Gaining insight into the implications of the microbiome on human health requires not only a precise characterization of the microbial communities at the structural level, but also to generate knowledge on the metabolic pathways driving the effect. A spectrum of -OMICS techniques (i.e., 16S rDNA sequencing, metagenomic shotgun sequencing, metatranscriptomics, metaproteomics, meta-metabolomics) are becoming increasingly available, which different pros and cons for each methodology.
What is on you opinion the best approach -OMIC approach when studying the relationship of the microbiota with a disease?
Thanks. I understand the issues between the different techniques, but it would be nice to have a sense of what technique do researchers in the field would choose if available resources were not a limitation.
Actually, I don't think there is a best approach but probably if you have enough resources and you are working in a multidisciplinary group you should considere to use both metagenomics and metaproteomics (maybe also metabolomics). By the way shotgun metagenomics can give you a clear view.
I would advise a gradual approach to test which particular questions I want to answer in my patient group. I would begin with 16S rDNA sequencing to see a broad picture, so that I can decide decide whether further characterization requires shotgun metagenomics, metatranscriptomics or metaproteomics. Since I am a geneticist, I consider that meta-metabolomics is least likely to help me, but it may be of great interest if particular metabolic pathways do influence the phenomenon I want to study.
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