婴儿和成人粪便微生物群中整合前噬菌体的扩展目录显示溶原性的高流行率。

An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny.

作者信息

Dikareva Evgenia, Matharu Dollwin, Lahtinen Emilia, Kolho Kaija-Leena, De Vos Willem M, Salonen Anne, Ponsero Alise J

机构信息

Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.

Children's Hospital, Paediatric Research Centre, University of Helsinki and HUS, Helsinki, Finland.

出版信息

Front Microbiol. 2023 Sep 5;14:1254535. doi: 10.3389/fmicb.2023.1254535. eCollection 2023.

DOI:10.3389/fmicb.2023.1254535

PMID:37731926

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10508911/

Abstract

BACKGROUND AND AIMS

The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential to shape the gut bacterial communities. However, the complex ecological interactions between phages and their bacterial host are still poorly characterized. In this study, we investigated the abundance and diversity of integrated prophages in infant and adult gut bacteria by detecting integrated prophages in metagenome assembled genomes (MAGs) of commensal bacteria.

METHODS

Our study included 88 infants sampled at 3 weeks, 3 months, 6 months, and 12 months ( = 323 total samples), and their parents around delivery time ( = 138 total samples). Fecal DNA was extracted and characterized by using shotgun metagenomic sequencing, and a collection of prokaryotic MAGs was generated. The MAG collection was screened for the presence of integrated bacteriophage sequences, allowing their taxonomic and functional characterization.

RESULTS

A large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 prophage sequences longer than 10 kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed among , while a very high prevalence of lysogen MAGs were observed in . Interestingly for several bacterial families such as and , the prevalence of prophages in MAGs was higher in early infant time point (3 weeks and 3 months) than in later sampling points (6 and 12 months) and in adults. The prophage sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. Finally, we explored the functional repertoire of the potential auxiliary metabolic genes carried by these prophages, encoding functions involved in carbohydrate metabolism and degradation, amino acid metabolism and carbon metabolism.

CONCLUSION

Our study provides an enhanced understanding of the diversity and prevalence of lysogens in infant and adult gut microbiota and suggests a complex interplay between prophages and their bacterial hosts.

摘要

背景与目的

幼儿期肠道微生物群落的获得与逐渐成熟是个体健康发育的核心。噬菌体有可能塑造肠道细菌群落。然而，噬菌体与其细菌宿主之间复杂的生态相互作用仍未得到充分表征。在本研究中，我们通过检测共生细菌宏基因组组装基因组（MAG）中的整合噬菌体，调查了婴儿和成人肠道细菌中整合前噬菌体的丰度和多样性。

方法

我们的研究纳入了88名分别在3周、3个月、6个月和12个月时采样的婴儿（共323个样本），以及他们在分娩前后的父母（共138个样本）。提取粪便DNA并通过鸟枪法宏基因组测序进行表征，生成了一组原核MAG。对MAG集合进行筛选，以检测整合噬菌体序列的存在，从而对其进行分类学和功能表征。

结果

从婴儿和成人肠道微生物群中获得了大量的6186个MAG，并对其进行整合前噬菌体筛选，从而鉴定出7165个长度超过10 kb的前噬菌体序列。引人注目的是，超过70%的近乎完整的MAG被鉴定为溶原菌。MAG中前噬菌体的流行率因细菌家族而异，在……中观察到较低的流行率，而在……中观察到溶原菌MAG的流行率非常高。有趣的是，对于几个细菌家族，如……和……，MAG中前噬菌体的流行率在婴儿早期时间点（3周和3个月）高于后期采样点（6个月和12个月）以及成人。前噬菌体序列被聚类为5616个类物种vOTU，其中77%是新的。最后，我们探索了这些前噬菌体携带的潜在辅助代谢基因的功能库，这些基因编码参与碳水化合物代谢和降解、氨基酸代谢和碳代谢的功能。