Megaphages infect Prevotella and variants are widespread in gut microbiomes
Megaphages infect Prevotella and variants are widespread in gut microbiomes
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DOI：
10.1038/s41564-018-0338-9
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发表时间：
2019-04-01
影响因子：
28.3
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
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作者：
Devoto, Audra E.;Santini, Joanne M.;Banfield, Jillian F.
噬菌体（Bacteriophage，简称BPHs）通过宿主裂解作用显著地改变微生物群落的组成，重新分配营养物质，并通过水平基因转移推动进化。尽管它们很重要，但关于人类微生物组中的细菌仍有很多东西需要了解。我们调查了来自孟加拉国和坦桑尼亚的人类，两个非洲狒狒社会群体和丹麦猪的肠道微生物组;这些微生物组中的许多含有属于Glade的细菌，其基因组长度>540个细菌，这是人类微生物组中报道的最大的细菌，接近有史以来报道的最大细菌。我们称之为Lak。CRISPR间隔区靶向表明Lak感染普雷沃氏菌属的细菌。我们手动策划完成了从宏基因组回收的15个不同的Lak噬菌体基因组。基因组显示出几个有趣的特征，包括使用替代遗传密码，高表达的大基因间区域和多达35个推定的转移RNA，其中一些含有神秘的内含子。不同的个体具有不同的噬菌体基因型，并且在连续采样日内变异频率的变化反映了噬菌体亚群相对丰度的变化。最近的同源重组导致了广泛的基因组混合九狒狒Lak噬菌体种群。我们推断Lak噬菌体广泛存在于含有普雷沃菌属物种的肠道群落中，并得出结论，噬菌体具有令人着迷且未充分研究的生物学特性，可能是人类和动物肠道微生物组中常见但在很大程度上被忽视的组成部分。
Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a Glade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.