Conducting a Microbiome Study

By Julia Goodrich, Sara C. Di Rienzi, Angela C. Poole, Omry Koren, William Walters, J. Gregory Caporaso, Rob Knight, Ruth E. Ley. Cell, 2014

647 citations recorded by the source corpus.

Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.

Subfields: Molecular Biology, Physiology

View Paper: https://www.semanticscholar.org/paper/2dad5ebef6427ddf135d4ee596976788ee78ade2

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Citations in the corpus

Ecology and exploration of the rare biosphere (2015, background): “Overall, the most important step in minimizing bias in HTS studies of SSU rRNA genes was the development of a well‑designed computational protocol 167 .”
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing (2016, methodology): “…of community composition, the internal standard reads (those reads classi ﬁ ed as A. ﬁ scheri ) were removed from the original data, and the samples were rare ﬁ ed by sub-sampling a set number of 16S rRNA sequences per sample to control for differences in library size (Goodrich et al., 2014).”
The healthy human microbiome (2016, background): “Large-scale epidemiology in other areas of human health, such as nutrition and lifestyle, has built a solid foundation for prospective, long-running cohorts, painstaking analyses, and carefully validated measurement instruments [119–121], all of which represent particularly promising avenues of expl”
Current challenges and best-practice protocols for microbiome analysis (2019, background): “scenarios: one producing observations without interferences, while the others remain targeted manipulations [38, 39].”
The Gut Microbiota and Inflammation: An Overview (2020, methodology): “An OTU clustering algorithm is applied to identify bacterial genera and species [11].”