Animal microbiome最新文献

Background: In aquaculture, several functional mushrooms have been efficiently used as prebiotics, impacting gut microbiota, increasing growth, and delivering antioxidant advantages to a variety of finfish species. However, the potential of Boletus edulis, the 'porcini' or 'penny bun' to influence the gut microbiota of Salmo salar has yet to be studied. Here, we investigated the prebiotic effect of Boletus edulis extract (BEE) on the gut microbiota of farmed Atlantic salmon via an in vitro gut model (SalmoSim).

Results: Notable changes in the production of short-chain fatty acids and microbial diversity were observed upon the addition of BEE. In particular, increased fiber fermentation was suggested by the decreasing concentrations of ammonia and increasing levels of acetate and propionate. Moreover, the 10% BEE improved the absorption of amino acids and increased the digestibility of crude protein, promoting a more diverse microbial community and reducing the accumulation of nitrogenous waste.

Conclusions: The results of the present study revealed that the addition of BEE efficiently altered the gut microbiota, increasing microbial diversity, supporting beneficial short-chain fatty acid synthesis, and improving nutritional absorption in Atlantic salmon.

Background: Most research into the development of the canine gut microbiota has featured cross-sectional studies, and there has been limited exploratory research into how it is affected by external factors. We aimed to longitudinally characterise the gut microbiota and its development in Labrador Retriever puppies and identify whether alterations in the gut microbiota are associated with factors related to demography, lifestyle, antibiotic usage and gastrointestinal health.

Results: 76 Labrador Retriever puppies were recruited via Dogslife, a UK-based online cohort study. Faecal samples were collected at three to four, seven, and 12 months of age and analysed using 16 S rRNA gene sequencing alongside questionnaire data. Alpha and beta diversity were assessed using linear mixed effects models and permutational multivariate analysis, accounting for repeated measures. Differential abundance was evaluated using multivariable association with linear models. Associations were identified between puppies' gut microbiota and age, sex, coat colour, household smoking status, dietary indiscretions (e.g. household waste, coprophagia), contact with other dogs and horses, recent oral/injected antibiotic use, and recent vomiting and diarrhoea. The greatest source of variation was individual identity, explaining approximately 25% of alpha diversity and 50% of beta diversity. Alpha diversity declined between three and 12 months, with age-related shifts in community composition and dispersion. Coprophagia was associated with increased alpha diversity and contributed to variation in community structure. Antibiotic use was associated with reduced alpha diversity, altered composition, and changes in taxa across Firmicutes, Proteobacteria, and Tenericutes. These effects were largely transient, with the largest shifts occurring within one week of treatment. Puppies with recent diarrhoea showed increased alpha diversity and differential abundance in several taxa within four weeks of the episode. Helicobacter was more frequently detected in samples from puppies with recent diarrhoea.

Conclusions: This longitudinal study characterises the development of gut microbiota in Labrador Retriever puppies and identifies associations with demographic, environmental, and health-related factors. These findings underscore the value of longitudinal sampling in microbiome research, offer novel insights for owners and veterinarians, and lay a foundation for future studies investigating causal mechanisms and potential interventions.

Infections of swine enteric coronavirus (SECoV), including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), cause severe diarrhea in piglets and result in substantial losses to the pig industry. The intestinal microbiota plays a crucial role in SECoV disease progression and outcomes, yet current research largely focuses on specific age groups or intestinal segments. This review provides a comprehensive analysis of the dynamic microbiota changes in piglets after SECoV infections across different ages and intestinal regions. It discusses differential microbiota analyses, functional changes, metabolic products, alongside their effects on immune responses. Additionally, we explore fecal bacterial transplantation as a potential intervention and highlight the role of the microbiota in either promoting or inhibiting SECoV infections. The development of advanced research tools, including culturomics, sequencing technologies, and multi-omics approaches, is pivotal in understanding the intricate relationship between the porcine intestinal microbiota and SECoV infections, offering potential strategies for preventing and controlling SECoV-related diseases.

Background: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.

Results: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.

Conclusions: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.

Background: Artificial diet-reared silkworms (Bombyx mori) exhibit reduced gut microbial diversity and impaired growth performance compared to mulberry-fed counterparts. While Bacillus subtilis is widely used as a probiotic in livestock and aquaculture, its impact on silkworms remains unexplored. This study investigates whether dietary supplementation with B. subtilis enhances larval development and elucidates the underlying mechanisms involving gut microbiota and metabolic pathways.

Results: Supplementing artificial diets with B. subtilis (6 × 10⁵ CFU/g) significantly increased larval body weight by 9.1-22.1% during instar stages and improved feed utilization efficiency (FUE) by 4.09%-6.80% compared to controls. Cocoon quality metrics, including cocoon shell weight (+ 9.77% in females) and cocoon shell ratio (+ 6.56%), also improved. Mechanistically, B. subtilis did not colonize the midgut but transiently modulated gut physiology: it elevated midgut fluid pH and enhanced α-amylase, trypsin, and lipase activities. 16 S rRNA sequencing revealed reduced gut microbial diversity (Shannon index, P < 0.01) and shifts in community structure, with decreased abundances of potential pathogens (e.g., Pseudomonas) and commensals (e.g., Lactobacillus). Targeted metabolomics identified a 3.1-fold increase in phenylalanine levels in hemolymph, linked to upregulated aromatic amino acid metabolism pathways (KEGG). Dietary phenylalanine supplementation (0.4%) replicated B. subtilis-induced growth promotion, confirming its pivotal role in host-microbe interactions.

Conclusions: B. subtilis enhances silkworm growth and silk production through multi-faceted mechanisms: reshaping gut microbiota composition, improving digestive enzyme activity, and elevating phenylalanine biosynthesis. These findings establish B. subtilis as a promising probiotic for optimizing artificial diet systems in Lepidoptera and highlight the central role of amino acid metabolism in insect-microbiome symbiosis.

Background: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.

Results: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.

Conclusions: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.