Learning from clinical microbiologists: culturomics and metagenomics
Clinical microbiologists have started using new, non-conventional methods to study the microbiology of the human gut. In this article, Jeanne Moldenhauer discusses the intricacies of culturomic and metagenomic studies and how this can advance current research.
In recent years there has been significant interest in the sequencing of the human microbiome and what can be learned from this project. One of the areas of interest includes those normally occurring microorganisms in the human gut. It is believed that the human gut microbiota is responsible for maintaining health as well as disease pathogenesis.1 However, study of the gut microbiota has required the development of new culture and evaluation methods. Research has indicated that as many as 80 percent of the human gut bacteria are unknown and considered “unculturable”.1 This is similar to the term used by many pharmaceutical microbiologists – viable but not culturable (VBNC). To remedy this, clinical microbiologists started using new, non-conventional methods; referred to as the “rebirth of culture in microbiology”.1
Metagenomics is a term that refers to the study of genetic material that comes directly from environmental samples, rather than pure colonies of organisms. This is followed by sequencing, depicted in Figure 1, which allows for the detection of a largely unbiased sample of all genes from the sampled communities (ie, they may not be pure cultures).2 The sequencing process in metagenomics includes use of shotgun or PCR-directed sequencing. Shotgun sequencing involves sampling environmental growth from its natural habitat, filtering the particles, lysis and DNA extraction, construction of the cloning library, sequencing of the clones and assembly of the sequence into contigs and scaffolds. This flow is depicted in Figure 2.2