Animal microbiome最新文献

{"title":"Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.","authors":"Kayla C Evens, Ingrid Bakke, Brendan J M Bohannan","doi":"10.1186/s42523-026-00573-6","DOIUrl":"https://doi.org/10.1186/s42523-026-00573-6","url":null,"abstract":"<p><strong>Background: </strong>Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.</p><p><strong>Results: </strong>We compared water and zebrafish gut microbiomes across five aquaculture facilities two in the United States and three in Norway- using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity analyses revealed significant clustering by sample type, facility, and geographic location, with facility identity explaining the largest proportion of compositional variance. Multivariate dispersion also differed significantly across facilities, indicating that observed compositional differences reflect both shifts in community composition and differences in within-facility variability. Each facility harbored a distinct microbial community in both water and fish gut samples, with geographic location further structuring community composition between Oregon and Norwegian facilities. Similarity Percentage analysis identified key taxa driving facility differences, including Cetobacterium, Vibrio, and Aeromonas in fish gut microbiomes and Pseudomonas and Rheinheimera in tank water. Microbial source tracking using FEAST revealed that facility-level tank water contributed measurably to fish gut microbiome composition in most facilities, though unknown sources dominated estimates across all facilities (71-99%) and the strength of fish-water microbiome association varied substantially across facilities.</p><p><strong>Conclusions: </strong>This study demonstrates that zebrafish aquaculture facilities harbor unique microbial communities shaped by both environmental and geographic factors. While tank water microbiomes show associations with zebrafish gut microbiome composition, the dominant contribution of unknown sources to gut microbiome composition suggests that factors beyond the immediate tank water environment- including diet, host physiology, and other facility-specific conditions- are primary drivers of gut microbiome variation. The strength of this association varied considerably across facilities and appeared related to fish domestication history, a pattern that warrants direct experimental investigation. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration,","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacillus amyloliquefaciens regulates oxidative damage through ssc-miR-10390 by targeting WT1 in the intestine of piglets.","authors":"Junmeng Yuan, Yu Liu, Yaowei Sun, Huawei Liu, Kai Zhang, Jinshan Zhao, Weifen Li, Yang Wang","doi":"10.1186/s42523-025-00505-w","DOIUrl":"https://doi.org/10.1186/s42523-025-00505-w","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147823826","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 regulation on gut resistome linked with microbial amino acid metabolism in pigs.","authors":"Ziyu Liu, Chengming Meng, Junhua Shen, Huisong Wang, Jiaqing Guo, Jiangchao Zhao, Chunlong Mu, Weiyun Zhu","doi":"10.1186/s42523-026-00542-z","DOIUrl":"https://doi.org/10.1186/s42523-026-00542-z","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824064","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 uropygial gland of the European hoopoe as a symbiotic organ.","authors":"Manuel Martín-Vivaldi, Ángela Martínez-García, Juan M Peralta-Sánchez, Michael Schaub, Raphaël Arlettaz, Antonio M Martín-Platero, Ester Martínez-Renau, María Dolores Barón, Magdalena Ruiz-Rodríguez, Estefanía López-Hernández, Manuel Martínez-Bueno, Eva Valdivia, Juan J Soler","doi":"10.1186/s42523-026-00543-y","DOIUrl":"https://doi.org/10.1186/s42523-026-00543-y","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13130528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824030","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":"Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.","authors":"Mirena Ivanova, Birgitta Svensmark, Emilie Egholm Bruun Jensen, Frank M Aarestrup, Håkan Vigre, Saria Otani","doi":"10.1186/s42523-026-00577-2","DOIUrl":"https://doi.org/10.1186/s42523-026-00577-2","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal dynamics shifts in multi-kingdom rumen microbiota and fermentation profiles of water buffalo under heat stress.","authors":"Yanzhi Wu, Jian Li, Jinchi Yu, Chengjian Yang, Shengyong Mao","doi":"10.1186/s42523-026-00570-9","DOIUrl":"https://doi.org/10.1186/s42523-026-00570-9","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of dietary chitin supplementation on body weight, haematology and serum biochemistry, fecal scores and gut microbiota of captive pangolins.","authors":"Xinmei Wang, Chungang Xie, Rongquan Zheng, Shanjian Zheng, Yanni Wang, Jia Xu","doi":"10.1186/s42523-026-00576-3","DOIUrl":"https://doi.org/10.1186/s42523-026-00576-3","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.","authors":"Anitha Ravi, Violetta Shestivska, Priscila Thiago Dobbler, Hana Sechovcová, Martina Maixnerová, Jaroslav Semerád, Alena Nehasilová, Mariana Vadroňová, Iñaki Odriozola, Hana Šubrtová Salmonová, Tomáš Větrovský, Šárka Musilová, Tomáš Cajthaml, Eva Pěchoučková, Alexandr Nemec, Martina Kyselková","doi":"10.1186/s42523-026-00568-3","DOIUrl":"https://doi.org/10.1186/s42523-026-00568-3","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alleviation of heat stress-induced microbial dysbiosis in pigs through dietary supplementation with vitamins and trace elements.","authors":"Peter Fauszt, Endre Szilagyi, Maja Mikolas, Emese Szilagyi-Tolnai, Peter David, Ildiko Noemi Kovacs-Forgacs, Brigitta Csernus, Ferenc Gal, Laszlo Stundl, Sandor Biro, Csaba Szabo, Judit Remenyik, Laszlo Babinszky, Melinda Paholcsek","doi":"10.1186/s42523-026-00575-4","DOIUrl":"https://doi.org/10.1186/s42523-026-00575-4","url":null,"abstract":"<p><strong>Background: </strong>Chronic heat stress (HS) is known to impair animal health and productivity, in part by altering gut microbiota. This study investigated how HS affects the pig gut microbiome and whether dietary supplementation with antioxidants and trace elements (vitamins E, C, selenium, and zinc) at moderate (D1) or high (D2) doses can mitigate these effects.</p><p><strong>Results: </strong>During the adaptation phase, feed efficiency was similar across groups, but as the experiment progressed, the thermoneutral control improved while the heat-stressed control deteriorated. Supplemented diets (D1/D2) partially alleviated this efficiency loss. Microbiome analysis revealed that HS progressively reduced diversity, reaching the lowest Shannon index during exposure. High-dose supplementation markedly increased richness, exceeding control levels. Total microbial abundance declined under HS, with opportunistic pathogens enriched particularly during early exposure. Guild-level indices further indicated a shift under HS. Aerotolerance indices decreased (ATi: TC > D1 > D2 > HSC), reflecting hypoxia-prone conditions favoring obligate anaerobes and SCFA producers. Among supplemented groups, D1 most closely stabilized aerotolerance toward control levels, while D2 maintained an SCFA-dominant community and enhanced butyrate capacity. Genus-level correlations with qPCR-based host gene-expression markers were assessed across all groups. HSP70 was the dominant correlate, and the most extreme associations were confined to a few taxa, indicating marked group specificity.</p><p><strong>Conclusion: </strong>Chronic HS in pigs induced microbial dysbiosis characterized by reduced diversity, loss of beneficial SCFA producers, and expansion of opportunistic pathogens. Dietary supplementation counteracted these adverse changes in a dose-dependent manner. While moderate supplementation provided partial stabilization, high-dose supplementation more effectively restored microbial diversity and enriched beneficial taxa, making it the more effective strategy for mitigating HS-induced microbiome disruption.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.","authors":"Chi Sun Yun, Jae-Kyeom Kim, Hyojung Kwon, Moon Her, Jin San Moon","doi":"10.1186/s42523-026-00565-6","DOIUrl":"https://doi.org/10.1186/s42523-026-00565-6","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}