Animal microbiome最新文献

{"title":"Differences in composition and potential function of the bacterial communities of cave- and surface-dwelling Mexican salamanders.","authors":"Julio César García-Sánchez, Sean M Rovito","doi":"10.1186/s42523-025-00423-x","DOIUrl":"10.1186/s42523-025-00423-x","url":null,"abstract":"<p><p>Caves are a challenging environment for many organisms to inhabit, and many cave-dwelling animals are endemic to particular cave systems. Microorganisms in caves have been shown to have a high biosynthetic capacity, likely as a result of intense biological interactions to deal with resource scarcity. Although cave salamanders have been studied extensively in other parts of the world, they have received relatively little attention in Mexico. Declines of some cave-dwelling species may be due to outbreaks of fungal disease, and a better understanding of their cutaneous microbiome could help with future conservation efforts in the face of disease outbreaks. We characterized the cutaneous microbiome of 11 cave-dwelling Mexican salamanders and their relatives from surface environments using high-throughput 16S amplicon sequencing. We expected cave salamanders to have a more diverse microbiome containing more bacteria with potential antifungal capacity compared to forest salamanders. We also estimated networks of associations between bacteria to test the hypothesis that there are more positive associations in caves. Finally, we used a bioinformatic approach to see if bacteria in caves potentially have more metabolic pathways associated with microbial communication as a result of more intense biological interactions in caves. Although we do not find higher skin bacterial diversity in caves compared to forests, we do find differences in microbiome composition between environments, more positive associations between bacteria, and a slightly higher number of metabolic pathways associated with microbial communication in caves. Our results provide some support for an impact of the cave environment on the skin microbiome of Mexican salamanders.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"56"},"PeriodicalIF":4.9,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217677","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":"Novel insight into the impact of black soldier fly larvae meal and protease on cecal microbiome, SCFAs, and excreta composition in laying hens.","authors":"Jing Lu, Renée Maxine Petri, Janice Leigh MacIsaac, Stephanie Anne Collins","doi":"10.1186/s42523-025-00421-z","DOIUrl":"10.1186/s42523-025-00421-z","url":null,"abstract":"<p><strong>Background: </strong>Insect farming represents a sustainable loop that recycles organic wastes back to the food chain while requiring minimal inputs such as land and water. Insect products are not only low in environment footprint, but also nutrient-dense and contain health-promoting bioactives. Black soldier fly larvae meal (BSFLM) stands out as an excellent source of protein and chitin, and the latter is a polysaccharide associated with promoting gut health. A 20-week feeding trial evaluated the effects of three dietary inclusion levels of BSFLM (0%, 6.5%, and 13%), with and without protease enzyme (Concentrase-P) supplementation, on two commercial laying hen strains: Lohmann Brown-Lite (brown hens) and Lohmann LSL-Lite White (white hens). The two strains of 52-week-old hens (mean weight = 2.2 kg) were housed in one production room, with each strain distributed across 36 conventional cages (5 birds per cage). Each treatment was randomly assigned to six cages (n = 6). At the end of the trial, cecal microbiome, SCFA production and excreta composition were studied.</p><p><strong>Results: </strong>White hens exhibited a distinct cecal microbiome compared to brown hens (p < 0.05), characterized by enhanced diversity, increased relative abundance of Actinobacteriota, and an altered cecal SCFA profile with increased butyric acid and reduced acetic acid levels (p < 0.05). Independent from strain, both 6.5% and 13% BSFLM inclusion promoted cecal microbial richness and evenness, shifting the community to produce more acetic acid and less butyric acid (p < 0.05). Excreta analysis showed significantly higher concentrations and daily excretion of nitrogen, ammoniacal nitrogen and non-ammoniacal nitrogen in both strains on the 13% BSFLM diet. Concentrase-P supplementation effectively ameliorated the elevated nitrogen and ammoniacal nitrogen excretion linked to the 13% BSFLM diet, despite having minimal effects on the cecal microbiome and SCFA production.</p><p><strong>Conclusion: </strong>Our study provides a novel perspective on the enhanced cecal microbiome diversity in laying hens fed high levels of BSFLM, linking it to suboptimal protein digestion and an undesired increase in protein fermentation, which we have demonstrated can be partially addressed by protease supplementation. Our findings highlight the need to consider interactions between host nutrition, gut microbiome, and sustainability when evaluating novel feed ingredients.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"55"},"PeriodicalIF":4.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12126888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192542","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":"Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms.","authors":"Urška Kuhar, Uroš Krapež, Brigita Slavec, Joško Račnik, Petra Šenica Kavčič, Urska Jamnikar-Ciglenecki","doi":"10.1186/s42523-025-00428-6","DOIUrl":"10.1186/s42523-025-00428-6","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"54"},"PeriodicalIF":4.9,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12126904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192543","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":"Cardiac function of colorectal cancer mice is remotely controlled by gut microbiota: regulating serum metabolites and myocardial cytokines.","authors":"Zhan-Kui Gao, Chao-Yuan Fan, Bo-Wen Zhang, Jia-Xin Geng, Xing Han, Dan-Qi Xu, Muhammad Arshad, Hao-Xuan Sun, Jiong-Yi Li, Xiangyuan Jin, Xiao-Qin Mu","doi":"10.1186/s42523-025-00405-z","DOIUrl":"10.1186/s42523-025-00405-z","url":null,"abstract":"<p><p>Several studies have indicated that the dysregulation of microbial metabolites and the inflammatory environment resulting from microbial dysbiosis may contribute to the occurrence and progression of cardiovascular diseases. Therefore, restoring the disordered gut microbiota in patients with colorectal cancer by fecal microbiota transplantation (FMT) has the potential to reduce the incidence of cardiac disease. In this study, we identified cardiac dysfunction in azomethane and dextran sodium sulfate-induced colorectal cancer mice. Intestinal microbes from healthy mice were transferred to colorectal cancer mice, which vastly reversed the disorder of the gut microbiota and effectively alleviated cardiac dysfunction. Moreover, FMT regulated the expression of serum metabolites such as uridine triphosphate (UTP), tiamulin, andrographolide, and N-Acetyl-D-glucosamine, as well as cytokines like TGF-β, IRF5, and β-MHC in the heart. These findings uncover that the disturbed gut microbiota causes cardiac dysfunction in colorectal cancer mice by modulating the expression of serum metabolites and cytokines, which could be alleviated by treatment with FMT.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"53"},"PeriodicalIF":4.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188564","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":"From mother to piglet: the lasting influence of the maternal microbiome.","authors":"Alessandra Tancredi, Thomas Matthijs, Eric Cox, Filip Van Immerseel, Evy Goossens","doi":"10.1186/s42523-025-00420-0","DOIUrl":"10.1186/s42523-025-00420-0","url":null,"abstract":"<p><strong>Background: </strong>Given their crucial roles in agriculture and biomedical research, promoting pig health is essential. A balanced gut microbiota is vital for immune development, metabolism and pathogen resistance, and requires optimal initial colonization by beneficial bacteria. This becomes particularly evident during early life stages, like suckling and weaning, where disruptions can lead to long-term health issues. Understanding the factors influencing microbiome development during these phases is fundamental for enhancing pig health. On these basis, rectal swab samples from eighteen sow-piglet pairs were collected at multiple time points from 7 days after birth to 10 days post-weaning, and analyzed through 16S rRNA gene sequencing. This study aims to understand the maternal influence on piglet microbiota development during the suckling-weaning period, exploring microbial diversity, composition and additional influencing factors such as age, piglet and weaning.</p><p><strong>Results: </strong>α diversity significantly increased with piglet age (p < 0.001) and stabilized upon weaning, with maternal influence and differences between individual piglet affecting variability before weaning. Post-weaning α diversity was influenced by the pen environment (contributing to 14.5-16% of the variability between piglets) rather than age. Both the sow (~ 9.6%) and age of the piglets (20-30%) had a significant impact on the microbial β diversity over the entire timeframe. Moreover, at 10 days post-weaning a significant influence of the cage mates on piglets microbial β diversity was observed (~ 24.6%). Source-tracking analysis revealed a significant maternal contribution to piglet microbiome at 7 days (31.68%), which decreased over time but remained at 13.33% post-weaning. Piglet microbiome exhibited consistency across time, with 22.55-61.23% of bacteria retained from previous stages. Cage mates contributed 53.54% to the microbiome at 10 days post-weaning. Additionally, 68.32% of piglets microbiome at 7 days was derived from sources not included in the study, decreasing to 37.6% by 10 days post-weaning. ASV-level analysis showed that the majority of maternally transmitted ASVs pre-weaning persisted until the last time point, with both beneficial bacteria and pathobionts being transmitted.</p><p><strong>Conclusions: </strong>This study highlights the significant influence of maternal microbiota on piglet gut microbiome development, affecting both diversity and composition. Beneficial bacteria are transmitted from mothers to offspring and persist through early developmental stages, thereby emphasizing the long-lasting impact of maternal microbiome and the importance of early microbial colonization for piglet health.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"52"},"PeriodicalIF":4.9,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144152973","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":"Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep.","authors":"Ximei Xie, Huan Yang, Xingang Zhao, Li Teng, Yuze Yang, Hailing Luo","doi":"10.1186/s42523-025-00412-0","DOIUrl":"10.1186/s42523-025-00412-0","url":null,"abstract":"<p><strong>Background: </strong>Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.</p><p><strong>Results: </strong>The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.</p><p><strong>Conclusions: </strong>In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"51"},"PeriodicalIF":4.9,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144364","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":"Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective.","authors":"Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Sandra Romero-Hidalgo, Alonso A Lopez-Zavala, Andrés Cota-Huízar, Melany Cervantes-Echeverría, Rogerio R Sotelo-Mundo, Adrian Ochoa-Leyva","doi":"10.1186/s42523-025-00414-y","DOIUrl":"10.1186/s42523-025-00414-y","url":null,"abstract":"<p><strong>Background: </strong>Pacific Whiteleg shrimp (Litopenaeus vannamei) is an important model for breeding programs to improve global aquaculture productivity. However, the interaction between host genetics and microbiota in enhancing productivity remains poorly understood. We investigated the effect of two shrimp genetic lines, Fast-Growth (Gen1) and Disease-Resistant (Gen2), on the microbiota of L. vannamei.</p><p><strong>Results: </strong>Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. After confirming that the rearing pond did not significantly influence the microbiota composition, we determined that genetic differences explained 15.8% of the microbiota variability, with a stronger selective pressure in the hepatopancreas than in the intestine. Gen1, which exhibited better farm productivity, fostered a microbiota with greater richness, diversity, and resilience than Gen2, along with a higher abundance of beneficial microbes. Further, we demonstrated that a higher abundance of beneficial microbes was associated with healthier shrimp vs. diseased specimens, suggesting that Gen1 could improve shrimp's health and productivity by promoting beneficial microbes. Finally, we determined that the microbiota of both genetic lines was significantly different from their wild-type counterparts, suggesting farm environments and selective breeding programs strongly alter the natural microbiome.</p><p><strong>Conclusions: </strong>This study highlights the importance of exploring the hologenome perspective, where integrating host genetics and microbiome composition can enhance breeding programs and farming practices.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"50"},"PeriodicalIF":4.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129652","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":"Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.","authors":"C Purse, A Parker, S A James, D J Baker, C J Moss, R Evans, J Durham, S G P Funnell, S R Carding","doi":"10.1186/s42523-025-00409-9","DOIUrl":"https://doi.org/10.1186/s42523-025-00409-9","url":null,"abstract":"<p><strong>Background: </strong>Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.</p><p><strong>Results: </strong>Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.</p><p><strong>Conclusions: </strong>We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"47"},"PeriodicalIF":4.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081886","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":"Characterization of bacterial communities of ewe's vaginal tract and its potential impact on reproductive efficiency.","authors":"E L Reinoso-Peláez, F Puente-Sánchez, M Serrano, J H Calvo, M Ramón, M Saura","doi":"10.1186/s42523-025-00383-2","DOIUrl":"https://doi.org/10.1186/s42523-025-00383-2","url":null,"abstract":"<p><p>The success rate of artificial insemination in sheep remains suboptimal, which has led to an emerging interest in the impact of the reproductive tract microbiome on this process. This research aims to identify the ewes' vaginal core bacterial community, examine the factors influencing bacterial composition, and to determine the association between vaginal bacteria and pregnancy success. By using a robust dataset comprising 331 multiparous ewes from three Spanish breeds (Latxa, Manchega, Rasa Aragonesa) across four herds, this study performed the sequencing of the hypervariable regions V3-V4 of the 16S ribosomal RNA gene and the identification of Amplicon Sequence Variants (ASV) to analyze the bacterial community. Our analysis revealed a core bacterial primarily consisting of the genera Streptobacillus, Histophilus, Fusobacterium, Oceanivirga, and Parvimonas. Alpha and beta diversity, as well as Random Forest analysis, identified that herd and breed were the main drivers of bacterial variability. PERMANOVA analysis also showed significant differences in bacterial composition and abundance associated with pregnancy outcomes. Notably, specific ASVs associated with Fusobacterium, Leptotrichia, Histophilus, Escherichia, and Bacteroides were predominantly found in non-pregnant ewes, while genera such as Pseudomonas, Acinetobacter, and Brevundimonas were more abundant in pregnant ewes. This study contributes to the knowledge about the critical roles of specific bacteria in determining reproductive success in sheep and provides novel insights about the importance of different factors involved in the composition of ewes' vaginal bacterial communities.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"48"},"PeriodicalIF":4.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082486","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":"Temperature-dependent shifts in gut microbiota and metabolome of olive flounder (Paralichthys olivaceus): implications for cold-water aquaculture expansion and probiotic applications.","authors":"Che-Chun Chen, Yu-Ping Chen, Hsiao-Tsu Yang, Yu-Ling Chen, Chen-Wei Wu, Hong-Yi Gong, Yuan-Shing Ho, Ying-Ning Ho","doi":"10.1186/s42523-025-00417-9","DOIUrl":"https://doi.org/10.1186/s42523-025-00417-9","url":null,"abstract":"<p><strong>Background: </strong>In recent years, rising temperatures due to climate change have become significant stressors in aquatic environments, impacting disease incidence, growth, and gut microbiota in fish. Cold-water species, such as the olive flounder (Paralichthys olivaceus), are particularly vulnerable to increasing water temperatures. Despite its economic importance as a species farmed in East Asia, research on temperature-dependent shifts in the gut microbiota and metabolome of olive flounder remains limited. This study investigates the effects of water temperature on the gut microbiota and metabolome of olive flounder using full-length 16 S rRNA sequencing with Oxford Nanopore Technologies and metabolomics analysis with high-resolution liquid chromatography-mass spectrometry (LC-MS). The analysis compares individuals exposed to three water temperatures (18 °C, 22 °C, and 26 °C).</p><p><strong>Results: </strong>Temperature significantly influenced the composition of gut microbiota, with an increase in Gammaproteobacteria abundance at higher temperatures. Potential pathogens such as Vibrio and Photobacterium increased from 22 °C to 26 °C, while Pseudomonas declined, suggesting an elevated risk of pathogen infection at 26 °C. Functional predictions revealed that gut bacteria regulated host metabolism, particularly carbohydrate, amino acid, and lipid pathways. Metabolomic analysis showed reduced levels of polyunsaturated fatty acids (PUFAs) and phosphatidylcholine (PC)-related metabolites at higher temperatures. Notably, the umami flavor-related compound aspartic acid decreased, while the bitter flavor-related compound phenylalanine increased. Correlation analysis identified significant associations between bacterial genera, such as Comamonas,Pseudomonas,Sphingomonas, and Stentotrophomonas (positive correlation), and Legionella and Phaeobacter (negative correlation), with shifts in PUFAs and PC metabolites.</p><p><strong>Conclusions: </strong>This study demonstrates that environmental temperature significantly affects the gut microbiota and muscle metabolites of olive flounder. Higher temperatures diversified gut bacterial communities and altered metabolite profiles, with reductions in PUFAs and PC-related compounds linked to specific bacterial genera. These findings highlight the potential of these bacterial genera as biomarkers or probiotics for improving aquaculture practices and environmental adaptation strategies. By establishing a strong correlation between gut microbiota and muscle metabolites, this research provides insights that could contribute to sustainable flounder farming and enhance resilience to climate change.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"49"},"PeriodicalIF":4.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081920","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}