The Pig’s other genome: a reference gene catalogue of the gut microbiome

Pig is a main species for livestock and biomedicine. The pig genome sequence was recently reported. To boost research, we established a catalogue of the genes of the gut microbiome based on faecal samples of 287 pigs from France, Denmark and China. More than 7.6 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing, highlighting more similarities with the human than with the mouse catalogue. The pig and human catalogues share only 12.6 and 9.3 % of their genes, respectively, but 70 and 95% of their functional pathways. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotics resistance genes (ARGs) reflected antibiotics supplementation in each farm system, and revealed that non-antibiotics-fed animals still harbour ARGs. The pig catalogue creates a resource for whole metagenomics-based studies, highly valuable for research in biomedicine and for sustainable knowledge-based pig farming.

猪是畜牧养殖与生物医药研究中的核心物种之一，其基因组序列已于近期被解析并公开。为推动相关研究进展，我们基于采自法国、丹麦与中国的287头猪的粪便样本，构建了猪肠道微生物组基因目录。通过深度宏基因组测序，本研究共鉴定出超过760万个非冗余基因，对应719个宏基因组物种；该目录与人类肠道微生物组基因目录的相似性显著高于其与小鼠相关目录的相似性。猪肠道微生物组基因目录与人类肠道微生物组基因目录的基因重叠率分别仅为各自总基因集的12.6%与9.3%，但二者功能通路的重叠率则分别可达70%与95%。猪肠道菌群的组成会受到性别、年龄与品种的显著影响。对抗生素抗性基因（antibiotics resistance genes, ARGs）携带率的分析结果反映了各养殖系统的抗生素使用情况，同时发现未饲喂抗生素的生猪仍携带ARGs。本猪肠道微生物组基因目录为全宏基因组学相关研究提供了核心资源，对生物医药研究以及可持续知识型生猪养殖均具有极高的应用价值。

搜集汇总

背景与挑战

背景概述

该数据集是一个猪肠道微生物组参考基因目录，基于来自法国、丹麦和中国的287头猪的粪便样本，通过深度宏基因组测序识别了超过760万个非冗余基因和719个宏基因组物种。研究发现猪与人类肠道微生物组在功能通路上高度相似（共享70%和95%），但基因共享率较低，并分析了抗生素抗性基因的流行情况，为生物医学研究和可持续养猪提供了重要资源。