Variation and transmission of the human gut microbiota across generations - shotgun data

Although composition and functional potential of the human gut microbiota evolve over lifespan, kinship has been identified as a key covariate of microbial community diversification. To date, sharing of microbiota features within families has however mostly been assessed between parents and their direct offspring. Here, we investigate potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (N=102) spanning three to five generations over the same female bloodline. We observe microbiome community composition to be associated with kinship, with seven (low-abundant) genera displaying familial distribution patterns. While kinship and current cohabitation emerged as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter’s age, and being higher among cohabiting pairs than those living apart. Although rare, we do detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.EGA study EGAS00001005649

尽管人类肠道菌群的组成与功能潜力随生命周期动态演变，但亲缘关系已被证实为微生物群落多样化的关键协变量。迄今为止，学界对家族内菌群特征共享情况的评估大多局限于父母与其直系后代之间。本研究针对同一母系血统下跨越3至5代的102个家庭队列（N=102），探究家族微生物组模式与微生物基因型的潜在传播及留存情况。研究发现，微生物群落组成与亲缘关系显著相关，其中7个（低丰度）菌属呈现家族特异性分布模式。尽管亲缘关系与当前共同居住状态呈现高度相关的混杂变量，但我们针对微生物基因型分布与传播概率的探索性分析表明，后者才是菌株传播的关键协变量。研究估算显示，姐妹间以及母女间的潜在传播率最高，且传播率随女儿年龄增长而降低；共同居住的家庭成员间的传播率高于分居者。尽管此类事件较为罕见，但我们确实检测到了跨越3代乃至4代的潜在传播事件，这些事件主要涉及另枝菌属（Alistipes）和拟杆菌属（Bacteroides）的物种。总体而言，本研究分析证实了家族特异性微生物组群落特征的存在，但细菌菌株的传播或共同获得似乎与共同居住状态密切相关。本研究关联EGA研究编号EGAS00001005649。