Animal microbiome最新文献

Background: Recent advancements in sequencing technologies and associated bioinformatic tools have eased the analyses of the factors influencing variability in host-associated microbial communities in the gastrointestinal tract (GIT). Although extensive research has focused on fecal microbiota, the small intestine represents a critical, yet less explored, site for understanding the interplay between microbiota, diet, and host health. Study 1 employed CapSa, a non-invasive sampling capsule, to collect microbiota at five distinct administration time points. The aim was to use amplicon sequencing to investigate changes in the small intestine microbiome composition throughout the grower-finisher pig lifespan. Study 2 examined the long-term impact of enterotoxigenic Escherichia coli (ETEC) F4 infections, which cause post-weaning diarrhea (PWD), on small intestine microbiota dynamics. The study provides insights into the long-term responses of microbiota after a short pathological challenge.

Results: In both studies, microbiota analysis of the small intestinal content revealed that Firmicutes predominated across all samples, and at weaning, Lactobacillaceae and Lactobacillus were the most abundant. In Study 1, following CapSa administration, Clostridium sensu stricto 1 and Terrisporobacter increased with age/body weight and at slaughter, Streptococcaceae dominated. Significant differences in microbial composition were observed based on sample type and diet, indicating dynamic shifts throughout the pigs' lives under normal conditions. In Study 2, the abundance of Lactobacillaceae was consistently lower in ETEC-infected pigs. At slaughter, only minimal differences in microbial composition emerged based on the early post-weaning infection status in specific small intestine segments, indicating dynamic infection-induced shifts in the gut microbiota composition. The CapSa sampling method was successful, with a retrieval rate higher than 70% in both studies.

Conclusions: This study monitored porcine intestinal microbiota dynamics using an ingestible capsule. In healthy pigs, microbial composition changes occurred from post-weaning to slaughter. In contrast, ETEC infection only minimally altered communities, though small differences at slaughter suggest lasting impacts.

We investigated the early-life interplay between microbiota, host, and environment by longitudinally monitoring nasal and gut microbiota in 30 veal calves over their first five months of life. Microbial composition and stability were highly compartmentalized. Fecal communities showed increasing biomass, diversity, and homogeneity with age. Conversely, nasal microbiota remained less diverse and highly variable between individuals, likely influenced by mucociliary clearance and transient colonization. Environmental factors, diet, and clinical indicators were associated with both microbial communities, alongside distinct cytokine profiles. As calves matured, microbiota dynamics and composition covaried across body sites, reflecting systemic immune development and environmental adaptations. This study provides a comprehensive, multi-layered characterization of microbial dynamics, identifying the first month of life as a critical window for interventions targeting the fecal microbiota. The nasal microbiota, by contrast, remains flexible and amenable to modulation throughout the production cycle.

Background: Early life represents an unparalleled window in the life of the pig in which the gut microbiota interacts with its host's naïve immune system. Yet, modern swine production often favours conditions that promote production efficiency rather than enriched microbiota development, the long-term consequences of which remain poorly understood. This study sought to analyse the long-term impacts of early-life rearing conditions on the gut microbiota until day 90, and in turn, its physiological and immunological consequences. We established two rearing conditions from farrowing until day 90: enriched, microbiota-enhancing husbandry characterised by weaning at 6 weeks and the provision of litter material throughout; and restricted, microbiota-depleting husbandry comprising weaning at 3 weeks and antibiotic administration from days 2 to 9. The day 42 faecal, and day 90 ileal and faecal microbiotas underwent 16 S V1-V9 rRNA gene sequencing. Intestinal and faecal volatile fatty acids were measured via gas chromatography, haematological parameters were assessed from whole blood, and serum immunoglobulin G was measured. Immune-focused gene expression in the spleen and ileum was also measured via qPCR.

Results: The faecal microbiota exhibited differential β-diversity by group at both timepoints. On day 90, enriched pigs exhibited significantly elevated ileal villus height to crypt depth ratios, which were negatively correlated with serum IgG. Conversely, restricted pigs had more branched-chain fatty acids in the colon and faeces, alongside signs of heightened immune activity, with haematology showing enhanced neutrophil activation, and elevated lymphocyte and IgG levels. In the spleen, gene sets comprising genes for the pro-inflammatory cytokines IL-6, IL-15 and IFN-γ were upregulated among restricted pigs, while enriched pigs exhibited better-primed innate immune systems.

Conclusions: These findings demonstrate long-term impacts of early-life rearing on faecal microbiota composition. We furthermore observed a potential shift towards inflammation and altered haematology associated with the microbiota.

Background: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.

Results: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.

Conclusions: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.

Background: The gut microbiota of the silkworm (Bombyx mori) plays a vital role in metabolic processes, including nutrient digestion and immune regulation. However, the specific bacterial communities that enhance feed utilization and improve amino acid composition in silk and pupae remain unclear. In this study, we explored the mechanisms through which gut bacteria influence nutritional efficiency and the biosynthesis of high-quality silk and pupae by exposing fifth-instar silkworms to magnetic Fe₃O₄@urease-doped nanoconjugates.

Results: Our findings revealed that Fe₃O₄@urease nanoconjugates had no detrimental effects on the silkworm gut. Dominant genera in the MF group included Enterococcus, Staphylococcus, Pantoea, Klebsiella and Glutamicibacter (p < 0.05), while Linear Discriminant Analysis (LDA) and Effect Size (LEfSe) identified Dialister, Rhizobium and Parabacteroides as biomarkers. Functional prediction revealed bacteria in the Fe₃O₄@urease nanoconjugates treatment group were involved in metabolic activities, including amino acid synthesis, protein degradation and immune development. HPLC-LC-MS analysis revealed significantly higher levels of the amino acids Histidine (1077.06%) and Arginine (1020.45%) in the Fe₃O₄@urease nanoconjugates treatment group.

Conclusion: In summary, magnetic Fe₃O₄@urease-doped nanoconjugates effectively modulated B. mori gut microbiota, enhancing digestion and nutrient assimilation, and providing a scientific basis for the rational implementation of bacteria control for enhancing amino acid contents in silk and pupae.