Animal microbiome最新文献

Background: Sustainable pig farming balances animal welfare, productivity, and social acceptance. Organic systems offer enriched environments for the pigs and represent a model for sustainable production, but require an understanding of how breed, intestinal microbiome, and housing interact. In this study, we compared a commercial breed (German Landrace, GL) and a traditional breed (German Saddleback, GS) reared in different housing systems (Conventional, CON; Organic, ECO). Jejunal mucosa transcriptomes (n = 56) and digesta microbiota (n = 100) were collected from growing pigs at 70 days of life; 54 samples overlapped between the two datasets and were used for all integrated host-microbiome analyses. Data from RNA-seq and 16 S-seq were evaluated through differential expression analysis, microbial community profiling, and DIABLO-based data integration.

Results: Jejunal transcriptome variation was influenced primarily by breed. GL pigs exhibited a profile supporting anabolic pathways, including upregulated oxidative phosphorylation, whereas GS pigs showed a profile focused on lipid metabolism and a shift toward energy storage as an adaptation. In contrast, the housing system was the main driver of microbial composition, with ECO housing enriching fermentative taxa such as Lactobacillus and Campylobacter, presumably due to outdoor exposure, while CON housing enriched fewer Lactobacillus but more Clostridium. Breed-Housing combinations analysis revealed distinct adaptive strategies: the modern GL breed responded strongly to housing conditions at both the transcriptional and microbial levels, whereas the traditional GS breed, while also transcriptionally responsive, maintained a more stable microbial community phenotype across environments. Integrated host-microbiome analysis identified a core set of host genes (e.g., PCSK9 and SCD) that were strongly correlated with housing-specific microbes, defining a lipid-inflammation axis.

Conclusion: Breed and rearing environment jointly shape the porcine jejunal transcriptome and microbiota through distinct strategies. Together, these data provide molecular insight into how traditional and modern breeds differentially respond and potentially adapt to divergent husbandry systems, with implications for health and productivity.

Clinical trial number: Not applicable.

Background: Viruses play a key role in cattle respiratory tract (RT) health, yet, profiling the upper respiratory tract (URT) virome (DNA and RNA viruses) from deep nasopharyngeal swabs (DNS) remains challenging due to their low biomass, lack of well-defined enrichment approaches, and a high proportion of unclassified viral sequences. This study aimed to optimize DNS preservation, nucleic acid extraction, and bioinformatics pipelines to enhance URT virome characterization in beef calves.

Results: Three DNS preservation methods were tested (RNAlater, brain heart infusion (BHI) medium/glycerol at -80 °C, and BHI medium/glycerol followed by RNAlater). Three nucleic acid extraction kits (QIAamp Fast DNA Stool Mini Kit, GeneJET Genomic DNA Purification Kit, and mirVana™ miRNA Isolation Kit) were evaluated to compare total nucleic acid yields. Viral DNA and RNA were extracted separately using the NucleoSpin Virus Kit, which was optimized for viral nucleic acid recovery. The DNS samples that preserved in RNAlater and extracted using the NucleoSpin Virus kit generated highest viral DNA (1.35 ± 0.12 µg) and RNA (1.57 ± 0.09 µg) (mean ± SEM) yields for metagenomics sequencing. Metagenomic sequencing and viral taxonomic assignment using Kraken2 and Kaiju, respectively showed that Kaiju allowed maximum exact matches for viral taxonomy assignment and provided high-resolution outputs for the profiling of cattle URT viromes.

Conclusion: The use of an optimized nucleic acid extraction method and Kaiju-based classification enhanced viral nucleic acid recovery and taxonomic classification from low-biomass DNS samples. The findings highlighted the importance of effective storage conditions and extraction methods in maximizing viral nucleic acid yield, while demonstrating that Kaiju provided more reliable viral taxonomic assignments than Kraken2. These advancements provide a framework for more accurate assessment of the URT virome in cattle and other farm animals, enabling deeper investigation into the roles of viruses in RT health.

Background: Red 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.

Results: 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.

Conclusions: 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.

Symbiotic 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.

Background: Colobine monkey species have a multi-cavity forestomach adapted to a folivorous diet and foregut fermentation, making their gut microbiome essential for efficient digestion of plant fibre. In captivity, these species frequently experience gastrointestinal disorders associated with dietary changes and microbial dysbiosis. Understanding how their microbiome differs from that of other primates is therefore critical for improving health and husbandry. This study used a meta-analysis of global primate microbiome data to compare the faecal microbiome of colobines with those of other herbivorous primates, focusing on the effects of captivity.

Results: Data from 16 studies involving 35 primate species and 7 primate families/subfamilies, comprising 1,690 faecal samples generated using 16 S rRNA amplicon sequencing, were re-analysed using standardised bioinformatic and compositional-statistical pipelines. Significant differences in microbial diversity and composition were observed among wild primates across families/subfamilies, diets, and fermentation strategies. Colobinae had a distinctive microbiome characterised by low Shannon diversity and high relative abundance of Firmicutes, particularly Ruminococcaceae and Lachnospiraceae, which were also prominent members of the wild colobinae core microbiome. Across all families/subfamilies and within colobinae, observed Shannon diversity was lower in captivity; however, multivariable mixed-effects models showed that alpha-diversity estimates were highly sensitive to study identity, species representation and methodological covariates. In contrast, beta-diversity and ALDEx2 analyses provided consistent evidence of captivity-associated compositional restructuring. Captive colobinae were enriched in Bacteroidetes and Spirochaetes, and families such as Prevotellaceae, Rikenellaceae, Methanobacteriaceae, Spirochaetaceae and Bacteroidaceae, whereas wild colobines were enriched in fibre-associated taxa, including Ruminococcaceae and Lachnospiraceae.

Conclusions: Captivity alters the gut microbiota of colobine primates, affecting microbial diversity and core fibre-fermenting taxa important for gastrointestinal health. However, adjusted alpha-diversity models revealed substantial confounding by study, species, and methodological variables, indicating that diversity effects should be interpreted cautiously. Their specialised folivorous diet and foregut-fermenting physiology appear to produce a highly efficient yet fragile microbial ecosystem poorly adapted to ex-situ conditions. The strongest evidence for captivity-associated disruption was consistent alterations in faecal microbial composition, highlighting the need for diet formulations and microbiome-based health monitoring tailored to the unique digestive ecology of colobines to mitigate the high prevalence of gastrointestinal disorders in captivity.

The intensification of poultry production has led to an increased prevalence of necrotic enteritis (NE), a costly disease caused by Clostridium perfringens, traditionally managed through antibiotic use. However, concerns over antibiotic resistance have driven the search for alternative solutions. This study evaluates the efficacy of a three-strain Bacillus probiotic blend as an alternative for preventing NE in broiler chickens. The three Bacillus strains, Bacillus subtilis ATCC PTA126786, B. velezensis ATCC PTA127064, and B. velezensis ATCC PTA 127065, were selected based on their probiotic attributes, especially their ability to inhibit the growth of C. perfringens and other poultry pathogens. Our results from in vivo experiments showed that dietary supplementation with the probiotic blend significantly reduced NE-associated mortality and improved growth performance metrics such as average daily gain and feed conversion ratio. Metagenomic analyses of ileal contents of chickens supplemented with the Bacillus blend revealed a significant reduction in the abundances of C. perfringens, Enterococcus cecorum, and Eimeria acervulina following NE challenge, despite modest changes in overall microbiome composition. Importantly, the observed probiotic efficacy was strongly associated with the Bacillus strains colonization in the gut, as measured by the Bacillus genome recovery in ileal content samples. These findings highlight the potential of Bacillus-based probiotics as an effective alternative to antibiotics in poultry production, contributing to improved animal health and sustainability.

This study investigated the effects of microencapsulated sodium butyrate (MSB) on production performance, reproductive hormone profiles, and gut microbiota-metabolite interactions in late-laying quails. Dietary MSB supplementation significantly increased laying rate and early egg weight and elevated serum FSH and LH concentrations, suggesting a potential involvement of reproductive endocrine regulation. MSB enhanced gut microbial richness and enriched fiber-fermenting, SCFA-associated taxa such as Lachnospiraceae, Ruminococcaceae and Bacteroides, while co-occurrence network analysis revealed increased connectivity and robustness of the microbial community. Untargeted metabolomics showed coordinated changes in amino acid derivatives, short peptides and lipid-like molecules. Exploratory mediation analysis further suggested that specific metabolites may be involved in the associations between MSB-responsive bacteria and host reproductive traits. Specifically, the dipeptide Pro-Trp and N-arachidonoyl phenylalanine were potentially associated with the relationship between decreased s__uncultured_bacterium_o__RF39 and improved laying rate, whereas N-docosahexaenoyl tryptophan appeared to link increased s__unclassified_f__Lachnospiraceae to higher FSH concentrations. These findings indicate that MSB may improve reproductive performance in aging quails by reshaping the gut microbiota and its metabolite outputs in a manner that supports reproductive endocrine function. Overall, this study provides novel insights supporting the use of microencapsulated sodium butyrate as a functional feed additive for extending the productive lifespan of laying quails.

Background: The redbelly tilapia (Coptodon zillii) is a highly invasive fish species posing serious ecological risks to freshwater systems in China. To uncover mechanisms behind its invasion success, this study investigated spatiotemporal plasticity of its gut microbiome and explored the drivers of such plasticity. Using high-throughput 16 S rRNA sequencing, gut microbiota of C. zillii from five water bodies (two rivers, three reservoirs) and from Shuikou Reservoir across four seasons were compared.

Results: Among populations from different habitats, 6 of the top 10 abundant phyla and 17 of the top 30 genera varied significantly (P < 0.05). Gut microbiota differed significantly (P < 0.05) in all pairwise population comparisons. Alpha diversity indices also showed significant differences among some populations (P < 0.05). Of 24 digestion-related KEGG pathways identified, 23 exhibited significant abundance variations across populations. Relative gene abundances of beta-glucosidase (P = 0.0025) and chitinase (P = 0.022) also differed significantly. Water temperature, dissolved oxygen, and conductivity were key environmental drivers of gut microbiota variation. Notably, microbial community assembly was predominantly governed by deterministic processes (> 60%), with heterogeneous selection contributing 42%-63%. In seasonal samples from Shuikou Reservoir, 6 of the top 10 phyla and 15 of the top 30 genera showed significant seasonal variation (P < 0.05). PERMANOVA indicated significant differences (P < 0.05) in all pairwise seasonal comparisons. Of 19 digestion-related KEGG pathways, 13 exhibited significant abundance variations across seasons. Chitinase-coding gene abundance varied significantly among populations (P < 0.0001). Key factors driving seasonal differentiation were pH, conductivity, turbidity degree, and total nitrogen.

Conclusions: The gut microbiome of invasive C. zillii displays significant spatiotemporal variation in structure, diversity, and functional gene composition. This pronounced plasticity-rather than a stable, specialized microbiota-likely serves as a key adaptive strategy, enabling the species to thrive in heterogeneous environments.

Background: This study primarily investigated the differences in rumen microbial composition and functional profiles among goats with varying degrees of rumen bloat under a high-concentrate diets (HCDs) feeding condition. Forty Nubian goats fed a HCDs were selected as experimental animals and subjected to rumen bloating (RB) scoring. From these, six goats with high bloat scores (HB group) and six goats without obvious bloat (NB group) were selected. Rumen content samples were collected via oral stomach tubes. Rumen fluid foaming characteristics and pH values were measured, and metatranscriptome sequencing was conducted to analyze microbial functions.

Results: The results demonstrated that compared to the NB group, the HB group exhibited significantly higher foaming capacity, foam stability, and viscosity of ruminal fluid, along with a significantly lower pH value (P < 0.05). Additionally, α-diversity indices (Chao1, ACE, and observed_species) were significantly elevated in the HB group (P < 0.05). Annotation of rumen microbial species showed that the relative abundance of Ascomycota, Basidiomycota, Dialister, and Dialister sp. CAG:486 was significantly higher in the HB group, whereas Bacteroidetes, Proteobacteria, Spirochaetes, Prevotella, Bacteroides, Treponema, Lactobacillus, Leptotrichia hofstadii and Prevotella oralis were significantly reduced (P < 0.05). Functional analysis of differentially expressed genes (DEGs) revealed significant enrichment in several biological processes. In the Gene Ontology (GO) database, DEGs were predominantly associated with cellular protein modification, protein maturation, and ribosome biogenesis. According to KEGG pathway analysis, DEGs were mainly enriched in pathways related to endocytosis, ubiquitin-mediated proteolysis, and protein processing in the endoplasmic reticulum.

Conclusion: In summary, under uniform feeding conditions, individual variations in goat rumen microbiota functions are associated with differences in microbial community structure and gene expression patterns. Alterations in the protein metabolism function of the rumen microbiome are associated with the presence of foaming proteins, which in turn are linked to individual differences in rumen foam production capacity. Ultimately, these associations may result in differing susceptibility and severity of RB among animals.