New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract

Q1 Medicine

Human Microbiome Journal Pub Date : 2018-12-01 DOI:10.1016/j.humic.2018.10.002

Ranjit Kumar , Jayleen Grams , Daniel I. Chu , David K. Crossman , Richard Stahl , Peter Eipers , Kelly Goldsmith , Michael Crowley , Elliot J. Lefkowitz , Casey D. Morrow

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引用次数: 9

Abstract

Recent studies have shown that microbe strains in normal individuals fecal microbe community are relatively stable over time. Given the role the gut microbe community plays in human health, it is important to understand if disruption of the gastrointestinal tract environment results in emergence of new genomic variants. To address this, we have used a new technique called Window-based single nucleotide similarity (WSS) to analyze the impact of several surgical procedures of the human gastrointestinal tract on the stability of the fecal microbes. Previously, we established a WSS boundary score cutoff to determine if microbe genomic variants were similar. Based on analysis of normal individuals from the Human Microbiome Project, 93% of microbes in paired fecal samples up to 1 year apart were above the cutoff, indicating similar (stable) microbes. For the current study, we analyzed fecal samples from 18 patients undergoing Roux-en-Y gastric bypass (RYGB) or 6 patients undergoing gastric sleeve for extreme obesity. From comparison of the pre-RYGB versus 1–2 year post RYGB samples from the same patients, 65% of the WSS were above the boundary cutoff, while for pre versus 1–2 year samples post surgery for patients undergoing sleeve gastrectomy, 75% of the WSS were above the cutoff. In contrast, analysis of fecal samples from 5 patients pre and post removal of segments of the sigmoid colon revealed that 97% of WSS scores were above the cutoff. Our study establishes emergence of new microbe genomic variants in the fecal community following alteration of the upper gastrointestinal environment.

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上消化道手术中断后患者粪便群落中新的微生物基因组变异

最近的研究表明，随着时间的推移，正常个体粪便微生物群落中的微生物菌株相对稳定。鉴于肠道微生物群落在人类健康中的作用，了解胃肠道环境的破坏是否会导致新的基因组变异的出现是很重要的。为了解决这个问题，我们使用了一种称为基于窗口的单核苷酸相似性(WSS)的新技术来分析人类胃肠道的几种外科手术对粪便微生物稳定性的影响。之前，我们建立了一个WSS边界评分截止值来确定微生物基因组变异是否相似。根据人类微生物组计划对正常个体的分析，在相隔1 年的配对粪便样本中，93%的微生物高于临界值，表明微生物相似(稳定)。在目前的研究中，我们分析了18例接受Roux-en-Y胃旁路术(RYGB)或6例接受胃套管术治疗的极度肥胖患者的粪便样本。通过比较来自同一患者的RYGB前和RYGB后1-2 年的样本，65%的WSS高于边界截断，而对于接受袖胃切除术的患者，术前和术后1-2 年的样本，75%的WSS高于边界截断。相比之下，对5例乙状结肠切除前后患者的粪便样本分析显示，97%的WSS评分高于临界值。我们的研究表明，随着上消化道环境的改变，粪便群落中出现了新的微生物基因组变异。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Human Microbiome Journal Medicine-Infectious Diseases

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期刊介绍： The innumerable microbes living in and on our bodies are known to affect human wellbeing, but our knowledge of their role is still at the very early stages of understanding. Human Microbiome is a new open access journal dedicated to research on the impact of the microbiome on human health and disease. The journal will publish original research, reviews, comments, human microbe descriptions and genome, and letters. Topics covered will include: the repertoire of human-associated microbes, therapeutic intervention, pathophysiology, experimental models, physiological, geographical, and pathological changes, and technical reports; genomic, metabolomic, transcriptomic, and culturomic approaches are welcome.