Animal microbiome最新文献

{"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}

{"title":"Microbial diversity and pigment synthesis in the accessory nidamental gland: species-specific and color-associated patterns in bigfin reef squid (Sepioteuthis lessoniana).","authors":"Ling Chiu, Jei-Lin Guo, Hau-Wen Li, Hai-Jin Chang, Shan-Hua Yang, Sylvie Dufour, Ching-Fong Chang, Yung-Che Tseng, Guan-Chung Wu","doi":"10.1186/s42523-025-00402-2","DOIUrl":"https://doi.org/10.1186/s42523-025-00402-2","url":null,"abstract":"<p><strong>Background: </strong>In certain cephalopod species, two distinct symbiotic organs host large populations of microorganisms: the light organ, regulated by the daily cycle, and the accessory nidamental gland (ANG), regulated by the female reproductive cycle. While host-microbiota interactions in the light organ of the bobtail squid are well understood, the dynamics within the ANG remain largely unexplored. This study uses the bigfin reef squid, Sepioteuthis lessoniana, as a model to investigate the microbiomes associated with specific regions of the ANG, capitalizing on its relatively large gland size compared to the bobtail squid. Our goal was to characterize species-specific microbiomes in the ANG and explore how pigmented region-dependent microbes contribute to reproductive fitness in bigfin reef squid.</p><p><strong>Results: </strong>Histological results indicate that four types of epithelial cells were observed in the secondary tubules of inner ANG layer. Using an amplicon-based approach, we found that Alphaproteobacteria were highly abundant in different cephalopod species. Beta diversity analyses revealed significant interspecies differences in microbiomes, while alpha diversity showed that the bigfin reef squid harbored a richer bacterial community than the other two species. Notably, pigmented regions of the ANG exhibited lower microbial diversity compared to whole ANG tissues, with Alphaproteobacteria significantly enriched in these regions. Hyphomicrobiaceae (Alphaproteobacteria) were unique to the orange regions, while Fodinicurvataceae (Alphaproteobacteria) and Flavobacteriaceae (Bacteroidia) were exclusive to the white regions. qPCR results showed higher transcription levels of immune response-associated genes in the orange region compared to other pigmented regions, suggesting localized immune interactions.</p><p><strong>Conclusions: </strong>These findings suggest that Alphaproteobacteria, particularly the Hyphomicrobiaceae clade, may correlated to the synthesis orange pigmentation in the ANG of the bigfin reef squid. The roles of Hyphomicrobiaceae in ANG symbiosis and reproductive fitness still needs further investigation. With this knowledge, we propose further investigations using in situ hybridization to detect host-expressed genes and pigmented region-dependent bacteria as markers. This approach will facilitate the study of localized host-microbiota interactions in distinct pigmented regions of the ANG, providing deeper insights into the mechanism of host-microbe communication.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"36"},"PeriodicalIF":4.9,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029210","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":"Metagenomic analysis reveals microbial drivers of heat resistance in dairy cattle.","authors":"Mingxun Li, Zhiwei Wang, Zheng Ma, Yangyang Wang, Haoran Jia, Lei Zhang, Peng Chen, Yongjiang Mao, Zhangping Yang","doi":"10.1186/s42523-025-00399-8","DOIUrl":"https://doi.org/10.1186/s42523-025-00399-8","url":null,"abstract":"<p><p>Heat stress poses a significant challenge to dairy cattle, leading to adverse physiological effects, reduced milk yield, impaired reproduction performance and economic losses. This study investigates the role of the rumen microbiome in mediating heat resistance in dairy cows. Using the entropy-weighted TOPSIS method, we classified 120 dairy cows into heat-resistant (HR) and heat-sensitive (HS) groups based on physiological and biochemical markers, including rectal temperature (RT), respiratory rate (RR), salivation index (SI) and serum levels of potassium ion (K⁺), heat shock protein 70 (HSP70) and cortisol. Metagenomic sequencing of rumen fluid samples revealed distinct microbial compositions and functional profiles between the two groups. HR cows exhibited a more cohesive and functionally stable microbiome, dominated by taxa such as Ruminococcus flavefaciens and Succiniclasticum, which are key players in fiber degradation and short-chain fatty acid production. Functional analysis highlighted the enrichment of the pentose phosphate pathway (PPP) in HR cows, suggesting a metabolic adaptation that enhances oxidative stress management. In contrast, HS cows showed increased activity in the tricarboxylic acid (TCA) cycle, pyruvate metabolism and other energy-intensive pathways, indicating a higher metabolic burden under heat stress. These findings underscore the critical role of the rumen microbiome in modulating heat resistance and suggest potential microbiome-based strategies for improving dairy cattle resilience to climate change.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"35"},"PeriodicalIF":4.9,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11984055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012132","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":"Oregano essential oil enhanced body weight and well-being by modulating the HPA axis and 23-nordeoxycholic acid of cecal microbiota in Holstein steers under cold stress.","authors":"Yongliang Huang, Siyu Cheng, Jinping Shi, Pengjia He, Yue Ma, Xu Zhang, Yongzhi Cao, Zhaomin Lei","doi":"10.1186/s42523-025-00401-3","DOIUrl":"10.1186/s42523-025-00401-3","url":null,"abstract":"<p><strong>Background: </strong>Prolonged exposure to cold stress in cattle increases basal energy consumption and impedes optimal production. Consequently, herds require adequate attention during cold, extended winters to alleviate cold stress and maintain profitability. This study investigated the effects of oregano essential oil (EO) on body weight (BW), well-being, blood parameters, and cecal microbiota. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CK) or the same diet supplemented with 20 g/(d·head) EO for 270 days.</p><p><strong>Results: </strong>EO increased BW by increasing cecal microbial abundance and carbohydrate metabolism CAZymes, leading to elevated the total volatile fatty acids (VFA) levels. Cold stress activated the HPA axis, and mitigated stress by reducing serum levels of cortisol (COR), corticosterone (CORT), adrenocorticotropic hormone (ACTH), and dopamine (DA). EO increased well-being by decreasing viral species without apparent contribution to drug or antibiotic resistance development, and cecal metabolites were primarily enriched in growth, carbohydrate metabolism, and amino acid metabolism pathways. Specifically, tryptophan metabolism (2-picolinic acid, quinolinic acid, and oxindole) enhanced steer well-being by increasing antioxidants (superoxide dismutase (SOD), peroxidases (POD), and glutathione (GSH)) and reducing inflammatory factors (interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α)) following EO treatment. Notably, low-abundance microorganisms (s_Streptomyces_gardneri, s_Paenibacillus_sp._S09, and s_Nocardia_sp._Root136) may play a significant role in growth and immunity.</p><p><strong>Conclusion: </strong>These findings provide fundamental insights into how EO alleviates cold stress by modulating the HPA axis, promotes growth and well-being of steers under cold stress by influencing mediates tryptophan metabolism of cecal microbiota in Holstein steers.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"34"},"PeriodicalIF":4.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765910","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":"Deep culturing the fecal microbiota of healthy laying hens.","authors":"Zhixuan Feng, Natalia Lorenc, Bridget O'Brien, Guangwen Sun, Zhiwei Li, Dongyun Jung, Jennifer Ronholm","doi":"10.1186/s42523-025-00395-y","DOIUrl":"10.1186/s42523-025-00395-y","url":null,"abstract":"<p><strong>Background: </strong>The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.</p><p><strong>Results: </strong>In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.</p><p><strong>Conclusions: </strong>Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733412","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":"Causal estimation of the relationship between reproductive performance and the fecal bacteriome in cattle.","authors":"Yutaka Taguchi, Haruki Yamano, Yudai Inabu, Hirokuni Miyamoto, Koki Hayasaki, Noriyuki Maeda, Yoshiro Kanmera, Seiji Yamasaki, Noboru Ota, Kenji Mukawa, Atsushi Kurotani, Shigeharu Moriya, Teruno Nakaguma, Chitose Ishii, Makiko Matsuura, Tetsuji Etoh, Yuji Shiotsuka, Ryoichi Fujino, Motoaki Udagawa, Satoshi Wada, Jun Kikuchi, Hiroshi Ohno, Hideyuki Takahashi","doi":"10.1186/s42523-025-00396-x","DOIUrl":"https://doi.org/10.1186/s42523-025-00396-x","url":null,"abstract":"<p><strong>Background: </strong>The gut bacteriome influences host metabolic and physiological functions. However, its relationship with reproductive performance remains unclear. In this study, we evaluated the relationship between the gut bacteriome and reproductive performance in beef cattle, such as Japanese black heifers. Artificial insemination (AI) was performed after 300 days of age, and the number of AI required for pregnancy (AI number) was evaluated. The relationship of the fecal bacteriome at 150 and 300 days of age and reproductive performance was visualized using statistical structural equation modelling between traits based on four types of machine-learning algorithms (linear discriminant analysis, association analysis, random forest, and XGBoost).</p><p><strong>Results: </strong>The heifers were classified into superior (1.04 ± 0.04 cycles, n = 26) and inferior groups (3.87 ± 0.27 cycles, n = 23) according to the median frequency of AI. The fecal bacteria of the two groups were examined and compared using differential analysis, which demonstrated that the genera Rikenellaceae RC9 gut group and Christensenellaceae R-7 group were increased in the superior group. Subsequently, correlation analysis evaluated the interrelationships between bacteriomes, which demonstrated that the patterns exhibited distinct characteristics. Therefore, four machine-learning algorithms were employed to identify the distinctive factors between the two groups. The directed acyclic graphs carried out by DirectLiNGAM based on these extracted factors inferred that the family Erysipelotrichaceae and the genera Clostridium sensu stricto 1 and Family XIII AD3011 group at 150 days of age were strongly associated with an increase in AI number. Furthermore, a pathway involved in creatinine degradation (PWY-4722) at 150 days of age was related to an increase in AI number. However, bacteriomes and/or pathways at 300 days of age were not necessarily related to AI number.</p><p><strong>Conclusions: </strong>In this study, a causal inference methodology was applied to investigate AI-dependent gut bacterial communities in pregnant cattle. These findings suggest that AI numbers, which are crucial for beef cattle production management, could be inferred from the fecal bacterial patterns nearly six months before the AI, rather than immediately before. This study provides a novel perspective of the gut environment and its role in reproductive performance.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"33"},"PeriodicalIF":4.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744584","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":"Idiopathic epilepsy in dogs is associated with dysbiotic faecal microbiota.","authors":"Marco Silvestrino, Mattia Pirolo, Angelica Bianco, Stefano Castellana, Laura Del Sambro, Viviana Domenica Tarallo, Luca Guardabassi, Andrea Zatelli, Floriana Gernone","doi":"10.1186/s42523-025-00397-w","DOIUrl":"10.1186/s42523-025-00397-w","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays a crucial role in modulating various physiological and pathological processes through its metabolites, including short-chain fatty acids (SCFA), which impact immune system development, gastrointestinal health, and brain functions via the gut-brain axis. Dysbiosis, an imbalance in gut microbiota composition, has been linked to neuroinflammatory and neurodegenerative conditions, including epilepsy. In dogs, idiopathic epilepsy has been hypothesized to be influenced by gut microbiota composition, although studies on this association are limited and show inconsistent results. Here, we compared the faecal microbiota of idiopathic epileptic drug-naïve dogs and healthy controls. To this aim, we recruited 19 idiopathic epileptic dogs and 17 healthy controls which met stringent inclusion criteria and characterized their faecal microbiome by 16 S rRNA sequencing.</p><p><strong>Results: </strong>No significant differences were observed between the two groups regarding age, breed, body condition score, diet, or reproductive status, though males were significantly overrepresented in the idiopathic epileptic group. Epileptic dogs showed a marked reduction in bacterial richness and a trend towards lower evenness (α-diversity) compared to healthy controls, while no differences in community composition (β-diversity) were observed between the two groups. Moreover, a decrease in SCFA-producing bacteria, namely Faecalibacterium, Prevotella, and Blautia, was observed alongside an increase in Escherichia coli, Clostridium perfringens, and Bacteroides in epileptic dogs.</p><p><strong>Conclusions: </strong>Idiopathic epileptic dogs exhibit dysbiosis, with reduced bacterial diversity, loss of beneficial genera, and overgrowth of opportunistic pathogens. These alterations in microbiota diversity and composition may contribute to epilepsy via the gut-brain axis, highlighting the need for further research to explore dietary or probiotic interventions targeting gut microbiota modulation as adjunctive therapies for managing epilepsy in dogs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"31"},"PeriodicalIF":4.9,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733413","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}