The impact of the gut microbiota in human health is affected by several factors including its composition, drug administrations, therapeutic interventions and underlying diseases. Unfortunately, many human microbiota datasets available publicly were collected to study the impact of single variables, and typically consist of outpatients in cross-sectional studies, have small sample numbers and/or lack metadata to account for confounders. These limitations can complicate reusing the data for questions outside their original focus. Here, we provide comprehensive longitudinal patient dataset that overcomes those limitations: a collection of fecal microbiota compositions (>10,000 microbiota samples from >1,000 patients) and a rich description of the “hospitalome” experienced by the hosts, i.e., their drug exposures and other metadata from patients with cancer, hospitalized to receive allogeneic hematopoietic cell transplantation (allo-HCT) at a large cancer center in the United States. We present five examples of how to apply these data to address clinical and scientific questions on host-associated microbial communities.

肠道微生物群对人类健康的影响受到多种因素的影响，包括其组成、药物管理、治疗干预和潜在疾病。不幸的是，收集了许多公开可用的人类微生物群数据集以研究单一变量的影响，并且通常由横断面研究中的门诊患者组成，样本数量少和/或缺乏元数据来解释混杂因素。这些限制可能会使将数据重复用于其原始重点之外的问题变得复杂。在这里，我们提供了克服这些限制的全面的纵向患者数据集：粪便微生物群组成的集合（来自 >1,000 名患者的 >10,000 个微生物群样本）和对宿主经历的“医院生活”的丰富描述，即，他们的药物暴露和其他来自癌症患者的元数据，这些患者在美国一家大型癌症中心住院接受同种异体造血细胞移植 (allo-HCT)。我们提供了五个示例，说明如何应用这些数据来解决有关宿主相关微生物群落的临床和科学问题。