Animal microbiome最新文献

{"title":"Temporal microbial colonization on different forages is driven by the rumen environmental conditions.","authors":"X Xie, J K Wang, J X Liu, L L Guan, A L A Neves","doi":"10.1186/s42523-025-00407-x","DOIUrl":"https://doi.org/10.1186/s42523-025-00407-x","url":null,"abstract":"<p><p>The rumen is one of the four compartments of the ruminant stomach and houses a diverse array of anaerobic microbes that play a crucial role in feed digestion and volatile fatty acid (VFA) production. The aim of this study was to explore how two different in vivo rumen environmental conditions, AHR (created from sheep-fed alfalfa hay) and CSR (created from sheep-fed corn stover), affect fiber digestion and rumen bacterial colonization in relation to two types of forage, alfalfa hay (AH) and corn stover (CS). Both AH and CS forages were subjected to in-sacco incubation in AHR and CSR conditions for a period of 48 h. The results revealed that CSR exhibited a less variant pH, lower total VFA concentration, and higher acetate-to-propionate ratio than AHR. CSR significantly enhanced the degradation of neutral detergent fiber and acid detergent fiber in both incubated forages (AH and CS). Although CSR did not improve the degradation of dry matter (DM) or crude protein (CP) on AH, it improved the degradation of DM and CP on CS. Both CS and AH incubated under CSR were found to have a greater abundance of fibrolytic bacteria (e.g., Fibrobacter and Butyrivibrio 2) compared to the same forage incubated under AHR, especially during the initial stages of incubation. However, CS and AH incubated under AHR were colonized by bacteria specialized in breaking down soluble carbohydrates (e.g., Prevotella and Succinivibrio). Compared with AHR, CSR enhanced the degradation rates of both incubated forages (CS and AH). These findings underscore the role of the rumen microenvironment in affecting the composition of adherent microbial communities and enhancing the breakdown of forages. Therefore, optimizing the rumen microenvironment to promote the attachment of fibrolytic bacteria during the early fermentation stages while minimizing hydrogen accumulation to stabilize the pH could lead to improved forage fermentation and animal performance.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"46"},"PeriodicalIF":4.9,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043602","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":"Interactions between time on diet, antibiotic treatment, and liver abscess development on the fecal microbiome of beef cattle.","authors":"Germán Plata, Nielson T Baxter, Troy B Hawkins, Lucas Huntimer, Akshitha Nagireddy, Dwi Susanti, James B Reinbold","doi":"10.1186/s42523-025-00413-z","DOIUrl":"https://doi.org/10.1186/s42523-025-00413-z","url":null,"abstract":"<p><strong>Background: </strong>Liver abscesses caused by polymicrobial infections of the liver are a widespread problem in feedlot cattle production. There are currently no effective methods for the early detection of liver abscesses or to predict antibiotic efficacy for their control. Although gene expression and microbiome differences have been reported in the rumen of abscessed and normal animals, liver abscess biomarkers using less invasive tools can facilitate managing of the disease in the field.</p><p><strong>Results: </strong>Here we report the results of two studies measuring the fecal microbiome composition of steers that did or did not develop liver abscesses, with or without antibiotic treatment, along a 7-month feeding period on a high-concentrate diet. Our results indicate a limited impact of liver abscesses or tylosin on fecal microbiome composition, with time on diet explaining most variance in the fecal microbiome. Interestingly, in both studies, antibiotic treatment led to larger differences in the variability of the fecal microbiomes between abscessed and normal animals compared to controls. These differences were limited to specific sampling times in each of the two studies. Although multiple amplicon sequence variants with differential abundances according to liver abscess state were identified, there was no overlap between the two studies.</p><p><strong>Conclusions: </strong>Our results suggest that the fecal abundance of individual microorganisms may not be a robust predictor of liver abscess susceptibility across sampling times or diet regimes. Fecal biomarkers of liver abscess susceptibility might be developed with a focus on other aspects of the hindgut microbiome, especially for animals receiving preventive antibiotics.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"45"},"PeriodicalIF":4.9,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063446","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":"Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism.","authors":"Yongliang Huang, Siyu Cheng, Jinping Shi, Pengjia He, Yue Ma, Ruixin Yang, Xu Zhang, Yongzhi Cao, Zhaomin Lei","doi":"10.1186/s42523-025-00415-x","DOIUrl":"https://doi.org/10.1186/s42523-025-00415-x","url":null,"abstract":"<p><strong>Background: </strong>Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.</p><p><strong>Results: </strong>OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P = 0.011), propionate (P = 0.008), butyrate (P = 0.018)) and digestive enzymes activity (cellulase (P = 0.018), protease and β-glucosidase (P < 0.001)), and improved rumen development (papillae width (P = 0.008) and micropapillary density (P = 0.001)), which reasons contribute to increase body weight (BW, P = 0.022), average daily gain (ADG, P = 0.021), carcass weight (P = 0.001), dressing percentage (P < 0.001), and net meat production (P = 0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.</p><p><strong>Conclusion: </strong>These results suggest that feed with 20 g/(d·head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"44"},"PeriodicalIF":4.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060516","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":"Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics.","authors":"Bernardo Duarte, Eduardo Feijão, Ana Cruz-Silva, Pedro Pascoal, Mónica Nunes, Marcelo Pereira, Andreia Figueiredo, Ricardo P Dias, Susanne E Tanner, Vanessa F Fonseca","doi":"10.1186/s42523-025-00398-9","DOIUrl":"https://doi.org/10.1186/s42523-025-00398-9","url":null,"abstract":"<p><p>The commercial demand for small pelagic fish, such as Atlantic chub mackerel (Scomber colias), renders them susceptible to provenance fraud. Scomber colias specimens intestinal tract bacteriome from five distinct fishing areas along the Portuguese Atlantic coastline were analyzed by 4th-generation sequencing. Bacteria diversity indices and differential abundance revealed dissimilarities in operational taxonomic unit (OTU) abundance among specimens from distinct fishing sites. Random forest-based model yielded an 85% accuracy rate in attributing sample provenance based on intestinal tract bacteriome OTU relative abundance. Further refinement of microbial features using Indicator Species Analysis, Linear Discriminant Analysis Effect Size (LEfSe) and OTU Gini scores enabled the identification of 3-5 bacterial OTU location biomarkers per fishing site. The intestinal tract bacteriome revealed sequences linked to pathogenic bacteria, particularly in specimens from Center-North and Center-South fishing areas. While this doesn't imply active pathogens, it highlights potential public health concerns and complements efforts to improve seafood microbiological quality and traceability.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"43"},"PeriodicalIF":4.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997829","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":"Superspreaders have lower gut microbial alpha-diversity and distinct gut microbial composition in a natural rodent population.","authors":"Klara M Wanelik, Mike Begon, Janette E Bradley, Jonathan Fenn, Joseph A Jackson, Steve Paterson","doi":"10.1186/s42523-025-00411-1","DOIUrl":"https://doi.org/10.1186/s42523-025-00411-1","url":null,"abstract":"<p><p>The microbiome is well known to drive variation in host states (e.g. behaviour, immunity) that would be expected to modulate the spread of infectious disease-but the role of microbiotal interactions in promoting superspreading is poorly understood. Superspreaders are individuals with a strongly disproportionate contribution to pathogen transmission, and come in two forms. Supershedders transmit infection to more individuals because they shed higher levels of pathogen. Supercontacters transmit infection to more individuals because they have larger numbers of social contacts. We explore associations between the gut microbiota and these two forms of superspreading in a wild rodent model-Bartonella spp. bacteraemia in the field vole (Microtus agrestis). We find evidence that individuals fall into distinct shedding and contacting clusters, and that higher-contacters have lower and more variable gut microbial alpha-diversity than lower-contacters. We also show evidence that both higher-shedders and higher-contacters have distinct gut microbial composition and identify OTUs that are differentially abundant in the gut microbiota of these two classes of individuals when compared to lower-shedders and lower-contacters respectively. We find that the Muribaculaceae are associated with differences in both shedding and contacting, and discuss potential mechanisms by which they may be acting on these host traits.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"42"},"PeriodicalIF":4.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061129","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":"Honey bee (Apis mellifera) queen quality: host-microbial transcriptomes exploring the influence of age and hindgut symbiont Commensalibacter melissae.","authors":"Duan C Copeland, Oliver L Kortenkamp, Brendon M Mott, Charles J Mason, Kirk E Anderson","doi":"10.1186/s42523-025-00408-w","DOIUrl":"https://doi.org/10.1186/s42523-025-00408-w","url":null,"abstract":"<p><p>Understanding the biological mechanisms underlying extreme lifespan variation within species remains a fundamental challenge in aging research. Here, we investigated the role of gut microbiota and age in honey bee (Apis mellifera) queens combining 16S rRNA gene sequencing and transcriptomics. Analysis of 40 queen hindguts revealed that Commensalibacter melissae (Alpha 2.1) relative abundance was significantly higher in young queens compared to old queens. Using queens with the highest and lowest C. melissae relative abundance, RNA sequencing identified 1451 differentially expressed genes associated with C. melissae abundance, twice the number associated with age alone (719 genes). Queens with high C. melissae abundance showed distinct transcriptional profiles related to stress response, protein homeostasis, and longevity-regulating pathways, particularly genes involved in oxidative stress response and cellular maintenance. Our analysis revealed complex relationships between age, C. melissae abundance, and gene expression patterns, suggesting that multiple interacting factors contribute to queen quality. These findings contribute to our understanding of host-microbe interactions in honey bee queens and highlight the intricate relationship between gut microbiota composition and host physiology in honey bees.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"41"},"PeriodicalIF":4.9,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059621","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":"AI for rapid identification of major butyrate-producing bacteria in rhesus macaques (Macaca mulatta).","authors":"Annemiek Maaskant, Donghyeok Lee, Huy Ngo, Roy C Montijn, Jaco Bakker, Jan A M Langermans, Evgeni Levin","doi":"10.1186/s42523-025-00410-2","DOIUrl":"https://doi.org/10.1186/s42523-025-00410-2","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome plays a crucial role in health and disease, influencing digestion, metabolism, and immune function. Traditional microbiome analysis methods are often expensive, time-consuming, and require specialized expertise, limiting their practical application in clinical settings. Evolving artificial intelligence (AI) technologies present opportunities for developing alternative methods. However, the lack of transparency in these technologies limits the ability of clinicians to incorporate AI-driven diagnostic tools into their healthcare systems. The aim of this study was to investigate an AI approach that rapidly predicts different bacterial genera and bacterial groups, specifically butyrate producers, from digital images of fecal smears of rhesus macaques (Macaca mulatta). In addition, to improve transparency, we employed explainability analysis to uncover the image features influencing the model's predictions.</p><p><strong>Results: </strong>By integrating fecal image data with corresponding metagenomic sequencing information, the deep learning (DL) and machine learning (ML) algorithms successfully predicted 16 individual bacterial genera (area under the curve (AUC) > 0.7) among the 50 most abundant genera in rhesus macaques (Macaca mulatta). The model was successful in predicting functional groups, major butyrate producers (AUC 0.75) and a mixed group including fermenters and short-chain fatty acid (SCFA) producers (AUC 0.81). For both models of butyrate producers and mixed fermenters, the explainability experiments revealed no decline in the AUC when random noise was added to the images. Increased blurring led to a gradual decline in the AUC. The model's performance was robust against the impact of fecal shape from smearing, with a stable AUC maintained until patch 4 for all groups, as assessed through scrambling. No significant correlation was detected between the prediction probabilities and the total fecal weight used in the smear; r = 0.30 ± 0.3 (p > 0.1) and r = 0.04 ± 0.36 (p > 0.8) for the butyrate producers and mixed fermenters, respectively.</p><p><strong>Conclusion: </strong>Our approach demonstrated the ability to predict a wide range of clinically relevant microbial genera and microbial groups in the gut microbiome based on digital images from a fecal smear. The models proved to be robust to the smearing method, random noise and the amount of fecal matter. This study introduces a rapid, non-invasive, and cost-effective method for microbiome profiling, with potential applications in veterinary diagnostics.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"39"},"PeriodicalIF":4.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12020216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060515","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":"Organ-specific microbiomes of Biomphalaria snails.","authors":"Lauren V Carruthers, Stephanie C Nordmeyer, Timothy Jc Anderson, Frédéric D Chevalier, Winka Le Clec'h","doi":"10.1186/s42523-025-00403-1","DOIUrl":"https://doi.org/10.1186/s42523-025-00403-1","url":null,"abstract":"<p><strong>Background: </strong>The microbiome is increasingly recognized to shape many aspects of its host biology and is a key determinant of health and disease. The microbiome may influence transmission of pathogens by their vectors, such as mosquitoes or aquatic snails. We previously sequenced the V4 region of the bacterial 16S rRNA gene from the hemolymph (blood) of Biomphalaria spp. snails, vectors of the human blood fluke (schistosomes). We showed that snail hemolymph harbored an abundant and diverse microbiome. This microbiome is distinct from the water environment and can discriminate snail species and populations. As hemolymph bathes snail organs, we then investigated the heterogeneity of the microbiome in these organs.</p><p><strong>Results: </strong>We dissected ten snails for each of two different species (B. alexandrina and B. glabrata) and collected their hemolymph and organs (ovotestis, hepatopancreas, gut, and stomach). We also ground in liquid nitrogen four whole snails of each species. We sampled the water in which the snails were living (environmental controls). Sequencing the 16S rRNA gene revealed organ-specific microbiomes. These microbiomes harbored a lower diversity than the hemolymph microbiome, and the whole-snail microbiome. The organ microbiomes tend to cluster by physiological function. In addition, we showed that the whole-snail microbiome is more similar to hemolymph microbiome.</p><p><strong>Conclusions: </strong>These results are critical for future work on snail microbiomes and show the necessity of sampling individual organ microbiomes to provide a complete description of snail microbiomes.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"40"},"PeriodicalIF":4.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993603","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":"Cooling redistributed endotoxin across different biofluids via modulating the ruminal microbiota and metabolome without altering quorum sensing signal levels in heat-stressed beef bulls.","authors":"Zuo Wang, Qingyang Wu, Weijun Shen, Fachun Wan, Jianhua He, Lei Liu, Shaoxun Tang, Zhiliang Tan","doi":"10.1186/s42523-025-00400-4","DOIUrl":"https://doi.org/10.1186/s42523-025-00400-4","url":null,"abstract":"<p><strong>Background: </strong>Cooling is one of the most common and economical methods to ameliorate heat stress (HS), and it has been discovered to alter the lipopolysaccharide (LPS) endotoxin level in ruminants. However, whether the endotoxin variation induced by cooling relates to the quorum sensing (QS) within the ruminal microflora remains unknown. The current study was consequently performed to examine whether cooling could influence the endotoxin distribution across different biofluids, ruminal microbiota, and ruminal metabolisms through affecting the QS of rumen microorganisms in beef cattle exposed to HS. Thirty-two Simmental bulls were used as experimental animals and randomly assigned to either the control (CON) group, or the mechanical ventilation and water spray (MVWS) treatment. The temperature-humidity index (THI) was recorded throughout this trial, and samples of the rumen liquid, blood, and urine were collected.</p><p><strong>Results: </strong>Cooling significantly lowered (P < 0.05) the temperature-humidity index (THI), ruminal endotoxin, and endotoxin concentration and excretion in urine, and significantly raised endotoxin level in blood (P < 0.05), but did not change the ruminal concentrations of QS signals including 3-OXO-C6-HSL and the AI-2 (P > 0.05). The linear discriminant analysis effect size (LEfSe) analysis revealed that Prevotellaceae, Rikenellaceae, Monoglobales and their affiliated members, as well as other bacterial taxa were significantly differently (P < 0.05) enriched between the two treatments. The Tax4Fun2 prediction suggested that QS function was upregulated in MVWS compared to CON. The metabolomic analysis indicated that cooling altered the ruminal metabolism profile and downregulated the pathways of lysine degradation, phenylalanine, tyrosine and tryptophan biosynthesis, and ubiquinone and other terpenoid-quinone biosynthesis. The significant (P < 0.05) correlations of the differential bacteria and metabolites with endotoxin and QS molecules were also demonstrated through Spearman analysis.</p><p><strong>Conclusions: </strong>Based on the results of this trial, it could be speculated that the cooling reshaped the endotoxin distribution across different biofluids through manipulating ruminal microbiota and metabolome, which might involve the participation of QS. Further investigations are warranted to disclose and verify the mechanisms for those correlations found in this study.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"38"},"PeriodicalIF":4.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043581","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":"Seasonal variation in gut microbiota of migratory wild raptors: a case study in white-tailed eagles.","authors":"Xiaoqi Ouyang, Yu Guan, Jianchi Pei, Jianping Ge, Hongfang Wang, Lei Bao","doi":"10.1186/s42523-025-00406-y","DOIUrl":"https://doi.org/10.1186/s42523-025-00406-y","url":null,"abstract":"<p><strong>Background: </strong>Migration poses significant energetic challenges for migratory birds, during which both intrinsic and extrinsic factors affecting the gut microbiota alter substantially. While the temporal dynamics of gut microbiota in wild birds across migration seasons have garnered increasing attention, research on the seasonal variation in wild raptors remains limited despite their distinct gut microbiota structures. Furthermore, raptors, being the highest trophic level in the food chain, have been found to harbor more pathogens and antibiotic resistance genes (ARGs). In this study, we characterized the diversity and composition of the gut microbiota of wild white-tailed eagles at a critical stopover site along the East Asian Flyway (EAF). Fecal samples were collected during both autumn and spring migration seasons and microbial compositions were analyzed using high-throughput sequencing.</p><p><strong>Results: </strong>The most prevalent bacterial phylum in the gut microbiome of white-tailed eagles during both migration seasons was Firmicutes. The diversity of the gut microbiota is elevated in the spring migration season and the bacterial community composition significantly differed between two seasons. Individuals in spring migration show elevated levels of Clostridium_sensu_stricto_13 and Brochothrix, most likely related to the consumption of carrion. Conversely, individuals in autumn migration showed a higher prevalence of potential pathogens such as Fusobacterium and Escherichia-Shigella. Furthermore, we found that specific genera were seasonally enriched, probably reflecting distinct environmental exposures along migration routes.</p><p><strong>Conclusions: </strong>This study revealed substantial seasonal variation in the gut microbiota of migratory white-tailed eagles, most likely shaped by dietary shifts, environmental factors, and physiological stress during migration. The higher prevalence of pathogens during autumn migration highlights potential health risks for eagles and their ecosystems, emphasizing the need for targeted conservation strategies at stopover sites. These findings contribute to understanding the dynamic interactions between migration and gut microbiota in wild raptors and provide valuable insights into their ecological and health management. While dietary differences may play a role, further research is needed to directly assess their impact.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"37"},"PeriodicalIF":4.9,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997801","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}