2 Analyzing Microbiomes
Analyzing Microbiomes
Choosing the correct approach when characterizing a microbiome is important when considering what questions are trying to be answered. Who are the players? What is the function? What genes are being expressed? How do they interact?
Even though when assessing a microbiome all members of the microbiota should be considered, some insight can be gained by viewing individual groups, such as the prokaryotic component, which can be further compartmentalized into the bacteriome and archaeome. In some cases, it is difficult to completely characterize all of the members due to inherent biological differences between these communities, and in other situations, certain groups may be absent or irrelevant to the study. In so, analyzing these individual pieces could help reveal their distinct importance and contribution to the overall big picture.
The type of analysis also depends on the research question. If the sole interest is to identify all the bacteria in a sample, then a metagenomic approach may work best. Whereas, if an interest lies in what the microorganisms are doing, then a metatranscriptomics or metaproteomics approach would be more appropriate. If there is an interest in one or a few particular members of the microbiome, culture-based techniques (culturomics) could be implemented, which can often catch rare microbes that are missed using sequencing techniques because of data filtering protocols (Lagier et al., 2012, Allaband et al., 2019). However, it is usually difficult to characterize an entire microbiome based on just a few microbes and achieving multiple isolations is extremely difficult as a ‘one-size-fits-all’ type media does not exist.
Sample Collection
Depending on the type of research questions and the particular microbiome of interest, there are different ways to collect microbial communities that will be subjected to analysis. That is, the approach to collecting microbes from the human gut is much different than getting a soil sample. Really, there is no perfect method for any one microbiome, though some may be more difficult to obtain than others, and will depend on a variety of factors such as feasibility, cost, patient acceptance, and downstream analytical methods (Allaband et al., 2019). It can also be very difficult to capture all microbes within a microbiome sample, as inevitably some will be missed or cannot be collected by a particular technique. For example, when analyzing the gut microbiome, stool collection is preferred due to its ease and frequent accessibility, but this method often misses microbes in the small intestine and others which are mucosally adherent as opposed to excreted (Eckburg et al., 2005, de Carcer et al., 2010, Allaband et al., 2019). Additionally, collection and storage materials, storage time, and transport options should be considered as these can compromise sample integrity and create problems for various analytical approaches (Costello et al., 2009, Capor