Gut microbes!

The importance of microbial communities is becoming increasingly recognized, and one location in which the role of microscopic symbionts is especially fascinating is in our guts! These tiny organisms, invisible to the human eye, may include bacteria, archaea, protists, and even viruses. For example, bacteria in our intestines help to break down parts of our food that may be particularly difficult to digest—like plant cell walls—and in doing so enable us to consume a wider variety of resources. Over time a suite of bacteria may evolve to be quite specific in the types of cell wall glycans, or polysaccharides, that they can break down, and Martens et al. (2011) found that these unique metabolic capacities are driven by different “gene clusters” that produce the proteins necessary to break down specific polysaccharides. In this way, these symbiotic gut bacteria have evolved in order to occupy specific “carbohydrate niches” in order to coexist within the human gut (Martens et al. 2011). In fact, the diversity of symbiotic gut bacteria in mammals has been found to be greater in herbivores as compared to carnivores with omnivores falling in between (Ley et al. 2008).

Curiosity about the role of microbes in the human body has driven a formibable body of research and has led to massive collaborative enterprises, such as the Human Microbiome Project (NIH Human Microbiome Project 2016). Though they comprise only 1-3% of our body mass, the number of cells and genes belonging to symbiotic microbes far exceeds those of our own bodies (NIH HMP 2016)! With these numbers in mind it’s easy to understand why they might be so vital to the function of our bodies and minds. Shifts in the composition the microbial community in an individual’s gut may be influenced by their weight (Armougom et al. 2009). Interestingly, Armougom et al. (2009) found significantly higher abundance of Lactobacillus species—which are used by farmers to promote growth in livestock—in obese humans as compared to non-obese humans. In comparison, individuals with anorexia had significantly higher abundance of the methanogen, Methanobrevibacter smithii, which could be a result of their ability to use limited or different nutrients in these individuals.

Now how, you may ask, does all of this relate to marine science?! Well, unsurprisingly, fish rely on the contribution of symbiotic microbes for digestion just like humans! These microbes allow for fermentative digestion, which helps with nutrient cycling and is seen in other herbivores, such as cows (Clements et al. 2014). Interestingly, the microbial communities found in fishes may be more closely related to those found in humans than those found in the surrounding environment (Clements et al. 2014), which suggests that the symbionts likely coevolved with their hosts rather than being environmentally acquired. With this in mind, it’s thought that the transfer of intestinal microbes may be a result of coprophagy, in which the juvenile fishes consume the feces of adult fishes. Like humans, fish species with different diets (i.e., detritivores versus herbivores) are home to different microbial communities that are specifically adapted to digest those resources (Clements et al. 2014).

One of the largest bacteria known, Epulopiscium fishelsoni (epulos), is found in the guts of Acanthurus nigrofuscus (brown surgeonfish), which is a very common herbivorous reef fish in Hawaiʻi (Bresler & Fishelson 2006). These eubacteria have a huge amount of DNA per nucleoid and high levels of polyploidy, and this may help E. fishelsoni thrive in the guts of these fishes, which contain a large range of potential food-derived chemicals, or xenobiotics (Bresler & Fishelson 2006). The pH of the intestine of A. nigrofuscus appears to be tied to the presence or absence of protozoan symbionts as well (Montgomery & Pollack 1988). Changes in pH related to symbionts can be seen in extremely short time frames, such as overnight, and this is thought to be due to the aggregation of microbial symbionts around a ball of food, or bolus, maintained in the intestine when the fish is not actively eating (Montgomery & Pollack 1988).

In conclusion, while we know some really interesting stuff about the microbial communities inhabiting the intestines of fishes, we have so much more to learn! Using new, accessible technology, such as next-generation sequencing, we now have the ability to understand a tremendous amount about the invisible world of microbes. As someone interested in the diet of reef herbivores, I cannot wait to see what the future holds for us!



Armougom F, Henry M, Vialettes B, Raccah D, Raoult D (2009) Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients. PLoS ONE 4(9): e7125.

Bresler V & L Fishelson. (2006) Export pumps in Epulopiscium fishelsoni, the symbiotic giant gut bacterium in Acanthurus nigrofuscus. Naturwissenschaften 93: 181- 184.

Clements KD, Angert ER, Montomery WL, and JH Choat. (2014) Intestinal microbiota in fishes: what’s known and what’s not. Molecular Ecology 23: 1891-1898.

Ley RE, Hamady M, Lozupone C, Turnbaugh P, Ramey RR, Bircher S, et al. (2008) Evolution of mammals and their gut microbes. Science 320(5883): 1647-1651.

Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, et al. (2011) Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts. PLoS Biol 9(12): e1001221.

Montgomery WL and PE Pollak. (1988) Gut anatomy and pH in a Red Sea surgeonfish, Acanthurus nigrofuscus. MEPS 44: 7-13.

NIH Human Microbiome Project. (2016)