Animal microbiome最新文献

{"title":"Geographic and cross-species transmission of Mamastroviruses from multiple hosts.","authors":"Yong Wang, Haiqiang Wu, Xunbi Liu, Hongfu Ma, Aolin Li, Yongdong Li, Xu Guo","doi":"10.1186/s42523-026-00517-0","DOIUrl":"10.1186/s42523-026-00517-0","url":null,"abstract":"<p><p>BACKGROUND: Astroviruses (AstVs) are single-stranded RNA viruses belonging to the family Astroviridae, which comprises two genera: Mamastrovirus (MaAstV) and Avastrovirus. These viruses circulate globally and infect multiple hosts, enabling cross-species transmission that poses significant risks to both humans and animals. In this study, we comprehensively analyze the evolution, global geographic transmission, and cross-species transmission of MaAstVs. RESULTS: Our analysis reveals that a broad distribution and diverse host range for AstVs, with a noticeable decline in detection after 2017. Phylogenetic analyses uncover complex relationships, suggesting potential host spillover events. The evolutionary rates of different MaAstVs vary. Most MaAstVs exhibited a decreasing trend in effective population size, with minor fluctuations observed in a few instances. Furthermore, our global transmission analysis demonstrates the spread of MaAstVs across Asia, Europe, the Americas, Africa, and Oceania, identifying specific countries as key nodes within the transmission network. Analyses of cross-species transmission in Groups 1, 2, and 3 reveal distinct ancestral origins and trace the cross-species transmission history of MaAstVs among domestic animals, humans, companion animals, and wildlife. CONCLUSIONS: This study offers a detailed examination of the evolution, global transmission, and cross-species transmission of MaAstVs across multiple hosts. Our findings provide valuable insights into their circulation across species and regions, as well as their evolutionary dynamics. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12930795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota remodeling by Astragalus membranaceus stems and leaves correlates dual modulation of arachidonic acid and tryptophan metabolism to counteract perinatal stress-induced hemometabolic dysregulation in sows.","authors":"Zhiyuan He, Ning Guo, Chenyun Yu, Tong Zou, Hongde Lu, Yanzhuo Lv, Tao Wang, Hong Dong","doi":"10.1186/s42523-026-00518-z","DOIUrl":"10.1186/s42523-026-00518-z","url":null,"abstract":"<p><p>Perinatal stress (PS) commonly occurring in high-yielding sows has gradually become a factor threatening the reproductive and immunoreactive performances by impairing their fecundity. Despite the Astragalus membranaceus, a herb native to northern China, has been applied to relieve PS, it is still unclear whether its aerial parts, i.e., Astragalus membranaceus stems and leaves (AMSL), protects against reproductive damage induced by PS in sows and how it works. Here, we aims to evaluate the novel roles of AMSL in alleviating PS-induced reproductive disorders in sows (n = 45) and their offsprings (n = 45). Amplicon-based microbiota analysis revealed that maternal dietary supplementation of AMSL significantly induced affluent Prevotella, Limosilactobacillus, Rikenellaceae_RC9_gut_group, and Clostridium_sensu_sticto_1 in perinatal sows and was correlated with accelerated maturation of gut microbiota in preweaning piglets. Untargeted metabolomics were used to profile serum and fecal metabolites, and serum arachidonic acid (AA)-related metabolites were markedly diminished on the day of farrowing and from neonatal piglets at birth post AMSL administration in sows. Pearson correlation analyses indicated that enriched indole-related metabolites and fewer kynurenine-related metabolites were strongly positively correlated with these four bacteria. Then, fecal microbiota transplantation (FMT) in pregnant mice were conducted to illustrate whether the protective role of AMSL is mediated by remodeling gut microbiota. PS and immunosuppressive symptoms were both largely ameliorated in mice that had received fecal bacteria of sows pretreated with AMSL. These results support the notion that the beneficial effects of AMSL were primarily achieved via gut microbiota modulation, which related to improved tryptophan metabolism and inhibited the excessive synthesis of AA in blood circulation. Our findings provide new insights into the potential application of AMSL as a sustainable feed additive.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"21"},"PeriodicalIF":4.5,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12910787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146042236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the potential for competitive exclusion of commensal probiotic candidates against the insidious swine pathogen Brachyspira hyodysenteriae.","authors":"Samuel Gómez-Martínez, Lucía Pérez-Pérez, Alejandro Ucero-Carrretón, Álvaro López-García, Cristina Galisteo, Ana Carvajal, Héctor Argüello","doi":"10.1186/s42523-025-00511-y","DOIUrl":"10.1186/s42523-025-00511-y","url":null,"abstract":"<p><p>BACKGROUND: Research into animal microbiota reveals the intricate relationships between commensal bacteria and enteric pathogens. Metagenomics and culturomics offer novel opportunities in probiotic research, which is particularly interesting for diseases where treatment alternatives are limited, such as swine dysentery (SD), which is caused by Brachyspira hyodysenteriae (B. hyo). This study evaluates the potential ability of a collection of 28 isolates from species of interest to outcompete the anaerobic pathogen B. hyo by an array of in vitro assays designed to characterize their competitive exclusion capacity in co-cultures, alongside assessing the antimicrobial activity of the isolates cell-free supernatants (CFS) and the mechanisms by which they inhibit B. hyo growth. RESULTS: 20 of the 28 isolates tested were able to reduce the growth of B. hyo by more than one log10 bacteria/mL after 96 h of co-culture, with different inhibitory dynamics observed. Notably, Intestinibaculum porci (J1/23 CM6), Dorea longicatena (J1/23 YB16), Bifidobacterium thermoacidophilum (J1/23 YB69), Mobilitalea sibirica (J1/23 YB21), Clostridium butyricum (CECT 361), and Parabacteroides goldsteinii (DSMZ 29187) reduced B. hyo growth in more than 2 log10 units (bacteria/mL). The anti-B. hyo activity of the tested CFS demonstrated that the mechanisms involved went beyond nutrient competition, with a CFS concentration-dependent reduction. CFS from 11 isolates achieved a reduction of over 2 log10 bacteria/mL, with C. butyricum and Paraprevotella clara (DSMZ 19731) CFS standing out with values of 2–3 log10 bacteria/mL. A pH-dependent effect was disclosed for part of the isolates tested, while C. butyricum, Limosilactobacillus mucosae, B. thermoacidophilum and Lactiplantibacillus plantarum maintained part of their anti-B. hyo activity at fixed pH (7.0). A combined analysis of the short chain fatty acid profile and pH on B. hyo growth inhibition revealed differences between isolates, with similar effect for CFS of isolates with similar production of lactic and acetic acids and no clear effect of the pH. CONCLUSIONS: This study demonstrates the potential of pig gut commensals to outcompete B. hyo and discloses part of the mechanisms involved in the growth inhibition, providing a foundation into future research in competitive exclusion as strategy to control SD. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"19"},"PeriodicalIF":4.5,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12903595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary muramidase leads to the downregulation of peptidoglycan biosynthesis and to caecal microbial modulation in laying hens.","authors":"Salvatore Galgano, Murtala Umar Faruk, Irene Eising, Jos G M Houdijk, Farina Khattak","doi":"10.1186/s42523-025-00506-9","DOIUrl":"10.1186/s42523-025-00506-9","url":null,"abstract":"<p><p>BACKGROUND: In-feed muramidase enzyme has been linked to numerous advantages in several animal species. In the past years, muramidase has been shown to be effective in hydrolyzing peptidoglycan fragments, especially at small-intestine level in broilers, and to improve digestibility and performance. Moreover, previous studies also showed a possible anti-inflammatory effect of some secondary metabolites derived from the hydrolysis of peptidoglycan. Although a major effort has been carried out to unravel the in vivo mechanism of action of muramidase, there is currently little information on its metabolic interactions in laying hens, especially considering the fundamental differences with broilers in terms of microbiota and host genetics. Therefore, we conducted a 20-week study, testing five different levels of inclusion of muramidase, from 0 mg/kg to 600 mg/kg. We analyzed dry matter and nitrogen digestibility, apparent metabolizable energy, body weight gain, caecal microbiota and microbiome. RESULTS: The intervention with muramidase (Balancius®, DSM Nutritional Products Ltd., Basel, Switzerland) led to a drop in α-diversity (Shannon index; P < 0.05) and to microbial composition changes, with a decrease in Lactobacillus and an increase in Collinsella, amongst others (Q < 0.05), at all the muramidase concentrations compared to 0 mg/kg. In parallel, we found that muramidase led to an increased protein digestibility as revealed by the increased nitrogen retention, together with a dose-dependent amelioration of body weight, dry matter digestibility and metabolizable energy (P < 0.05). At functional gene level, we observed a net decrease in the microbial potential to metabolize amino acids, likely as a direct consequence of the lower amino acid availability at caecal level, as linked to the increased nitrogen retention. Moreover, muramidase also led to a decreased microbial functional potential to synthesize peptidoglycan. CONCLUSION: This study is the first to investigate the effects of dietary muramidase supplementation on nutrient digestibility and metagenomics in laying hens. Our findings align perfectly with the previous studies in broilers, especially in terms of increased protein digestibility. Moreover, for the first time, a direct correlation between the observed phenotype and both microbiota and microbiome has allowed us to gain further insights into the mechanism of action of muramidase in laying hens. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"7"},"PeriodicalIF":4.5,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12821794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiome- targeted intervention ameliorates structural and transcriptomic changes in the kidney of hindlimb unloaded mouse model.","authors":"Anu V Ranade, Grisilda Vidya Bernhardt, Megna Srinivas, Damodara Gowda K M, Firdos Ahmad, Suni Ebby, Asima Karim, Naveed Ahmed Khan, Josemin Jose, Gopika Ramachandran, Hezlin Marzook, Rizwan Qaisar","doi":"10.1186/s42523-025-00503-y","DOIUrl":"10.1186/s42523-025-00503-y","url":null,"abstract":"<p><p>The human body is adapted to Earth's gravity, but space microgravity significantly alters kidney function, with the hindlimb unloaded (HU) mouse model serving as a valuable tool for studying these effects. During space travel, changes in gut microbiota can lead to health-related issues. In this study, we explored the protective role of crocodile gut microbiome media on kidney health in a HU mouse model, given the known impact of space travel on gut microbiota and related health issues. Male C57BL/6 mice (four months old) were divided into a ground-based control group (GC), HU mice fed with distilled water (HU), and HU mice fed with crocodile bacterial conditioned media (HU-CP). All groups were maintained in a controlled environment for three weeks. At the end of the experiment, mice were euthanized, kidney tissues were dissected for histopathological examination and transcriptomic analysis. Statistical analysis was performed using one-way ANOVA followed by Tukey's multiple comparison test, with p < 0.05 considered significant. Transcriptomic analysis revealed distinct gene expression profiles across GC, HU, and HU-CP groups, with HU-CP inducing both unique (4325 genes) and differential (975 genes) expression compared to HU group. The treatment partially restored glomerular morphology, reduced inflammation, and reversed gene expression alterations associated with oxidative stress, apoptosis, fibrosis, and inflammation. The crocodile bacterial conditioned media demonstrated potential therapeutic benefits in mitigating renal injury induced by simulated microgravity in HU mice. Further research is needed to elucidate the specific mechanisms involved and explore the potential clinical applications of this approach.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"6"},"PeriodicalIF":4.4,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12817730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146004884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The function of Toll-like receptor 2 in control of transcriptome responses to the microbiome and microbiome composition.","authors":"Li Liu, Herman P Spaink","doi":"10.1186/s42523-025-00502-z","DOIUrl":"10.1186/s42523-025-00502-z","url":null,"abstract":"<p><p>BACKGROUND: Toll-like receptor 2 (TLR2) plays a pivotal role in innate immunity and has recently emerged as a critical regulator of host-microbiome interactions. However, how TLR2 influences host transcriptional responses to colonized microbiome and microbial community dynamics remains largely unclear. A comparison between germ free (GF) and conventionalized zebrafish (Danio rerio) larvae provides a valuable system to investigate how the microbiome influences host transcriptomic responses in a tlr2 mutant versus wild-type control. Vice versa, to understand the role of Tlr2 in regulating the microbiome, we have analyzed microbial community composition in both tlr2 mutant and wild-type zebrafish at larval and adult stages. RESULTS: RNAseq analysis revealed that approximately 2.6% of the zebrafish genome (827 genes) exhibited transcriptomic alterations in tlr2 mutant larvae compared to the wild type under microbiome-colonized conditions, whereas around 2% of the genome (639 genes) showed differential expression under GF conditions. KEGG enrichment analyses show that under both microbiome-colonized and GF conditions major differences between the tlr2 mutant and wild type are related to metabolism. Furthermore, there is a striking difference in endoplasmic reticulum stress responses, including well-known markers for inflammatory bowel disease which are all downregulated in the mutant under the microbiome-colonized condition. Microbiome colonization elicited a broader transcriptional response in tlr2 wild-type larvae than in the mutant, with specifically the ferroptosis, apoptosis and inflammation related pathways differently regulated. In terms of how Tlr2 influences microbial composition, 16 S rRNA gene sequencing showed large differences in beta diversity between the tlr2 mutant and wild type. The tlr2 mutant exhibited higher microbial alpha diversity during early development, whereas alpha diversity was higher in wild-type adults. For larvae at the genus level, tlr2 mutant larvae showed increased Chryseobacterium and Flectobacillus but reduced Gracilibacteria abundance relative to wild-type controls. For adult gut samples, the relative abundance of Cetobacterium was higher in the tlr2 mutants, indicating a developmental stage-specific restructuring of the microbiome. CONCLUSIONS: TLR2 not only modulates host transcriptional responses to microbial colonization, but also shapes gut microbial diversity, composition, and metabolic potential. Our findings highlight the critical role of TLR2 in orchestrating immune-metabolic homeostasis and provide new insights into its broader function in maintaining host-microbiota symbiosis across developmental stages. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"5"},"PeriodicalIF":4.5,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12817729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146004847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of dietary Bacillus amyloliquefaciens Y02 supplementation on the growth performance, immunity, intestinal morphology, and cecal microbiota of 1 to 42 days Langya chickens.","authors":"Lumin Yu, Shanpeng Zhang, Mengjie Yu, Yangzhe Zhao, Chao Wang, Yanyun Wang, Jiahao Wen, Chaojie Chen, Xinglin Zhang","doi":"10.1186/s42523-026-00519-y","DOIUrl":"10.1186/s42523-026-00519-y","url":null,"abstract":"<p><p>BACKGROUND: Bacillus amyloliquefaciens (B. amyloliquefaciens) has garnered significant attention and application as a feed additive in poultry production for improving the chickens’ production performance and intestinal health. However, it remains unclear whether B. amyloliquefaciens influences the production performance and intestinal health of Langya chickens, a Chinese local chicken breed. The present study aims to investigate the effect of dietary B. amyloliquefaciens supplementation on the growth performance, immune function, intestinal morphology, and cecal microbiota in Langya chickens. RESULTS: Dietary supplementation with B. amyloliquefaciens Y02 had no effects on the final body weight, weight gain (WG), average daily gain (ADG), average daily feed intake (ADFI), and feed-to-gain ratio (F/G) of Langya chickens at 42 days of age in the treatment group (BAT) compared to the the control group (CON) (p > 0.05). However, the addition of B. amyloliquefaciens Y02 in the BAT group resulted in a 40% decrease in mortality of Langya chickens compared to the CON group. The serum immunoglobulin G (IgG) levels were increased by 31.56% and IgM by 32.36% in the BAT group in comparison to the CON group (p < 0.05), but tumor necrosis factor-α (TNF-α), interleukin-2 (IL), and IL-6 levels had no changes (p > 0.05). Compared to the CON group, the BAT group with B. amyloliquefaciens Y02 resulted in a 8.43% increase in the duodenal villus height (p < 0.01), a 24.13% increase in the duodenal villus height to crypt depth ratio (V/C) (p < 0.01), and a 15.83% decrease in the duodenal crypt depth (p < 0.05), as well as a 19.14% increase in the jejunal villus height (p < 0.01). Notably, the addition of B. amyloliquefaciens Y02 enriched the abundance of Bacteroides, Clostridum, and Alistipes at the genus level, resulting in the production of certain beneficial metabolites that play pivotal roles in maintaining the intestinal health, promoting the immune function, and reducing the colonization of harmful bacteria. CONCLUSIONS: This study demonstrates that B. amyloliquefaciens Y02 has many beneficial effects in terms of enhancing the immune defense mechanisms, improving the intestinal morphology, altering the cecal microbial composition, and maintaining the cecal microbiota balance in Langya chickens. CLINICAL TRIAL NUMBER: Not applicable. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"16"},"PeriodicalIF":4.5,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12895774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated microbiota and metabolomic analysis demonstrates the growth-promoting effects of Lactobacillus plantarum in Nile tilapia (Oreochromis nilotica).","authors":"Lukuan Li, Yuexin Wang, Yanfeng Li, Tong Wang, Zhe Wang, Nannan Zhou, Fang Qiao, Zhen-Yu Du, Mei-Ling Zhang","doi":"10.1186/s42523-026-00516-1","DOIUrl":"10.1186/s42523-026-00516-1","url":null,"abstract":"<p><p>Lactobacillus plantarum, a well-characterized probiotic from terrestrial animals, shows promising effects on fish growth and lipid metabolism. However, its role in promoting protein deposition in fish remains unclear. In this study, 180 juvenile Nile tilapia were randomly assigned to two groups and fed for eight weeks with either a control diet (CK) or a diet supplemented with L. plantarum (LR). The results showed that L. plantarum significantly improved final body weight, weight gain rate, body length, carcass rate, intestinal index, whole-body protein content, and villus length (P < 0.05), accompanied by increased expression of growth-related genes and activation of the mechanistic target of rapamycin (mTOR) pathway. Conversely, the hepatosomatic index, condition factor, mesenteric fat index, hepatic lipid droplets, liver and serum triglycerides were significantly reduced (P < 0.05). The L. plantarum group exhibited downregulated expression of lipogenic genes and upregulation of genes involved in lipolysis, β-oxidation, and fatty acid transport (P < 0.05). Gut microbiota analysis revealed higher α-diversity and increased relative abundances of Pseudomonas and Diaphorobacter, while Cetobacterium, Aestuariivirga, and Aurantimicrobium at the genus level were reduced (P < 0.05). Metabolomic profiling showed elevated bile acids, uridine, phosphatidylcholine, and carnitine derivatives (P < 0.05). To confirm strain-specific effects, germ-free zebrafish were mono-colonized with L. plantarum, leading to suppressed lipogenesis and enhanced lipolysis and growth-related gene expression. Overall, L. plantarum promoted growth while simultaneously reducing fat accumulation, indicating a non-adipogenic growth-promoting effects in Nile tilapia.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"14"},"PeriodicalIF":4.5,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12888601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145971473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Responses of rumen bacterial microflora to aflatoxin B1 challenge: potential roles of AHLs/AI-2 mediated quorum sensing.","authors":"Zuo Wang, Haikang Guo, Jianhua He, Zhijun Zhang, Sharon Huws, Tongjun Guo, Weijun Shen, Fachun Wan","doi":"10.1186/s42523-026-00515-2","DOIUrl":"10.1186/s42523-026-00515-2","url":null,"abstract":"<p><p>BACKGROUND: As a universal cell-to-cell communication mode in the diverse microbial communities, quorum sensing (QS) has been discovered in the ruminal microbiome and supposed to play a significant role in feed digestion and microorganism adaptation during rumen fermentation. Besides, the mycotoxin aflatoxin B1 (AFB1) has been reported to cause rumen dysbacteriosis and alter the abundance of some specific ruminal bacteria that possess the QS-related genes. Threfore, we hypothesized that QS is involved in the responses of rumen bacterial microbiota to AFB1 exposure, and employed the rumen simulation technique (RUSITEC) to investigate the potential roles of QS in the AFB1-induced shifts in ruminal microbiota and relevant metabolisms. RESULTS: AFB1 raised ruminal pH and NH3-N concentration, but decreased total volatile fatty acid (TVFA) production, the molar proportions of acetate, propionate, butyrate, isobutyrate, valerate, isovalerate, and the disappearance of acid detergent fiber (ADF). The concentrations of QS signaling molecules including AI-2, C4-HSL, C6-HSL, and 3-oxo-C6-HSL were reduced by AFB1, whereas the microbial protein and lipopolysaccharide (LPS) were unchanged. The copy numbers of Ruminococcus flavefaciens, methanogens, and fungi dropped, while the density of Selenomonas ruminantium rose in response to AFB1. LEfSe analysis showed that the species of unclassified_Prevotella, UCG_004_bacterium_YGB2007, Cenchrus americanus, uncultured_rumen_bacterium affiliated to the class Kiritimatiella, Butyrivibrio fibrisolvens, and Anaerovibrio_sp_JC8 were differentially enriched in the rumen liquid of different treatments, whilst another uncultured_rumen_bacterium was the only distinctively enriched species in the rumen solid. Further, the metabolomics analysis indicated that ascorbate and aldarate metabolism, histidine metabolism, sphingolipid metabolism, pyruvate metabolism, glycine, serine and threonine metabolism, biosynthesis of unsaturated fatty acids, and arginine and proline metabolism were the commonly differential metabolic pathways. As illustrated by the Spearman analysis, the AI-2 and C6-HSL were positively correlated with the volatile fatty acids (VFAs), and C6-HSL was positively correlated with the copy numbers of Selenomonas ruminantium and Ruminococcus flavefaciens. Moreover, the positive or negative interconnections between the QS signal molecules and the relative abundances of differential bacterial taxa were also exhibited. CONCLUSIONS: The present RUSITEC fermentation study revealed the potential involvements of AHLs/AI-2 mediated QS in the fluctuations of ruminal microbes and relevant rumen metabolisms under the AFB1 challenge, which could lead to the overall impairment of ruminal microbial fermentation. Future studies are necessitated to elucidate and testify the mechanisms of those correlations discovered in the current trial. CLINICAL TRIAL NUMBER: Not applicable. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"15"},"PeriodicalIF":4.5,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12888296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145971547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.","authors":"Matteo Buffoni, Jesse J Kerkvliet, Henk Enting, Jannigje G Kers, Malbert Rogers, J Arjan G M de Visser, Fernanda L Paganelli, Rob J L Willems, Anita C Schürch","doi":"10.1186/s42523-025-00497-7","DOIUrl":"10.1186/s42523-025-00497-7","url":null,"abstract":"<p><p>BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons. RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans. CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"3"},"PeriodicalIF":4.5,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12797969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145960794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}