Collection Methods for Microbiome Samples

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Overview of the Human Microbiome

Analysis of the human microbiome is an exciting and rapidly expanding field of research. The human microbiome includes microbes and their genes and metabolites that colonize different body niches, such as the gut, mouth, skin, respiratory tract, and genitals. The microbiome is known to have beneficial roles in normal homeostasis, such as assisting in the bioconversion of nutrients, detoxification, protection from pathogenic microorganisms, supporting immunity, and maintaining host development, metabolism, and physiology. Microorganisms are important factors affecting human health and disease, and they are studied to develop new treatments. Therefore, accurate qualitative and quantitative measurements and inferences about microbial community composition and function are essential to provide reliable and meaningful biological conclusions.

Overview of strategies for interrogating the microbiome.Fig.1 Overview of strategies for interrogating the microbiome. (Poussin, 2018)

DNA-based Microbiome Studies

DNA-based microbiome studies generally fall into two categories. Targeted amplicon studies focus on one or a few marker genes and use these markers to reveal the composition and diversity of the microbiota. Other studies have used a whole metagenomic approach. This is sometimes called shotgun metagenomics because of the random nature of obtaining genome sequences.

  • Taxonomic Profiling Studies

In principle, longer sequences should yield higher resolution for applications such as classification, defining novel taxa, or identifying specific biomarker organisms based on a culture-independent approach. However, changes in community composition can often be assessed based on a gene fragment as small as 100 bp.

  • Functional Profiling Studies

Compared with the typical 16S-rDNA-based classification analysis methods, the sequencing requirements of metagenomic functional analysis methods are different. Initial studies involved sequencing clones of large-insert libraries that were derived from genomic DNA extracted from a microbial community.

Human Microbiome Samples Collection

Because different sampling environments may introduce different types of systematic bias, it is especially important to consider the method of sample collection.

To facilitate human microbiome research, in prospective cohort studies, researchers need to collect samples, including stool samples, that can be used to assess the role of the microbiome in disease etiology. Stool samples are representative of the distal gut microbiome.

A comprehensive understanding of the interactions of the oral microbiome with environmental and host factors may help unravel the role the oral microbiome plays in health and disease.

Exhaustive analyses of skin microbiota can not only provide a better understanding of cutaneous processes and diseases but can also suggest targets for developing therapies. The use of prebiotics and probiotics on the skin is a promising area of research.

The vaginal microbiota contains a wide variety of microbial communities known as the vaginal microbiota. Alterations in the vaginal microbiota and host-microbe interactions have been implicated in many gynecological and obstetric conditions.

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  1. Poussin, C.; et al. Interrogating the microbiome: experimental and computational considerations in support of study reproducibility. Drug discovery today. 2018, 23(9): 1644-1657.

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