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

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 wide use of antibiotic in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in elite racehorses than that in normal horses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fiber fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. Conclusions Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalog for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.

研究背景 作为对人类至关重要的驯化物种，马在全球范围内被饲养，用于体育、休闲、食品生产与交通运输，作为机械动力来源。肠道菌群对马的健康、疾病、运动表现及行为均发挥关键作用。
研究结果 本研究利用来自242匹马肠道样本的约2.2 Tb宏基因组测序数据，其中包含110份盲肠样本与132份直肠（粪便）样本，共组装得到4142个微生物宏基因组组装基因组（metagenome-assembled genome, MAG），其中4015个（占比96.93%）疑似为全新物种。基于长读长测序数据，我们成功组装得到13个环状完整细菌染色体基因组，均代表尚未被报道的新物种。本研究在这些MAG中共预测得到超过313568个碳水化合物活性酶（carbohydrate-active enzyme, CAZy），其中超59.77%的序列在公共CAZy数据库中仅表现出较低的相似性匹配。我们在MAG中鉴定出丰度与多样性均较高的抗生素抗性基因（antibiotic resistance gene, ARG），这一结果大概率与马饲养管理中抗生素的广泛使用相关。至少36个MAG（例如隶属于毛螺菌科Lachnospiraceae、颤螺菌科Oscillospiraceae以及瘤胃球菌属Ruminococcus的MAG）在顶级赛马中的丰度显著高于普通马。这些在赛马中富集的MAG包含了纤维发酵产乙酸与丁酸的核心通路中的全部基因，具备产生更多短链脂肪酸以支撑运动表现的潜力。
研究结论 综上，本研究基于短读长与长读长测序数据，从马肠道样本中组装得到4142个MAG。本数据集构建了一套全面的马肠道微生物基因组目录，可为高性能运动相关微生物的发掘以及马肠道微生物组研究提供极具价值的资源。