Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse

Abstract

Background As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. Results Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. Conclusion Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.

Phenolics from Dendrobium officinale Leaf Ameliorate Dextran Sulfate Sodium-Induced Chronic Colitis by Regulating Gut Microbiota and Intestinal Barrier

“…Previous studies have clarified that Lachnospiraceae_NK4A136_group can increase SCFAs, IL-10, SOD, and Occludin levels to relieve inflammation in UC mice Oscillospiraceae is a key bacterium in the acetate and butyrate production pathway, and DOPL treatment restored the decrease in the relative abundance of unclassified_Oscillospiraceae caused by DSS, which may be closely related to the final increase in the level of SCFAs in DOP groups. Previous reports categorized Colidextribacter as the beneficial bacterium that promotes the production of SCFAs .…”

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties

“…Recent studies have emphasized the crucial role of the gut microbiome in host health and disease [38,39]. However, the majority of gut microbes cannot be cultured in the laboratory, limiting our understanding of their functions, including those related to substance metabolism and antibiotic resistance [15]. Metagenomic sequencing technology can effectively study the functional gene composition of microbial communities.…”

“…Consequently, our understanding of the composition and function of gut microbiota in Jianghan chickens remains limited. The advent of highthroughput sequencing and metagenomic sorting technologies has made it possible to obtain nearly complete metagenomic assembled genomes (Mags) on a large scale [15]. This technology has generated thousands of Mags from chicken cecal microbes, making the metagenomic sequencing approach a reliable and effective method for investigating chicken gut microbiota [16].…”

Jumbo phages possess independent synthesis and utilization systems of NAD+

“…Bacteriophages (phages), as viruses that infect bacteria, are key components in natural microbiomes because they can shape microbial composition and structure, alter host’s metabolisms, spread antibiotic resistance genes, and mediate gene transfer [1–3]. Metagenomic investigations have showed that diverse and abundant gut virome was observed in livestock gut [4, 5]. Recent studies also demonstrated that phages in livestock microbiome may impact the major functions of gut such as feed digestion, microbial protein synthesis, methane emissions [6, 7].…”

“…Metagenomic investigations have showed that diverse and abundant gut virome was observed in livestock gut [4,5]. Recent studies also demonstrated that phages in livestock microbiome may impact the major functions of gut such as feed digestion, microbial protein synthesis, methane emissions [6,7].…”