培养富集+测序可揭示肠道细菌核心及附属基因
创作:热心肠 审核:szx 2019年04月18日
  • 结合液体培养及深度鸟枪法测序,可研究肠道菌群中低丰度细菌的基因组;
  • 在培养富集的菌群(CEM)中,组装出187个细菌物种,相比于非培养富集的菌群(CIM),CEM中可鉴定出更多(1.3倍)的抗性基因;
  • 泛基因组分析发现,阴沟肠杆菌抗性基因与其核心基因组相关,而与潜在的可移动元件无关,大肠杆菌刚好相反;
  • 运用这种方法可推断抗生素耐药基因是固有的,还是潜在的基因水平转移的结果。
主编推荐语
szx
《Microbiome》上发表的一项最新研究,报道了结合液体培养与鸟枪法测序,可研究肠道菌群中低丰度细菌的基因组,并通过此方法鉴定出了阴沟肠杆菌及大肠杆菌的耐药基因,并可推断基因水平转移可能性。该方法对于研究肠道细菌耐药性以及获得方式具有参考价值。
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Microbiome [IF:11.607]

Culture-enriched human gut microbiomes reveal core and accessory resistance genes

人体肠道菌群的培养富集揭示了核心和附属抗性基因

10.1186/s40168-019-0669-7

2019-04-05, Article

Abstract & Authors:展开

Abstract:收起
BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.
RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.
CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.

First Authors:
Frédéric Raymond

Correspondence Authors:
Frédéric Raymond

All Authors:
Frédéric Raymond,Maurice Boissinot,Amin Ahmed Ouameur,Maxime Deraspe,Pier-Luc Plante,Sewagnouin Rogia Kpanou,Ève Bérubé,Ann Huletsky,Paul H Roy,Marc Ouellette,Michel G Bergeron,Jacques Corbeil

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