Animal microbiome最新文献

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).

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.

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.

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.

BACKGROUND: The gut microbiome is an ecosystem of microbes that live within the host’s digestive tract and are a vital component of host health. An increasing number of studies are investigating microbiome differences in wild and captive-managed populations to assist in species conservation and improve captive welfare. The gut microbiota of Australian marsupials has not been extensively studied but has long been recognised as having an important functional role in the digestive physiology and health of those in care. We used 16S rRNA gene sequencing to characterise and compare the faecal bacterial communities of six species of Australian marsupials from captive or wild origins over a large temporal and spatial scale. RESULTS: We found the microbiome of captive marsupials had reduced microbial richness and diversity in two species, the brushtail possum and the Eastern grey kangaroo. Captivity was associated with gut microbiome compositional differences for half of the species tested. These compositional changes were accompanied by less pronounced seasonal variability in captivity. CONCLUSIONS: This study provides valuable baseline data and demonstrates that captivity significantly alters the gut microbiota, suppressing its natural seasonal variability. These findings enhance our understanding of the gut microbiome in Australian marsupials. Future research should focus on determining the functional importance of these microbial communities and develop strategies to address any microbiome deficiencies in managed populations. Such efforts could ultimately improve the success of captive rearing and reintroduction programs.

The gut microbiome is a dynamic and complex ecosystem that plays an important role in determining ruminant health, productivity, and environmental footprint. Its plasticity during early life presents a critical window for potential programming of long-term physiological and functional capacities, with early interventions demonstrating greater effectiveness compared to those applied in the stable adult microbiome. This review synthesizes current evidence on the assembly of the early-life gut microbiome, elucidates the mechanisms and effectiveness of various interventions (including nutritional, microbial, and genetic approaches), and evaluates their impacts on feed efficiency, animal health, and methane emissions. While various intervention strategies offer promise for advancing ruminant production, challenges remain due to the inconsistency and variability in the persistence and long-term efficacy of these protocols. We highlight the urgent need for integrated and standardized intervention strategies, alongside longitudinal, multi-omics research, and the application of artificial intelligence, to fully unlock the transformative potential of early-life microbiome modulation. Such efforts are essential to aligning ruminant production systems with global food security and climate sustainability goals.

Specific maternal gut microbiota can activate immune responses in the gut-associated lymphoid tissues, driving the secretion of maternal immunoglobulins into the milk and facilitating the passive immunity of the offspring via the entero-mammary axis. This study aims to investigate the distinct gut microbiota profiles between large white (LW) sows and Ningxiang (NX) sows, and to explore probiotic for maternal and offspring intestinal health. Lactobacillus reuteri (LR) was significantly enriched in the feces of NX sows and positively correlated with colostral immunoglobulin (Ig) levels, specifically IgG (r = 0.568, P = 0.014), IgA (r = 0.573, P = 0.013), and IgM (r = 0.721, P = 0.0007). Maternal supplementation with LR isolated from NX pigs enhanced mammary IgA production and elevated secretory IgA (sIgA) levels in both colostrum and the ileum of mice. Importantly, maternal dietary LR supplementation improved immune functions of offspring mice challenged with enterotoxigenic escherichia coli (ETEC), as evidenced by reduced systemic inflammation (TNF-α, IFN-γ) and preserved intestinal barrier function. These results support the potential of NX pig-derived LR as a probiotic to improve the health of maternal and offspring via the gut-mammary axis.

Background: Intestinal microbial homeostasis and metabolic balance play a crucial role in maintaining normal physiological function in horses. Exogenous stress involving abrupt turns and jumps during show jumping significantly impacts intestinal microbial homeostasis and metabolic balance in these animals.

Results: By comparing rectal (faecal) samples from 10 Warmblood horses collected before and immediately after a show jumping competition on the same day, we observed substantial alterations in intestinal microbial homeostasis and metabolic balance post-exercise. Microbial evenness significantly increased following the competition, accompanied by enrichment of specific taxa such as Bacteroides, Ruminococcus, Prevotella, and Fibrobacter. Metabolite analysis revealed a marked decrease in antioxidant-related compounds, including orsellinic acid, 2,3-dimethyl-2-cyclohexen-1-one, and (1 R,6 R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate. Conversely, glucosan and thiamine pyrophosphate levels increased. Post-competition, membrane lipid metabolism pathways were significantly downregulated, while antioxidant responses and energy metabolism pathways were upregulated. Spearman correlation analysis indicated positive associations between Fibrobacter, Ruminococcus, and Prevotella with energy metabolism-related metabolites, whereas Lysinibacillus correlated positively with metabolites involved in antioxidant activity and intestinal mucosal protection.

Conclusion: Collectively, our findings demonstrate that show jumping induces shifts in intestinal microbial homeostasis and metabolic balance in Warmblood horses. These adaptations appear conducive to preserving epithelial integrity and enhancing energy provision to meet the demands of high-intensity exercise. This study provides novel insights into the impact of acute high-intensity exercise on equine gut microbial dynamics and metabolism, offering a theoretical basis for probiotic-based interventions to support intestinal health in sport horses.

Background: Mammalian gut microbiomes are essential for supporting digestion, nutrient absorption and overall host health. While diet and phylogeny are the two main influences on gut microbial composition, other factors, including life history and environment also contribute. Here, we characterised and compared the gut (faecal) bacterial microbiomes of two baleen whale species with contrasting life histories: the Bryde's whale (Balaenoptera edeni brydei), a non-migratory, year-round generalist forager; and the southern right whale (Eubalaena australis; SRW), a seasonal migrating species with a specialised diet of krill and copepods.

Results: We found that each species harboured distinct gut microbiomes with potential links to their different feeding and migratory strategies. The Bryde's whale gut microbiome bore a strong resemblance to that of toothed whales, with relatively lower bacterial richness and diversity and a high proportion of Proteobacteria after Firmicutes. The core microbiome of these whales included taxa supporting a protein-rich diet and year-round foraging lifestyle, e.g. Carnobacterium and Faecalitalea. In contrast, the SRW had a gut microbiome similar to other baleen whale species, with a higher richness and diversity, and dominated by Firmicutes and Bacteroidetes. The SRW core microbiome featured taxa associated with lipid metabolism, e.g. Erysipelotrichaceae and Coriobacteriia, reflecting a lipid-rich diet and reliance on blubber reserves during migration. We also found that SRWs sampled at different stages in the migratory cycle had significantly different gut microbial compositions. Functional analyses further supported these results, with Bryde's whales being broadly enriched in enzymatic functions including protein digestion and SRWs showing more selective enrichment.

Conclusions: Along with species-specific microbiomes, our findings also suggest that migratory behaviour and foraging patterns - key aspects of cetacean life history - may substantially influence gut microbiome composition. The characterisation of the gut microbiomes of the two whales provides a valuable baseline for the future monitoring of cetaceans and their environments.

BACKGROUND: Gut microbial dysbiosis is a common cause of calf diarrhea, a major contributor to calf mortality. Additionally, the early gut microbiota in calves is considered a hotspot for antimicrobial resistance, potentially leading to the failure of antibiotic treatments. Most prior research investigating the associations between calf microbiota and diarrhea has relied on partial 16S rRNA gene amplicon sequencing, which offers limited taxonomic resolution. In this study, we collected fecal samples from 25 Holstein-Angus crossbred neonatal calves on days 4, 7, 11, 14, and 30 and analyzed the gut microbiota using full-length 16S rRNA gene amplicon sequencing. A machine-learning approach was employed to identify potential bacterial markers associated with diarrhea. RESULTS: A significant increase in gut microbial diversity (P < 0.05) was observed with the calves’ age; however, days 11 and 14 showed similar diversity levels, coinciding with the peak prevalence of diarrhea. Differences in gut microbiota features between healthy (n = 5) and diarrheic calves (n = 8), determined by fecal scores on days 11 and 14, were also detected at earlier (day 4) and later (day 30) stages of life. Seven diarrhea-associated species (e.g., Fusobacterium spp. and Bacteroides fragilis) and four health-associated species (e.g., Megasphaera elsdenii and Enterococcus faecium) were consistently identified by both Linear Discriminant Analysis Effect Size (LEfSe) analysis and Boruta feature selection. Machine learning models trained on Boruta-selected bacterial features using Random Forest and Support Vector Machine algorithms achieved high classification accuracy (87–100%) in distinguishing diarrheic from healthy fecal samples. Moreover, the concentration of gut bacteria resistant to the cephalosporin antibiotic cefotaxime was significantly higher in diarrheic calves that harbored a greater abundance of pathogens (P < 0.05), particularly on days 11 and 14, when the prevalence of diarrhea was high, which may be attributed to the co-localization of virulence genes and antimicrobial resistance genes. CONCLUSIONS: This study provided a comprehensive characterization of the neonatal calf gut microbiota, identified potential bacterial species as biomarkers to predict diarrhea and probiotic candidates, and indicated early, immediate, and long-term microbiota changes associated with diarrhea. Additionally, it highlighted the increased risk of antimicrobial resistance to antibiotic treatment in diarrheic calves.