Javier del Campo: Microbiomes are more than bacteria, unveiling the eukaryome

In our latest Insight, Javier del Campo of the University of Miami talks about this new Review paper: The eukaryome: Diversity and role of micro‐eukaryotic organisms associated with animal hosts.

The paper

We live in the middle of the microbiome hype. We see the word microbiome showing up everywhere and we commonly associate it to the human gut, and that is correct because the word was coined and popularized by the studies of the human gut microbial communities. That is why most of the public, and some scientist, forget that the study of the microbiome is nothing more than the study of the microbial communities using molecular methods, mostly metabarcoding, and these approaches where adopted by clinical microbiologist from microbial ecology. Thus, we should remind everybody that the boom of the microbiome is as well the boom of ecology, and the integrated way in which ecologist study the environment, including the human gut or any other animal-associated environment.

However, the aforementioned integrated view of the community is not such for most of the microbiome studies. The field is mostly focused on the study of only one compartment of the microbial communities associated to a host, and that compartment is the bacterial one, so it would be probably more correct to call it the bacteriome. Fungi and Protists, the microeukaryotic fraction, has been virtually ignored if we compare the number of studies available that includes this fraction of the microbiome with all the published works on the topic. In recent years, Fungi have started to be targeted in some studies in what has been called the mycobiome, but still the number of publications is extremely small compared with the ones focused on bacteria. In the meantime the rest of the microeukaryotes, what we commonly known as protist still, are extremely understudied despite we know, after centuries of research on parasites and mutualists, that they play crucial roles as symbionts of many animals.

In our publication we present the state of the art of the study of what has been called the eukaryome, the microeukaryotic fraction of the microbiome. Another newly coined term that might seem unnecessary but it is needed because the concept microbiome has been predated by prokaryotes and few people think further than bacteria when they read that word. We can find animal symbionts in all the major groups of eukaryotes, being the alveolates and the excavates the two groups that contain the most. Within both groups we find charismatic symbionts that have been studying for years. For example, the parasite that causes malaria, Plasmodium sp. or the coral mutualist algae, the zooxanthellae, both are alveolates. As part of the excavates we find other well know symbionts such as the brain eating amoeba, Naegleria fowleri or the thermite gut mutualistic protists that help termites digest lignin allowing them to feed on wood. The examples I am providing here are parasites and mutualists, two extremes of the “symbiotic continuum”. Parasites have negative effects on their hosts while mutualists are beneficial to them. These types of symbiotic interactions are the ones that have been more explored but are most likely not the most abundant in nature.

The current view we have of the eukaryome is dominated by parasites and mutualists, this is a result of decades of targeted studies focused on this kind of symbionts and driven mostly by the interest of clinical parasitologists. Whit the introduction of non-targeted approaches, such as the used in bacteria microbiome studies, we will probably see has happened for prokaryotes, that most of the symbionts are commensal, so they are not pernicious or provide any benefit to the host most of the time. I am saying most of the time, because that is another aspect of symbiosis that we need to embrace, is not an static feature but a dynamic one that depends on the symbiont, the host and their environment. As mentioned before, symbiosis is a continuum and certain organisms can transit from one extreme to the opposite of the spectrum, such as the coral endolithic algae Ostreobium sp. at the very beginning of a bleaching event can provide nutrients to its coral host but if the bleaching is to long it will end up killing the coral by overgrowing it. Another example is Blastocysts that for years has been considered a human parasite but recently using metabarcoding has been reported in many healthy individuals, most likely being a commensal.

Eukaryotes play many important roles as symbionts of animals and are key members of their microbiome. Furthermore, they also interact with the bacterial component of the microbiome and studying this interaction is needed to understand comprehensively the processes occurring within this particular ecosystem and how are affecting their host. Novel non-targeted genomic approaches will give us access to the microeukaryotic compartment  of the microbiome and in the coming years we will see how the eukaryotes rise and claim the place they deserve in this microbiome era.

The author

When I decided to study Biology as a high school student I wanted to be a geneticists. I was interested in genetic manipulation, particularly of animals, it sounded to me like science fiction and very exciting. However, in my second year at the University of Barcelona I studied microbiology and I discovered microbial ecology and evolution trough the work of Lynn Margulis among others. Since then I became obsessed with ecological processes at the microscale and I decided that I wanted to become a microbial ecologist. During my PhD I started working mostly with bacteria in marine intertidal systems until I discovered protists. Protist were, and are, mysterious and were severely understudied compared to their non-nucleated counterparts. On top of that its taxonomy was extremely messy, so I found that this particular part of microbial ecosystems could be an interesting challenge. I have been working on microeukaryotes ever since. I started studying them in the oligotrophic ocean water and through my career I moved more and more towards animal-associated environments. Currently I focus my research on the study of marine animal microbiomes including both prokaryotes and eukaryotes.

Read the paper in full here. This paper is part of the Special Feature: Evolution and Ecology of Microbiomes – browse the plain language summaries for this special feature here.

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