infection with E faecium (odds ratio, 1.14; P = .02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E faecium infection (odds ratio, 1.27; P < .01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.},
}

Humans
*Gastrointestinal Microbiome
*Hematopoietic Stem Cell Transplantation/adverse effects
Male
Female
Middle Aged
Adult
Feces/microbiology
Anti-Bacterial Agents/pharmacology
Enterococcus faecium/drug effects/isolation & purification
Enterococcus faecalis/drug effects/isolation & purification
Metagenomics
*Drug Resistance, Bacterial
Young Adult
Escherichia coli/drug effects/isolation & purification
Aged
Gram-Positive Bacterial Infections/microbiology
Transplant Recipients

@article {pmid40468098,
year = {2025},
author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R},
title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {7},
pages = {2129-2150},
pmid = {40468098},
issn = {1618-1905},
mesh = {*Rivers/virology ; Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Phylogeny ; *Virome ; },
abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).},
}

*Rivers/virology
Metagenomics
*Viruses/genetics/classification/isolation & purification
*Biodiversity
Phylogeny
*Virome

@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 = {28},
number = {7},
pages = {2095-2103},
pmid = {40439813},
issn = {1618-1905},
support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Oil and Gas Fields/microbiology ; *Petroleum/microbiology/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; DNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; },
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.},
}

*Oil and Gas Fields/microbiology
*Petroleum/microbiology/analysis
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota
DNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Anaerobiosis

@article {pmid40411710,
year = {2025},
author = {Chen, L and Chen, C and Bai, Y and Li, C and Wei, C and Wei, R and Luo, R and Li, R and Ma, Q and Geng, Y},
title = {Evaluation of the effects of different formulations of protectants on the preservation of the microbiota in fecal microbiota transplantation.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {7},
pages = {2057-2079},
pmid = {40411710},
issn = {1618-1905},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics/growth & development ; *Protective Agents/pharmacology/chemistry ; Microbial Viability/drug effects ; *Preservation, Biological/methods ; Freeze Drying ; Male ; },
abstract = {BACKGROUND: With the increasing indications for fecal microbiota transplantation for the treatment of diseases, there is a growing demand for the preparation of frozen or lyophilized fecal microbiota products that are viable and can stably colonize the recipient. The addition of protective agents plays an important role in the preparation. However, there has been no systematic evaluation of the protective agents used in fecal microbiota sample transplantation preparation for transplantation.

METHODS: We were used the donor bacterial flora containing 10 different formulations of protective agents were frozen, lyophilized, and stored. Plate counting, CCK8 assay, flow cytometry after LIVE/DEAD staining, and fluorescence intensity were used to assess viable bacteria in vitro. In addition, the donor bacterial flora samples containing different formulations protective agents were transplanted into antibiotic-treated SPF mice, with 3 mice in each group and a total of 5 groups. Fecal samples were collected for metagenomic sequencing to observe the colonization of the bacterial flora in the recipient mice.

RESULTS: The preliminary screening results showed that the survival rate of bacteria in the 5% trehalose (T) groups, and 5% sucrose, 5% inulin, and 1% cysteine hydrochloride (SI) groups was slightly higher than that in the other groups. SI groups tended to be more protective against anaerobes than T groups. The donor gut microbiota containing the SI groups protective agent exhibited the best colonization of the recipient mice. The protective effects of different formulations of protective agents on the colonized probiotic strains and the metabolic function of the bacterial flora in recipient mice were found to be species specific.

CONCLUSIONS: SI groups can not only better protect the activity of anaerobic bacteria in the intestine, but also effectively promote the effective colonization of donor intestinal bacteria in the recipient mice, and the effect of frozen storage method is less, and can be used at the same time as frozen and freeze-dried preparation. It can be used as a reference for the selection of protective agents in the preparation of fecal microbiota transplantation samples.},
}

Animals
*Fecal Microbiota Transplantation/methods
Mice
*Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Bacteria/drug effects/genetics/growth & development
*Protective Agents/pharmacology/chemistry
Microbial Viability/drug effects
*Preservation, Biological/methods
Freeze Drying
Male

@article {pmid40402820,
year = {2025},
author = {Alberdi, A and Limborg, MT and Groussin, M and Aizpurua, O and Gilbert, MTP},
title = {Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {10},
pages = {1285-1298},
doi = {10.1093/jeb/voaf063},
pmid = {40402820},
issn = {1420-9101},
support = {DNRF143//Danish National Research Foundation/ ; R250-2017-1351//Lundbeckfonden/ ; CF20-0460//Carlsbergfondet/ ; H2020-SFS-2018-1//European Union/ ; HoloFood-817729//European Union/ ; 901436//Norwegian Seafood Research Fund/ ; 1182//German Science Foundation/ ; 261376515-SFB 1182//German Science Foundation/ ; },
mesh = {Animals ; *Biological Evolution ; *Microbiota ; *Metagenomics ; *Vertebrates/microbiology ; Host Microbial Interactions ; },
abstract = {Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand the ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called "metagenomic space" concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterization of microbial communities. This provides the basis to study more complex attributes, such as "potential metagenomic space" and "fundamental metagenomic space," "metagenomic plasticity," and "metagenomic evolvability," which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatiotemporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary, and applied processes.},
}

Animals
*Biological Evolution
*Microbiota
*Metagenomics
*Vertebrates/microbiology
Host Microbial Interactions

@article {pmid40266232,
year = {2025},
author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y},
title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf076},
pmid = {40266232},
issn = {1751-7370},
support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; //Shandong Provincial Key Research and Development Program of China/ ; //National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Chickens/microbiology/immunology ; *Gastrointestinal Microbiome ; *Homeostasis ; *Intestines/microbiology/immunology ; *Bacteria/genetics/classification ; *Salmonella Infections, Animal/immunology/prevention & control/microbiology ; Phylogeny ; Poultry Diseases/immunology/microbiology ; *Salmonella/immunology ; },
abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a 10-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early-life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria (SFB), which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of SFB from the chicken gut microbiota, which displayed common metabolic deficiencies with SFB of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of SFB in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.},
}

Animals
*Chickens/microbiology/immunology
*Gastrointestinal Microbiome
*Homeostasis
*Intestines/microbiology/immunology
*Bacteria/genetics/classification
*Salmonella Infections, Animal/immunology/prevention & control/microbiology
Phylogeny
Poultry Diseases/immunology/microbiology
*Salmonella/immunology

@article {pmid40134271,
year = {2025},
author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A},
title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.},
journal = {The Journal of neuropsychiatry and clinical neurosciences},
volume = {37},
number = {4},
pages = {349-358},
doi = {10.1176/appi.neuropsych.20240126},
pmid = {40134271},
issn = {1545-7222},
support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Inpatients ; *Personality/physiology ; *Mental Disorders/microbiology ; Machine Learning ; Feces/microbiology ; Young Adult ; *Personality Disorders/microbiology ; },
abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.

METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.

RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.

CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Adult
Middle Aged
Inpatients
*Personality/physiology
*Mental Disorders/microbiology
Machine Learning
Feces/microbiology
Young Adult
*Personality Disorders/microbiology

@article {pmid41087370,
year = {2025},
author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D},
title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35782},
pmid = {41087370},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; },
abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.},
}

*Metagenomics/methods
*Metagenome
*Phosphates/metabolism
*Geologic Sediments/microbiology
Bacteria/genetics
Microbiota/genetics
Phosphoric Monoester Hydrolases/genetics/metabolism

@article {pmid41085703,
year = {2025},
author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J},
title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.},
journal = {Molecular genetics and genomics : MGG},
volume = {300},
number = {1},
pages = {97},
pmid = {41085703},
issn = {1617-4623},
support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&IC/J/14/2022/160//JKST&IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; },
mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; },
abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.},
}

*Crocus/microbiology/genetics
*Software
*Metagenome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Algorithms

@article {pmid41084448,
year = {2025},
author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP},
title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {15},
pages = {4315-4324},
doi = {10.19540/j.cnki.cjcmm.20250421.401},
pmid = {41084448},
issn = {1001-5302},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; },
abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Intestinal Mucosa/drug effects/metabolism/microbiology
Male
*Drugs, Chinese Herbal/administration & dosage
Mice, Inbred C57BL
Humans
*Glycolipids/metabolism
Lipid Metabolism/drug effects
Administration, Oral
Disease Models, Animal

@article {pmid41032855,
year = {2025},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M},
title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.},
journal = {Environmental science & technology},
volume = {59},
number = {40},
pages = {21540-21554},
doi = {10.1021/acs.est.5c01564},
pmid = {41032855},
issn = {1520-5851},
mesh = {*Wetlands ; *Microbiota ; Archaea ; Bacteria ; China ; Ecosystem ; Metagenome ; },
abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.},
}

*Wetlands
*Microbiota
Archaea
Bacteria
China
Ecosystem
Metagenome

@article {pmid40726432,
year = {2025},
author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T},
title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {38},
pages = {e01707},
doi = {10.1002/advs.202501707},
pmid = {40726432},
issn = {2198-3844},
support = {2021YFA1301201//National Key R&D Program of China/ ; 2021YFA0805400//National Key R&D Program of China/ ; 2024YFA1307004//National Key R&D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; },
mesh = {*Atherosclerosis/metabolism/microbiology ; Animals ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Pyroptosis/drug effects/physiology ; Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; *Macrophages/metabolism ; Probiotics/pharmacology ; Humans ; *Lactobacillus johnsonii/metabolism ; Mice, Inbred C57BL ; *Lactobacillus/metabolism ; Male ; Disease Models, Animal ; },
abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.},
}

*Atherosclerosis/metabolism/microbiology
Animals
Mice
*Receptors, G-Protein-Coupled/metabolism/genetics
*Pyroptosis/drug effects/physiology
Gastrointestinal Microbiome/physiology
*Butyrates/metabolism
*Macrophages/metabolism
Probiotics/pharmacology
Humans
*Lactobacillus johnsonii/metabolism
Mice, Inbred C57BL
*Lactobacillus/metabolism
Male
Disease Models, Animal

@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Symbiosis
Phylogeny
Metagenome/genetics
*Evolution, Molecular
Biological Evolution

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41080577,
year = {2025},
author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z},
title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636876},
pmid = {41080577},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.},
}

Humans
*Gastrointestinal Microbiome/immunology
Child
*Lung/immunology/microbiology/metabolism
*Lung Diseases/therapy/microbiology/immunology/etiology/metabolism
Dysbiosis
Animals
Fatty Acids, Volatile/metabolism

@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.

METHODS: We performed metagenomic whole genome sequencing (mWGS; > 25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.

RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p = 0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p = 0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p = 0.05) but reduced compared to healthy individuals (0.20; p < 0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p = 0.06) and healthy (0.01; p = 0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.

CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Renal Insufficiency, Chronic/microbiology
*Acute Kidney Injury/microbiology
Metagenomics/methods
Precision Medicine/methods
Female
Male
Middle Aged
Adult
Feces/microbiology

@article {pmid41061488,
year = {2026},
author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N},
title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111479},
doi = {10.1016/j.ijfoodmicro.2025.111479},
pmid = {41061488},
issn = {1879-3460},
mesh = {*Raphanus/microbiology/virology ; Fermentation ; *Bacteriophages/genetics/physiology/isolation & purification/classification ; *Bacteria/virology/genetics/classification/isolation & purification ; Food Microbiology ; Fermented Foods/microbiology/virology ; Fungi/isolation & purification/genetics/classification/virology ; Microbiota ; },
abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.},
}

*Raphanus/microbiology/virology
Fermentation
*Bacteriophages/genetics/physiology/isolation & purification/classification
*Bacteria/virology/genetics/classification/isolation & purification
Food Microbiology
Fermented Foods/microbiology/virology
Fungi/isolation & purification/genetics/classification/virology
Microbiota

@article {pmid40972462,
year = {2026},
author = {Wang, X and Luo, Y and Gu, Y and Ren, T and Liu, Y and Wang, X and Zhao, N and Nie, X and Liu, D and Zhao, Z},
title = {Physicochemical properties, microbial diversity, metabolites and their potential relationships of traditional Chinese Zhacai fermented for different periods.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111447},
doi = {10.1016/j.ijfoodmicro.2025.111447},
pmid = {40972462},
issn = {1879-3460},
mesh = {Fermentation ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Fungi/metabolism/classification/isolation & purification/genetics ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Amino Acids/analysis ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {In this study, we investigated the physicochemical properties, dominant microorganisms, non-volatile metabolites and their relationships of traditional Chinese Zhacai (TCZ) at the "second-time pickling and pressing" stage fermentation. pH and amino acid nitrogen contents exhibited an increasing and then decreasing trend. Metagenomics analysis revealed the dominant bacterial species Lactiplantibacillus (Lpb.) plantarum and Latilactobacillus (Lat.) sakei, and fungal species Debaryomyces (D.) hansenii. LEfSe analysis identified a total of 47 differentially abundant bacteria, including Lpb. plantarum and Lat. Sakei. Metabolomics analysis indicated organic acids and their derivatives, organic heterocyclic compounds, lipids and lipid-like molecules as the major differential metabolites. Spearman's correlation results showed significant correlations among differential bacteria, non-volatile metabolites and physicochemical properties. Unexpectedly, differential fungi were not observed in TCZ at this fermentation period. Pathway enrichment identified phenylpropanoid biosynthesis and tryptophan metabolism as dominant metabolic pathways, both influencing the TCZ flavor development. This study contributes to further understanding of quality formation of TCZ, providing a foundational resource for future optimization and industrial application.},
}

Fermentation
*Bacteria/metabolism/classification/genetics/isolation & purification
*Fungi/metabolism/classification/isolation & purification/genetics
Food Microbiology
*Fermented Foods/microbiology/analysis
Amino Acids/analysis
Biodiversity
Hydrogen-Ion Concentration

@article {pmid40886575,
year = {2025},
author = {Agga, GE and Looft, T and Sistani, KR},
title = {Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application.},
journal = {The Science of the total environment},
volume = {999},
number = {},
pages = {180306},
doi = {10.1016/j.scitotenv.2025.180306},
pmid = {40886575},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Microbiota ; Animals ; Poultry ; *Drug Resistance, Microbial/genetics ; Fertilizers ; *Manure/microbiology ; Soil/chemistry ; },
abstract = {Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.},
}

*Soil Microbiology
*Microbiota
Animals
Poultry
*Drug Resistance, Microbial/genetics
Fertilizers
*Manure/microbiology
Soil/chemistry

@article {pmid40879860,
year = {2025},
author = {Liu, Y and Wang, Q and Zhang, Y and Duo, R and Bian, X and Tian, J and Hao, J and Zheng, J and Shen, H},
title = {Multi-omics characterization of gut microbiota and fecal and plasma metabolites in patients with primary Sjögren's syndrome.},
journal = {Clinical rheumatology},
volume = {44},
number = {10},
pages = {4103-4118},
pmid = {40879860},
issn = {1434-9949},
support = {CY2021-QN-A10//the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital/ ; 2022-ZD-101//Science and Technology Program of Lanzhou city/ ; GSWSKY2023-08//Health Industry Scientific Research Project of Gansu Province/ ; },
mesh = {Humans ; *Sjogren's Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology/chemistry ; Middle Aged ; Male ; Adult ; Metabolomics ; *Metabolome ; Case-Control Studies ; Metagenomics ; Aged ; Multiomics ; },
abstract = {INTRODUCTION: Accumulating evidence has implicated gut microbiota and their metabolites in primary Sjögren's syndrome (pSS) pathogenesis. However, no study simultaneously explores the gut microbiome, microbial, and plasma metabolome in pSS patients.

METHOD: Thirty pSS patients and 60 healthy controls (HCs) were recruited. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool and plasma samples.

RESULTS: pSS patients exhibited significant reduction in microbial richness and diversity. Bacteroidetes and Firmicutes accounted for over 80% of all phyla. Four phyla, 48 genera, and 106 species with significant differences were identified (P < 0.05). Proteobacteria, Ascomycota, Fusobacteria, and 31 genera (e.g., Escherichia, Veillonella, Prevotella, Klebsiella) were enriched in pSS, while Actinobacteria, Bifidobacterium, Dorea, and Blautia were depleted. Opportunistic pathogens (e.g., Escherichia coli, Prevotella copri, Streptococcus oralis, Klebsiella pneumoniae, Enterococcus faecalis) and pathogenic Clostridium bolteae and Fusobacterium nucleatum were more abundant in pSS, whereas beneficial Bifidobacterium longum and butyrate-producing Eubacterium hallii and Anaerostipes hadrus were in HCs. Notably, Lactobacillus spp. were enriched in pSS. Of 298 differential functional pathways, 239 pSS-enriched pathways were focused on nutrient and energy metabolism, while amino acid biosynthesis in HCs. During 881 differential fecal metabolites (pSS: HCs = 631:250), fatty acyls were enriched in pSS, and glycerophospholipids in HCs. Among the 712 differential plasma metabolites (pSS: HCs = 438:274), heterocyclic compounds and benzene derivatives were more abundant in pSS, while fatty acyls and glycerophospholipids prevailed in HCs. Amino acids and organic acids were predominant in both samples.

CONCLUSIONS: This study characterized gut microbiome and fecal/plasma metabolome in pSS patients, providing theoretical support for regional pSS prevention and treatment. Key Points • This is the first study to systematically characterize the gut microbiome and fecal and plasma metabolomes of primary Sjögren's syndrome (pSS) patients in Northwest China via multi-omics integration analysis. • Significant reduction in gut microbial diversity and probiotic bacteria, enrichment of opportunistic and infectious pathogens, and microbial dysfunction were observed in pSS patients. • Much more differential fecal and plasma metabolites were observed in pSS patients, with amino acids, organic acids and derivatives, nucleotides, and metabolites being the main altered metabolites in both samples.},
}

Humans
*Sjogren's Syndrome/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Female
*Feces/microbiology/chemistry
Middle Aged
Male
Adult
Metabolomics
*Metabolome
Case-Control Studies
Metagenomics
Aged
Multiomics

@article {pmid40202358,
year = {2025},
author = {Alexandre, A and Gerard, À and Sergio, I and Wim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L},
title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.},
journal = {Journal of periodontal research},
volume = {60},
number = {9},
pages = {910-922},
doi = {10.1111/jre.13406},
pmid = {40202358},
issn = {1600-0765},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota/genetics ; *Metagenomics ; Female ; Male ; *Gingiva/microbiology ; Peru ; Chile ; Adult ; Spain ; Middle Aged ; Belgium ; Porphyromonas gingivalis/isolation & purification/genetics ; Tannerella forsythia/isolation & purification/genetics ; },
abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.

METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.

RESULTS: The results indicated significant variation in α-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, β-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.

CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.},
}

Humans
*Periodontitis/microbiology
*Microbiota/genetics
*Metagenomics
Female
Male
*Gingiva/microbiology
Peru
Chile
Adult
Spain
Middle Aged
Belgium
Porphyromonas gingivalis/isolation & purification/genetics
Tannerella forsythia/isolation & purification/genetics

@article {pmid40987427,
year = {2025},
author = {Hsu, BM and Chen, JS and Wang, WY and Chen, CJ and Fan, CW and Wu, CC and Hussain, B and Tsai, HC},
title = {An integral view of gut microbiome diversity and functional metabolic changes of a gut-brain axis associated with dementia based on metagenomic analysis.},
journal = {Physiology & behavior},
volume = {302},
number = {},
pages = {115112},
doi = {10.1016/j.physbeh.2025.115112},
pmid = {40987427},
issn = {1873-507X},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; *Dementia/microbiology/metabolism ; Middle Aged ; Female ; Aged ; Aged, 80 and over ; Metagenomics ; *Brain/metabolism ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Brain-Gut Axis/physiology ; },
abstract = {BACKGROUND: Growing evidence highlights the vital role by gut microbiota in brain health through the gut-brain axis, which involves neural, immune, endocrine, and metabolic signaling pathways. Disruption of this axis through microbial dysbiosis is increasingly linked to cognitive disorders, including dementia. However, the specific taxa and pathways involved remain poorly characterized. This study investigates taxonomic and functional shifts in the gut microbiome across healthy individuals, mild dementia, and dementia patients, aiming to identify microbial signatures and metabolic alterations associated with cognitive decline.

METHODS: A total of 184 participants (aged 60-98) were recruited and grouped into healthy, mild dementia, and dementia categories based on Clinical Dementia Rating scores. Demographic and clinical data were collected through structured interviews. Fecal samples were collected from participants and DNA was extracted and subjected to 16S rRNA gene sequencing. Sequencing data were processed using QIIME2 and classified using the SILVA database. Alpha (Shannon, Inverse Simpson) and beta diversity (Bray-Curtis PCoA) were analyzed between participant groups. Functional prediction was performed with PICRUSt2 to estimate KEGG orthologs from normalized ASVs. Statistical analyses were conducted in R using Kruskal-Wallis and PERMANOVA tests to assess group-level differences.

RESULTS: Dementia patients exhibited the highest proportion of unique ASVs (32.1 %) but showed reduced alpha diversity compared to mild dementia and healthy controls. PCoA revealed distinct microbial clustering across groups, explaining 19.3 % of total variance, with dementia samples forming a unique cluster. Taxonomically, dementia samples were enriched in Firmicutes and pro-inflammatory genera such as Peptoclostridium and Scardovia, while healthy controls harbored more SCFA-producing taxa like Lachnospiraceae_UCG-001. Co-occurrence networks in dementia were more complex, with increased inter-species connectivity and key drivers including Dorea and Clostridium innocuum. Functionally, dementia samples showed enrichment of vanillate degradation pathways and depletion of neuroprotective pathways like ergothioneine and vitamin E biosynthesis, correlating with specific microbial signatures.

CONCLUSIONS: Cognitive decline was associated with reduced microbial diversity and selective enrichment of pro-inflammatory taxa, reflecting gut ecological instability due to dementia. Microbial composition shifted progressively with dementia severity, indicating disease-specific gut microbial restructuring. Moreover, the loss of key functional microbial metabolites such as neuroprotective and anti-inflammatory metabolites supports targeting such metabolites and their producing gut microbiota as a therapeutic strategy for dementia. Future studies should ensure generalization by recruiting multi-center participants with strict guidelines for monitoring confounders.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Male
*Dementia/microbiology/metabolism
Middle Aged
Female
Aged
Aged, 80 and over
Metagenomics
*Brain/metabolism
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Brain-Gut Axis/physiology

@article {pmid40939728,
year = {2025},
author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB},
title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.},
journal = {Physiology & behavior},
volume = {302},
number = {},
pages = {115102},
doi = {10.1016/j.physbeh.2025.115102},
pmid = {40939728},
issn = {1873-507X},
mesh = {Animals ; Male ; *Gastrointestinal Microbiome/drug effects/physiology ; *Physical Conditioning, Animal/physiology ; *Cardiovascular Diseases/prevention & control ; Rats ; *Arecaceae ; Liver/metabolism/drug effects ; Oxidative Stress/drug effects ; Rats, Wistar ; Fruit ; Blood Glucose ; Cholesterol/blood ; Heart Disease Risk Factors ; },
abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.

METHODOLOGY: Forty-four male rats were divided into four groups (n= 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 min and progressing to 60 min. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.

RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.

CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.},
}

Animals
Male
*Gastrointestinal Microbiome/drug effects/physiology
*Physical Conditioning, Animal/physiology
*Cardiovascular Diseases/prevention & control
Rats
*Arecaceae
Liver/metabolism/drug effects
Oxidative Stress/drug effects
Rats, Wistar
Fruit
Blood Glucose
Cholesterol/blood
Heart Disease Risk Factors

@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}

Humans
Adolescent
*Dysbiosis/microbiology
Female
Male
*Mouth/microbiology
*Obesity/microbiology
Microbiota/genetics
Saliva/microbiology
Body Mass Index
Kuwait

@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf216},
pmid = {41074769},
issn = {1751-7370},
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}

@article {pmid41074341,
year = {2025},
author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z},
title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117155},
doi = {10.1016/j.foodres.2025.117155},
pmid = {41074341},
issn = {1873-7145},
mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; },
abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.},
}

*Taste
China
*Hot Temperature
*Wine/microbiology/analysis
Odorants/analysis
*Food Microbiology
Bacteria/classification/genetics/metabolism
Metagenomics
Microbiota
Fermentation
Humans

@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}

Animals
Cattle/growth & development/microbiology
Rumen/microbiology/metabolism
*Creatine/pharmacology/administration & dosage
Metabolomics
Metagenomics
Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Animal Feed/analysis
*Pyruvic Acid/pharmacology
Bacteria/genetics/classification/metabolism

@article {pmid40712732,
year = {2025},
author = {Pérez-Molina, JA and Moreno, E and Crespillo-Andújar, C and Chamorro-Tojeiro, S and Arsuaga, M and Olavarrieta, L and Martín, O and Monge-Maillo, B and Norman, F and Lanza, VF and Serrano-Villar, S},
title = {Chagas disease induces gut microbial metabolic stress: Disruption of energy and nucleotide pathways and partial reversal by antiparasitic therapy (TRIPOBIOME-2 study).},
journal = {Travel medicine and infectious disease},
volume = {67},
number = {},
pages = {102881},
doi = {10.1016/j.tmaid.2025.102881},
pmid = {40712732},
issn = {1873-0442},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Chagas Disease/drug therapy/microbiology/metabolism ; Adult ; Male ; Female ; Middle Aged ; *Nitroimidazoles/therapeutic use ; Feces/microbiology ; Energy Metabolism ; *Nucleotides/metabolism ; Aged ; Trypanosoma cruzi ; Stress, Physiological ; },
abstract = {Chagas disease (CD) can alter gut microbiota composition, although its functional impact is poorly defined. We conducted whole-genome metagenomic sequencing of stool samples from 55 adults with chronic CD (23 treated with benznidazole) and 17 non-infected controls. Functional pathways were annotated with HUMAnN 3, and their differential abundance was assessed using ANCOM-BC2. Diversity metrics (Chao1/ACE indices and multidimensional scaling) and sPLS-DA modelling were used to explore community structure. No significant group differences were observed for alpha- and beta-diversity of bacterial functions; only 6-7 % of variance was attributable to infection status or prior benznidazole therapy. Nevertheless, chronic CD produced a distinctive functional signature marked by depletion of energy-yielding pathways (reductive and canonical tricarboxylic-acid cycles, fatty-acid β-oxidation, haem and 2-methylcitrate metabolism) and modest enrichment of purine and pyrimidine biosynthetic routes. These shifts may imply a microbiome adapting to hypoxia, nutrient scarcity, and metabolic competition with Trypanosoma cruzi. Compared with untreated patients and controls, benznidazole-treated individuals exhibited partial metabolic restoration, namely, up-regulated nucleotide and carbohydrate-degradation pathways, enhanced (5Z)-dodecenoate synthesis, and reduced reliance on the reductive tricarboxylic acid cycle, suggesting renewed microbial growth and improved short-chain-fatty-acid potential. Collectively, our results seem to portray a resource-limited, metabolically stressed gut ecosystem in chronic CD whose functional imbalance is partially reversible with antiparasitic therapy. The affected pathways, particularly those governing energy and nucleotide metabolism, could be used as candidate surrogate markers for disease monitoring and therapeutic response and as targets for microbiota-directed adjuvant strategies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Chagas Disease/drug therapy/microbiology/metabolism
Adult
Male
Female
Middle Aged
*Nitroimidazoles/therapeutic use
Feces/microbiology
Energy Metabolism
*Nucleotides/metabolism
Aged
Trypanosoma cruzi
Stress, Physiological

@article {pmid40662533,
year = {2025},
author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E},
title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).},
journal = {Zoo biology},
volume = {44},
number = {5},
pages = {504-515},
doi = {10.1002/zoo.70014},
pmid = {40662533},
issn = {1098-2361},
support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G250407)./ ; },
mesh = {Animals ; *Spheniscidae/microbiology/physiology ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolome/physiology ; Animals, Zoo/microbiology ; *Aging/physiology ; Age Factors ; Male ; },
abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.},
}

Animals
*Spheniscidae/microbiology/physiology
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Metabolome/physiology
Animals, Zoo/microbiology
*Aging/physiology
Age Factors
Male

@article {pmid41072198,
year = {2025},
author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E},
title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180681},
doi = {10.1016/j.scitotenv.2025.180681},
pmid = {41072198},
issn = {1879-1026},
abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.},
}

@article {pmid41069707,
year = {2025},
author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A},
title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf157},
pmid = {41069707},
issn = {2730-6151},
abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.},
}

@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.

RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.

CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}

Animals
*Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
*Gastrointestinal Microbiome
Epithelium/metabolism/microbiology
Fatty Acids, Volatile/metabolism
Female
*Goat Diseases/microbiology
Hydrogen-Ion Concentration
*Microbiota
Transcriptome
Multiomics

@article {pmid41068590,
year = {2025},
author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B},
title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {653},
pmid = {41068590},
issn = {1471-2180},
support = {2023ZSLC24//Zhongshan Hospital/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; },
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.

METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.

RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio = 0.29; 95% confidence interval = 0.12-0.73; P = 0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score = 1.0; log2FoldChange = 3.6) and Dolosigranulum (NetMoss score = 0.6; log2FoldChange = 1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.

CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.},
}

Humans
Male
*Microbiota
Female
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
*Lung/microbiology
Prognosis
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Nontuberculous Mycobacteria/genetics/isolation & purification/classification
Bacteria/classification/genetics/isolation & purification
Metagenomics
Adult

@article {pmid41031025,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41031025},
issn = {2692-8205},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.},
}

@article {pmid40882788,
year = {2026},
author = {Wu, J and Li, X and Huang, X and Zhu, Y and Yu, H and Xia, Y and Guo, S and Wang, X and Dong, T and Keung Tsim, KW and Zhu, Y},
title = {Kai-Xin-San, an ancient herbal mixture for anti-depression, mitigates the fluoxetine-induced gut dysbiosis and intestinal damage in chronic unpredictable mild stressed mice.},
journal = {Journal of ethnopharmacology},
volume = {354},
number = {},
pages = {120484},
doi = {10.1016/j.jep.2025.120484},
pmid = {40882788},
issn = {1872-7573},
mesh = {Animals ; *Fluoxetine/adverse effects/toxicity ; *Dysbiosis/chemically induced/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Depression/drug therapy/microbiology ; *Antidepressive Agents/pharmacology ; Intestines/drug effects/pathology ; Behavior, Animal/drug effects ; Disease Models, Animal ; },
abstract = {The gut microbiome plays a crucial role in the pathology of depression. The intestinal dysbiosis associated with prolonged use of antidepressants, such as fluoxetine, can adversely affect the efficacy of these medications. Kai-Xin-San (KXS), a traditional Chinese herbal decoction, has been utilized to treat mental disorders with a long history in China. The modulation of the gut microbiome by KXS could underlie its antidepressant effect. In the context of combining with fluoxetine, KXS could potentially mitigate fluoxetine-associated intestinal side effects during depression treatment.

AIM OF THE STUDY: This study investigates the impact of KXS on the gut of depressive mice, with a particular emphasis on its potential to mitigate fluoxetine-induced intestinal side effects.

MATERIALS AND METHODS: A high dose of fluoxetine was applied to the chronic unpredictable mild stress (CUMS)-induced mice, alone or in combination with KXS. Behavior tests were conducted to confirm the anti-depressant efficiencies. The feces of mice were collected and subjected to 16S rDNA and metagenomic sequencing. The gastrointestinal morphology and functions were assessed. The potential mechanistic action of KXS on alleviating the intestinal dysbiosis was probed.

RESULTS: Notable imbalance of microbiome and disruption of intestinal barrier were observed in CUMS mice. The intake of fluoxetine exacerbated the dysbiosis, as evidenced by the increased ratio of Firmicutes/Bacteroidetes and the elevated abundance of antibiotic-resistant genes in the gut microbiome. In addition, fluoxetine treatment further compromised the intestinal integrity and functions. Significantly, KXS treatment effectively mitigated the impairment of intestinal barrier induced by fluoxetine. These protective effects appeared to be mediated through multiple mechanisms, including the restoration of microbial homeostasis and the direct cytoprotective action on intestinal epithelial cells.

CONCLUSIONS: These findings particularly provide support for the combined usage of KXS and fluoxetine in depression treatment.},
}

Animals
*Fluoxetine/adverse effects/toxicity
*Dysbiosis/chemically induced/drug therapy
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Male
Mice
*Stress, Psychological/drug therapy
*Depression/drug therapy/microbiology
*Antidepressive Agents/pharmacology
Intestines/drug effects/pathology
Behavior, Animal/drug effects
Disease Models, Animal

@article {pmid40883605,
year = {2025},
author = {Yi, H and Lu, X and Chang, Q},
title = {MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations.},
journal = {Nature computational science},
volume = {5},
number = {10},
pages = {884-897},
pmid = {40883605},
issn = {2662-8457},
mesh = {*Metagenomics/methods ; *Databases, Genetic ; Humans ; Microbiota/genetics ; Metagenome ; Software ; Computational Biology/methods ; Cluster Analysis ; },
abstract = {The performance of metagenomic profiling is constrained by the diversity of taxa present in the reference taxonomic marker database (MarkerDB) used. However, continually updating MarkerDB to include newly determined taxa using existing approaches faces increasing difficulties and will soon become impractical. Here we introduce MetaKSSD, which redefines MarkerDB construction and metagenomic profiling using sketch operations, enhancing MarkerDB scalability and profiling performance. MetaKSSD encompasses 85,202 species in its MarkerDB using just 0.17 GB of storage and profiles 10 GB of data within seconds. Leveraging its comprehensive MarkerDB, MetaKSSD substantially improves profiling results. In a microbiome-phenotype association study, MetaKSSD identified more effective associations than MetaPhlAn4. We profiled 382,016 metagenomic runs using MetaKSSD, conducted extensive sample clustering analyses and suggested potential yet-to-be-discovered niches. MetaKSSD offers functionality for instantaneous searching of similar profiles. It enables the swift transmission of metagenome sketches over the network and real-time online metagenomic analysis, facilitating use by non-expert users.},
}

*Metagenomics/methods
*Databases, Genetic
Humans
Microbiota/genetics
Metagenome
Software
Computational Biology/methods
Cluster Analysis

@article {pmid40695364,
year = {2025},
author = {Kabil, AK and Liu, LT and Xu, C and Nayyar, N and González, L and Chopra, S and Brassard, J and Beaulieu, MJ and Li, Y and Damji, A and Zandstra, PW and Blanchet, MR and Hughes, MR and McNagny, KM},
title = {Microbial dysbiosis sculpts a systemic ILC3/IL-17 axis governing lung inflammatory responses and central hematopoiesis.},
journal = {Mucosal immunology},
volume = {18},
number = {5},
pages = {1139-1158},
doi = {10.1016/j.mucimm.2025.07.002},
pmid = {40695364},
issn = {1935-3456},
mesh = {Animals ; *Dysbiosis/immunology ; Mice ; *Interleukin-17/metabolism ; *Th17 Cells/immunology ; *Hematopoiesis ; *Lung/immunology ; Mice, Inbred C57BL ; Streptomycin ; Disease Models, Animal ; Microbiota ; Immunity, Innate ; },
abstract = {Advancements in vaccination and sanitation have significantly reduced the prevalence and burden of infectious diseases; however, these benefits have coincided with a marked rise in autoimmune and allergic disorders. Recent studies have investigated these linked trends through the lens of host-microbiome alterations, proposing these shifts as a potential explanatory mechanism. Previously, we demonstrated that vancomycin-induced depletion of short-chain fatty acid (SCFA) producing bacteria results in hyperactivation of ILC2s and exacerbated allergic responses. Here we investigate the effects of low-dose streptomycin on innate and adaptive immune cell populations and their activation states. Although streptomycin-treated mice exhibit normal allergic responses, they display heightened susceptibility to Th1/Th17-mediated disease, specifically hypersensitivity pneumonitis (HP). This is characterized by a two-fold increase in ILC3s and Th17 cells in the lungs, alongside activation of antigen-presenting cells (APCs) at steady state, an effect that is further amplified upon exposure to HP-inducing agents. Shotgun metagenomic analysis revealed that streptomycin-induced dysbiosis reduces microbial diversity, depletes bile acid-metabolizing bacteria, and enriches for metabolic pathways involved in branched-chain amino acid biosynthesis, including leucine, a known activator of mTORC1. Strikingly, administration of the secondary bile acid metabolite isolithocholic acid (an inverse agonist of RORγt), or an IL-23 neutralizing antibody, reverses the enhanced susceptibility to HP. Inhibition of mTORC1 also significantly reduced Th17/ILC3 responses and histopathology. Our findings underscore microbial equilibrium as a key determinant of susceptibility to HP and uncover a positive feedback loop between IL-23-producing APCs and ILC3/Th17 cells that mechanistically links dysbiosis to sustained type 3 inflammation; and we identify a simple, actionable means of intervention.},
}

Animals
*Dysbiosis/immunology
Mice
*Interleukin-17/metabolism
*Th17 Cells/immunology
*Hematopoiesis
*Lung/immunology
Mice, Inbred C57BL
Streptomycin
Disease Models, Animal
Microbiota
Immunity, Innate

@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism
Female
*Gastrointestinal Microbiome
Male
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Adult
Middle Aged
Bile Acids and Salts/metabolism
Constipation/microbiology
Metagenome
Diarrhea/microbiology
Bacteria/classification/genetics/metabolism

@article {pmid41068233,
year = {2025},
author = {Giovannini, N and Limena, A and Ercolino, C and Renteria, SCU and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D},
title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35306},
pmid = {41068233},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation & purification ; *Pregnancy Complications, Infectious/microbiology/virology ; },
abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.},
}

Humans
Female
Pregnancy
*COVID-19/microbiology/virology
*Nasopharynx/microbiology
Adult
*Microbiota
*Mouth/microbiology
SARS-CoV-2/isolation & purification
*Pregnancy Complications, Infectious/microbiology/virology

@article {pmid41068119,
year = {2025},
author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y},
title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {196},
pmid = {41068119},
issn = {2055-5008},
support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; },
abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Metagenome
*Genome, Bacterial
Interspersed Repetitive Sequences
Phylogeny
Metagenomics

@article {pmid41066275,
year = {2025},
author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S},
title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002065},
pmid = {41066275},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; },
abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*Periodontitis/therapy/microbiology
Middle Aged
Adult
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology

@article {pmid41066109,
year = {2025},
author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y},
title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2511071122},
doi = {10.1073/pnas.2511071122},
pmid = {41066109},
issn = {1091-6490},
support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; },
abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.},
}

*Soil Microbiology
*Microbiota/physiology
*Ecosystem
*Desert Climate
Soil/chemistry

@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}

China
*Museums
*Air Microbiology
*Bacteria/genetics/classification/isolation & purification/drug effects
Microbiota

@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}

Humans
*Bile Acids and Salts/blood
*Gastrointestinal Microbiome
*Crohn Disease/blood/microbiology
*Colitis, Ulcerative/blood/microbiology
Female
Male
Adult
Biomarkers/blood
Middle Aged
*Inflammation/blood
Case-Control Studies
Feces/microbiology

@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R15LM013460//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}

*Deep Learning
*Proteomics/methods
*Peptides/analysis
Humans
Gastrointestinal Microbiome
Neural Networks, Computer
Databases, Protein
Metagenome

@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}

Animals
*Sus scrofa/virology
*Animals, Wild/virology
Swine/virology
*Animals, Domestic/virology
China/epidemiology
Disease Reservoirs/virology
Virome/genetics
Humans
*Viruses/genetics/classification/isolation & purification
*Swine Diseases/virology
Zoonoses/virology
Phylogeny

@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}

@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}

Humans
*Respiratory Tract Infections/virology/microbiology/complications
*Metagenomics
Male
Middle Aged
Female
Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Virome
Bronchoalveolar Lavage Fluid/virology/microbiology
Microbiota
Aged
*Respiratory Insufficiency/virology/microbiology
Adult

@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigación/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}

*Models, Biological
*Ecosystem
Bayes Theorem
*Microbiota
Humans

@article {pmid40985550,
year = {2025},
author = {He, Y and Baltar, F and Wang, Y},
title = {Seasonal variability in community structure and metabolism of active deep-sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf214},
pmid = {40985550},
issn = {1751-7370},
support = {ZDSYS20230626091459009//Shenzhen Key Laboratory of Advanced Technology for Marine Ecology/ ; //National Natural Science Foundation of China/ ; },
mesh = {*Seasons ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; China ; *Microbiota ; Archaea/classification/metabolism/genetics ; Metagenome ; },
abstract = {Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales, and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate to nutrient source variations as reflected by the different levels of microbial network complexity between the two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.},
}

*Seasons
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
China
*Microbiota
Archaea/classification/metabolism/genetics
Metagenome

@article {pmid40972887,
year = {2025},
author = {Hitch, TCA and Bosch, J and Bolsega, S and Deschamps, C and Etienne-Mesmin, L and Treichel, N and Blanquet-Diot, S and Ocvirk, S and Basic, M and Clavel, T},
title = {Function-based selection of synthetic communities enables mechanistic microbiome studies.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf209},
pmid = {40972887},
issn = {1751-7370},
support = {CA23110//European Union, COST action INFOGUT/ ; 513892404//German Research Foundation/ ; 460129525//German Research Foundation/ ; NFDI4Microbiota//German Research Foundation/ ; 403224013//German Research Foundation/ ; SFB1382//German Research Foundation/ ; 395357507//German Research Foundation/ ; SFB1371//German Research Foundation/ ; 01KA2103//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Mice ; Humans ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; *Host Microbial Interactions ; Metagenome ; Germ-Free Life ; *Gastrointestinal Microbiome ; Colitis/microbiology ; },
abstract = {Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.},
}

Animals
Mice
Humans
*Microbiota
Inflammatory Bowel Diseases/microbiology
*Host Microbial Interactions
Metagenome
Germ-Free Life
*Gastrointestinal Microbiome
Colitis/microbiology

@article {pmid40956094,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling bile acids in the stools of humans and animal models of cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0145125},
pmid = {40956094},
issn = {2165-0497},
support = {ES 033988-01A1/NH/NIH HHS/United States ; 05912G223//Cystic Fibrosis Foundation/ ; T32HL134598/NH/NIH HHS/United States ; R01AI164772, U01AI163063, P30DK117469/NH/NIH HHS/United States ; P20-GM130454/NH/NIH HHS/United States ; },
mesh = {*Cystic Fibrosis/microbiology/metabolism ; Animals ; *Bile Acids and Salts/metabolism/analysis ; *Feces/chemistry/microbiology ; Humans ; Mice ; Disease Models, Animal ; Ferrets ; Male ; Gastrointestinal Microbiome ; Female ; Child ; Bacteria/classification/genetics/metabolism/isolation & purification ; Child, Preschool ; Adolescent ; },
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with aberrant bile acid (BA) metabolism. As little is known about BA in children with CF (cwCF), we performed both comprehensive (n = 89) and focused (n = 21) BA profiling in stool of children with or without CF. Our results reveal select BA species and metabolites are significantly different between cwCF and nonCF controls. Focused BA profiling revealed a significant increase in total BA levels and selected changes in a subset of BA classes for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in this small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroidetes (lower in cwCF) phylum are consistent with prior reports. A trend was noted toward reduced abundance of bsh gene families, a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Observed modest changes in both BAs and microbial BA metabolism-related gene abundances may suggest a possible combination of defects in host and microbial BA metabolic pathways in cwCF. Fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, and while the ferret model reproduced significant differences between CF and nonCF animals, the nonCF animals showed higher levels of BA (opposite of what is observed in humans), indicating that neither model recapitulated BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF and highlight limitations of CF animal models for BA functional studies.

IMPORTANCE: Changes in the abundance and/or composition of intestinal BAs may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for cwCF. Matched metagenomic analysis suggests possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}

*Cystic Fibrosis/microbiology/metabolism
Animals
*Bile Acids and Salts/metabolism/analysis
*Feces/chemistry/microbiology
Humans
Mice
Disease Models, Animal
Ferrets
Male
Gastrointestinal Microbiome
Female
Child
Bacteria/classification/genetics/metabolism/isolation & purification
Child, Preschool
Adolescent

@article {pmid40914155,
year = {2025},
author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR},
title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.},
journal = {Cell metabolism},
volume = {37},
number = {10},
pages = {2048-2065.e6},
doi = {10.1016/j.cmet.2025.08.005},
pmid = {40914155},
issn = {1932-7420},
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; Diet, High-Fat/adverse effects ; Male ; Humans ; *Portal Vein/metabolism ; Gluconeogenesis ; Hepatocytes/metabolism/drug effects ; Vancomycin/pharmacology ; Liver/metabolism ; Obesity/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.},
}

Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
Diet, High-Fat/adverse effects
Male
Humans
*Portal Vein/metabolism
Gluconeogenesis
Hepatocytes/metabolism/drug effects
Vancomycin/pharmacology
Liver/metabolism
Obesity/metabolism
Diabetes Mellitus, Type 2/metabolism
Anti-Bacterial Agents/pharmacology

@article {pmid40862625,
year = {2025},
author = {Ao, J and Tang, X and Li, Z and Tang, Z},
title = {Shrub encroachment alters microbial community composition and soil carbon and nitrogen cycling functional genes in northern peatlands.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0054225},
pmid = {40862625},
issn = {2165-0497},
support = {2023YFF1304604-3//National Key Research and Development Program of China/ ; XZ202401ZY0110//Key R&D Program of Tibet Autonomous Region, China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; Wetlands ; *Microbiota/genetics ; Fungi/genetics/classification/metabolism/isolation & purification ; Carbon Cycle/genetics ; Nitrogen Fixation/genetics ; Ecosystem ; },
abstract = {Changes in vegetation, such as shrub encroachment in grassland and wetland ecosystems, significantly influence soil microbial communities and biogeochemical processes. However, the specific impact of shrub encroachment on peatland ecosystems remains poorly understood. This study used a "space-for-time" approach, collecting soil samples from three encroachment stages-uninvaded, shrub invasion, and shrub invasion expansion-at two depths (0-30 cm and 30-60 cm). Metagenomic sequencing was used to assess the microbial community composition and functional gene dynamics. Shrub encroachment significantly alters soil physicochemical properties, nutrient availability, and microbial communities. Alpha diversity of bacteria and fungi was influenced by shrub encroachment and depth, whereas beta diversity varied mainly with depth. Functional carbon fixation genes (korA and pps) increased during shrub encroachment, while methane oxidation (hdrA2) and carbon degradation genes (GH31 and GH51) decreased before increasing. In addition, functional genes linked to nitrogen cycling (nifD, nifH, amoA, and amoC) declined, indicating a reduction in nitrogen fixation and nitrification pathways. Correlation and Mantel tests revealed that the total soil carbon content was the primary driver of these functional changes. These findings highlight the dynamic microbial responses to shrub encroachment and offer insights into the soil carbon and nitrogen-cycling mechanisms in peatlands.IMPORTANCEShrub encroachment is transforming peatlands and altering their ecological and biogeochemical functions. This study provides critical insights into how shrub invasion affects microbial communities and functional genes responsible for carbon and nitrogen cycling in peatland soils. By revealing the underlying genetic mechanisms, this study enhances our understanding of the consequences of vegetation shifts on ecosystem processes. These findings are essential for predicting and managing peatland responses to environmental changes, helping to preserve their role as vital carbon and nutrient reservoirs.},
}

*Soil Microbiology
*Carbon/metabolism/analysis
*Soil/chemistry
*Bacteria/genetics/classification/metabolism/isolation & purification
*Nitrogen Cycle/genetics
Nitrogen/metabolism
Wetlands
*Microbiota/genetics
Fungi/genetics/classification/metabolism/isolation & purification
Carbon Cycle/genetics
Nitrogen Fixation/genetics
Ecosystem

@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0311924},
pmid = {40833093},
issn = {2165-0497},
mesh = {*Metagenomics/methods/standards ; Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *DNA Contamination ; *Microbiota/genetics ; Workflow ; *DNA, Bacterial/genetics/isolation & purification ; Indicators and Reagents ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}

*Metagenomics/methods/standards
Humans
*High-Throughput Nucleotide Sequencing/methods/standards
*DNA Contamination
*Microbiota/genetics
Workflow
*DNA, Bacterial/genetics/isolation & purification
Indicators and Reagents
Bacteria/genetics/classification/isolation & purification

@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}

Humans
Male
Female
*Dysbiosis/microbiology
*Ischemic Attack, Transient/microbiology
*Microbiota/genetics
Middle Aged
Case-Control Studies
Aged
*Ischemic Stroke/microbiology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Saliva/microbiology
Bacteria/genetics/classification
*Mouth/microbiology

@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}

Humans
*Cystic Fibrosis/microbiology/complications
*Microbiota
Male
Female
Adult
Sputum/microbiology
*Diabetes Mellitus/microbiology/etiology
Glucose Tolerance Test
Young Adult
Lung/microbiology
Respiratory Function Tests
Pseudomonas aeruginosa

@article {pmid40919785,
year = {2025},
author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y},
title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0129925},
doi = {10.1128/spectrum.01299-25},
pmid = {40919785},
issn = {2165-0497},
support = {No.82370661//National Natural Science Foundation of China/ ; YFYKCTDPY202202//Science and Technology Innovation Team Cultivation Project of the First Affiliated Hospital of Nanchang University/ ; },
mesh = {Animals ; *Rifaximin ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; Humans ; Disease Models, Animal ; Female ; *Pancreatitis/drug therapy/microbiology/pathology ; Middle Aged ; *Inflammation/drug therapy ; Adult ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; },
abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.

IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.},
}

Animals
*Rifaximin
*Gastrointestinal Microbiome/drug effects
Mice
Male
Humans
Disease Models, Animal
Female
*Pancreatitis/drug therapy/microbiology/pathology
Middle Aged
*Inflammation/drug therapy
Adult
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Mice, Inbred C57BL
Dysbiosis/drug therapy

@article {pmid40915262,
year = {2025},
author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D},
title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139776},
doi = {10.1016/j.jhazmat.2025.139776},
pmid = {40915262},
issn = {1873-3336},
mesh = {*Biofilms ; *Ammonia/metabolism ; *Microbiota ; *Manganese/metabolism ; *Dioxanes ; *Water Pollutants, Chemical/metabolism ; Filtration ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Electrochemical Techniques ; Water Purification/methods ; },
abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.},
}

*Biofilms
*Ammonia/metabolism
*Microbiota
*Manganese/metabolism
*Dioxanes
*Water Pollutants, Chemical/metabolism
Filtration
Biodegradation, Environmental
Bacteria/genetics/metabolism
Electrochemical Techniques
Water Purification/methods

@article {pmid40910779,
year = {2025},
author = {Hanawa, S and Son, A and Kato, T and Matsuo, Y and Omae, T and Omori, Y and Yoshikawa, K and Yamanegi, K and Hirota, K and Ohno, H and Ogura, H and Ishido, S and Noguchi, K and Kishimoto, H},
title = {Identification of beneficial symbiont candidates in commensalism as potential oral gatekeepers.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0158825},
doi = {10.1128/spectrum.01588-25},
pmid = {40910779},
issn = {2165-0497},
support = {JP23H05357//Japan Society for the Promotion of Science/ ; JP22K09106//Japan Society for the Promotion of Science/ ; //Hyogo College of Medicine/ ; },
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; Microbiota ; Male ; Female ; *Mouth Neoplasms/microbiology ; Middle Aged ; Probiotics ; *Bacteria/classification/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; Healthy Volunteers ; Aged ; Dysbiosis/microbiology ; },
abstract = {The basis of the development of oral cancer has been reported to be inflammation (e.g., periodontitis) caused by dysbiosis of the oral microbiota (i.e., a decrease in beneficial oral symbionts). Since a decrease in beneficial symbionts is connected to oral cancer, restoring these bacteria may help prevent it. Based on this, oral probiotics using beneficial oral symbionts are under development. Therefore, it is necessary to understand how beneficial oral symbionts are maintained in a healthy oral cavity. We evaluated a cohort consisting of 42 healthy volunteers and 39 oral cancer patients via 16S metagenomic analysis. Beneficial symbiont candidates were mined by comparing the oral microbiota of healthy volunteers with that of oral cancer patients, and the interaction mode among the beneficial symbiont candidates was further examined. Cancer patients exhibited decreased relative abundance of the genera Rothia and Streptococcus. In addition, both bacterial genera further decreased in advanced cancer, highlighting them as beneficial candidates. Furthermore, these two bacterial genera demonstrated a positive correlation in terms of relative abundance. Rothia dentocariosa isolated from a representative healthy volunteer was suggested to support the survival of Streptococcus salivarius through possible syntrophic interaction. Thus, we report a potential syntrophic interaction between Streptococcus spp. and Rothia spp. as a possible mechanism underlying oral health maintenance. Given that S. salivarius is currently employed as an oral probiotic, our findings provide insights into the development of probiotics for oral cancer.IMPORTANCEPathobiont candidates associated with oral cancer are currently being thoroughly investigated. However, it is not clear which bacteria and how their interactions contribute to preventing the development of oral cancer. In this report, we demonstrate for the first time the presence of a potential syntrophic interaction between Rothia spp. and Streptococcus spp., both of which were identified as beneficial symbiont candidates in the oral cavity.},
}

Humans
*Symbiosis
*Mouth/microbiology
Microbiota
Male
Female
*Mouth Neoplasms/microbiology
Middle Aged
Probiotics
*Bacteria/classification/genetics/isolation & purification
Adult
RNA, Ribosomal, 16S/genetics
Healthy Volunteers
Aged
Dysbiosis/microbiology

@article {pmid40886530,
year = {2025},
author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C},
title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139709},
doi = {10.1016/j.jhazmat.2025.139709},
pmid = {40886530},
issn = {1873-3336},
mesh = {Metagenomics ; *Soil Microbiology ; Biodegradation, Environmental ; *Estradiol/metabolism ; *Microbiota ; Rhodococcus/metabolism/genetics ; *Soil Pollutants/metabolism ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; },
abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.},
}

Metagenomics
*Soil Microbiology
Biodegradation, Environmental
*Estradiol/metabolism
*Microbiota
Rhodococcus/metabolism/genetics
*Soil Pollutants/metabolism
Microbial Consortia
RNA, Ribosomal, 16S/genetics

@article {pmid40882374,
year = {2025},
author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X},
title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139681},
doi = {10.1016/j.jhazmat.2025.139681},
pmid = {40882374},
issn = {1873-3336},
mesh = {Mining ; *Metals, Rare Earth/toxicity ; *Water Pollutants, Chemical/toxicity/metabolism ; Bioreactors ; *Microbial Consortia/drug effects ; Wastewater ; *Ferrous Compounds/chemistry ; Biodegradation, Environmental ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; Water Purification/methods ; *Iron ; },
abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.},
}

Mining
*Metals, Rare Earth/toxicity
*Water Pollutants, Chemical/toxicity/metabolism
Bioreactors
*Microbial Consortia/drug effects
Wastewater
*Ferrous Compounds/chemistry
Biodegradation, Environmental
Waste Disposal, Fluid/methods
Oxidation-Reduction
Water Purification/methods
*Iron

@article {pmid40865218,
year = {2025},
author = {Yang, H and Fu, H and Zhao, Y and Li, R and Cao, M and Liu, Y and Ni, Y and Song, W and Liang, Y and Cai, P and Chang, W and Tao, F and Wang, H and Liu, K},
title = {Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139604},
doi = {10.1016/j.jhazmat.2025.139604},
pmid = {40865218},
issn = {1873-3336},
mesh = {*Lakes/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Animals ; Pharmaceutical Preparations/analysis ; Microbiota ; Spatio-Temporal Analysis ; Fishes ; China ; },
abstract = {This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.},
}

*Lakes/microbiology/chemistry
*Water Pollutants, Chemical/analysis
*Pesticides/analysis
*Drug Resistance, Microbial/genetics
Environmental Monitoring
*Genes, Bacterial
Geologic Sediments/microbiology
Animals
Pharmaceutical Preparations/analysis
Microbiota
Spatio-Temporal Analysis
Fishes
China

@article {pmid40824084,
year = {2025},
author = {Li, J and Liang, L and Ye, J and Miao, Y and Zhao, K and Tian, Y and Li, X and Li, X and Chen, X and Wen, B and He, Y and Chen, B and Qin, L and Wang, Y and Fu, X},
title = {Gastric microbiota transplantation enhanced the eradication of refractory Helicobacter pylori infection by modulating the gastric microbiota: a pilot study.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0326324},
doi = {10.1128/spectrum.03263-24},
pmid = {40824084},
issn = {2165-0497},
support = {2024ZYD0144 and 24ZYZYTS0389//Central Government-Directed Project for Local Science and Technology Development/ ; 24WXXT05//Health Commission of Sichuan Province/ ; },
mesh = {Humans ; *Helicobacter Infections/therapy/microbiology ; Pilot Projects ; *Helicobacter pylori ; Male ; Middle Aged ; Female ; Adult ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Gastritis, Atrophic/therapy/microbiology ; *Stomach/microbiology ; Aged ; Dysbiosis/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {UNLABELLED: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. In this study, we investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. We performed a metagenomic analysis of the microecological systems across different regions of the stomach, including the gastric fluid (GF), the gastric mucus layer (GML), and the gastric mucosa (GM). We initiated a clinical GMT intervention by transplanting microbial communities from healthy individuals' GML into patients exhibiting refractory H. pylori infection and chronic atrophic gastritis. Our findings demonstrated significant disparities in species richness among the GF, GML, and GM, with the GML exhibiting the highest diversity of unique microbial genera. H. pylori infection primarily influenced the relative species abundance within the GML community, without altering its fundamental composition. Clinically, GMT was well-tolerated by all recipients and showed substantial synergistic efficacy against refractory H. pylori infection, achieving a 100% eradication rate in all patients, and significantly alleviating symptoms in individuals with H. pylori-positive atrophic gastritis (P < 0.05). Compared with the gastric microbiota of H. pylori-negative patients, the gastric microbiota of H. pylori-positive patients treated with GMT exhibited closer alignment with those of healthy donors. In conclusion, GMT utilizing GML enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis through modulating the gastric microbiota.

IMPORTANCE: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. We investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. GMT significantly enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis. GMT demonstrated improvements in the cure rate of refractory H. pylori infection, potentially offering a new clinical treatment approach. This finding provides new insights and a potential therapeutic direction for treating dysbiosis related chronic gastric diseases.},
}

Humans
*Helicobacter Infections/therapy/microbiology
Pilot Projects
*Helicobacter pylori
Male
Middle Aged
Female
Adult
Gastric Mucosa/microbiology
*Gastrointestinal Microbiome
Gastritis, Atrophic/therapy/microbiology
*Stomach/microbiology
Aged
Dysbiosis/therapy/microbiology
Anti-Bacterial Agents/therapeutic use

@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}

Humans
*Skin/radiation effects/microbiology/metabolism
Animals
Mice
Microbiota/radiation effects
Bioengineering
Cell Proliferation/radiation effects
Dose-Response Relationship, Radiation

@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}

Animals
*Methane/metabolism/biosynthesis
*Fermentation/drug effects
*Rumen/microbiology/metabolism
Cattle
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Animal Feed
*Ruminants/microbiology/metabolism
Microbiota/drug effects
Fatty Acids, Volatile/metabolism

@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}

Humans
*Mucormycosis/diagnosis/microbiology/drug therapy
*Mucorales/genetics/isolation & purification/classification
Male
Female
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Adult
ROC Curve
Antifungal Agents/therapeutic use
Microbiota

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}

@article {pmid40966609,
year = {2025},
author = {Wu, L and Bao, D and Liao, H and Yan, M and Ge, Y and Han, Z and Xia, X},
title = {Pore-scale mass transfer heterogeneity shapes nutrient accessibility and functional assembly in porous microbial ecosystems.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf205},
pmid = {40966609},
issn = {1751-7370},
support = {2023YFF1103701//National Key Research and Development Program of China/ ; },
mesh = {*Ecosystem ; *Microbiota ; Porosity ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenomics ; Soil Microbiology ; Amino Acids/metabolism ; Biomass ; },
abstract = {Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.},
}

*Ecosystem
*Microbiota
Porosity
*Nutrients/metabolism
*Bacteria/metabolism/genetics/classification
Metagenomics
Soil Microbiology
Amino Acids/metabolism
Biomass

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {49},
number = {8},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
mesh = {Humans ; *Appendicitis/microbiology/diagnosis/surgery ; Prospective Studies ; Male ; Adult ; Female ; *Rectum/microbiology ; *Microbiota ; Middle Aged ; Appendectomy ; Cohort Studies ; Aged ; Young Adult ; },
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}

Humans
*Appendicitis/microbiology/diagnosis/surgery
Prospective Studies
Male
Adult
Female
*Rectum/microbiology
*Microbiota
Middle Aged
Appendectomy
Cohort Studies
Aged
Young Adult

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}

@article {pmid41044010,
year = {2025},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}

*Soil Microbiology
*Phosphorus/metabolism
China
Soil/chemistry
Grassland
*Carbon/metabolism
Desert Climate
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Microbiota
Metagenomics

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}