The woman’s gut microbiota during pregnancy may support nutrient acquisition, is associated with diseases, and has been linked to infant health. However, there is limited information on gut microbial characteristics and dependence in pregnant women. In this study, we provide a comprehensive overview of the gut microbial characteristics of 1479 pregnant women using 16S rRNA gene sequencing of fecal samples. We identify a core microbiota of pregnant women, which displays a similar overall structure to that of age-matched nonpregnant women. Our data show that the gestational age-associated variation in the gut microbiota, from the ninth week of gestation to antepartum, is relatively limited. Building upon rich metadata, we reveal a set of exogenous and intrinsic host factors that are highly correlated with the variation in gut microbial community composition and function. These microbiota covariates are concentrated in basic host properties (e.g., age and residency status) and blood clinical parameters, suggesting that individual heterogeneity is the major force shaping the gut microbiome during pregnancy. Moreover, we identify microbial and functional markers that are associated with age, pre-pregnancy body mass index, residency status, and pre-pregnancy and gestational diseases. The gut microbiota during pregnancy is also different between women with high or low gestational weight gain. Our study demonstrates the structure, gestational age-associated variation, and associations with host factors of the gut microbiota during pregnancy and strengthens the understanding of microbe–host interactions. The results from this study offer new materials and prospects for gut microbiome research in clinical and diagnostic fields.

女性在怀孕期间的肠道微生物群可能支持营养获取，与疾病有关，并与婴儿健康有关。然而，关于孕妇肠道微生物特征和依赖性的信息有限。在这项研究中，我们使用粪便样本的 16S rRNA 基因测序，全面概述了 1479 名孕妇的肠道微生物特征。我们确定了孕妇的核心微生物群，其整体结构与年龄匹配的非孕妇相似。我们的数据显示，从妊娠第 9 周到产前，肠道微生物群与孕龄相关的变化相对有限。基于丰富的元数据，我们揭示了一组与肠道微生物群落组成和功能变化高度相关的外源性和内在宿主因素。这些微生物群协变量集中在基本宿主特性（例如，年龄和居住状况）和血液临床参数中，表明个体异质性是塑造怀孕期间肠道微生物群的主要力量。此外，我们确定了与年龄、孕前体重指数、居住状况以及孕前和妊娠疾病相关的微生物和功能标记。妊娠期体重增加高或低的女性在怀孕期间的肠道微生物群也不同。我们的研究证明了结构、与孕龄相关的变异、以及与怀孕期间肠道微生物群宿主因素的关联，并加强对微生物-宿主相互作用的理解。这项研究的结果为临床和诊断领域的肠道微生物组研究提供了新材料和前景。