Animal microbiome最新文献

{"title":"Host genetic architecture and gut microbiota cooperatively regulate early growth in goats.","authors":"Hui-Long Mou, Zi-Xuan Wang, Ming-Ding Zhang, Yao-Long Liu, Tao Ren, Peng-Cheng Ruan, Yan-Guo Han, Yan Zeng, Hao-Yuan Zhang, Jia-Guo Lu, Yang Zhang, Cheng-Li Liu, Yong-Fu Huang, Yong-Ju Zhao, Zhong-Quan Zhao, Xiao Pan, Li-Ping Zhou, Simone Ceccobelli, Guang-Xin E","doi":"10.1186/s42523-026-00597-y","DOIUrl":"10.1186/s42523-026-00597-y","url":null,"abstract":"<p><p>Early postnatal growth is a critical determinant of meat production efficiency and long-term genetic improvement in goats; however, the molecular mechanisms underlying individual variation in growth performance remain poorly understood. In this study, a total of 123 Hechuan white goats were included. First, a genome-wide association study (GWAS) for average daily gain (ADG) was performed using all 123 individuals. Subsequently, based on the coefficient of variation of ADG (CV = 65.6%), an extreme phenotype sampling (EPS) strategy was applied to select 39 individuals with extreme growth phenotypes for subsequent metabolomic, microbiome, and integrated mGWAS analyses.The results showed that ADG approximately followed a normal distribution across the 123 goats. GWAS identified 22 loci significantly associated with ADG, mapping to genes including DLK1, NCAPG2, LCORL, CNTNAP2, and SLC8A1, which are involved in pathways related to skeletal muscle development, cell cycle regulation, ion transport, and immune function. Metabolomic profiling detected 1,589 putative metabolites, revealing differential enrichment of lipid, amino acid, and bile acid metabolic pathways between fast- and slow-growing goats. Gut microbiome analysis demonstrated that Christensenellaceae_R-7_group and Monoglobus were significantly enriched in fast-growing individuals, whereas Desulfovibrio was more abundant in slow-growing goats.Integrated mGWAS analysis further revealed extensive effects of host genetic variation on gut microbiota and fecal metabolites. Specifically, 11 bacterial genera were significantly associated with host genomic variants, among which Desulfovibrio exhibited the highest number of associated loci. Integration of multiple variant types consistently linked Desulfovibrio, Eubacterium_hallii_group, and Candidatus_Saccharimonas with genes such as ARHGAP24 and IGF2BP2. In addition, 14 metabolites were significantly associated with host genetic variants, with Lysopc(14:1(9Z)/0:0) and glycocholic acid showing the strongest associations. Notably, the peak signal for Lysopc was located within HMGA2.Collectively, these findings define a coordinated host genome-gut microbiota-metabolite network underlying early growth variation in goats and provide a mechanistic foundation for precision breeding and targeted nutritional strategies in goat production systems.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13483726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148426803","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":"Gut microbiome alterations in canine idiopathic epilepsy: a pairwise case-control study.","authors":"Yixuan Yang, Julie Nettifee, M Andrea Azcarate-Peril, Karen R Muñana, Benjamin Callahan","doi":"10.1186/s42523-026-00594-1","DOIUrl":"10.1186/s42523-026-00594-1","url":null,"abstract":"<p><strong>Background: </strong>Idiopathic epilepsy (IE) is the most common chronic nervous system disorder of dogs, and its cause is poorly understood. Emerging evidence suggests that microbiome alterations can occur with IE via the microbiota-gut-brain axis. Therefore, we analyzed the fecal microbiomes of 98 dogs (49 IE, 49 control) in a pairwise case-control observational study using 16S rRNA gene sequencing.</p><p><strong>Results: </strong>Although the microbial community was mostly similar between groups, IE was associated with a modest but significant shift in weighted UniFrac distance (p = 0.042). We used six differential abundance (DA) methods to identify differentially abundant amplicon sequencing variants (ASVs) between IE and control groups. Notably, one Collinsella ASV was found to be significantly more abundant in IE dogs by all six methods. The gut microbial compositions varied drastically across households (accounting for about 69% of the total variation), but did not have significant differences between sex, age, or breed. Phenobarbital administration in IE dogs had a significant effect on seizure control, and was not associated with changes in the microbiome.</p><p><strong>Conclusion: </strong>Our findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148426864","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":"Using sequence-derived microbiome information from bulk tank milk samples to assess the influence of post-milking teat disinfection in New Zealand dairy herds.","authors":"Hong Ling, John Williamson, Sean Gatenby, Seren Pruden, Catherine Neeley, Chad Harland, Andrew Wallace, Christine Couldrey","doi":"10.1186/s42523-026-00557-6","DOIUrl":"10.1186/s42523-026-00557-6","url":null,"abstract":"<p><strong>Background: </strong>Post-milking teat spraying plays an important role in the control of mastitis within New Zealand dairy herds. We examined the sample-level associations between post-milking teat spraying and bacterial levels in bulk tank milk (BTM) microbiomes, using shotgun DNA sequencing data within a non-experimental framework.</p><p><strong>Methods: </strong>A total of 1325 BTM samples were collected from 219 pasture-based commercial herds voluntarily enrolled across New Zealand, over the 2021 and 2022 dairy seasons. Bacterial levels of Staphylococcus and Streptococcus species and Corynebacterium bovis were quantified (cells/ml) and compared along with two post-milking teat spray actives (iodine and chlorhexidine) and two application methods (manual and automatic). Analyses were performed at the BTM sample level using log-transformed abundances and the Wilcoxon rank-sum test; Benjamini-Hochberg FDR was applied per individual species. A univariate PERMANOVA (Euclidean distance, 9,999 permutations) was used as a permutation-based robustness check.</p><p><strong>Results: </strong>These data show that post-milking teat spraying was associated with lower BTM levels of Corynebacterium bovis and lower levels across Staphylococcus species compared with samples without teat disinfection, across both seasons. At the teat spray active level, Chlorhexidine-based teat disinfectant was associated with lower Corynebacterium bovis, Staphylococcus aureus, and Streptococcus dysgalactiae than the iodine-based teat disinfectant, while no consistent differences were observed for Streptococcus uberis, Streptococcus agalactiae, Streptococcus chromogenes, or Streptococcus epidermidis. For the teat spray application method, patterns varied by species. Findings were consistent across two seasons and directionally consistent between Wilcoxon and PERMANOVA.</p><p><strong>Conclusions: </strong>We demonstrate that sequencing-based BTM microbiome profiling can reveal sample-level associations between teat spray practices and mastitis-associated bacteria. While causal inference is constrained by the observational design and uncertain sources contribution within BTM, these findings suggest that BTM sequencing may complement herd-level monitoring of teat spray performance. Further controlled studies incorporating key covariates are warranted.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148392652","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":"Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.","authors":"Gladys Maria Pangga, Anne Richmond, Callie Hughes, Androniki Psifidi, Dong Xia, Damer Blake, Umer Zeeshan Ijaz, Ozan Gundogdu","doi":"10.1186/s42523-026-00596-z","DOIUrl":"10.1186/s42523-026-00596-z","url":null,"abstract":"<p><strong>Background: </strong>The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.</p><p><strong>Results: </strong>We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.</p><p><strong>Conclusion: </strong>Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148388410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing sheep rumen health with Przewalskia tangutica: boosting fermentation and microbial diversity in saline-alkali sown pastures.","authors":"Xiaoyun Zhang, Kaili Xie, Yuhong Jiang, Bifang Xu, Wanhe Zhu, Fujiang Hou","doi":"10.1186/s42523-026-00592-3","DOIUrl":"10.1186/s42523-026-00592-3","url":null,"abstract":"<p><strong>Background: </strong>Livestock grazing on saline-alkali pastures frequently encounter nutritional challenges due to inadequate forage quality and imbalanced rumen function. Phytogenic feed additives, which are abundant in bioactive compounds such as tropane alkaloids and flavonoids, have demonstrated potential in enhancing rumen fermentation and improving animal performance. Przewalskia tangutica, a desert plant rich in these compounds, remains largely unexplored concerning its effects on microbiota and metabolism in sheep under saline-alkali conditions. This study aims to evaluate the impact of graded supplementation of Przewalskia tangutica on rumen fermentation, microbial dynamics, digestive enzyme activity, and growth performance in sheep grazing on degraded saline-alkali pastures.</p><p><strong>Results: </strong>Supplementation with Przewalskia tangutica significantly increased the average daily gain (ADG, P < 0.001) and reduced the feed conversion ratio (FCR, P < 0.001). The high-dose group (HP) exhibited the highest ADG at 139.94 g/d. Additionally, the concentrations of total volatile fatty acids (VFAs), including acetate, isobutyrate, and butyrate, were significantly elevated (P < 0.001), peaking at 1.46 mmol/L in the HP group. Furthermore, the activities of amylases, lipase, cellulase, and protease increased significantly (P < 0.05). While the bacterial alpha diversity remained unchanged, beta diversity analysis revealed structural shifts characterized by increased abundances of Verrucomicrobiota, Proteobacteria, and Fibrobacterota (P < 0.05). Fungal diversity also increased under the HP treatment (P < 0.05), whereas a reduction in Cladosporium abundance was correlated with enhanced fiber degradation. Moreover, microbial co-occurrence networks demonstrated more balanced interactions in the treated groups, with significant correlations among taxa, enzymes, and VFAs.</p><p><strong>Conclusions: </strong>Przewalskia tangutica improves rumen fermentation and sheep performance in saline-alkali environments through targeted modulation of microbial communities and enzymatic activity, particularly at the high dose, significantly improved sheep growth performance by increasing average daily gain and reducing the feed conversion ratio, suggesting a sustainable strategy for livestock production in challenging ecosystems.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148383379","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 placebo-controlled study of the effects of Saccharomyces cerevisiae var. boulardii CNCM I-1079 probiotic on faecal quality, microbiota and immunity in weaned kittens.","authors":"Virginie Gaillard, Ana Rodiles, Amélie Mugnier, Jérémy Laxalde, Diana Knight, Willy Joly, Franck Péron","doi":"10.1186/s42523-026-00574-5","DOIUrl":"10.1186/s42523-026-00574-5","url":null,"abstract":"<p><strong>Background: </strong>Acute diarrhoea or soft stools can occur in kittens after environmental challenges. The effects of a probiotic on gastrointestinal and immune biomarkers in kittens exposed to three study events were investigated. Healthy weaned 10-week-old kittens were fed a daily dietary supplement of Saccharomyces cerevisiae var. boulardii CNCM I-1079 (SB-1079) or placebo for 7 weeks (20 kittens/group). The study events were a routine booster vaccination (Week 3), a change in housing (Week 5), and a diet transition (Week 6). Outcomes included faecal scores and percentage dry matter (DM%), total serum IgG, faecal IgA, and faecal microbiota. Statistical analyses included Linear Mixed Models and Generalized Linear Mixed Models with group, time and group × time interaction as fixed effects; longitudinal Kruskal-Wallis test corrected for false discovery rate was used for microbiota outcomes.</p><p><strong>Results: </strong>Faecal scores were optimal throughout the whole study for 12/20 supplemented kittens vs 8/20 control kittens. Overall, group and group × time did not affect faecal quality or moisture, but in Week 5 (housing change) supplemented kittens had firmer stools (P=0.007) and lower faecal DM% (P=0.032) than placebo kittens. Total serum IgG concentration was affected by group (P=0.028), time (P<0.001) and group × time (P=0.001), and was higher in the probiotic vs placebo group (P<0.039) at Week 7, having increased 250% vs 62% from Week 0. Faecal IgA concentration tended to be higher in the probiotic vs placebo group after booster vaccination (P=0.068). Microbiota composition (weighted Unifrac beta diversity) differed between groups overall (P=0.025), at Week 4 (P=0.017), and in the differences between Week 6 and 7 (P=0.008). In supplemented kittens, relative abundances of Veillonellaceae and Actinobacteria remained stable over the first weeks, and abundance of potential pathogens in the Desulfovibrionaceae family decreased. A decrease in Shannon alpha diversity of faecal microbiota post diet transition was significant in supplemented kittens only (P = 0.008) due to a rapid increase in abundance of the Helicobacteraceae family.</p><p><strong>Conclusions: </strong>The impacts of SB-1079 on biomarkers of gastrointestinal and immunological health suggest its potential to promote resilience of these systems in young kittens experiencing physiological challenges like new environments and diet transitions.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148354856","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":"Bat skin microbiome and the association of ecoregion and bat species that impacted isolation of members with bioactivity against Pseudogymnoascus destructans.","authors":"Paris S Salazar-Hamm, María-José Romero-Jiménez, Nicole A Caimi, Kevin R Amses, Jennifer J Marshall Hathaway, Debbie C Buecher, Ernest W Valdez, Lindsay K Caesar, Andrea Porras-Alfaro, Diana E Northup","doi":"10.1186/s42523-026-00591-4","DOIUrl":"10.1186/s42523-026-00591-4","url":null,"abstract":"<p><strong>Background: </strong>Microbiome constituents can serve as a primary defense against vertebrate pathogens. This may be crucial to the protection of North American bats who have been devastated over the last two decades by the fungal pathogen, Pseudogymnoascus destructans (Pd), which causes white-nose syndrome (WNS). The objectives of this study were to isolate members of the external microbiome of bats post-hibernation in Arizona and New Mexico before the arrival of WNS, to identify those bacteria with bioactivity against Pd, and to determine the variables associated with antifungal strains.</p><p><strong>Results: </strong>In this study we isolated 2,936 bacteria from the fur and skin of 314 bats across 12 bat species at 6 sites across New Mexico and Arizona from 2013 to 2016. Selective media were used to promote the isolation of Actinomycetota (2,594 isolates, 88.4%), particularly species of Streptomyces (2,045 isolates, 69.7%) known for their bioactivity. Although Actinomycetota isolation was targeted, this collection includes representatives from Pseudomonadota (Alpha-, Beta-, and Gamma-Proteobacteria), Bacillota, and Bacteroidota phyla also common to the bat microbiome. A bi-layer challenge assay performed on 1,089 isolates identified 61 bat-associated bacteria with activity against Pd. These results were pooled with efforts by Hamm et al. [1] to determine what metrics impacted isolation of bacteria that inhibit Pd (n = 97). Ecoregion and bat species were determinant variables associated with Pd inhibition.</p><p><strong>Conclusions: </strong>This study represents, to our best knowledge, the largest culture collection of bacteria from bats' skin and fur before the impact of WNS. We identified bacteria with antifungal activity against Pd and found significant associations of bioactive strains with bat species and ecoregions.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148334889","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 bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity.","authors":"Samat Amat, Devin B Holman, Sarah M Luecke, Katherine E Gzyl, Muhammad Anas, Gerald Stokka","doi":"10.1186/s42523-026-00587-0","DOIUrl":"10.1186/s42523-026-00587-0","url":null,"abstract":"<p><strong>Background: </strong>Despite widespread use of antimicrobials and vaccines, the incidence of infectious bovine keratoconjunctivitis (IBK), or pinkeye, continues to increase in North American beef cow-calf operations. Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit Moraxella spp. in vitro. Ocular swabs (n = 143) were collected from IBK-affected (n = 102) and healthy cattle (n = 41) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including Moraxella bovoculi, Moraxella bovis, and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of Moraxella spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.</p><p><strong>Results: </strong>The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to Bacillus (25.9%), Streptococcus (11.1%), Staphylococcus (10.1%), and Moraxella (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R² = 0.05; P = 0.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included Cutibacterium acnes, Mannheimia pernigra, Mesomycoplasma bovoculi, Moraxella bovis, and Moraxella bovoculi. Eight bacterial species, including Bifidobacterium globosum and Bacillus licheniformis, were more abundant in healthy cattle, while Arthrobacter luteus was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as Mesomycoplasma bovoculi. Moraxella spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited Moraxella, with Weizmannia coagulans, Lentilactobacillus buchneri, and Paenibacillus polymyxa showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.</p><p><strong>Conclusion: </strong>The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":" ","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13330061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148260720","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":"Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.","authors":"Raha Abedini, Ghasem Hosseini Salekdeh, Maryam Hashemi","doi":"10.1186/s42523-026-00547-8","DOIUrl":"10.1186/s42523-026-00547-8","url":null,"abstract":"<p><p>While metagenomics has transformed our view of microbial ecosystems, culture-based methods remain indispensable for accessing microbial functionality and biotechnological potential. In this study, we applied a culturomics strategy to explore the diversity, abundance, and distribution of culturable aerobic and facultative anaerobic bacteria along the gastrointestinal tract of dromedary camels (Camelus dromedarius) grazing on pristine desert flora. Using six culture media-including modified YCFA formulations-we isolated 97 bacterial species across 42 genera, 31 families, and four phyla: Firmicutes, Proteobacteria, Actinomycetota, and Bacteroidota. Strikingly, 88.6% of this diversity was recovered using YCFA-based media, and four candidate novel species were identified. The rumen harbored the most diverse and Gram-positive-dominated community, whereas the small intestine was enriched with Gram-negative taxa, many with pathogenic potential. These findings highlight the camel's unique physiological adaptation to extreme arid environments, characterized by efficient fiber degradation under nutrient- and water-limited conditions and the presence of stress-tolerant gut microbes capable of resisting acidic and osmotic challenges. Overall, this study establishes a foundational understanding of the camel gut microbiota and underscores the complementary power of culture-dependent methods to metagenomics. Future integration with anaerobic culturing and multi-omics analyses will further unveil the ecological and biotechnological potential of desert-adapted microbial life.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13262223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240639","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":"Optimization of solid-state fermentation process of diets and its effects on growth performance and intestinal function in growing pigs.","authors":"Mengting Ji, Jingchao Liu, Qinglin Wang, Tianye Gong, Jiaqi Zhang, Meng Li, Xiaohong Guo, Yang Yang, Bugao Li","doi":"10.1186/s42523-026-00540-1","DOIUrl":"10.1186/s42523-026-00540-1","url":null,"abstract":"<p><strong>Background: </strong>Biological fermentation can improve animal growth performance and meat quality by optimizing feed nutritional properties. However, the complex fermentation parameters require further systematic optimization. This study aimed to establish and optimize a solid-state fermentation (SSF) process, evaluate changes in the feed microbial community and flavor metabolites, and investigate their effects on muscle development and intestinal barrier function in growing pigs. Here, we developed a synergistic SSF strategy for pig feed using combinations of 4 probiotics and 11 enzymatic preparations, 16S rDNA-seq and flavoromics-seq were employed to investigate the dynamic changes in microbial communities and flavor compounds post-fermentation. Subsequently, 32 Duroc × Jinfen White pigs were fed diets containing 10% SSF to assess growth performance, intestinal health and muscle development.</p><p><strong>Results: </strong>The optimal fermentation ratio of Bacillus subtilis, Lactobacillus plantarum, Saccharomyces cerevisiae and Aspergillus niger is 1:2:3:3, with a temperature of 36 °C, an inoculation rate of 93%, a moisture content of 72%, and a time of 4.1 days. SSF significantly enhanced the nutritional value of feed by increasing the ash, organic matter (OM), crude protein (CP), and ether extract (EE) content, while simultaneously reducing the concentration of anti-nutritional factors. Sequencing identified 17 differential microbes and 116 flavor compounds, with the relative abundance of Lactobacillus and the Firmicutes significantly increased, 2-octenal and vanillin imparting sweet, fruity, and grassy notes to the feed. Meanwhile, RNA-seq revealed 320 DEGs in muscle tissue following fermented feed supplementation, which are mainly enriched in pathways related to cytochrome P450 drug metabolism and arginine biosynthesis. Additionally, H&E staining results indicated that fermentation significantly increased the villus height, crypt depth, and villus-to-crypt ratio in the small intestine of growing pigs, and the levels of tight junction proteins Claudin-1 and ZO-1 in the jejunum were significantly higher than those in the ctrl group. Subsequent correlation analysis indicated that Firmicutes may influence pig growth performance and IL-6, TNF-α levels by affecting their metabolites.</p><p><strong>Conclusion: </strong>Our findings establish and optimize an SSF process that markedly elevates feed nutritional value, enriches beneficial microbes, and fosters the production of unique flavor metabolites. When fed to growing pigs, it effectively enhances growth performance and antioxidant capacity while improving small-intestinal morphology and barrier function.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"8 1","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13262001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240683","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}