Dini Hu, Chenghang Sun, Tong Xin, Yixin Liu, Tianchun Pu, Shunfu He, Yanqiang Yin, Yibo Hu
{"title":"Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.","authors":"Dini Hu, Chenghang Sun, Tong Xin, Yixin Liu, Tianchun Pu, Shunfu He, Yanqiang Yin, Yibo Hu","doi":"10.1038/s41522-026-01066-9","DOIUrl":"10.1038/s41522-026-01066-9","url":null,"abstract":"<p><p>The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148331753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Beyond estrobolome 1.0: unraveling endocrine-microbiome axis as a driver and therapeutic target in hormone-driven cancers.","authors":"Exian Mou, Rui Guo, Yong Yi, Yang Li, Yutang Yao, Jia Xu","doi":"10.1038/s41522-026-01074-9","DOIUrl":"10.1038/s41522-026-01074-9","url":null,"abstract":"<p><p>The endocrine-microbiome axis extends the estrobolome concept, recognizing gut microbes as active endocrine partners. Bacteria modulate estrogen recycling via diverse enzymes and produce SERM-like metabolites, while host hormones shape microbial communities. This bidirectional crosstalk influences hormone-driven carcinogenesis through inflammation, genomic instability, and epigenetic changes. Therapeutic opportunities include precision probiotics and selective enzymatic inhibition. Advancing the field requires causal models, multi-omics integration, and sex as a biological variable.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148318367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christina Schäfer, Maria L Bonatelli, Idun Maria Tokvam Burgos, Sabine Kleinsteuber, Daniel Machado, Ove Øyås, Hauke Harms, Heike Sträuber
{"title":"Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.","authors":"Christina Schäfer, Maria L Bonatelli, Idun Maria Tokvam Burgos, Sabine Kleinsteuber, Daniel Machado, Ove Øyås, Hauke Harms, Heike Sträuber","doi":"10.1038/s41522-026-01072-x","DOIUrl":"10.1038/s41522-026-01072-x","url":null,"abstract":"<p><p>Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l<sup>-1</sup>) and CO<sub>2</sub> were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l<sup>-1</sup>), lactic acid (up to 1.2 g l<sup>-1</sup>), ethanol (up to 1.2 g l<sup>-1</sup>), CO<sub>2</sub>, and H<sub>2</sub>. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13294492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148318372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chunli Hu, Xuehu Ma, Xixi Li, Dezhi Wang, Shengru Wu, Jianan Dong, Yanfen Ma
{"title":"Linoleic acid enhances ruminal carbohydrate metabolism and biohydrogenation to promote rumen epithelial development in calves.","authors":"Chunli Hu, Xuehu Ma, Xixi Li, Dezhi Wang, Shengru Wu, Jianan Dong, Yanfen Ma","doi":"10.1038/s41522-026-01063-y","DOIUrl":"10.1038/s41522-026-01063-y","url":null,"abstract":"<p><p>Unlike mature ruminant, pre-weaned calves have limited ruminal biohydrogenation during early microbial establishment. Since linoleic acid (LA) is known to promote calf growth, elucidating whether dietary LA supplementation during this plastic phase can actively shape rumen biohydrogenation function, restructure the microbiota, and drive epithelial development represents a pivotal unanswered question. This study determined the optimal dietary supplementation dose of LA and elucidated its regulatory effects on the rumen microbiota, metabolites and gene expression in preweaning calves. LA supplementation reshaped the rumen microbial community of calves and enhanced microbial carbohydrate metabolism by increasing the abundance of carbohydrate-active enzymes, thereby promoting acetate synthesis. Hydrogen generated during carbohydrate fermentation further facilitated LA biohydrogenation. The metabolites generated from this process activate the microbial phosphatidylcholine synthesis pathway in the rumen, increasing PC concentrations in both rumen fluid and tissue. CYP3A24 was identified as a core rumen gene involved in the PC-CYP3A24 regulatory axis. PC promoted bovine rumen epithelial cells (BRECs) proliferation, barrier function, antioxidant capacity and inflammation suppression, while CYP3A24 silencing diminishes these effects. In conclusion, optimal LA supplementation regulates rumen metabolism, enhances PC synthesis via functional microbiota, and activates the PC-CYP3A24 axis, thereby improving rumen development and calf growth performance.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148318396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Radka Roubalová, Janet Luthar, Petra Procházková, Kateřina Zadáková, Kristýna Coufalová, Jakub Kreisinger, Jaroslav Semerád, Alena Nehasilová, Hynek Mácha, Dominika Luptáková, Helena Tlaskalová-Hogenová, Petra Holanová, Alena Lambertová, Hana Papežová
{"title":"Gut microbiota contributions to anorexia nervosa pathogenesis: insights from the activity-based anorexia model.","authors":"Radka Roubalová, Janet Luthar, Petra Procházková, Kateřina Zadáková, Kristýna Coufalová, Jakub Kreisinger, Jaroslav Semerád, Alena Nehasilová, Hynek Mácha, Dominika Luptáková, Helena Tlaskalová-Hogenová, Petra Holanová, Alena Lambertová, Hana Papežová","doi":"10.1038/s41522-026-01055-y","DOIUrl":"10.1038/s41522-026-01055-y","url":null,"abstract":"<p><p>Anorexia nervosa (AN) is a severe eating disorder that profoundly affects quality of life. Despite increasing understanding of the neurobiological basis of the disease, many patients develop a chronic course of illness accompanied by a variety of physical and psychiatric comorbidities. To investigate the contribution of the gut microbiome to disease progression, we employed the activity-based anorexia (ABA) mouse model of AN. We performed fecal microbiota transplantation using samples from three donor groups: healthy controls, patients with acute AN, and patients with severe and enduring AN (SEAN). We continuously assessed changes in the gut microbiota and fecal metabolites (e.g., short-chain fatty acids, serotonin, and GABA) throughout the experiment, along with behavioral traits across the three groups of mice. Mice colonized with microbiota from acute AN patients exhibited reduced hunger signaling (via NPY, AgRP, MCH, and orexin), accompanied by decreased food intake. In contrast, mice transplanted with microbiota from SEAN patients showed appetite signaling and food consumption comparable to those colonized with microbiota from healthy controls but displayed significantly higher running activity relative to the other groups. However, the distinct microbiota did not affect the development of the ABA phenotype. Overall, our findings suggest that changes in the gut microbiome during disease development contribute to disease progression. Our results also indicate that restoration of a healthy gut microbiome is essential for complete recovery.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Foliar metal micronutrients reshape rhizosphere soil multifunctionality by filtering microbial life-history strategies.","authors":"Ye Liu, Gao Xiong, Lifang Gao, Ying Li, Xi Zhou, Hui Yao, Guangfei Wei, Miyi Yang, Yulong Yin, Jingjing Peng, Linlin Dong, Guozhuang Zhang","doi":"10.1038/s41522-026-01071-y","DOIUrl":"10.1038/s41522-026-01071-y","url":null,"abstract":"<p><p>Foliar application of metal micronutrients is increasingly adopted in intensive cultivation systems, yet its potential ecological risks to rhizosphere functions remain poorly understood. Here, using the medicinal plant Panax notoginseng as a model, we conducted a gradient foliar amendment experiment with iron (Fe), zinc (Zn), and copper (Cu) to evaluate how aboveground metal inputs regulate rhizosphere soil multifunctionality (MF) through microbial life-history strategies. By integrating 16S rRNA amplicon sequencing, metagenomics, root transcriptomics, and a newly developed quantitative Yield-Acquisition-Stress tolerance (qYAS) framework, we disentangled the microbial mechanisms underlying divergent functional responses to metal amendments. Foliar Fe significantly enhanced multifunctionality, including nutrient provision and element cycling, while Cu and Zn reduced nutrient provision and element cycling, but enhanced plant pathogen abundances. These changes were closely associated with shifts in bacterial life-history strategies: Fe promoted Y-strategists characterized by efficient carbon use, streamlined genomes, and high network connectivity, whereas Cu and Zn enriched AS-strategists with larger genomes and negative associations with multifunctionality. Partial least squares path modeling (PLS-PM) further identified microbial strategies as key mediators linking foliar metal inputs, plant performance, soil properties, and multifunctionality. This study provides a trait-based microbial framework for evaluating foliar metal fertilization and guiding safer nutrient management.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Oxygen homeostasis: new insight of gut microbiota-host interactions.","authors":"Zhipeng Yang, Juan Yang, Jian Peng, Hongkui Wei","doi":"10.1038/s41522-026-01062-z","DOIUrl":"10.1038/s41522-026-01062-z","url":null,"abstract":"<p><p>Oxygen homeostasis is a key ecological factor shaping microbial composition, epithelial function, and immune balance in the gut. Spatial and developmental oxygen gradients drive the transition from facultative to obligate anaerobes. Gut hypoxia is maintained by epithelial oxygen consumption and microbial metabolism, forming a positive feedback loop that supports barrier integrity and immune homeostasis. Disruption by inflammation, antibiotics, or diet elevates oxygen availability, promoting dysbiosis, pathogen expansion, and disease risk.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.","authors":"Chenqionglu Feng, Huanhuan Lu, Jiaxuan Bian, Hui Wang, Huiqun Jia, Xiaoying Li, Mingjuan Yang, Hongbin Song, Weilong Tan, Ligui Wang","doi":"10.1038/s41522-026-01054-z","DOIUrl":"10.1038/s41522-026-01054-z","url":null,"abstract":"<p><p>Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ryan Bournes, Suzie Hingley-Wilson, Bing Guo, Cayla Harris, Umar Abubacar, Mark Chambers, Roman Bauer
{"title":"Agent-based modeling of erosion and sloughing during growth of Pseudomonas aeruginosa biofilms.","authors":"Ryan Bournes, Suzie Hingley-Wilson, Bing Guo, Cayla Harris, Umar Abubacar, Mark Chambers, Roman Bauer","doi":"10.1038/s41522-026-01052-1","DOIUrl":"10.1038/s41522-026-01052-1","url":null,"abstract":"<p><p>Pseudomonas aeruginosa is a prevalent healthcare pathogen. It forms biofilms, which significantly increase antibiotic resistance, escalating the burden on healthcare systems. While global biofilm phenomena are observable experimentally, understanding local behaviours of bacteria and their environment, and how these factors drive biofilm formation, is challenging. Agent-based modelling (ABM) offers a computational solution to simulate these local behaviours and resulting large-scale phenomena. ABMs can simulate physical mechanisms like erosion and sloughing but often lack the ability to capture them during biofilm growth and validate them experimentally. We present a three-dimensional ABM of P. aeruginosa biofilms growing under constant flow. This model is the first of its kind to accurately capture the change in physical shape of biofilms growing under constant flow, as well as capture erosion and sloughing as natural byproducts of local bacteria interactions. The model is validated both qualitatively and quantitatively against experimental culture results, providing a general framework that can be adapted to simulate different environments or other biofilm-forming species.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148302525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Rattus norvegicus and Rattus tanezumi as hub hosts for viral diversity and potential spillover on Hainan Island, China.","authors":"Haoyue Huangfu, Ji Pu, Mengqi Jiao, Qianjin Fan, Huiwei Deng, Qian Ling, Hao Zhou, Xuelian Luo, Jianguo Xu","doi":"10.1038/s41522-026-01056-x","DOIUrl":"10.1038/s41522-026-01056-x","url":null,"abstract":"<p><p>Rodents, which account for over 40% of mammalian species and occupy diverse terrestrial ecosystems, are major reservoirs for zoonotic viruses, including Coronaviridae, Hantaviridae, and Arenaviridae. However, the rodent species acting as central hubs for viral diversity and transmission remain poorly defined. To address this, we conducted systematic sampling across 18 counties and cities on Hainan Island between 2023 and 2024. A total of 2550 animals were collected, representing 14 Rodentia species, one Erinaceomorpha species, and one Scandentian species. Based on a statistical sampling framework, 1284 individuals were selected to generate 125 pooled gut samples for virome analysis. We identified 527 viral RNA species and recovered 175 complete or near-complete viral genomes. Remarkably, Rattus norvegicus and Rattus tanezumi accounted for 83.9% (442/527) of detected viral species, 68.6% (72/105) of novel viral sequences, and 88.6% (93/105) of cross-species viruses. Eight novel viruses showed recombination signals, seven originating from these two species. Among 13 human pathogenic viruses identified, 12 were detected in Rattus norvegicus and Rattus tanezumi. These findings suggest that these species may function as hub hosts for viral maintenance and spread, emphasizing the value of targeted surveillance to reduce future potential spillover risks.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13649783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148302541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}