Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes.
Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes.
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DOI：
10.1128/msystems.00911-20
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发表时间：
2020-09-29
期刊：
影响因子：
6.4
通讯作者：
Ley RE
中科院分区：
文献类型：
--
作者：
Schmidt V;Enav H;Spector TD;Youngblut ND;Ley RE
当人类驯养动物时，一些动物在基因上适应了消化牛奶直到成年（乳糖酶持续性）。具有乳糖酶持久性基因型（AA或AG）的人的肠道微生物组与具有乳糖酶非持久性基因型（GG）的人的肠道微生物组不同，因为含有较少的属于双歧杆菌的细菌，这是一组含有有益物种的细菌。在这里，我们询问了GG和AA/AG基因型成人的肠道微生物组是否在存在的双歧杆菌物种中存在差异。特别是，我们使用了一种新的技术，使我们能够在菌株水平上比较成年人中的双歧杆菌，而不需要传统的培养。我们的研究结果表明，GG基因型提高了丰度的biobacteria的物种无关。我们还注意到，一个人的特定菌株可以在几年后恢复，双胞胎可以共享相同的菌株。考虑到双歧杆菌是从母亲遗传给孩子的，成年后随着时间的推移菌株的稳定性表明了长期的、多代遗传。人类遗传学与肠道微生物组之间最强的关联之一是具有乳糖酶基因（LCT）单核苷酸多态性（SNP）的成人中双歧杆菌的相对丰度更高，与乳糖酶非持久性（GG基因型）相比，乳糖酶持久性（AA/AG基因型）。为了获得这种关联的更细粒度的系统发育分辨率，我们询问了1，680个16 S rRNA文库和245个来自具有各种乳糖酶持久性基因型的成年人肠道微生物组的宏基因组。我们进一步采用了一种新的基于基因组捕获的富集双歧杆菌DNA的方法，该方法来自这些宏基因组的一个子集，包括单卵（MZ）双胞胎对，每个双胞胎对采样2或3次。B。我和B。无论宿主LCT基因型如何，长双歧杆菌都是最丰富的双歧杆菌物种。LCT基因型不能根据双歧杆菌物种的相对丰度或双歧杆菌群落结构来区分。富集双歧杆菌DNA的三种不同宏基因组分析方法揭示了B的个体内时间稳定性。longum，B.和B。两歧菌株对一个可变的微生物组的背景。我们的三种方法中的两种还观察到，对于B，MZ双胞胎对内的菌株共享比无关个体内的菌株共享更大。然而，没有方法揭示宿主LCT基因型对双歧杆菌菌株组成的影响。我们的研究结果支持一个“涨潮举起所有的船”模型的优势biobacteria在成人肠道：他们的高丰度的乳糖酶非持久性比乳糖酶持久性的个人的结果从属水平的扩张。已知双歧杆菌属物种可从母亲传播给儿童，并且在婴儿期和儿童期的个体内稳定：我们的研究结果将这种稳定性延长到成年期。当人类驯养动物时，一些动物在基因上适应了消化牛奶直到成年（乳糖酶持续性）。具有乳糖酶持久性基因型（AA或AG）的人的肠道微生物组与具有乳糖酶非持久性基因型（GG）的人的肠道微生物组不同，因为含有较少的属于双歧杆菌的细菌，这是一组含有有益物种的细菌。在这里，我们询问了GG和AA/AG基因型成人的肠道微生物组是否在存在的双歧杆菌物种中存在差异。特别是，我们使用了一种新的技术，使我们能够在菌株水平上比较成年人中的双歧杆菌，而不需要传统的培养。我们的研究结果表明，GG基因型提高了丰度的biobacteria的物种无关。我们还注意到，一个人的特定菌株可以在几年后恢复，双胞胎可以共享相同的菌株。考虑到双歧杆菌是从母亲遗传给孩子的，成年后随着时间的推移菌株的稳定性表明了长期的、多代遗传。
When humans domesticated animals, some adapted genetically to digest milk into adulthood (lactase persistence). The gut microbiomes of people with lactase-persistent genotypes (AA or AG) differ from those with lactase-nonpersistent genotypes (GG) by containing fewer bacteria belonging to the bifidobacteria, a group which contains beneficial species. Here, we asked if the gut microbiomes of adults with GG and AA/AG genotypes differ in the species of bifidobacteria present. In particular, we used a novel technique which allowed us to compare bifidobacteria in adults at the strain level, without the traditional need for culturing. Our results show that the GG genotype enhances the abundance of bifidobacteria regardless of species. We also noted that a person’s specific strains are recoverable several years later, and twins can share the same ones. Given that bifidobacteria are inherited from mother to child, strain stability over time in adulthood suggests long-term, multigenerational inheritance. One of the strongest associations between human genetics and the gut microbiome is a greater relative abundance of Bifidobacterium in adults with lactase gene (LCT) single nucleotide polymorphisms (SNPs) associated with lactase nonpersistence (GG genotypes), versus lactase persistence (AA/AG genotypes). To gain a finer-grained phylogenetic resolution of this association, we interrogated 1,680 16S rRNA libraries and 245 metagenomes from gut microbiomes of adults with various lactase persistence genotypes. We further employed a novel genome-capture-based enrichment of Bifidobacterium DNA from a subset of these metagenomes, including monozygotic (MZ) twin pairs, each sampled 2 or 3 times. B. adolescentis and B. longum were the most abundant Bifidobacterium species regardless of host LCT genotype. LCT genotypes could not be discriminated based on relative abundances of Bifidobacterium species or Bifidobacterium community structure. Three distinct metagenomic analysis methods of Bifidobacterium-enriched DNA revealed intraindividual temporal stability of B. longum, B. adolescentis, and B. bifidum strains against the background of a changeable microbiome. Two of our three methods also observed greater strain sharing within MZ twin pairs than within unrelated individuals for B. adolescentis, while no method revealed an effect of host LCT genotype on Bifidobacterium strain composition. Our results support a “rising tide lifts all boats” model for the dominant bifidobacteria in the adult gut: their higher abundance in lactase-nonpersistent than in lactase-persistent individuals results from an expansion at the genus level. Bifidobacterium species are known to be transmitted from mother to child and stable within individuals in infancy and childhood: our results extend this stability into adulthood. IMPORTANCE When humans domesticated animals, some adapted genetically to digest milk into adulthood (lactase persistence). The gut microbiomes of people with lactase-persistent genotypes (AA or AG) differ from those with lactase-nonpersistent genotypes (GG) by containing fewer bacteria belonging to the bifidobacteria, a group which contains beneficial species. Here, we asked if the gut microbiomes of adults with GG and AA/AG genotypes differ in the species of bifidobacteria present. In particular, we used a novel technique which allowed us to compare bifidobacteria in adults at the strain level, without the traditional need for culturing. Our results show that the GG genotype enhances the abundance of bifidobacteria regardless of species. We also noted that a person’s specific strains are recoverable several years later, and twins can share the same ones. Given that bifidobacteria are inherited from mother to child, strain stability over time in adulthood suggests long-term, multigenerational inheritance.