Animal microbiome最新文献

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.

Background: Schistosomiasis is a snail-borne disease affecting over 200 million people worldwide. Despite dedicated control efforts and effective diagnostic tools, schistosomiasis remains prevalent. Novel and sustainable control measures are urgently needed. Bacteria might offer such a solution as links between bacteria, disease resistance and transmission potential of intermediate hosts have been established in other systems. To better understand the tripartite interaction potentially driving snail-schistosome compatibility patterns, microbial communities must be investigated throughout and across various parasite exposure conditions. Therefore, we studied Biomphalaria glabrata snails exposed to a high- and low-shedder population of Schistosoma mansoni and Schistosoma rodhaini in single and co-exposure experiments. Snails were sacrificed at different time points post-exposure and their bacterial communities and trematode (co-)infection status were determined through metabarcoding tools.

Results: Snails infected by low- and high-shedder S. mansoni populations were more likely to have bacterial community dysbiosis than those infected by S. rodhaini but this was also affected by miracidial load. Moreover, the single-infection hierarchical effect on the bacterial component of the microbiome is not maintained under co-infection with S. rodhaini, which appears to stabilize the snail's bacterial profile even after being outcompeted by high-shedder S. mansoni. Finally, alpha diversity differed significantly between infected and uninfected snails around the onset period of shedding at 30 days post-miracidial exposure.

Conclusion: The timing of this bacterial shift suggests an intricate parasite-snail interaction around key parasite development moments. Future studies investigating the tripartite interaction are advised to consider the effect of outcompeted or prepatent infections on the snail's microbiome.

Background: Growing insights into gut microbiota reveal their surprising role in shaping external traits in fish, including the regulation of skin pigmentation. This study explores whether black-spot pigmentation influences the abundance of gut microbiota. We investigate how black-spot pigmentation in Oujiang color common carp shapes gut microbiome composition, gene expression, and metabolite, revealing a coordinated gut-skin color axis. To validate these findings, we used a TYR knockout group, which included both mutant black-spotted (TYR ^+/-) and non black-spotted (TYR ^-/-) fish, enabling functional comparison across pigmentation phenotypes.

Results: We demonstrate that black-spotted (RB and WB) fish groups contained less total microbiome composition among them. We observed significant differences in microbiota composition, with genera such as Acinetobacter, Bacillus, and Staphylococcus being more less abundant in wild black-spotted (RB and WB) groups. Gene expression profiling revealed significant differential regulation, with 27 genes markedly upregulated in the black-spotted group. Interestingly, we identified RAB9B, JUN, EGR1, PURB, HS2ST1, and ARL8 as key genes functionally correlated with the gut microbiome and metabolite profiles. Notably, Xanthine metabolites were significantly upregulated in RB and WB groups, highlighting a strong connection to purine metabolism. These genes are primarily involved in tyrosine signaling transduction, the immune system, and metabolic pathways. In parallel, blood metabolomic analysis identified 3 significantly elevated metabolites associated with nucleotide, amino acid, and lipid metabolism. Furthermore, 9 lipid-derived nutrients from muscle tissue were significantly upregulated in the black-spotted group, underscoring a strong link between pigmentation phenotype and systemic metabolic alterations. To support this, knocking out TYR converted black-spotted fish to a white phenotype and showed total microbiome profiles, 5 selective bacterial taxa, and 4 consistently expressed genes that mirrored those of wild-type black-spotted fish. Moreover, human gut microbiome data showed Bacillus and Pseudomonas were less abundant in black skin populations, reflecting patterns seen in fish.

Conclusions: Our results draw a root map to uncover a potential gut-skin-color axis, where black-spot pigmentation not only marks external phenotypic variation but also aligns with distinct microbial signatures.

Background: There is an intricate relationship between pig nutrition and gut microbiome. For technical, cost and societal reasons, in vitro gut models can be advantageously used as an alternative to in vivo experiments to perform mechanistic studies on the interactions between gut microbes and nutrients. In this context, the aim of the present study was to develop a new in vitro model of the healthy adult pig colon integrating both luminal and mucosal microenvironments. The model was further used to evaluate feed ingredients (lactose and lactose + sucrose). Gut Microbiota composition and metabolic activities were followed by 16S Metabarcoding and short chain fatty acid (SCFA) / gas measurement, respectively. Then, the effect of the both feedstuffs on skatole production, responsible for boar taint in male pigs, was also investigated.

Results: Based on in vivo data, the new MPigut-IVM was set-up to reproduce the main physicochemical (pH, transit time, self-maintained anaerobiosis), nutritional (composition of ileal effluents, bile salts) and microbial (lumen and mucus-associated microbiota) parameters of the large intestine in healthy adult pigs. The model was validated through in vitro-in vivo comparisons regarding SCFA concentrations and bacterial profiles at the phylum and family levels. Lactose and lactose + sucrose had no significant impact on SCFAs but increased gas production (P < 0.01 with lactose). Both sugars, particularly lactose + sucrose, tended to reduce skatole concentrations while increasing indole levels (P > 0.05). This was associated to a slight reduction of the numbers of skatole-producing bacteria Olsenella scatoligenes (P > 0.05). Both feed ingredients induced a decrease in bacterial α-diversity (P < 0.05).

Conclusion: Despite obvious limitations such as lack of host interactions, the adult MPigut-IVM represents a powerful platform for Microbiome studies in the pig colonic environment. In Line with the 3R regulations, this in vitro model can be useful to perform preliminary screening of innovative feed strategies to improve pig health and help to elucidate their mechanisms of action in relation with gut microbiota, taking into account inter-individual variabilities.

Background: Gut microbiota plays a crucial role in swine health and performance, with diet as a key modulator. Euglena gracilis supplementation has shown immunomodulatory effects that benefit sows and piglets. However, its prebiotic effect on gut microbiota remains unclear. This study investigated the impact of maternal E. gracilis supplementation on gut microbiota, piglet body weight, and the incidence of diarrhea.

Methods: Sixty-one crossbred sows (Landrace × Yorkshire) were assigned to either a standard diet (Control; n = 30) or a standard diet supplemented with 1 g/sow/day of E. gracilis (E. gracilis; n = 31) from day 85 of gestation until day 21 of lactation. On day 109 of gestation, 30 sows (15/group) were randomly selected for performance assessment and fecal sample collection. After farrowing, one corresponding piglet per selected sow (15/group) was randomly chosen for fecal sampling. In total, 180 fecal samples were collected, 90 from sows and 90 from piglets. Sow samples (15/group/timepoint) were collected on day 109 of gestation and days 3 and 21 of lactation, while piglet samples (15/group/timepoint) were collected on days 3, 10, and 21 of age. Gut microbial composition was determined by 16S ribosomal RNA gene sequencing. Piglet body weight was measured from birth until weaning, while the incidence of diarrhea was monitored from days 1 to 21 of age.

Results: On average, the number of piglets alive at birth and weaning was 13.9 ± 2.4 and 10.9 ± 2.2 piglets/litter, respectively. Piglets nursed by E. gracilis-supplemented sows had greater body weight at weaning (+ 0.28 kg; P = 0.100) and a lower incidence of diarrhea on days 10 (P ≤ 0.05), 11 (P ≤ 0.10), and 12 (P ≤ 0.05) of age. For alpha diversity, E. gracilis-supplemented sows exhibited a lower Chao1 index on day 21 of lactation (P ≤ 0.05), while a higher Inverse Simpson index on day 3 (P ≤ 0.05) and both Inverse Simpson and Shannon indices on day 21 (P ≤ 0.05) of lactation. In piglets, the Inverse Simpson index was lower on day 10 of age in those nursed by E. gracilis-supplemented sows (P ≤ 0.10). Gut microbial composition revealed that E. gracilis-supplemented sows exhibited a higher relative abundance of Bacteroidetes (g_Prevotella and o_Bacteroidales) and Spirochaetes (g_Treponema), while lower Firmicutes (g_Clostridium and f_Peptostreptococcaceae) than control sows, during the lactation period. Similarly, piglets nursed by E. gracilis-supplemented sows had higher Bacteroidetes (g_Bacteroides) and Proteobacteria (g_Escherichia) but lower Firmicutes (g_Lactobacillus) during the suckling period than those nursed by control sows. The non-metric multidimensional scaling analysis showed a correlation between piglet gut microbiota in those nursed by E. gracilis-supplemented sows and their body weight on days 10 (P = 0.094) and 21 (P = 0.031) of age.

Conclusion: Maternal E. gracilis supplementation d

Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.

Background: Declines in honey bee queen quality and variability in drone (male) reproductive performance are contributing factors to colony losses reported by beekeepers. While the causes of reduced reproductive fitness remain unclear, recent evidence implicates agrichemical exposure. Oxytetracycline (OTC), an antibiotic used in apiculture for over 70 years to treat brood diseases, is classified as an endocrine-disrupting compound due to its inhibition of mitochondrial function in reproductive cells. In other animals, OTC exposure has been associated with impaired reproductive development, reduced sperm viability, and broader reproductive dysfunction. Although the effects of OTC on worker bee gut microbiota and physiology are well documented, its impact on drone gut microbiota has never been characterized. Additionally, we recently discovered microbial communities in drone reproductive tissues, which could be impacted by OTC exposure. The goal of this study was to determine if OTC has the potential to impact drone development, survival, fecundity, and microbiota composition.

Results: Using an in vitro rearing system, we found that larval OTC exposure delays drone development, reduces survival, and results in detectable residues in the gut and reproductive tissues of newly emerged adults. In mature drones, oral exposure to conservative field-relevant OTC concentrations significantly reduced gut bacterial abundance and diversity, although reproductive tissue-associated microbiota appeared largely unaffected. In vitro assays further revealed that OTC is highly toxic to drone sperm at environmentally relevant concentrations.

Conclusion: Our findings demonstrate that OTC exposure has the potential to negatively affect drone development, survival, gut microbiota, and sperm viability. These results support our hypothesis that the use of OTC in beekeeping may contribute to reduced male reproductive health. Importantly, this work highlights the need for additional studies, particularly field-based investigations, to better understand the impacts of OTC on drone reproductive health and microbiomes. Such research will be critical for evaluating the broader consequences of antibiotic use in apiculture and for developing sustainable strategies to manage brood diseases.

Background: The intestinal microbiota influences nutritional metabolism, immunity, and disease resistance of fish hosts, while the host reciprocally regulates it. The compositional patterns of intestinal microbiota in groupers are influenced by multiple factors, with the core and stable interacting microbiota playing a crucial role in maintaining host growth stability. Asia is renowned for the grouper aquaculture industry, highlighting the importance of studying grouper intestinal microbes for both aquaculture development and conservation efforts.

Result: We integrated and re-analyzed 936 sequencing files of six grouper species (purebred species: Epinephelus akaara, E. coidides, Plectropomus leopardus, and hybrid: E. fuscoguttatus♀ × E. polyphekadion♂, E. lanceolatus♂ × E. fuscoguttatus♀, E. moara♀ × E. lanceolatus♂) from both our experiments and public databases, covering samples from the South China Sea, East China Sea, and Bohai Sea. For aqua-cultured groupers, differences in core intestinal microbiota were mainly determined by host genetics rather than the aquaculture environment. Additionally, a clear purebred-hybrid dichotomy existed in the intestinal microbiota network: hybrids had more intricate, competitive, and stable intestinal microbiota, whereas purebreds possessed simpler yet highly positive intestinal microbiota. Further analysis summarized the common effects of external factors on the core co-occurrence of intestinal microbiota: disease markedly diminished the complexity and positive interactions; antibiotics also weakened microbial community structure; in contrast, probiotics enhanced diversity and stability. Both lipid and plant protein substitutions increased negative interactions and reduced bacterial synergy, with plant protein significantly simplifying the microbiota network. Under varying conditions, the intestinal microbiota balanced between beneficial and potentially harmful two competing guilds. Cluster 1 containing more keystone ASVs was positively correlated with the control group, while Cluster 2 showed a correlation with external factors. Although some factors influenced the core intestinal microbiota, they strived to maintain a balance between two clusters, such as probiotics, plant proteins, and alternative oil groups. In contrast, both disease and antibiotic groups exhibited significant reductions in two clusters, consistent with the marked simplification of core co-occurrence structure.

Conclusion: Generally, understanding the core intestinal microbiota and its changing patterns under influences provides valuable insights into exploring grouper health and improving aquaculture strategies.