Animal microbiome最新文献

{"title":"Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa.","authors":"Mikaella L Grant, Renee M Petri, Tristan M Baecklund, Gregory A Wilson, Christopher J Kyle","doi":"10.1186/s42523-025-00451-7","DOIUrl":"10.1186/s42523-025-00451-7","url":null,"abstract":"","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"89"},"PeriodicalIF":4.4,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980658","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 ocular surface microbiome of rhesus macaques.","authors":"Joelle K Hass, Arthur G Fernandes, Michael J Montague, Armando Burgos-Rodriguez, Melween I Martinez, Lauren J N Brent, Noah Snyder-Mackler, John Danias, Gadi Wollstein, James P Higham, Amanda D Melin","doi":"10.1186/s42523-025-00454-4","DOIUrl":"10.1186/s42523-025-00454-4","url":null,"abstract":"<p><strong>Background: </strong>The ocular surface microbiota (OSM) is important for eye health, and variations in OSM composition have been associated with multiple diseases in humans. Studies of OSM-disease dynamics in humans are confounded by lifestyle factors. Animal models provide a complementary approach to understanding biological systems, free from many confounds of human studies. Here, we provide the first study of the OSM of rhesus macaques, a premier animal model for eye health and disease. We describe the taxonomy of the rhesus macaque OSM, and explore compositional correlations with age, sex, and living condition.</p><p><strong>Methods: </strong>We analyzed eyelid and conjunctival microbiota swabs from 132 individual rhesus macaques (Macaca mulatta) (57 males, 75 females, 1-26 years old) from one captive and one free-ranging group using 16 S rRNA V3/V4 MiSeq sequencing. We investigated alpha diversity, beta diversity, and differential abundance.</p><p><strong>Results: </strong>We found several similarities between the top Phyla and Genera of the rhesus macaque OSM and those reported in human literature. Significantly higher alpha diversity, which may reflect age-related ocular surface mucous membrane integrity and immune function, was present in younger individuals compared to older ones. Higher alpha diversity was also present in free-ranging rhesus macaques compared to ones in captivity, possibly related to differences in diet, exercise, and medical exposures between macaques in different living conditions. Beta diversity was most strongly influenced by individual identity, followed by living conditions. Sex did not correlate with any OSM variation.</p><p><strong>Conclusions: </strong>In this study we describe the taxonomic composition of the rhesus macaque OSM, and identify significant differences in alpha and beta diversity according to individual nonhuman primate host variables and the surrounding environment. Our findings suggest composition of the nonhuman primate OSM is shaped by age-related physiology, individual identity, and external living conditions. Our results offer novel insights into an underexplored region of the primate microbiome and highlight the utility of rhesus macaques as a model system for investigating the links between the OSM, ocular health, and disease.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"88"},"PeriodicalIF":4.4,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980167","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":"Unlocking microbiota potential: the role of organic copper in enhancing healthy white shrimp (Penaeus vannamei) farming.","authors":"Jinzhu Yang, Xiaoyang Yao, Zhonghao Zhang, Gang Lin, Mingzhu Li, Kangsen Mai, Yanjiao Zhang","doi":"10.1186/s42523-025-00450-8","DOIUrl":"10.1186/s42523-025-00450-8","url":null,"abstract":"<p><strong>Background: </strong>Microbiota sequencing has emerged a powerful tool for advancing aquatic nutrition research. However, few studies have comprehensively investigated the host microbiota's response to trace minerals. This study examined the role of organic copper supplementation in promoting the health of farmed white shrimp (Penaeus vannamei) from a microbiota perspective.</p><p><strong>Results: </strong>In an 8-week feeding trial, shrimp were fed diets supplemented with no copper, 30 mg/kg inorganic copper (CuSO₄·5H₂O) or organic copper (Cu-proteinate). The apparent digestibility coefficients of copper and zinc, along with carbon and nitrogen assimilation, were determined. The V3-V4 region of the 16S rRNA gene was sequenced from feeds, intestines, gills, and water samples. Shrimp that fed the organic copper diet demonstrated healthier physiological status, higher apparent digestibility coefficients of both copper and zinc, as well as greater accumulation of copper, zinc, carbon, and nitrogen. The organic copper group exhibited distinct microbial diversity and a more complex microbial co-occurrence network, characterized by enhanced natural connectivity and robustness. Keystone taxa, including Vibrio, Candidatus_Bacilloplasma, and Photobacterium, contributed to network stability. Taxa associated with nutrient metabolism, including Butyricicoccus, Lactobacillus, and genera in the family Lachnospiraceae, Prevotellaceae, Rikenellaceae and Ruminococcaceae, were significantly enriched, correlating well with improved nutritional profiles. In accordance, functional annotation revealed that the organic copper group exhibited higher abundances of functional modules associated with nutrient and energy metabolism such as carbon and nitrogen cycling. Furthermore, host-selective pressure shaped the unique microbiota composition in the intestine and gill, which differed from the surrounding water and water source, with the gill microbiota potentially serving as a transitional bridge shaping the intestinal microbiota.</p><p><strong>Conclusions: </strong>More stable host microbiota, enriched nutrient-metabolizing taxa, and enhanced ecological cycling in this study provide a potential strategy for innovative aqua-feed development. Our findings offer novel microbiota-centric insights into the role of organic copper in healthy shrimp farming.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"87"},"PeriodicalIF":4.4,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849935","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 influence of glutathione metabolism on alkaline adaptation of Amur ide (Leuciscus waleckii) and potential role of gut microbiota.","authors":"Zou Yuting, Li Chenghao, Huang Jing, Yang Haochen, Luo Liang, Liew Honjung, Chang Yumei","doi":"10.1186/s42523-025-00452-6","DOIUrl":"10.1186/s42523-025-00452-6","url":null,"abstract":"<p><p>Amur ide (Leuciscus waleckii), which inhabits Lake Dali, a soda lake in Northeast China with extremely high alkalinity (~ 53.57 mmol/L) and pH value (~ 9.6), is considered to be an ideal model for elucidating alkaline adaption mechanisms. To uncover the molecular mechanisms underlying this adaptation, we conducted a comparative study between the alkaline water ecotype (JY) and freshwater ecotype (DY). Both groups were exposed to a gradient of NaHCO₃ stress levels (0, 10, 30, and 50 mmol/L), and their responses were systematically assessed through integrated multi-omics analyses alongside physiological assays. Our results revealed that under low and moderate alkaline stress (10 and 30 mmol/L), JY group significantly upregulated the gene anpep, facilitating the hydrolysis of cysteinyl-glycine to release L-cysteine, thereby enhancing antioxidant capacity. Under high stress conditions (50 mmol/L), JY further synergistically upregulated gpx to activated the glutathione peroxidase (GPx) pathway to eliminate excess ROS. In contrast, the DY group predominantly relied on upregulating chac1-mediated γ-glutamyltransferase activity to facilitate glutathione cycling. Notably, while cysteinyl-glycine content significantly increased in the alkaline water ecotype (JY) under moderate and high alkalinity stress (30 and 50 mmol/L), the expression of its upstream gene chac1 was significantly downregulated. This paradox suggests alternative sources or regulatory mechanisms for cysteinyl-glycine accumulation in JY. Microbial tracing analysis revealed a positive correlation between cysteinyl-glycine levels and the gut microbiota genus Stenotrophomonas in JY, whose relative abundance increased progressively with elevated alkalinity. It is speculated that Stenotrophomonas may modulate host glutathione metabolism by regulating cysteinyl-glycine levels, thereby facilitating alkaline adaptation.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"86"},"PeriodicalIF":4.4,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838702","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":"A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages.","authors":"Varsha Kale, Germana Baldi, Martin Beracochea, Cecilie Clausen, Alejandra Escobar-Zepeda, Sabina Leanti La Rosa, Laurène A Lecaudey, Sen Li, Sarah S T Mak, Michael D Martin, Garazi Martin Bideguren, Louisa A Pless, Jacob A Rasmussen, Alexander B Rogers, Harald Sveier, Arturo Vera-Ponce de León, Ana Verissimo, M Thomas P Gilbert, Lorna Richardson, Morten T Limborg, Robert D Finn","doi":"10.1186/s42523-025-00453-5","DOIUrl":"10.1186/s42523-025-00453-5","url":null,"abstract":"<p><p>Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity. We profiled the salmon gut microbiome across 540 salmon samples in differing conditions with a view to capture the genomic diversity that can be resolved from the salmon gut. The salmon were exposed to 3 different nutritional additives: seaweed, blue mussel protein and silaged blue mussel protein, including both pre-smolts (30-60 g salmon reared in freshwater) as well as post-smolts (300-600 g salmon reared in saltwater). Using genome-resolved metagenomics, we generated a catalogue of 11 species-level bacterial MAGs from 188 input metagenome assembled genomes, with 5 species not found in other catalogues. This highlights that our understanding of salmon gut microbial diversity is still incomplete. A prevalent bacterial genome annotated as Mycoplasmoidaceae is present in adult fish, and a comparison of functions revealed significant sub-species variation. Juvenile fish have a different microbial diversity, dominated by a species of Pseudomonas aeruginosa. We also present the first viral catalogue for salmon including prophage sequences which can be linked to the bacterial MAGs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"85"},"PeriodicalIF":4.4,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12341145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823314","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 exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.","authors":"Lea Kauer, Panagiotis Sapountzis, Christian Imholt, Christian Berens, Ralph Kuehn","doi":"10.1186/s42523-025-00448-2","DOIUrl":"10.1186/s42523-025-00448-2","url":null,"abstract":"<p><p>The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"84"},"PeriodicalIF":4.4,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796269","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":"Natal soil consumption shifts gut microbiome in captive Ōkārito kiwi (Apteryx rowi).","authors":"Stephen P Rowe, Matthew B Stott, Bethany Brett, Priscilla A San Juan, Anastasija Podolyan, Manpreet K Dhami","doi":"10.1186/s42523-025-00445-5","DOIUrl":"10.1186/s42523-025-00445-5","url":null,"abstract":"<p><strong>Background: </strong>Captive-rearing programmes for endangered birds, such as those in place for kiwi conservation in Aotearoa-New Zealand, can unintentionally deprive the birds access to a microbially-diverse and 'natural' developmental environment i.e., their natal rohe (territory). These programmes introduce external variables such as increased exposure to diseases, unnatural and incomplete diets, antimicrobial usage, and artificial cohabited environments, which have the potential to impact rearing success outcomes. In this research, we investigated whether the introduction of natal soils, as a direct probiotic and a source of wild microorganisms, to the captive-reared ground-foraging Ōkārito kiwi (Apteryx rowi) chick diet would impact their gut microbiome. Using 16S rRNA gene and ITS sequencing to identify the key taxonomic groups present, we assess the community composition differences with the introduction of natal soils into the diet of captive-reared Ōkārito kiwi.</p><p><strong>Results: </strong>Results showed a distinct gut microbial community associated with Ōkārito kiwi in captivity. Bacterial diversity in Ōkārito kiwi gut increased with age, with the relative abundances of dominant taxonomic groups changing over time. Bacterial phyla Firmicutes, Proteobacteria and Actinobacteria, and the fungal orders Malasseziales and Trichosporon dominated the gut community. Exposure to natal Ōkārito soils influenced the composition of the gut microbiome in Ōkārito kiwi, especially on the temporal trends of key bacterial taxa. Kiwi with natal-soil-amended diets harboured an increased proportion of Firmicutes and Malasseziales compared to the 'Control' group. The fungal community in the Ōkārito kiwi gut was more transitory, changing rapidly following soil amendment. No significant changes to growth rates or overall health were found between 'Control' and 'Treatment' groups.</p><p><strong>Conclusions: </strong>The findings of this study represent the first description of the gut microbiome of the critically endangered Ōkārito kiwi, Apteryx rowi, and the first documented use of natal soil as a probiotic amendment for wild birds. Results show that mediation of the gut microbial communities of captive-reared ground-foraging birds can be achieved through the introduction of natal soils in their diet.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"83"},"PeriodicalIF":4.4,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12330010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796270","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 rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.","authors":"Abdallah Alaa Mousa, Han Zhang, Hongwei Duan, Jiyou Zhang, Shengyong Mao","doi":"10.1186/s42523-025-00439-3","DOIUrl":"10.1186/s42523-025-00439-3","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to investigate differences in the structure and function of the rumen microbiome and its associated changes in rumen fermentation patterns and apparent nutrient digestibility in dairy cattle with different sorting behavior. Twenty-four Holstein cows in mid-lactation were initially enrolled in the experiment. All cows were fed and milked three times daily throughout the entire 28-day experimental period, comprising a 7-day pre-trial and a 21-day main trial. On days 1, 7, 14, and 21 of the main trial, feed sorting behavior was measured, and feed and feces samples were collected to determine apparent nutrient digestibility. Rumen content samples were collected on day 21 to measure pH, volatile fatty acids (VFA), and rumen microbiome structure and function. Based on feed sorting behavior, twelve cows were selected and divided into two groups: six cows that were severely sorted for fine particles-severely rejected long particles (SES; n = 6) and six cows that were slightly sorted for fine particles-slightly rejected long particles (SLS; n = 6).</p><p><strong>Results: </strong>Comparative analysis revealed significant differences between the groups. The SES group exhibited lower rumen pH values and higher concentrations of total VFA (TVFA) and acetate (P < 0.05) than the SLS group. Data on apparent nutrient digestibility showed that compared to the SLS group, the SES group lowered the digestibility of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (P < 0.05). Differential analysis of rumen microbiota indicated that the SES group had a higher relative abundance of Prevotella, Lactobacillus, Bifidobacterium, Selenomonas, and Acetitomaculum by a lower relative abundance of Fibrobacter, Ruminobacter, Pseudobutyrivibrio, Butyrivibrio, and Ruminococcus. Carbohydrate-active enzyme (CAZyme) annotation revealed that the SES group showed increased abundance of GH13 and GH65 enzymes, while exhibiting decreased abundance of GH1, GH3, GH5, GH6, and GH94. Functional profiling of Kyoto encyclopedia of genes and genomes (KEGG) modules revealed that compared to the SLS group, the rumen microbiota in the SES group upregulated the abundance of carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism. In carbohydrate metabolism, the rumen microbiota in the SES group upregulated the abundance of starch and sucrose metabolism, the citrate cycle, and pyruvate metabolism, while downregulating the pentose phosphate pathway. Functional profiling of KEGG Orthology (KO) enzymes revealed that the microbiota in the SES group preferred energy production through increasing glycolysis and supported the metabolism changes toward acetate production and fatty acid biosynthesis.</p><p><strong>Conclusion: </strong>Our findings reveal that feed sorting behavior significantly alters the rumen microbial ecosystem and its metabolic functions, negatively impacting fermentation efficiency, fiber digesti","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"82"},"PeriodicalIF":4.4,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12302734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735810","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":"Strain-resolved comparison of beef and draft cattle rumen microbiomes using single-microbe genomics.","authors":"Feifei Guan, Jianhan Liu, Lincong Zhou, Qichang Tong, Ningfeng Wu, Tao Tu, Yuan Wang, Bin Yao, Huiying Luo, Jian Tian, Huoqing Huang","doi":"10.1186/s42523-025-00442-8","DOIUrl":"10.1186/s42523-025-00442-8","url":null,"abstract":"<p><strong>Background: </strong>Beef and draft cattle have distinct rumen microbiota that can influence their metabolic processes and body composition. However, traditional metagenomic sequencing methods only provide broad surveys of the rumen microbial genomic contents. In this study, we utilized high-throughput single-cell genome sequencing to investigate these differences at the strain level.</p><p><strong>Results: </strong>Following quality control and contig assembly, we obtained 97 bacterial genomes, 17 archaeal genomes, and 241 subspecies genomes from the rumen samples of Angus and Wuling cattle. Our analysis revealed a higher bacterial abundance in Angus rumen, characterized by an enrichment of the Succiniclasticum and Limivicinus genera. In contrast, the rumen of Wuling cattle exhibited a higher archaeal abundance. Additionally, we observed variations in the types and abundance of microbial-derived enzymes responsible for plant fiber degradation and volatile fatty acid (VFA) production between the two cattle breeds. The Angus rumen was found to harbor a higher diversity and abundance of cellulases and hemicellulases, particularly from the Ruminococcus unknown_0 genus. Furthermore, genera such as Succiniclasticum, Butyrivibrio, Limivicinus, UBA2868, and Prevotella were identified as key contributors to VFA production. Our findings suggest that the Angus rumen may have a stronger VFA production capacity due to the higher abundance of acidogenic genera. Interestingly, we also observed a greater abundance of Methanobrevibacter_A methanogens, which play a crucial role in energy flow in the rumen ecosystem, in Wuling cattle compared to Angus cattle.</p><p><strong>Conclusion: </strong>Our study highlights differences in the rumen microbiome of Angus and Wuling cattle. This difference could, at least partially, account for the variation in fat content that ultimately results in the superior meat quality of Angus cattle and the sustained muscle activity required by draft cattle. Overall, single-cell genome sequencing reveals distinct microbial composition and metabolic pathways between the two breeds, providing insights into their unique physiological and metabolic needs.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"80"},"PeriodicalIF":4.4,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12291375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719227","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":"Unlocking the potential of willow condensed tannins: effects on rumen fermentation, microbiome, and metabolome for sustainable ruminant nutrition.","authors":"Joshua P Thompson, Omar Cristobal-Carballo, Tianhai Yan, Katie Lawther, Nicholas J Dimonaco, Wayne E Zeller, Zhenbin Zhang, Sharon Huws, Laudina Safo, Andrew D Southam, Christian Ludwig, Gavin R Lloyd, Sokratis Stergiadis, Katerina Theodoridou","doi":"10.1186/s42523-025-00444-6","DOIUrl":"10.1186/s42523-025-00444-6","url":null,"abstract":"<p><strong>Background: </strong>Sustainable livestock production is essential for meeting the growing global protein demand while minimising environmental impacts. Exploring alternative forages that enhance nutrient utilisation and reduce reliance on imported feeds is a potential strategy. Condensed tannins (CTs) can bind to proteins in the rumen, protecting them from ruminal degradation resulting in decreased ammoniacal N and enhanced nitrogen uptake in the hindgut. This pioneering research is the first to explore the potential of willow (Salix) as an alternative feed for ruminant nutrition. The study involved feeding ewe hoggets a control grass silage (SIL) or a SIL mix containing a 20% dry matter (DM) dietary inclusion of leaves from two willow varieties to investigate the impact the willow CTs have on rumen fermentation, microbial populations, and metabolomic profiles. Willow treatments: Beagle (BG) and Terra Nova (TN) had an overall CT inclusion (CTI) of 1.1 and 0.1% DM with the control diet containing no CTs in a three-treatment x three-period Latin square design.</p><p><strong>Results: </strong>Although total dry matter and fibre intake were higher in BG and TN, there was no significant difference in ruminal CH₄ production between the treatments. However, fermentation was affected, with BG and TN showing lower acetate production and reduced total volatile fatty acid production compared to SIL. CTs may have impaired fibre digestion, as SIL had higher Fibrobacter abundance than BG. Heatmap visualisation indicated higher carbohydrate metabolite concentrations in SIL, with reduced metabolism observed in TN and BG. Ruminal ammonia did not differ significantly among treatments, despite higher nitrogen intake in BG and TN treatments. Proteolytic bacteria levels were similar across treatments, but TN and BG had higher ruminal metabolites associated with protein metabolism upon visualisation through heatmap analysis. TN showed higher abundance of Prevotella and Fibrobacter than BG, which had 10 times higher CT content and a greater prodelphinidin proportion.</p><p><strong>Conclusion: </strong>Feeding CT-containing willow enhanced feed intake, altered rumen microbiome composition and suggested visual changes in the analysis of protein metabolism, offering potential benefits for animal performance. While a reduction in CH₄ was not observed, this study highlights the potential of willow to alter ruminant nutrition while supporting sustainable agricultural practices.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"7 1","pages":"81"},"PeriodicalIF":4.4,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719228","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}