Animal Microbiome动物微生物组
Animal Microbiome(英文缩写 ANIM MICROBIOME),ISSN 2524-4671,eISSN 2524-4671,中文译名:动物微生物组 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-10-01 至 2026-09-30，按本站收录文献的发表日期统计。
期刊介绍
Animal Microbiome 最新收录文献
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2. From onset to healing: temporal dynamics of microbial communities pinpoint Midichloria-like organism's key role in the development of the fish skin disease red mark syndrome.
PMID:日期:2026-08-19Red mark syndrome (RMS) is an infectious disease affecting rainbow trout (Oncorhynchus mykiss), especially at market size, forcing farmers to downgrade the product with heavy economic repercussions. The causative agent of RMS has not been established according to Koch's postulates, since possible candidates have not been isolated and propagated in vitro. While the 16S rRNA gene of a Midichloria-like organism (MLO) is consistently detected in active skin lesions, the role of other bacteria in the disease has not been excluded. In this work, we provide a temporal perspective to elucidate the relationships between the bacteriome in rainbow trout skin and water, during the development and resolution of clinical disease in naive fish infected by cohabitation with RMS-affected fish in the same tank. We quantified the MLO by qPCR in skin and, for the first time, in water using environmental DNA, showing that its quantity in both sample types corresponds with disease progression. Using 16S rRNA gene profiling, we provide further evidence that the MLO is likely the primary pathogen triggering RMS, as it was the only significantly enriched taxon in active lesions. Furthermore, the skin microbiome of affected fish reverted to a control-like state during healing. RMS also caused changes in the overall skin microbiome at peak pathology: the relative abundance of "Ca. Branchiomonas" and an unclassified gammaproteobacterium increased in apparently healthy skin areas of RMS-affected fish while remaining low in controls, suggesting they may be opportunistic bacteria implicated in skin dysbiosis. Our findings on the temporal dynamics of the skin microbiome during disease progression and recovery strengthen the evidence that Midichloria-like organism is the primary pathogen of RMS. The observed shifts in other bacterial taxa suggest possible secondary roles in disease-associated skin dysbiosis. Finally, detection of MLO in environmental DNA from water provides new insights into RMS transmission and potential monitoring strategies.
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3. Differential skin-bacteriome-mediated defense against chytridiomycosis in two neotropical frog species.
PMID:日期:2026-08-04Symbiotic microbial communities have been implicated in host resistance to pathogens, but their effects are rarely demonstrated experimentally in wildlife. This study tested how skin-associated bacterial communities (i.e., bacteriomes) influence infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd) in two tropical frog species, Haddadus binotatus and Ischnocnema henselii, which differ in susceptibility to Bd. Using a 2x2 factorial experimental design, frogs of both species were assigned to treatments crossing Bd exposure and antibiotic-mediated bacteriome suppression. In parallel, we cultured 786 bacterial isolates from frog skin and assayed their ability to inhibit Bd in vitro, generating a functional database of Bd-inhibitory symbionts. Haddadus binotatus with an unsuppressed skin bacteriome and exposed to Bd showed no reduction in survival relative to Bd-unexposed controls, consistent with the lack of Bd infection previously observed in wild populations. In contrast, bacteriome suppression increased mortality and infection intensity under Bd exposure. Bd infection intensity in H. binotatus also decreased with the proportion of Bd-inhibitory sequence reads in the bacteriome, and a significant interaction between antibiotic treatment and Bd exposure affecting survival was detected, consistent with bacteriome-mediated protection in this species. In contrast, I. henselii experienced lower survival under Bd exposure in general. Species-specific log-rank tests revealed that bacteriome suppression significantly increased mortality under Bd exposure in H. binotatus but not in I. henselii, where survival was reduced under Bd exposure regardless of bacteriome state, suggesting fundamentally different defense strategies between species. Functional attributes of microbial communities, rather than diversity alone, appear to be key to disease outcomes. This work advances understanding of host-microbe-pathogen interactions and highlights microbiome function as a critical axis of wildlife disease defense.
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4. Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.
PMID:日期:2026-07-20Post-weaning estrus return is critical for sow reproductive efficiency. The gut microbiota is associated with post-weaning estrus of sows, potentially through effects on nutrient utilization and metabolic regulation. However, current microbial signatures associated with estrus return remain poorly resolved at the strain-level. Here, we explored the relationship between the gut microbiome and post-weaning estrus in sows using metagenomics and metabolomics profiling of 85 fecal samples. From 2,704 non-redundant metagenome-assembled genomes (MAGs), 608 estrus-associated MAGs were identified by LEfSe analysis. Among these, 48 high-quality MAGs were selected for co-abundance network analysis, which revealed two competing microbial functional guilds. Guild 1 was significantly enriched in the normal group, harboring more β-glucosidase and folate biosynthesis genes, but fewer antibiotic resistance genes and virulence factors than Guild 2. A random forest model based on these 48 MAGs demonstrated excellent performance in distinguishing between the normal and non-return sows (AUROC = 0.946) and was validated in an independent dataset (n = 29, AUROC = 0.818). Additionally, the guild-level microbiome index (GMI) derived from abundance differences between the two guilds also showed good discriminatory power (AUROC = 0.799). Integrated multi-omics analysis revealed alterations in fecal bile acid metabolism in non-return sows, characterized by a significantly increased ratio of secondary to primary bile acids and the accumulation of specific secondary bile acids. Notably, the enrichment of the Clostridia strain SFHK01 sp016296675, a member of Guild 2, and its encoded 12α-HSDH gene was positively associated with specific secondary bile acids, suggesting that this specific strain is involved in the distinct metabolic alterations observed in non-return sows. These findings provide the genome-resolved and guild-based insights into the gut microbial signatures associated with post-weaning estrus return, offering a basis for potential microbiota-targeted interventions to improve sow reproductive performance.
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5. The faecal microbiota and its influence on fur seal (Arctocephalus sp.) physiology.
PMID:日期:2026-07-15The gastrointestinal microbiota is a key determinant of vertebrate physiology, metabolism, and adaptation, forming a dynamic holobiont system that supports host health and resilience. However, while the gut microbiota of several fur seal species has been described, most studies have focused primarily on taxonomic composition, leaving a major gap in understanding how microbial communities influence host physiology in marine mammals. This study provides the first comprehensive comparison of the faecal microbiota and blood metabolomic profiles of Australian (Arctocephalus pusillus doriferus) and New Zealand fur seals (A. forsteri) across age classes (adult vs. pup), integrating 16S rRNA gene sequencing, and untargeted metabolomics and untargeted lipidomics to examine host-microbe interactions. Adult fur seals exhibited a conserved microbial structure dominated by the phyla Bacillota, Fusobacteriota, and Bacteroidota, while pups displayed lower microbial diversity and higher relative abundances of Actinobacteriota and Campylobacterota, alongside enrichment of metabolites involved in DNA synthesis (2-deoxy-D-ribose, 2-deoxycytidine, and 2-deoxyuridine) and lipid metabolism. Correlations between bacterial taxa and metabolites implicated in growth, fat deposition, and hair development suggest that it is possible that early-life microbial communities may play an important role in supporting rapid development and thermoregulation. Despite logistical constraints inherent to field-based sampling of wild marine mammals, our findings demonstrate consistent microbial patterns within the Arctocephalus genus and clear age-related differences in blood metabolic profiles. Together, these results enhance understanding of the complex interplay between host development, diet, and microbial ecology in fur seals, and establish a foundation for future research into the functional significance of microbiota in marine mammal health and adaptation. Not applicable.
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6. Gut microbiome alterations in canine idiopathic epilepsy: a pairwise case-control study.
PMID:日期:2026-07-11Idiopathic 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. 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. Our findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.
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7. Host genetic architecture and gut microbiota cooperatively regulate early growth in goats.
PMID:日期:2026-07-11Early 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.
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8. Enhancement of postpartum cow health and calf performance through maternal‒offspring interactions: effects on the immunity, antioxidants, and bacterial flora induced by Guiqi Yimu Powder.
PMID:日期:2026-07-11This study evaluated the effects of dietary supplementation with Guiqi Yimu powder (GYP) on the postpartum health of beef cows and the growth performance of their calves, with an emphasis on immune function, antioxidant capacity, and the bacterial flora. Twenty-two postpartum cows were randomly assigned on the day of calving to either the control group (CON) or the GYP group. The control group was fed a basal diet, and the GYP group was fed the basal diet supplemented with 300 g/day of GYP starting on the day of calving. After 7 days of supplementation, serum samples from the cows and calves were collected, and antioxidant indices [superoxide dismutase (SOD), malondialdehyde (MDA), and glutathione (GSH)] as well as immunoglobulins (IgA, IgM, and IgG) were analyzed. Fecal samples from cows were assessed for gut microbiota diversity and short-chain fatty acids (SCFAs) content; milk samples were analyzed for microbial composition and immunoglobulins. GYP was administered to the cows, and calves were exposed to GYP solely through suckling. Compared with those in the CON group, calves in the GYP group presented significantly greater weaning weights and average daily gains. The calf survival rate tended to increase, whereas the incidence of diarrhea tended to decrease in the GYP group. Among cows in the GYP group, both postpartum conception rates and estrus rates tended to increase; conversely, return-to-estrus rates and semen doses per conception tended to decrease. Serum levels of superoxide dismutase (SOD) and glutathione (GSH) were elevated, whereas malondialdehyde (MDA) levels were reduced (p < 0.05) in GYP cows. Moreover, supplementation with GYP significantly increased the serum IgG levels (p < 0.05), the milk IgM, IgA, and IgG levels (p < 0.05), and the serum IgG levels in calves (p < 0.05). Analysis of the gut microbiota of these cows revealed that, compared with CON, GYP improved the gut bacterial diversity and increased the relative abundances of UCG-002, Faecalibacterium, norank_f_F082, and Oscillibacter. Furthermore, examination of the milk microbiota revealed that GYP increased the relative abundances of Acetobacter, Lactobacillus, and Prevotellaceae_UCG-003. In addition, compared with CON, GYP significantly increased the contents of short-chain fatty acids (SCFAs), including acetic acid, propionic acid, isobutyric acid, n-butyric acid, isovaleric acid, and n-valeric acid, in the feces of postpartum cows (p < 0.05). GYP improves postpartum cow health and calf performance via (1) direct antioxidant and immunomodulatory effects, (2) gut microbiota remodeling and SCFAs promotion, and (3) vertical transfer of immunoglobulins and probiotics through milk. These findings support the use of GYP as a functional feed additive for optimizing postpartum management in beef cattle.
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9. Using sequence-derived microbiome information from bulk tank milk samples to assess the influence of post-milking teat disinfection in New Zealand dairy herds.
PMID:日期:2026-07-06Post-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. 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. 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. 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.
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10. Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.
PMID:日期:2026-07-04The 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. 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. 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.