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

Abstract

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 microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness

“…To obtain mouse skin bacterial strains, we used moist swabs to collect the total skin surface. After collection, the swab was thoroughly vortexed in 1.5-ml Eppendorf tubes, the solution was diluted and cultivated as described in a previous study (Fleming et al, 2021), and the bacterial isolate was identified by 16S rDNA sequencing.…”

New research frontiers pertaining to the infant gut microbiota

“…The establishment of cultivation-independent techniques, in particular 16S rRNA-based microbial profiling and shotgun metagenomics, facilitated the discovery of novel microbes residing in the human body. Most of these newly identified microbes had escaped detection because they were unculturable under the applied in vitro conditions [11][12][13][14][15][16] . This prompted the establishment of novel methodologies intended to cultivate these thus far unculturable bacteria [Figure 1].…”

“…The introduction of culturomics protocols in research projects aimed at exploring as yet unknown elements of the complex intestinal microbiota has provoked an approximately 23% increase in the current collection of cultivated gut microbes [11] . MALDI-TOF mass spectrometry allows very reliable and low-cost identification of bacterial isolates in high-throughput culturomics workflows such as those that need to be applied for the precise mapping of the microbial biodiversity of the human gut [11][12][13][14][15][16] . [ 35] .…”