Methods to study the intestinal microbiome

Recent technological advances have led to a revolution in microbiology: the detailed characterization of microbiomes in and on humans, animals, plants, in soil, and a myriad of other sites. Microbiomes are comprised of microbial communities (microbiota) and their associated genomes. Traditional low throughput methods to study complex microbial assemblages have been surpassed by high throughput technologies that can deliver information about microbiome compositions and functions in a much faster and more comprehensive way.

In this study, we have used low-throughput approaches such as traditional endpoint and quantitative PCR (qPCR) for molecular identification of microbes in fecal or intestinal material. As examples for modern high throughput analyses of microbiomes, massively parallel sequencing of 16S ribosomal RNA amplicons was employed (16S metagenomic sequencing). The latter methodology delivers immense amounts of sequence reads (amplicon sequence variants, ASVs) that require sophisticated bioinformatics for quality control and data analyses.

Results from these approaches will be presented with a discussion of advantages and drawbacks of utilizing the methods for small (summer) research projects by undergraduate, graduate and medical students. Furthermore, the potential for implementation of other modern technologies such as whole genome shotgun metagenomics, transcriptomics, proteomics, and metabolomics for small or larger research projects will be discussed.

In conclusion, microbiome research is not necessarily restricted to large and expensive research projects. Well planned, small projects are possible as part of larger studies or even as stand-alone studies that allow students to experience scientific research and discovery in this new and exciting field.