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.

中文翻译：

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双歧杆菌属的菌株水平分析。乳糖酶持久性基因型不同的成年人肠道微生物组的分离

人类遗传学与肠道微生物组之间最强的关联之一是成年人中双歧杆菌与乳糖酶非持久性（GG基因型）相关的乳糖酶基因（LCT）单核苷酸多态性（SNPs）与乳糖酶持久性（AA / AG基因型）相对较高）。为了获得更精细的系统发育关系解析，我们从具有各种乳糖酶持久性基因型的成年人肠道微生物区系中询问了1,680个16S rRNA文库和245个基因组。我们进一步从这些元基因组的子集中，包括双合子（MZ）双胞胎对，每对进行了2到3次采样，采用了基于双基因组DNA的新型基于双歧杆菌DNA的富集。青春双歧杆菌和长双歧杆菌不论宿主LCT基因型如何，它们都是最丰富的双歧杆菌物种。LCT基因型不能根据双歧杆菌种类或双歧杆菌群落结构的相对丰度来区分。富集双歧杆菌的DNA的三种不同的宏基因组学分析方法显示，在可变微生物组的背景下，长双歧杆菌，青春双歧杆菌和双歧双歧杆菌的个体内时间稳定性。我们的三种方法中的两种还观察到MZ双胞胎对中的菌株共享比不相关个体中的青春双歧杆菌更大。，但没有方法揭示宿主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了成年肠道中主要双歧杆菌的“潮起潮落”模式：乳糖酶非持久性个体比乳糖酶持久性个体的丰度更高，这归因于属水平的扩展。已知双歧杆菌是从母体传播到儿童的，在婴儿期和儿童期可在个体内稳定：我们的结果将这种稳定性扩展到成年。