Animal microbiome最新文献

{"title":"Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.","authors":"Nicolas Luna, Carolina Hernández, Angie L Ramírez, Plutarco Urbano, Karen Barragán, Catalina Ariza, Marina Muñoz, Luz H Patiño, Juan David Ramírez","doi":"10.1186/s42523-025-00504-x","DOIUrl":"10.1186/s42523-025-00504-x","url":null,"abstract":"<p><p>BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia. RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals. CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"22"},"PeriodicalIF":4.5,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228685","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":"Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments.","authors":"Sanling Fan, Haizhou Liu, Yi Yan, Meng Xu, Xiaoling Wan, Yujiang Hao, Cheng Gong, Chaoqun Wang, Yuan Zhang, Di Liu, Jinsong Zheng, Jianjun Chen","doi":"10.1186/s42523-026-00528-x","DOIUrl":"10.1186/s42523-026-00528-x","url":null,"abstract":"<p><p>BACKGROUND: The Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, but little is known about the microbiota and the influencing factors. Here, we performed metatranscriptomic sequencing on fecal samples collected from the YFPs under distinct environments to characterize the gut bacterial and viral communities, which consisted of 43 wild and 3 captive YFPs. RESULTS: Our analyses revealed that distinct environments of YFPs resulted in significant divergence in the gut microbiota. The captive adult YFPs inhabiting sanitized, stable environments exhibited consistent intestinal microbiota composition and structure, differing markedly from the wild adult YFPs. Notably, Romboutsia, a potential health-associated genus, was significantly prevalent in captive adult YFPs, whereas wild adult YFPs demonstrated higher relative abundances of known opportunistic pathogens. And the wild YFPs in a complex natural environment exhibited highly inter-individual variation with the absence of an age-specific pattern. High-abundance antibiotic resistance genes were prevalent in both captive and wild YFPs. Besides, less overlap in virus species between captive and wild populations was discovered, with one novel genus and two novel species identified. CONCLUSION: We aimed to comprehensively characterize the intestinal bacterial and viral communities of the YFP and to identify the influencing factors. Lifestyle differences were associated with distinct gut microbial compositions, while the individual specificity observed among the wild population may reflect environmental and host-specific influences. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13011329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146198269","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":"Lactobacillus fermentum supplementation modulates jejunal microbiota, metabolome, and morphology in yaks under high-energy feeding.","authors":"Qinran Yu, Chun Huang, Pengjia Bao, Ning Li, Minghao Zhang, Tong Wang, Chaofan Ma, Jingying Deng, Xinyu Cao, Jianlei Jia, Ping Yan","doi":"10.1186/s42523-025-00479-9","DOIUrl":"10.1186/s42523-025-00479-9","url":null,"abstract":"<p><p>Concentrated supplementary feeding is an effective strategy for addressing nutritional deficiencies in yaks during the cold-season grazing period. However, limited research has investigated whether long-term implementation may alter the gut microbiota and metabolite profiles of yaks, potentially posing health risks to the host. This study investigated the regulatory role of Lactobacillus fermentum in host metabolism through the gut microbiota, employing a “nutrition-gut-metabolism” perspective. Eighty healthy male Pamir yaks with similar body conditions were randomly divided into four groups (n = 20 per group), including Control (Con), Medium Energy (ME), High Energy (HE), and Medium Energy plus Lactobacillus fermentum (MEJ). Body weight was recorded every 30 days during the 150-day trial. Jejunal tissues and contents from nine yaks per group were collected for subsequent analyses. Key findings revealed that the HE group showed significantly increased crypt depth and elevated relative abundance of Clostridium_sensu_stricto_1 (P < 0.05). In contrast, the MEJ group reversed the decline in villus height and width observed in the ME group, while significantly enhancing muscularis thickness. Notably, MEJ yaks exhibited higher abundance of Paeniclostridium, Romboutsia and Treponema (P < 0.05) and markedly increased short-chain fatty acids concentrations (P < 0.001). Metabolomic analysis identified upregulated pathways, including D-amino acid metabolism and Neuroactive ligand-receptor interaction. Furthermore, comparative analyses pinpointed five critical microbial taxa (e.g., vadinBE97, Lachnospiraceae_UCG-008) and 18 key metabolites (e.g., 15-Deoxyprostaglandin J2, Lasalocid A) associated with these effects. In conclusion, Lactobacillus fermentum supplementation improved yak growth performance and mitigates metabolic risks linked to excessive energy intake. These findings provided a theoretical foundation for optimizing yak feeding strategies and advancing precision nutrition in ruminant production.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"17"},"PeriodicalIF":4.5,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12895861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146183703","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":"Maternal supplementation with rumen-protected arginine reshapes the ileal microbiome and enhances neonatal lamb growth.","authors":"Xiangjian Peng, Yuyang Xue, Hailiang Wang, Shanshan Nan, Yayin Qi, Cunxi Nie, Wenju Zhang","doi":"10.1186/s42523-026-00526-z","DOIUrl":"10.1186/s42523-026-00526-z","url":null,"abstract":"<p><strong>Background: </strong>The nutritional status of ewes during gestation and lactation is a key determinant of lamb growth performance. Supplementation with rumen-protected L-arginine (RP-Arg) during these stages induces maternal metabolic adaptation, thereby maintaining fetal developmental homeostasis. However, the sustained effects of such metabolic regulation on postnatal lamb growth and immune functions are currently unclear. Twenty-seven pregnant Chinese Merino ewes (at 60 days of gestation) were randomly assigned to one of three dietary treatments: (1) grazing only (control, CON), (2) grazing plus 300 g/day of concentrate feed (SF), or (3) SF diet supplemented with 30 g/day of RP-Arg (ARG). When the lambs reached 14 days of age, ileal and liver tissues were collected. The ileal microbiota was characterized using 16S rRNA gene amplicon sequencing, and untargeted metabolomics was used to examine the hepatic metabolism in the lambs.</p><p><strong>Results: </strong>Compared with the CON group, both SF and ARG group lambs showed significantly improved early growth performance (P < 0.05), and the ARG group exhibited significantly higher average daily gain and total weight gain (net weight gain) than the SF group (P < 0.05). Milk protein content was significantly higher in the SF and ARG groups than in the CON group (P < 0.05). Notably, compared with the SF group, ARG supplementation elevated colostrum lactoferrin and insulin-like growth factor-1 (IGF-1) concentrations by 28.4% and 34.1%, respectively (P < 0.05). Compared with SF group, ARG group showed a higher relative abundance of ileal Bacteroidota (+ 40%, P < 0.05) and Prevotella (+ 96%, least discriminant analysis > 3.2), increased hepatic glutamine, methionine, and malate (variable importance in projection > 1.3, P < 0.05), and upregulated arginine-proline metabolism and ABC transporters, indicating that RP-Arg was associated with a shift in both the ileal microbiota and hepatic metabolite profile, suggestive of a modest gut-liver metabolic interaction to enhance nitrogen and energy flux, resulting in superior lamb growth.</p><p><strong>Conclusions: </strong>RP-Arg specifically elevates colostrum IGF-1 and lactoferrin levels, enriches ileal Bacteroidota and Prevotella, and reprograms hepatic arginine-proline and ABC transporter metabolism. Overall, these changes were associated with an increased early growth rate of lambs without affecting milk protein production.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":"18"},"PeriodicalIF":4.4,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12895841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159501","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":"Dual probiotic intervention with Lactiplantibacillus plantarum Kmiate-6 and Pediococcus acidilactici Kmiate-15 improves periodontal health and oral microbiota balance in dogs.","authors":"Wanjin Hu, Rui Zhang, Saiwei Zhong, Weiyang Chen, Meiru Chen, Qinghua Yu","doi":"10.1186/s42523-026-00524-1","DOIUrl":"10.1186/s42523-026-00524-1","url":null,"abstract":"<p><p>BACKGROUND: Periodontal disease is highly prevalent in dogs, yet current treatments such as dental scaling and antibiotics carry limitations including anesthesia risks, high recurrence, and antibiotic resistance. Probiotics have emerged as a promising strategy to modulate oral microbiota and host inflammation. This study evaluated the effects of dual probiotic intervention with Lactiplantibacillus plantarum Kmiate-6 and Pediococcus acidilactici Kmiate-15 on canine oral health through in vitro and in vivo assays. RESULTS: Both strains exhibited antimicrobial activity against common oral pathogens, with Lactiplantibacillus plantarum Kmiate-6 showing stronger inhibition against Streptococcus mutans, Fusobacterium nucleatum, and Streptococcus mitis, while Pediococcus acidilactici Kmiate-15 demonstrated superior anti-inflammatory effects by reducing tumor necrosis factor-alpha and increasing interleukin-10 production. In vivo, 21-day oral administration of the probiotic combination significantly reduced dental plaque area and plaque index in dogs, along with decreased salivary tumor necrosis factor-alpha and elevated interleukin-10 levels. Microbiota analysis showed that probiotic intervention decreased the abundance of pathogenic genera such as Fusobacterium and Porphyromonas, and enriched beneficial taxa including Actinomyces and Weissella. Functional predictions based on 16S ribosomal RNA gene data indicated that probiotic treatment enhanced pathways related to detoxification, antioxidation, and propanoate metabolism, while reducing reliance on vitamin biosynthesis pathways typically exploited by pathogens. CONCLUSIONS: Combined oral administration of Lactiplantibacillus plantarum Kmiate-6 and Pediococcus acidilactici Kmiate-15 effectively improved canine periodontal health by inhibiting plaque formation, modulating inflammatory responses, and reshaping oral microbial composition and function. These findings support the potential of probiotic-based strategies as safe and effective alternatives for maintaining oral health in dogs. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12977619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138060","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":"Diel transcriptional dynamics of a marine sponge and its microbiome in a natural environment.","authors":"Gustavo A Ramírez, Rinat Bar-Shalom, Tzipora Perez, Reut Efrati Epchtien, Andrea Furlan, Roberto Romeo, Michelle Gavagnin, Arkadiy I Garber, Maya Lalzar, Laura Steindler","doi":"10.1186/s42523-025-00510-z","DOIUrl":"10.1186/s42523-025-00510-z","url":null,"abstract":"<p><p>BACKGROUND: Marine sponges are ecologically critical animals that host diverse microbial communities, forming complex symbiotic systems crucial to nutrient cycling and ecosystem functioning in the ocean. While several studies have started to delineate the interactions between sponges and their microbiomes, whether and how these interactions are influenced by night and day cycles remains unclear, particularly in natural environments. RESULTS: Here, we analyzed the in situ transcriptional changes of the demosponge species Aplysina aerophoba and its microbiome over a diel cycle, sampling four specimens each at four time points within a 24-hour period. At the global metatranscriptome level, microbiome activity clustered by animal subject, rather than time of sampling. However, diel transcriptional patterns were observed for a limited number of microbial genes, primarily involved in secondary metabolite biosynthesis and antibiotic efflux pumps. At the individual microbial lineage level, we identified diel patterns in cyanobacterial and alphaproteobacterial symbionts. Cyanobacterial symbionts exhibited canonical circadian regulation, with daytime expression of photosynthesis-related genes. At night upregulation of ammonium assimilation via glutamine synthetase coincided with induction of the oxidative pentose phosphate pathway and respiratory genes, indicating reliance on host-derived carbohydrates to generate ATP, NADPH, and the 2-oxoglutarate carbon backbone required for glutamate synthesis in the dark. This pattern contrasts with free-living cyanobacteria, where nitrogen assimilation is typically day-active and fueled by photosynthesis-derived energy and reducing power. The sponge host transcriptome displayed distinct diel regulation of key circadian genes (cry2 and PAR-bZIP), in addition to daytime upregulation of genes involved in sulfur metabolism and oxidative stress defense, patterns mirrored by alphaproteobacterial symbionts that together contribute to glutathione-based detoxification (sponge Glo2, bacterial GstB) and H2S management (SQOR). CONCLUSION: Our study demonstrates that diel environmental fluctuations modulate the transcriptome of the sponge hosts and only select microbial lineages - primarily Cyanobacteria and heterotrophic Alphaproteobacteria – highlighting targeted rather than community-wide diel transcriptional responses within the holobiont. Together, these lineage-specific responses reveal mechanistic links between nitrogen assimilation, sulfur metabolism, and oxidative stress detoxification. These findings provide novel insights into the metabolic integration and functional stability of one of the earliest evolved animal-microbe symbiotic systems. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"12"},"PeriodicalIF":4.5,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12879404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127755","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 developmental trajectory and maturation of the Hulunbuir sheep (Ovis aries) microbiome.","authors":"Aifei Yan, Xiunan Li, Jie Cheng, Yan Cheng, Kefyalew Gebeyew, Zhiliang Tan, Jinhe Kang, Zhixiong He","doi":"10.1186/s42523-025-00512-x","DOIUrl":"10.1186/s42523-025-00512-x","url":null,"abstract":"<p><p>The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"10"},"PeriodicalIF":4.4,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12869976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115122","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":"Lactobacillus plantarum (LPsca12) enhances growth phenotype and muscle nutrition in abalone (Haliotis discus hannai) by modulating microbial function and metabolism through the Amino Acid-Driven Gut-Muscle Axis.","authors":"Yangyang He, Lu Huang, Shiwei Han, Xiaoyu Yu, Chenlu Wu, Xianan Dai, Zhizhong Lv, Dafeng Song","doi":"10.1186/s42523-026-00521-4","DOIUrl":"10.1186/s42523-026-00521-4","url":null,"abstract":"<p><p>BACKGROUND: With the continuous expansion of abalone (Haliotis discus hannai) aquaculture, improving growth rate and muscle quality has become an increasingly important concern. Probiotic supplementation represents a promising strategy; however, the effects of probiotics on abalone remain poorly understood, particularly concerning their mechanisms of action on muscle physiology. This study employed a multi-omics investigation to explore the impact of the Lactobacillus plantarum (LPsca12) strain on hepatic metabolism and gut microbiota composition in abalone, and the potential associations between intestinal metabolites and short-chain fatty acids (SCFAs) in muscle. RESULTS: Our findings reveal that (I) probiotic supplementation induced notable shifts in gut microbiota composition, thereby enhancing abalone growth performance and reducing lipid accumulation by promoting hepatic lipid metabolism, (II) reshaped microbial community strongly linked to elevated concentrations of key amino acids in abalone, including L-leucine, L-isoleucine, L-valine, and L-arginine, which are considered potential precursors for SCFAs production, and (III) the elevated levels of SCFAs, such as acetate and propionate, in muscle tissue may activate the mTORC1 signaling pathway, thereby promoting protein synthesis and improving the nutritional status of abalone muscle. CONCLUSIONS: The results indicate that LPsca12 exerts beneficial effects on abalone by enhancing growth performance and improving lipid metabolism and promoting muscle nutritional status through an amino acid-driven gut–muscle axis. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12958711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115120","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":"Cotton farming affects ileal virome in a sedentary wild passerine.","authors":"Sergei V Drovetski, Brian P Bourke, Michelle L Hladik, Carolina F Ferreira, Koray Ergunay, Yvonne-Marie Linton, Dana W Kolpin, Gary Voelker","doi":"10.1186/s42523-026-00523-2","DOIUrl":"10.1186/s42523-026-00523-2","url":null,"abstract":"<p><p>Although a few studies have focused on avian gut virome variation in response to environmental stressors, none have assessed virome in relation to the production of chemically intensive crop-based agriculture that alters food resources and detrimentally affects various aspects of avian health and fitness. In this study, we used shotgun metatranscriptomics to assess whether exposure to cotton (Gossypium spp.) production had a deleterious effect on the ileal virome of sedentary northern mockingbirds (Mimus polyglottos) sampled from two cotton-producing areas (16 birds in total) and one uncultivated area (7 birds) in Texas, USA. We recovered 43 viruses representing 13 virus families, which included two viruses that appear to be potential vertebrate pathogens. Individual sample richness varied from 25 to 33 viruses. Both virome richness (Adj. r2 = 0.247, F(2, 20) = 4.615, P = 0.022) and composition (r2 = 0.370, F(2, 20) = 5.883, P = 0.001) differed among three sampling regions. Cotton production was associated with the increase of virome richness (Adj. r2 = 0.283, df = 22, P = 0.005). Pesticide occurrence data collected using silicone bands at the three sites suggest that virome compositional changes are not only associated with total pesticide exposure but are also particularly sensitive to the pesticide combinations detected at each location.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"8"},"PeriodicalIF":4.5,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12870179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115188","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":"Compost fermented with thermophilic Bacillaceae reduces heat stress-induced mortality in laying hens through gut microbial modulation.","authors":"Yudai Inabu, Hirokuni Miyamoto, Hideyuki Takahashi, Tamotsu Kato, Shigeharu Moriya, Atsushi Kurotani, Haruki Yamano, Teruno Nakaguma, Naoko Tsuji, Chitose Ishii, Makiko Matsuura, Satoshi Wada, Takashi Satoh, Motoaki Udagawa, Hisashi Miyamoto, Jun Kikuchi, Hiroaki Kodama, Hiroshi Ohno","doi":"10.1186/s42523-026-00520-5","DOIUrl":"10.1186/s42523-026-00520-5","url":null,"abstract":"<p><strong>Background: </strong>Heat stress (HS) adversely affects poultry health and productivity. Recently, it has been suggested that the gut microbiota may play a role in host resilience to HS, although the details of its mechanism remain unclear. Here, the heat tolerance-related effects of dietary supplementation of compost fermented by the thermophile Bacillaceae were explored using a laying hen model (601,474 hens in total).</p><p><strong>Results: </strong>In a field study conducted during the summer (maximum temperatures of approximately 35 °C) in eleven hen houses, oral administration of the compost extract resulted in a statistically significant reduction in mortality. Difference-in-differences analysis revealed that the abundances of the genera Lachnospiraceae NK3A20 group, Enterococcus, Ruminococcus 2, Blautia, Lactobacillus, Christensenellaceae R-7 group, and Tyzzerella 4 were significantly increased by compost administration, whereas those of the Prevotellaceae NK3B31 group, Prevotella 9, Romboutsia, Turicibacter, and Escherichia-Shigella were significantly reduced. In addition, to evaluate the relationship between short-chain fatty acids (SCFAs) metabolic profiles and the gut bacterial population, factor analysis combined with feature selection based on multiple machine learning (ML) algorithms was performed. The resulting optimal structural equation model suggested that compost administration led to increases in the levels of the SCFAs acetate and butyrate, as well as decreases in the levels of the genera Romboutsia and Turicibacter.</p><p><strong>Conclusion: </strong>Oral administration of thermophile-fermented compost to laying hens alleviated HS-induced mortality. Integrative computational evaluations further revealed that the reduction in mortality was linked to structural changes in the gut microbiota composition and SCFA concentrations.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":"9"},"PeriodicalIF":4.4,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12870368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115127","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}