16S rRNA data and sample metadata for "Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals"
This repository contains raw data for the manuscript "Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals".
While microbial communities inhabit a wide variety of complex natural environments, in vitro culturing enables highly controlled conditions and high-throughput interrogation for generating mechanistic insights. In vitro assemblies of gut commensals have recently been introduced as models for the intestinal microbiota, which plays fundamental roles in host health. However, a protocol for 16S rRNA sequencing and analysis of in vitro samples that optimizes financial cost, time/effort, and accuracy/reproducibility has yet to be established. Here, we systematically identify protocol elements that have significant impact, introduce bias, and/or can be simplified. Our results indicate that community diversity and composition are generally unaffected by substantial protocol streamlining. Additionally, we demonstrate that a strictly aerobic halophile is an effective spike-in for estimating absolute abundances in communities of anaerobic gut commensals. This time- and money-saving protocol should accelerate discovery by increasing 16S rRNA data reliability and comparability and through the incorporation of absolute abundance estimates.
|Type of resource
|[ca. 2019 - 2021]
|December 5, 2022
|January 7, 2022; December 1, 2021
|Celis Luna, Arianna
|in vitro communities
|16S rRNA sequencing
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- This work is licensed under an Open Data Commons Attribution License v1.0.
- Preferred citation
- Celis Luna, A., Aranda-Diaz, A., Culver, R., Xue, K., Relman, D., Shi, H., and Huang, K. (2021). 16S rRNA data for "Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals". Stanford Digital Repository. Available at https://purl.stanford.edu/ct503zg9433
Stanford Research DataView other items in this collection in SearchWorks
Also listed in
Loading usage metrics...