Since the second that Darwin stepped off the S.S. Beagle exhilarated by thoughts of how species diversity occurs, he received criticism. Now that the scientific community has had some time (over 180 years to be exact) to wrap their heads around his theory, new ideas on evolution have emerged. Darwin may have made some breakthrough observations about life on the Galapagos Islands but what he didn’t consider was all of the microbes living on and inside him, as well as inside his famous finches, and their role in the evolution of their host organisms.

I’m not going to bore you with debates on how the universe first came to be. There was a big bang maybe? Anyways, fast forward 750 million years or so to primitive prokaryotic cells. The leading hypothesis is that prokaryotic life emerged before eukaryotic life. The endosymbiotic theory proposes that mitochondria were once free-living prokaryotes that were phagocytosed, or engulfed by, and found their niche in a larger prokaryotic cell. BOOM! We have eukaryotic cells with membrane bound organelles and a mitochondrion that are making usable energy, and in return have a stable place to live. Because of this fateful union, eukaryotic cells started coming together to form multicellular organisms giving rise to all of the plants and animals of the modern world.

In 1991, Lynn Margulis coined the term holobiont. This term characterizes a host and all the microbial organisms that live on and inside it (Margulis & Fester, 1991). Since prokaryotic life is hypothesized to have existed before eukaryotic, one could hypothesize that even the first eukaryotic organisms were surrounded by prokaryotes. And so began the debate of holobiont evolution: when considering how certain organisms evolved and speciated, should we consider all of the microbes that were living in and on them? How big of an impact have they had? Were they evolving too? What if microbes were out-competed by eukaryotic cells and the earth was sterile? Would our world be the same? Would we exist?

Piggy-backing off of the term holobiont, the term hologenome refers to the genome of the host as well as the genome of all of the organisms living in the host. Since microbes have horizontal gene transfer, their genomes change more often than ours. Since the microbes that live inside of us are able to readily adapt to certain contexts, do we benefit from that when our environments change? Can we more readily adapt because of them? These are the over-arching questions driving new research (Simon, Marchesi, Mougel, & Selosse, 2019).

The microbiome can confer nutrients to the host, protect and aid in development (namely of the immune system). Colonization resistance occurs when bacteria that grows in a controlled manner and protects from harmful bacteria colonization. This happens inside the human gut. Good bacteria in the human gut not only aides in breaking down nutrients but does not leave space and nutrients for pathogens to colonize and harm the host. A nonhuman system that has been well characterized is that of the bobtail squid and Vibrio fisheri bacteria. V. fisheri is a bioluminescent bacteria that colonizes a special organ in the squid called the light organ.

Interestingly, large carnivorous predators often swim under the squid, closer to the ocean floor. The moonlight at night shines down and squid would be easily seen by predators looking up towards the moon. If they glow, they blend with the moonlight and are undetectable by predators. The bobtail squid is conferred with a huge benefit by their bacterial symbionts. Such a tight association between the two organisms may have influenced their evolution. What would happen to the squid without these glowing bacteria? Since the microbes are a key to survival in many cases, it is important they are studied (McFall-Ngai, 2014).

The field of microbiomics is evolving.Coupling molecular tools such as RT-PCR and qPCR (hyperlink Karens article) with the technology for high-throughput sequencing, methods for analyzing microbiomes are getting better and better making projects such as the Human Microbiome Project (HMP) possible. The Human Microbiome Project aims to establish what microbes are common among individuals and furthermore, what microbial genes are common among individuals (NIH HMP Working Group et al., 2009). Not only are studies being conducted on humans, but also on plants, insects, and animals. Establishing a “microbial core” may help to identify when a host organism is not healthy and identify characteristics of different diseases through microbial composition. It also creates new pathways for research in that if each organism of a certain species has a certain microbe in their gut, what benefit could it possibly be conferring to the host? And then questions could be answered on whether or not that symbiont influenced the hosts speciation or evolutionary pattern.

Many people are skeptical of this theory, specifically if host and microbiome components should be considered as one whole unit. Douglas and Werren argue that the mode of transmission of the microbe from host parent to offspring should be considered. They also argue that though the term holobiont is convenient, it does not take into consideration the selection process that the microbes are going through inside the host. Since it does not have a consistent ratio of each kind of bacteria at all times, it cannot be given this term referring to one living organism as a whole. The host and microbiome could be considered as a habitat in itself (Douglas & Werren, 2016). Because of its lack of consistency, the debate of whether organisms should be considered holobionts continues.

Only research and time will tell how big the impact microbes are having on their host fitness. Determining what organisms are there and how they are benefiting their hosts may give insight on how they may have influenced their fitness and furthermore, how they evolved.


Douglas, A. E., & Werren, J. H. (2016). Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts. MBio, 7(2), e02099-15.

Margulis, L., 1938-2011 (viaf)108159261, & Fester, R. (1991). Symbiosis as a source of evolutionary innovation: Speciation and morphogenesis. Retrieved from

McFall-Ngai, M. J. (2014). The importance of microbes in animal development: Lessons from the squid-vibrio symbiosis. Annual Review of Microbiology, 68, 177–194.

NIH HMP Working Group, Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., … Guyer, M. (2009). The NIH Human Microbiome Project. Genome Research, 19(12), 2317–2323.

Simon, J.-C., Marchesi, J. R., Mougel, C., & Selosse, M.-A. (2019). Host-microbiota interactions: From holobiont theory to analysis. Microbiome, 7(1), 5.