Thanks for sharing this perspective, Adriana. As a microbiologist focusing on bacteria, I’m definitely guilty of having tunnel vision to other microbes. This an issue for other fields of microbiology too and something the community as a whole needs to improve. It’s especially important to be considering diversity in metagenomic studies. When DNA is isolated from the microbiome (or any other environmental source), scientists can’t selectively isolate bacterial or fungal DNA. Likely, data about fungi and protists in the microbiome is already available and waiting for someone to use it with an inclusive perspective. Whether talking about fungi, protists, or even bacteria, I don’t think we know enough to make treatment decisions based on the microbiome  yet. It’s hard to understand an individual organism in a laboratory environment, let alone a population of interacting organisms in an environment we can’t easily access. 

Great article! You are highlighting something very important and something that is not talked about when considering these microbiome studies. I recently took a seminar on microbiome research and we did not discuss this whatsoever. Many of the nutrition-focused microbiome studies use 16S sequencing which is specific to bacteria and thus makes it impossible to capture our fungus friends. However, there are some who have done shotgun sequencing, which like Molly is suggesting, would offer the opportunity to expand upon the human microbiome research. Considering the current state of microbiome research, I think what you are highlighting will offer some possible answers to a field with many questions and add a lot more questions that need answering. But as you say, we cannot consider bacteria, fungi, and protists as independent of each other if we want to get to the bottom  of this. They function together as a community and so thus need to be considered as such. 

Adriana, this is a great read and a much needed perspective. All of the non-bacterial species in the gut have been sorely overlooked, and you’ve highlighted some examples where this can be dangerous.

I have enjoyed some articles, such as these published a while ago in EMBO and Microbiology & Molecular Biology Reviews, that point to this problem and suggest ways of changing our thinking about the gut microbiome. In microbial ecology, still very much an environmental rather than a medical science, microbes are studied in terms of how they relate to and interact with each other, as well as the biogeochemical  elements of their surroundings. We need to find ways to integrate terminology and modes of thinking from classical microbial ecology into the very modern era of microbiome study, or we’ll continue to miss important insights such as those you point out in your article here.

Interesting article, I think this is a huge gap in the field of microbiome research at the moment.

Since you cited studies regarding microbial shifts in Crohn’s  disease, I think it is worth mentioning a study that came out in Nature last month which provided a year long multi-omics study of the gut microbiome of patients with Crohn’s disease through the Integrative Human Microbiome Project.

In the study they focus primarily on bacterial loads, similar to your criticisms above, but they share a huge amount of data in the supplementary information including the observation of a spike in viral load preceding microbial dysbiosis. Additionally, they include data showing that subjects with dysbiotic Crohn’s disease have higher titers of anti-yeast antibodies, further highlighting your point that studying the microbiome in a more holistic manner is likely essential to moving forward as a field.