Animal microbiome最新文献

{"title":"Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.","authors":"Ying Yuan, He Cong, Tao Ren, Peng-Cheng Ruan, Lu Xu, Bai-Gao Yang, Hao-Yuan Zhang, Simone Ceccobelli, Zi-Xuan Wang, Yao-Long Liu, Kaushalendra, Yan-Guo Han, Yan Zeng, Hong Miao, De-Jun Xu, Guang-Xin E","doi":"10.1186/s42523-026-00559-4","DOIUrl":"10.1186/s42523-026-00559-4","url":null,"abstract":"<p><p>Mastitis poses a critical challenge to dairy goat production, impacting animal welfare, milk yield, and the microbiological safety of dairy products. This study employed a multi-omics approach to explore the genetic basis of mastitis resistance in Saanen goats, focusing on identifying functional copy number variants (CNVs) and their roles in immune regulation. A genome-wide scan identified 62,860 CNVs, with 115 exhibiting strong selection signals. Among these, two adjacent CNVs overlapping with the C-type lectin genes LOC108636060 and LOC108636138 were noteworthy due to their high deletion frequencies in the population of Saanen goats. Functional investigations involving lipopolysaccharide (LPS)-challenged goat mammary epithelial cells (GMECs) demonstrated that the overexpression of these two C-type lectin genes significantly potentiated NF-κB signaling pathway activation. This was accompanied by the marked upregulation of key inflammatory mediators, including CD14, CXCL8, and PTGS2. Integrated metabolomic analysis further validated their involvement in modulating immune-associated metabolic responses, such as alterations in lipid metabolism, amino acid derivatives, and inflammatory signaling molecules. These findings indicate that LOC108636060 and LOC108636138 could contribute to mastitis resistance through the regulation of innate immune pathways, with critical roles in orchestrating inflammatory responses. Their functional relevance suggests these genes may serve as promising candidates for selective breeding programs. Incorporating these markers into breeding strategies could facilitate the improvement of udder health, bolster mastitis resistance, and contribute to the overall safety of milk products in dairy goat production.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147618838","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":"Optimizing cetacean blow collection methods under controlled conditions: implications for further non-invasive UAV-based sampling of the cetacean respiratory microbiome in the wild.","authors":"Elyne Dugény, Luca Ceolotto, Rafaella Franch, Gaia Pesce, Eva Alvarez, Erika Esposti, Sandro Mazzariol, Cinzia Centelleghe","doi":"10.1186/s42523-026-00555-8","DOIUrl":"10.1186/s42523-026-00555-8","url":null,"abstract":"<p><p>BACKGROUND: Unmanned aerial vehicles (UAVs) are gaining attention as non-invasive tools for wildlife research, offering the ability to collect biological samples without physically handling animals. In cetaceans, drone-based sampling of exhaled breath condensate—or “blow”—has emerged as a promising method for assessing health, particularly through analysis of the respiratory microbiome. However, standardized protocols for effective and reliable blow collection are still lacking. RESULTS: This study aimed to evaluate and compare four different blow collection tools—DNA/RNA Shield, dry and pre-moistened biocide-free cellulose sponges, and indicating FTA cards—using controlled trials conducted 1 m above five bottlenose dolphins (Tursiops truncatus) under human care. Metabarcoding analyses of the captured microbial communities revealed that the type of sampling collection tool had a stronger influence on microbiome composition and structure than the individual dolphin or sample origin (blow, air, or water). FTA cards and DNA/RNA Shield consistently yielded the most informative and high-quality results. In contrast, both types of sponges showed evidence of overgrowth by copiotroph opportunistic bacteria, limiting their reliability. While DNA/RNA Shield offered superior DNA yield and storage conditions, FTA cards proved to be highly practical due to their ease of use, portability, and cost-effectiveness. CONCLUSIONS: The results underscore the critical role of sampling tool selection in shaping respiratory microbiome profiles obtained via UAV-based blow collection in dolphins. Both DNA/RNA Shield and FTA cards are valid options, with the final choice depending on specific logistical considerations, resource availability, and research priorities. This study provides a foundational step toward standardizing drone-assisted protocols for respiratory microbiome sampling in wild cetaceans. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13173833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147617205","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":"Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.","authors":"Alexandra Langlois, Mélissa Duplessis, Jennifer Ronholm, Antony T Vincent, Dominic Poulin-Laprade, Renée M Petri","doi":"10.1186/s42523-026-00554-9","DOIUrl":"10.1186/s42523-026-00554-9","url":null,"abstract":"<p><p>BACKGROUND: Dietary trace mineral (TM) concentrations for lactating cows often exceed national recommendations under commercial feeding practices. Excess TM supplementation may exert selection pressure on the gut microbiota, promoting metal resistance and potentially co-selecting for important antimicrobial resistance genes (ARGs). This study used a cross-over design to investigate the impact of overfeeding a commericially representative TM premix on the gut microbiome and resistome of lactating dairy cattle. Cows were fed either recommended or surplus TM levels for 31 days followed by sample collection from rumen papillae, whole rumen content, and feces. Targeted amplicon, shotgun metagenomic sequencing, and droplet digital PCR (ddPCR) were used to assess microbial community compositions and the associated resistome. RESULTS: While a surplus TM did not significantly affect the overall microbial diversity, specific taxa differed between the matrices and to a lesser extent by diet. Spirochaetota were more abundant in papillae of cows fed the recommended TM diet, whereas Bacillota were more prevalent in the rumen and feces from cows fed the surplus TM. Phosphorus had the greatest impact on prokaryotic taxa in rumen content. Cows fed surplus levels of TM showed increased abundances of Ruminococcus in their rumen, but decreased Campylobacter, Desulfovibrio, and Treponema adhered to their rumen papillae, Methanosphaera in their rumen and feces, as well as Treponema in their feces. Despite these changes, no significant differences in the presence of key ARGs or metal resistance genes were detected by metagenomics, and ddPCR showed no significant impact of TM supplementation on blaCTX−M, pcoA and zntA gene levels. CONCLUSIONS: Overfeeding TM in a commercial premix resulted in modest matrix specific shifts I the microbial composition without detectable enrichment of selected ARGs or metal resistance genes. These findings suggest short-term resilience of the rumen ecosystem to surplus TM supplementation. Additionally this work provides foundational knowledge to further guide mechanistic and long-term investigations. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13137713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517164","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":"Effects of Ligilactobacillus agilis W70 and dietary protein levels on feed efficiency, nitrogen metabolism, and rumen microbiota of lactating dairy cows.","authors":"Xiaowei Duan, Lu Ma, Calum Bridson, Zhijie Luo, Stafford Vigors, Dengpan Bu","doi":"10.1186/s42523-026-00548-7","DOIUrl":"10.1186/s42523-026-00548-7","url":null,"abstract":"<p><p>BACKGROUND: Efficient nitrogen utilization in dairy cows is essential for maximizing lactation performance while minimizing nitrogen losses. This experiment was conducted to evaluate the effects of the additive W70 and varying dietary protein levels on lactation performance, rumen fermentation, blood parameters, and nitrogen metabolism in lactating dairy cows. METHOD: 16 Holstein cows were utilised in a replicated 4 × 4 Latin square with 2 levels of crude protein (CP) (16 vs. 17%) and 2 levels of additive W70 (0 vs. 5 × 1010 cfu/g, 20 g/d). The cows were randomly assigned to 4 treatment groups: 16% CP no additive (16%C), 16% CP with additive W70 (16%A), 17% CP no additive (17%C), 17% CP with additive W70 (17%A). RESULTS: An interaction was observed between CP and additive W70. Specifically, additive W70 decreased dry matter intake (DMI) (P < 0.01), nitrogen (N) intake (P < 0.01), retained N content (P < 0.05), productive N content (P < 0.05), retained N proportion (P < 0.05), productive N proportion (P < 0.10), increased milk yield/DMI (P < 0.01) and nitrogen utilization efficiency (NUE) (P < 0.10) in the 16% CP diet, whereas no differences were observed in the 17% CP diet. The additive W70 increased fat corrected milk (FCM)/DMI (P < 0.10) and energy corrected milk (ECM)/DMI (P < 0.05), and reduced ruminal ammonia nitrogen (NH3-N) (P < 0.01), with no interaction with dietary CP level. The relative abundance of the genera Sphingomonas, Solibacillus, Desemzia, Peribacillus, Succinivibrionaceae UGG-001, Prevotella, and Succiniclasticum were higher in the rumen following the addition of additive W70 in both the 16% and 17% CP diets. Milk yield (P < 0.01), milk urea nitrogen (MUN) (P < 0.01), milk protein yield (P < 0.01), FCM yield (P < 0.05), ECM yield (P < 0.01), FCM/DMI (P < 0.10), and ECM/DMI (P < 0.05) were all increased in response to the 17% CP diet, whereas DMI and the content of milk fat, milk protein, and milk lactose were unaffected. The 17% CP diet increased the acetate to propionate ratio (P < 0.10) and NH3-N (P < 0.10), while reducing isovalerate (P < 0.10) and valerate (P < 0.10). The 17% CP diet increased blood urea nitrogen (BUN) (P < 0.01) and glucose (GLU) (P < 0.05). Cows fed a 17% CP diet had a higher milk N content (P < 0.05), fecal N content (P < 0.01), N loss content (P < 0.01), fecal N proportion (P < 0.01), urine N proportion (P < 0.10), and N loss proportion (P < 0.10) than those receiving 16% CP. The relative abundance of the genera Kandleria, Ligilactobacillus, and Escherichia-Shigella were lower in the 17% CP diet than in the 16% CP diet despite whether additive W70 was added or not. CONCLUSION: Supplementation with additive W70 improved feed conversion and NUE in a 16% CP diet, while the additive W70 modulated the rumen microbiota and reduced ruminal NH3-N. The 17% CP diet enhanced milk yield but increased N losses and altered rumen microbial composition. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517093","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 sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.","authors":"Guanyue Wei, Min Liu, Lusheng Huang, Congying Chen","doi":"10.1186/s42523-026-00551-y","DOIUrl":"10.1186/s42523-026-00551-y","url":null,"abstract":"<p><p>Fungi are crucial components of the pig gut microbiome, influencing host immunity and metabolism. However, the investigation about gut fungi via metagenomic sequencing remains challenging due to analytical complexity. Here, we characterized pig gut fungal profiles using 750 metagenomes collected from public repositories and our previous datasets based on a comprehensive collection of fungal reference genomes, and revealed dynamic compositional changes of pig gut fungi from birth to market (7d, 14d, 21d, 28d, 35d, 70d, and 140d). Weaning significantly shaped the gut fungal community, affecting key fungi like Lachancea kluyveri and Kazachstania slooffiae. Inter-kingdom interaction analysis revealed significant correlations between fungi and bacteria, such as between L. kluyveri and Lactobacillus amylovorus (r = -0.48) and between K. slooffiae and Lactobacillus johnsonii (r = 0.75). We identified 87 diarrhea-associated fungal species at the significance threshold of LDA > 2.0 in three experimental piglet cohorts. In antibiotic-free piglets, fungal species from Saccharomyces and Aspergillus, some of which have been considered as potential probiotics, were enriched in healthy individuals, whereas in antibiotic-treated groups, Saccharomyces spp. and K. slooffiae were higher in diarrheal piglets. Notably, K. slooffiae were negatively correlated with the pathogen M. circinelloides, suggesting a protective role during gut dysbiosis. This study provides a foundation for developing fungal-based interventions to improve pig health.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13137500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517153","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":"African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.","authors":"Laura E Peirson, Erin A McKenney, Jessica R Patterson, James C Beasley, Stéphanie Périquet-Pearce, Claudine Cloete, Madeline H Melton, Brennan PetersonWood, Rubén Portas, Ortwin Aschenborn, Diana J R Lafferty","doi":"10.1186/s42523-026-00553-w","DOIUrl":"10.1186/s42523-026-00553-w","url":null,"abstract":"<p><p>Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517120","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":"Temporal variability is an inherent feature of the healthy canine microbiome assessed by full-length 16S rRNA gene sequencing.","authors":"Connie A Rojas, Rebecca Smith, Rebecca Oliver, Guillaume Jospin, Isaac Corral, Holly H Ganz","doi":"10.1186/s42523-026-00546-9","DOIUrl":"10.1186/s42523-026-00546-9","url":null,"abstract":"<p><p>The canine gut microbiome plays a crucial role in host health, yet assessment of its temporal variability remains largely unexplored. Here, we used full-length 16S rRNA gene sequencing to evaluate long-term temporal variability of the fecal microbiomes of 35 healthy dogs sampled monthly over 1–2 years (median samples per dog: 10, range: 5–28 samples per dog, during the years 2020–2023). Analyses revealed that while individual-specific signatures in microbiome composition were observed (PERMANOVA R2 = 0.39, p = 0.001), fecal microbiomes exhibited substantial temporal fluctuations within individuals (9/35 dogs with microbiome dispersion ≥ 75%tile). Microbiome alpha-diversity was also not temporally stable (GAM F = 4.99, p = 0.025). The relative abundances of the 35 bacterial species varied considerably over time with Escherichia coli, and Enterococcus faecium especially dynamic (median CV 243–249%), and Peptacetobacter hiranonis and Collinsella intestinalis more stable (median CV 112–120%). Several taxa exhibited seasonal patterns, such as Fusobacterium spp. peaking in late summer and Peptacetobacter hiranonis declining in July. Collectively, these findings indicate that temporal fluctuations are an inherent feature of the healthy canine microbiome. Lastly, since our sampling captured occasional parasite or pathogen infections, we assessed whether transient C. perfringens, Giardia, or Campylobacter infections were correlated with microbiome alpha- and beta-diversity. We found no correlations with beta-diversity (p > 0.05), but a Giardia infection was associated with lower alpha-diversity (GLMM β= -0.37, p = 0.04).</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13069714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147505561","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":"Rubber seed cake supplementation alters meat quality, intestinal health, and gut microbiota in Hu sheep.","authors":"Huwei Zhao, Jinling Hua, Wenwen Lu, Xiaokang Lv, Chao Chen, Yan Liang","doi":"10.1186/s42523-026-00556-7","DOIUrl":"10.1186/s42523-026-00556-7","url":null,"abstract":"<p><p>This study aimed to investigate the effects of rubber seed cake (RSC) supplementation on slaughter performance, intestinal health, and gut microbiota in Hu sheep. Forty-eight Hu sheep (17.01 ± 0.57 kg; 3 months old) were randomly allocated to four dietary treatments: 0% (CON), 6% (R6), 12% (R12), and 18% (R18) RSC. Following an 80-day feeding trial, six sheep per group were randomly selected for slaughter. Samples of the longissimus dorsi, small intestine, and intestinal mucosa were collected for meat quality, morphological, and intestinal health analyses. Additionally, ileal contents were harvested and frozen for metagenomic sequencing. Dietary supplementation with RSC reduced the shear force of the longissimus dorsi muscle (P = 0.043) and lowered meat color L* (P = 0.044) and b* (P = 0.035) values in the R6 group compared to the CON group. Quadratic effects were observed for the villus height to crypt depth (VH/CD) ratio in the duodenum (P = 0.006), jejunum (P = 0.006), and ileum (P = 0.001) with increasing RSC supplementation, and the VH/CD ratio was significantly increased in the R6 and R12 groups (P < 0.05). Ileal pro-inflammatory cytokine concentrations, including tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6), decreased both linearly and quadratically with increasing RSC supplementation (P < 0.05). Quadratic effects (P < 0.05) were observed for the concentrations of mucin 2 (MUC2) and tight junction proteins such as zonula occludens-1 (ZO-1), occludin, and claudin in the jejunal and ileal mucosa with increasing RSC supplementation. Specifically, the concentrations of MUC2 and tight junction proteins in the jejunum, as well as MUC2 and ZO-1 in the ileum, were significantly higher in the R6 group (P < 0.05). RSC supplementation significantly altered the relative abundance of specific taxa, including Stenotrophomonas, Piromyces, Lichinomycetes, and Syntrophobacteria, as well as CAZyme gene sequences such as GH119, GT39, and GH13-8 (P < 0.05). In conclusion, these findings indicate that a 6% dietary supplementation of RSC is optimal in Hu sheep, as it improves meat quality and intestinal health by modulating the ileal microbiota composition and CAZyme abundance, thereby strengthening mucosal barrier function and alleviating inflammation.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13130676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147505543","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 lagging recovery: the delayed restoration of gut microbial diversity in Rhinolophus sinicus post-hibernation.","authors":"Yuting Wang, Wenqing Ling, Linxia Ouyang, Sheng Zhang, Huiqian Zhou, Tao Luo, Shurong Liu, Jiale Tang, Zixian Zhou, Liping Tang, Zhilin Wang, Fuwen Wei, Guangping Huang","doi":"10.1186/s42523-026-00552-x","DOIUrl":"10.1186/s42523-026-00552-x","url":null,"abstract":"<p><p>BACKGROUND: Hibernation enables animals to survive extreme environments, yet gut microbiome dynamics across the full hibernation cycle remain poorly understood, particularly in chiropterans with unique physiological traits. This study aimed to precisely characterize seasonal microbial succession in wild Rhinolophus sinicus using 16S rRNA gene sequencing across 6 physiological stages, with a focus on taxonomic and functional shifts linked to hibernation-associated fasting and post-hibernation activity. RESULTS: Alpha diversity followed a pronounced V-shaped trajectory, declining during hibernation and recovering only gradually—remaining suppressed in the early active stage and rebounding markedly by mid–late active stages. Beta diversity revealed a clear separation between hibernation and active phases, with physiological stage explaining 34.9% of community variation. At the phylum level, Pseudomonadota was the dominant taxon during hibernation, while Bacillota became the most abundant phylum in the active period. At the genus level, Yokenella was the core genus in the hibernation stage, and Lactococcus was the dominant genus in the active period. Functional predictions showed enrichment of lipid and amino acid metabolism during hibernation, supporting energy maintenance under fasting, while active-phase microbiota were oriented toward carbohydrate metabolism, matching increased energy demands. CONCLUSIONS: Our findings demonstrate that hibernation drives directional restructuring of the gut microbiota in R. sinicus, offering new insights into microecological strategies underlying bat survival under extreme conditions. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147492339","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":"Impact of 1,2-α-L-fucosidase on pig enteric methane production and growth performance.","authors":"D Georgaki, N Canibe, M E van der Heide, L Foldager, C H Poulsen, R Mejldal, D Velayudhan, J V Nørgaard, O Højberg","doi":"10.1186/s42523-025-00487-9","DOIUrl":"10.1186/s42523-025-00487-9","url":null,"abstract":"<p><p>BACKGROUND: Reducing the environmental and climatic impact while maintaining high growth performance is an urgent challenge in pig production. Limiting methane emissions from pigs through targeted strategies may help mitigate global methane emissions. Addition of a Bifidobacterium bifidum 1,2-α-L-fucosidase exoglycosidase to pig feed to cleave and release fucose from intestinal mucins into the gut lumen has previously been shown to promote specific beneficial gut bacteria and reduce methanogens. This study aimed to investigate the supplementation of the fucosidase to pig feed as a tool to reduce enteric methane production in pigs while improving growth performance. Four experimental groups were included: a control group (CON) fed Danish standard diets and three groups (Fuc2, Fuc7, Fuc16) fed the same standard diets amended with 100 mg fucosidase per kg feed for 2, 7, or 16 weeks, respectively, starting at weaning. The remaining period (up to 14 weeks), they received the control diets without fucosidase addition. A total of 240 crossbred piglets (weaning age 22 days) from 80 sows were included, and performance, counts of methanogens and methane emission were measured. RESULTS: When comparing all three groups fed with fucosidase together against the CON, a higher ADFI (p = 0.05) was observed in the fucosidase groups during the first two weeks. On day 106, the in vivo methane emission was lower in all three fucosidase groups compared to the CON (p < 0.05) when calculated per kg dry matter intake, and a tendency to reduce methane emission was observed when corrected for body weight (p ≤ 0.10). The in vitro methane production and the number of methanogens were not significantly different in the CON and the fucosidase groups (p >0.05). CONCLUSION: The results suggest that in-feed fucosidase may lead to lower methane emission at later pig production stages, despite neither affecting total methanogenic archaea numbers in the colon nor significantly impacting pig growth performance. </p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13001275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488794","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}