Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota

作者：Elizabeth Fleming, Victor Pabst, Zoe Scholar, Ruoyun Xiong, Anita Y. Voigt, Wei Zhou, Amelia Hoyt, Rachel Hardy, Anna K. Peterson, Ryan Beach, Yvette Ondouah-Nzutchi, Jinhong Dong, Lucinda Bateman, Suzanne D. Vernon, Julia Oh · 发表于：BMC Microbiology · 年份：2021 · DOI：10.1186/s12866-021-02314-y · 被引用次数：19 · 研究领域：Gut microbiota and health、Dermatology and Skin Diseases、Oral microbiology and periodontitis research

BACKGROUND: Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling. RESULTS: Of total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1-44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2-95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance. CONCLUSIONS: Use of a streamlined set of conditions selected for cultivation of skin, oral, and gut mi...