Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations
Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations
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DOI：
10.1038/ismej.2014.12
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发表时间：
2014-08-01
期刊：
影响因子：
11
通讯作者：
Stanton, Thaddeus B.
中科院分区：
文献类型：
--
作者：
Looft, Torey;Allen, Heather K.;Stanton, Thaddeus B.
对有益肠道微生物群落的干扰是抗生素的潜在附带效应，抗生素在动物农业中有许多用途（疾病的治疗或预防和饲料效率的提高）。了解抗生素对不同肠道部位细菌群落的影响对于充分认识饲料中抗生素的益处和后果至关重要。在本研究中，我们定义了来自小肠（回肠）和大肠（盲肠和结肠）以及粪便的肠道和粘膜细菌群落，并表征了饲料中抗生素（氯四环素、磺胺甲基嗪和青霉素（ASP250））对这些群落的影响。16S rRNA基因序列和细菌成员和功能的宏基因组分析显示，小肠和大肠的位置存在显著差异，包括在回肠中厚壁菌门和噬菌体编码基因的富集。大肠菌群编码了许多降解植物细胞壁成分的基因，而这些基因在回肠中是缺乏的。与粘膜相关的回肠微生物群比管腔具有更大的细菌多样性，但与大肠粘膜具有相似的隶属关系，这表明大多数肠道微生物可以与粘膜结合，并可能作为管腔的接种物。对抗生素喂养动物的微生物群的附带影响导致了与对照动物的差异，显著的变化是回肠大肠杆菌种群的增加，所有肠道部位的拉赫杆菌种群的增加，以及对未施用抗生素的耐药基因的增加。表征不同肠道位置的不同代谢能力和对扰动的反应将为改善肠道健康和食品安全的策略提供信息。
Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.