Animal microbiome最新文献

Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity. We profiled the salmon gut microbiome across 540 salmon samples in differing conditions with a view to capture the genomic diversity that can be resolved from the salmon gut. The salmon were exposed to 3 different nutritional additives: seaweed, blue mussel protein and silaged blue mussel protein, including both pre-smolts (30-60 g salmon reared in freshwater) as well as post-smolts (300-600 g salmon reared in saltwater). Using genome-resolved metagenomics, we generated a catalogue of 11 species-level bacterial MAGs from 188 input metagenome assembled genomes, with 5 species not found in other catalogues. This highlights that our understanding of salmon gut microbial diversity is still incomplete. A prevalent bacterial genome annotated as Mycoplasmoidaceae is present in adult fish, and a comparison of functions revealed significant sub-species variation. Juvenile fish have a different microbial diversity, dominated by a species of Pseudomonas aeruginosa. We also present the first viral catalogue for salmon including prophage sequences which can be linked to the bacterial MAGs.

The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.

Background: Captive-rearing programmes for endangered birds, such as those in place for kiwi conservation in Aotearoa-New Zealand, can unintentionally deprive the birds access to a microbially-diverse and 'natural' developmental environment i.e., their natal rohe (territory). These programmes introduce external variables such as increased exposure to diseases, unnatural and incomplete diets, antimicrobial usage, and artificial cohabited environments, which have the potential to impact rearing success outcomes. In this research, we investigated whether the introduction of natal soils, as a direct probiotic and a source of wild microorganisms, to the captive-reared ground-foraging Ōkārito kiwi (Apteryx rowi) chick diet would impact their gut microbiome. Using 16S rRNA gene and ITS sequencing to identify the key taxonomic groups present, we assess the community composition differences with the introduction of natal soils into the diet of captive-reared Ōkārito kiwi.

Results: Results showed a distinct gut microbial community associated with Ōkārito kiwi in captivity. Bacterial diversity in Ōkārito kiwi gut increased with age, with the relative abundances of dominant taxonomic groups changing over time. Bacterial phyla Firmicutes, Proteobacteria and Actinobacteria, and the fungal orders Malasseziales and Trichosporon dominated the gut community. Exposure to natal Ōkārito soils influenced the composition of the gut microbiome in Ōkārito kiwi, especially on the temporal trends of key bacterial taxa. Kiwi with natal-soil-amended diets harboured an increased proportion of Firmicutes and Malasseziales compared to the 'Control' group. The fungal community in the Ōkārito kiwi gut was more transitory, changing rapidly following soil amendment. No significant changes to growth rates or overall health were found between 'Control' and 'Treatment' groups.

Conclusions: The findings of this study represent the first description of the gut microbiome of the critically endangered Ōkārito kiwi, Apteryx rowi, and the first documented use of natal soil as a probiotic amendment for wild birds. Results show that mediation of the gut microbial communities of captive-reared ground-foraging birds can be achieved through the introduction of natal soils in their diet.

Background: This study aimed to investigate differences in the structure and function of the rumen microbiome and its associated changes in rumen fermentation patterns and apparent nutrient digestibility in dairy cattle with different sorting behavior. Twenty-four Holstein cows in mid-lactation were initially enrolled in the experiment. All cows were fed and milked three times daily throughout the entire 28-day experimental period, comprising a 7-day pre-trial and a 21-day main trial. On days 1, 7, 14, and 21 of the main trial, feed sorting behavior was measured, and feed and feces samples were collected to determine apparent nutrient digestibility. Rumen content samples were collected on day 21 to measure pH, volatile fatty acids (VFA), and rumen microbiome structure and function. Based on feed sorting behavior, twelve cows were selected and divided into two groups: six cows that were severely sorted for fine particles-severely rejected long particles (SES; n = 6) and six cows that were slightly sorted for fine particles-slightly rejected long particles (SLS; n = 6).

Results: Comparative analysis revealed significant differences between the groups. The SES group exhibited lower rumen pH values and higher concentrations of total VFA (TVFA) and acetate (P < 0.05) than the SLS group. Data on apparent nutrient digestibility showed that compared to the SLS group, the SES group lowered the digestibility of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (P < 0.05). Differential analysis of rumen microbiota indicated that the SES group had a higher relative abundance of Prevotella, Lactobacillus, Bifidobacterium, Selenomonas, and Acetitomaculum by a lower relative abundance of Fibrobacter, Ruminobacter, Pseudobutyrivibrio, Butyrivibrio, and Ruminococcus. Carbohydrate-active enzyme (CAZyme) annotation revealed that the SES group showed increased abundance of GH13 and GH65 enzymes, while exhibiting decreased abundance of GH1, GH3, GH5, GH6, and GH94. Functional profiling of Kyoto encyclopedia of genes and genomes (KEGG) modules revealed that compared to the SLS group, the rumen microbiota in the SES group upregulated the abundance of carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism. In carbohydrate metabolism, the rumen microbiota in the SES group upregulated the abundance of starch and sucrose metabolism, the citrate cycle, and pyruvate metabolism, while downregulating the pentose phosphate pathway. Functional profiling of KEGG Orthology (KO) enzymes revealed that the microbiota in the SES group preferred energy production through increasing glycolysis and supported the metabolism changes toward acetate production and fatty acid biosynthesis.

Conclusion: Our findings reveal that feed sorting behavior significantly alters the rumen microbial ecosystem and its metabolic functions, negatively impacting fermentation efficiency, fiber digesti

Background: Beef and draft cattle have distinct rumen microbiota that can influence their metabolic processes and body composition. However, traditional metagenomic sequencing methods only provide broad surveys of the rumen microbial genomic contents. In this study, we utilized high-throughput single-cell genome sequencing to investigate these differences at the strain level.

Results: Following quality control and contig assembly, we obtained 97 bacterial genomes, 17 archaeal genomes, and 241 subspecies genomes from the rumen samples of Angus and Wuling cattle. Our analysis revealed a higher bacterial abundance in Angus rumen, characterized by an enrichment of the Succiniclasticum and Limivicinus genera. In contrast, the rumen of Wuling cattle exhibited a higher archaeal abundance. Additionally, we observed variations in the types and abundance of microbial-derived enzymes responsible for plant fiber degradation and volatile fatty acid (VFA) production between the two cattle breeds. The Angus rumen was found to harbor a higher diversity and abundance of cellulases and hemicellulases, particularly from the Ruminococcus unknown_0 genus. Furthermore, genera such as Succiniclasticum, Butyrivibrio, Limivicinus, UBA2868, and Prevotella were identified as key contributors to VFA production. Our findings suggest that the Angus rumen may have a stronger VFA production capacity due to the higher abundance of acidogenic genera. Interestingly, we also observed a greater abundance of Methanobrevibacter_A methanogens, which play a crucial role in energy flow in the rumen ecosystem, in Wuling cattle compared to Angus cattle.

Conclusion: Our study highlights differences in the rumen microbiome of Angus and Wuling cattle. This difference could, at least partially, account for the variation in fat content that ultimately results in the superior meat quality of Angus cattle and the sustained muscle activity required by draft cattle. Overall, single-cell genome sequencing reveals distinct microbial composition and metabolic pathways between the two breeds, providing insights into their unique physiological and metabolic needs.

Background: Sustainable livestock production is essential for meeting the growing global protein demand while minimising environmental impacts. Exploring alternative forages that enhance nutrient utilisation and reduce reliance on imported feeds is a potential strategy. Condensed tannins (CTs) can bind to proteins in the rumen, protecting them from ruminal degradation resulting in decreased ammoniacal N and enhanced nitrogen uptake in the hindgut. This pioneering research is the first to explore the potential of willow (Salix) as an alternative feed for ruminant nutrition. The study involved feeding ewe hoggets a control grass silage (SIL) or a SIL mix containing a 20% dry matter (DM) dietary inclusion of leaves from two willow varieties to investigate the impact the willow CTs have on rumen fermentation, microbial populations, and metabolomic profiles. Willow treatments: Beagle (BG) and Terra Nova (TN) had an overall CT inclusion (CTI) of 1.1 and 0.1% DM with the control diet containing no CTs in a three-treatment x three-period Latin square design.

Results: Although total dry matter and fibre intake were higher in BG and TN, there was no significant difference in ruminal CH₄ production between the treatments. However, fermentation was affected, with BG and TN showing lower acetate production and reduced total volatile fatty acid production compared to SIL. CTs may have impaired fibre digestion, as SIL had higher Fibrobacter abundance than BG. Heatmap visualisation indicated higher carbohydrate metabolite concentrations in SIL, with reduced metabolism observed in TN and BG. Ruminal ammonia did not differ significantly among treatments, despite higher nitrogen intake in BG and TN treatments. Proteolytic bacteria levels were similar across treatments, but TN and BG had higher ruminal metabolites associated with protein metabolism upon visualisation through heatmap analysis. TN showed higher abundance of Prevotella and Fibrobacter than BG, which had 10 times higher CT content and a greater prodelphinidin proportion.

Conclusion: Feeding CT-containing willow enhanced feed intake, altered rumen microbiome composition and suggested visual changes in the analysis of protein metabolism, offering potential benefits for animal performance. While a reduction in CH₄ was not observed, this study highlights the potential of willow to alter ruminant nutrition while supporting sustainable agricultural practices.

Background: In dairy cows, the transition period around parturition is a critical period with the highest incidence of infectious and metabolic diseases compared to the rest of the lactation. Over the past few years, several studies have highlighted the central role of the microbiota in health and disease. In mammals, gut microbiota is typically studied by analysing faecal samples. In cattle, most research on the gastrointestinal microbiota has focused on the ruminal microbiota, while the composition and evolution of the faecal microbiota in transitioning dairy cows remain poorly studied. We aimed to describe the composition of the faecal bacterial microbiota in a large number of dairy cows around parturition on commercial farms. Faecal samples were collected three weeks before and one week after calving from a cohort of 411 Holstein dairy cows in their 2nd and 3rd lactations across 25 dairy herds. DNA was extracted from faeces, and the 16S rRNA gene (hypervariable region V3-V4) was sequenced after amplification.

Results: A loss of microbial diversity was observed after calving, with no significant association with the lactation rank. The analysis identified different genera when comparing pre- and post-calving samples, indicating significant changes in the faecal microbiota of dairy cows after calving compared to the dry period, closer to calving. Among the major changes, Verrucomicrobiota were less abundant in the two unknown genera from the phylum after calving. In contrast, the proportion of Bifidobacterium was higher after than before calving.

Conclusion: Shifts in faecal microbiota around calving may be attributed to changes in diet composition, feed intake modifications, or physiological changes from the dry period to lactation. However, other factors such as genetic background and health factors may also influence the microbiota composition. This could be further investigated to identify biomarkers for predicting imbalances or identifying maladaptation to the lactation stage.

Background: The combination of meglumine antimoniate and allopurinol is considered one of the most effective treatments for canine leishmaniosis caused by Leishmania infantum. This study investigated the effects of this treatment on the gut microbiome of 10 dogs from Spain, Portugal, and Italy via fecal shotgun metagenomic sequencing over six months.

Methods: Dogs were sampled at baseline (BL), after one month of combined treatment with meglumine antimoniate and allopurinol (M1) and after six months of allopurinol treatment (M6). Fecal samples had their total DNA extracted and sequenced by Illumina sequencing. Posteriorly, a microbiome analysis was conducted to analyze bacterial abundance, diversity and enrichment.

Results: The gut microbiome of Leishmania-infected dogs (BL) is dominated by Prevotella, Collinsella, Bacteroides, and Blautia, with individual variability being the primary determinant of microbiome composition. No significant changes in alpha diversity (Shannon index, gene number) or beta diversity (Bray-Curtis dissimilarity, UniFrac distance) were detected between pre- and post-treatment time points, suggesting that treatment with meglumine antimoniate and allopurinol does not disrupt the gut microbiota. Minor trends in taxonomic shifts were noted, with slight increases in Bifidobacterium pseudocantenulatum, Collinsella tanakaei, and Slackia piriformis after treatment, but these changes were not statistically significant after correction for multiple testing. Linear discriminant analysis and multivariable modeling confirmed that the microbial community structure was resilient to treatment effects. Individual-specific microbiome differences in diversity accounted for 52% of the observed variability, underscoring the personalized nature of the gut microbiota in dogs. Importantly, no adverse microbiome disruptions were detected, even with prolonged allopurinol use.

Conclusions: This study highlights the robustness of the canine gut microbiome during antileishmanial therapy and highlights the use of meglumine antimoniate and allopurinol without compromising gut microbial diversity or health. Further studies with larger cohorts are recommended to confirm these findings and explore the functional roles of the gut microbiota in modulating immune responses in Leishmania-infected dogs.

Fecal microbiota transplantation (FMT) is gaining attention as a method to modulate the gut microbiome in pigs, with the goal of enhancing health and production outcomes. While some studies indicate that FMT can enhance growth performance and intestinal health in piglets, others report minimal or even negative effects. This variability highlights the need for standardized protocols and further research to optimize FMT for swine applications. Currently, the use of FMT in pigs is still in its early stages, with limited studies showing considerable methodological differences. Although some evidence supports the effectiveness of FMT, significant gaps remain in our understanding of its approach and underlying mechanisms. Therefore, this review summarizes the role and development of gut microbiota in pigs, analyzes existing FMT research in pigs, emphasizes the varying outcomes, illustrates the potential mechanisms of action based on human and animal studies and discusses the innovative potential of using co-evolved microbial communities as a transplant material. As our understanding of pig gut microbiome advances, FMT and related microbiome-based interventions could become valuable tools in pig production. However, ongoing research is essential to elucidate their mechanisms and develop reliable protocols.