Gut Microbiota: a potential target for therapeutics

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Gut microbiota play both versatile and critical roles in the human body. Not only do they help in immune responses, but also contribute to energy metabolism by degrading complex carbohydrates for which humans do not possess the enzymes.1 These symbiotic microorganisms can degrade glycans and polysaccharides, producing short-chain fatty acids (SCFAs) that can be used by the body and are beneficial to the epithelium of the colon, as we learned in BCM441.

Although the characterization of the gut microbiome remains incomplete, it is estimated that over half of microorganisms residing in healthy human GI tracts belong to the Bacteroidetes phylum. Bacteria in this phylum can degrade starch using the starch utilization system. The starch utilization system (Sus) and Sus-like systems consist of several proteins that work to bind, degrade, and import starch into the cell via a multiprotein system (Fig. 1).2

Figure 1. This image, adapted from Santilli,, depicts the starch utilization system (Sus) and the eight proteins that comprise it. The Sus breaks down the polymer starch and imports the breakdown products into the cell using SusC. SusG is the target of acarbose, the small molecule inhibitor analyzed in this study.

Alteration of gut microbiota composition is implicated in a number of human diseases, including inflammatory bowel disease, colorectal cancer, and obesity, some of which have no cure, like Crohn’s disease. Dysbiosis describes abnormalities in gut microbiota populations that are associated with various disorders. Antibiotics are common therapeutics against bacterial infections. However, antibiotics tend to be indiscriminate in their attack against bacteria, sometimes leading to dysbiosis and potential consequences for the human host. Secondary opportunistic bacterial infections have been known to arise following antibiotic use that leads to dysbiosis, and these opportunistic infections are facilitated by alterations in carbohydrate availability.3 Additionally, past work has demonstrated that glycan availability affects microbiota composition. As presented in BCM441, a 2014 Nature paper showed that alteration of gut microbiota, prompted by artificial sweeteners, had systemic consequences, namely due to the development of glucose intolerance.4

Because of its implication in various human diseases, gut microbiota have become a new potential therapeutic target, departing from classical antibiotics and biochemical techniques. Composition of microbiota is readily changeable, unlike the human genome, which makes targeting of microbiota a potential strategy.1 Recent work has explored tungstate as a selective inhibitor of pathogenic bacteria that relieved symptoms of the bowel disease colitis in mice models, although, tungstate should not be ingested by humans.5 A new study by Santilli,, published in ACS Chemical Biology, describes the potential of targeting gut microbiota as a therapeutic agent for human diseases, particularly using small molecule nonmicrobicidal inhibitors.6

From the eight proteins (SusRABCDEFG) that comprise Bacteroides Sus, the protein SusG is an α-amylase located on the outer cellular surface that breaks α1,4-glycosidic bonds in starch-based polysaccharides. SusG is vital to Bacteroides thetaiotamicron growth on starch, even though other amylases are present.4

Santilli, used two species of bacteria from the Bacteroides phylum, B. thetaiotamicron (Bt) and B. fragilis (Bf) to investigate the effect of known human α-amylase inhibitors on growth and survival of these species. Bt and Bf were incubated in an anaerobic chamber with 100 µM of one of three human α-glucosidase inhibitors (acarbose, miglitol, and vogilbose), and one of four polysaccharides (potato starch, pullulan, chondroitin sulfate, and levan) in minimal media. By measuring optical density, the researchers found that acarbose can inhibit metabolism of potato starch and pullulan and thus bacterial growth. Bt and Bf could grow in the presence of miglitol and vogilbose and could metabolize chondroitin sulfate and levan even when treated with acarbose, the two of which are metabolized using not Sus, but Sus-like systems. Acarbose selectively acts on the Sus and does not actually kill the bacterial cells, as confirmed by the presence of viable cells in acarbose-treated cultures.

Fig. 2. Adapted from Santilli,, this image shows the known human α-amylase inhibitor acarbose and a component of acarbose called acarviosin. Both molecules inhibit Bacteroides starch metabolism by Sus.

Acarviosin is essentially acarbose without the maltose component (Fig. 2). A similar study as mentioned above investigated the effects of this small molecule on the growth of Bf and Bt in minimal media containing either potato starch or pullulan. This small molecule inhibits potato starch metabolism but exerts no inhibitory effects on Bt and Bf grown in pullulan-containing media. Not only does this show the selectivity of these small molecules for the Sus, but also the potential ability to target specific starches through chemical modification of acarbose. For both acarbose and acarviosin, a higher concentration of the small molecule leads to increased inhibition of Bacteroides growth.

Acarbose is selective not only considering the targeted system but also bacterial species. Activity of other prominent members of the gut microbiome, namely Ruminococcus bromii from the Firmicutes phylum, E.coli, and Lactobacillus reuteri, were assessed in the presence of acarbose. E. coli and L. reuteri do not metabolize starch and thus were not negatively impacted by acarbose, as expected. In contrast, R. bromii does degrade starch but uses a different protein system in the metabolic process and lacks homologs of Sus proteins. Although there was a small amount of inhibition in pullulan media, R. bromii growth was not affected in media containing either potato starch, fructose, or maltose. Acarbose selectively acts against Bacteroides growth, which differs from antibiotics that may harm more than one type of bacteria.

Gut microbiota composition is dynamic, flexible, and can change within a host’s lifetime, depending on diet and condition. This study contributes to the growing idea of targeting gut microbiota composition as a potential therapeutic avenue. Looking forward, the authors aim to identify the targets within Bt Sus responsible for acarbose inhibition of starch metabolism. Application of this strategy to other gut microbes and using different small molecules are also currently being investigated. Moreover, researchers can study the effects of acarbose, acarviosin, and other derivatives on gut microbes in both healthy and diseased animal models. Instead of using antibiotics and for conditions that involve detrimental alterations in gut microbiota composition, the use of small molecules that selectively inhibit growth of specific bacterial species is a potential option for therapeutic strategies.


1.Jia, W., Li, H., Zhao, L. & Nicholson, J. K. Gut microbiota: a potential new territory for drug targeting. Nature Reviews Drug Discovery 7, 123–129 (2008).

2. Koropatkin, N. M. & Smith, T. J. SusG: A Unique Cell-Membrane-Associated α-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules. Structure 18, 200–215 (2010).

3. Ng, K. M. et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96–99 (2013).

4. Suez, J. et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514, 181–186 (2014).

5. Zhu, W. et al. Precision editing of the gut microbiota ameliorates colitis. Nature 553, 208–211 (2018).

6. Santilli, A. D., Dawson, E. M., Whitehead, K. J. & Whitehead, D. C. Nonmicrobicidal Small Molecule Inhibition of Polysaccharide Metabolism in Human Gut Microbes: A Potential Therapeutic Avenue. ACS Chemical Biology 13, 1165–1172 (2018).

11 thoughts on “Gut Microbiota: a potential target for therapeutics”

  • I think the idea of using targeted non-microbicidal molecules to inhibit the growth of bacteria by removing their ability to process specific food sources rather than completely disrupt it by using bactericidals to outright kill them is a really interesting tactic. The different effects of acarbose and acarviosin based on the starch being used could point the way to discovering other targets for this system. The concern I have with the article is that they did not seem to test growth inhibition on mixed media, meaning media with several different food sources, which would be more reflective of the actual environment in the gut. Is it possible that the presence of different food sources in the gut would result in decreased inhibition or even little to no inhibition?

    • Hi Evan! Yes, in the intestinal environment, the bacteria would be exposed to multiple food sources, and as the paper found, little growth inhibition was observed when presented with chondroitin sulfate and levan, which are polysaccharides. From reading the immediate literature, it seems that the Bacteroides species only uses simple and complex sugars, so I do not think these bacteria would metabolize fats or proteins. So, in terms of the different polysaccharides present, acarbose would have a diminished inhibitory effect because of other sugars that are metabolized not using Sus. However, I think the goal of this article was to demonstrate that acarbose, a small molecule, can inhibit a specific system in the bacteria. For therapeutic uses in the future, media that is reflective of the actual gut environment should be considered!

  • This article was fascinating due to its focus being on targeting the gut bacteria to treat chronic illnesses which until recently were managed sole by dietary means. The fact that the Bt and Bf bacteria were still able to proliferate and survive while being inhibited, so the natural balance of the gut bacteria is still maintained something that is not thought about during antibiotic usage. However, during the study when culturing the bacteria Bt/Bf, E. coli, and Lactobacillus reuteri were they cultured in a medium of the same pH level as the intestines because depending on the answer that could future testing results or even the results seen in the study. In the future, if the research takes off, depending on administration methods, for instance, oral administration the acidity change between the stomach and intestine may degrade the molecule used to perform the inhibition.

    • That is an excellent point! I believe that the media they used was at a pH of 7. So, yes, it would be useful to study the effects of pH on these molecules if this ever does get to a clinical stage.

  • This is an interesting article; I’m curious to see what these authors figure out given they ended this paper by specifically outlining their ongoing explorations. A point in the paper that struck me in particular was that the Bacteroides genus they study is potentially connected to Type I diabetes: “a bloom in these bacteria appears to precede the initial stages of autoimmunity…” (1166). I think it would be really interesting for them to further study this avenue, maybe even by implementing studies in animal models. Perhaps they could use mice that are and aren’t genetically pre-disposed to Type I diabetes and then incorporate the Sus proteins to see whether to not they select for different species of the Bacteroides genus.

    • It would be interesting to study the effects of tailoring gut microbiota populations to possibly alleviate symptoms of Type I diabetes or to lead to a path for a cure. I like your idea about investigating this is mice models. However, what do you mean by “incoporat[ing] Sus proteins?” Are you thinking of knocking the entire Sus system out and then restoring it?

  • The specificity of Acarbose and Acarviosin is part of what makes this study so high impact- the ability of the authors to target the B.thetaiotamicron and B.fragilis bacteria without inhibiting other bacteria that do not metabolize starch preventing dysbiosis. The study mentions bacteria of the phylum Firmicutes that also have to ability to metabolize starch but do not contain the SusG amylase and therefor are not inhibited. Have you considered that inhibition of the Bacteriodetes species could lead to this Firmicutes species becoming more prevalent in the gut and presenting similar problems to those created by the Bacteriodetes species? The microbiota of the gut seem very sensitive to change and I am wondering if a decrease in prevalence of one would simply allow another species to take advantage of this absence and fill that role. However, possibly the specific niche of the SUS system would prevent this.

    • That’s a great question, Kelly! I’m not quite sure what would happen or if Firmicutes tend to be opportunistic. However, one thing the authors made note of was that the effect of acarbose was non-microbicidal – it didn’t kill the bacteria, only inhibited the metabolism of some starches. Because the Bacteroides bacteria are not dying, maybe the population ratio wouldn’t change noticeably. I do think it is difficult to predict what would happen in a person and it may be different with each individual and their own, varying microbial populations.

  • Very interesting article and clear review! First I thought acarbose inhibits well on disrupting all polysaccharide until R. bromii showed up. But in R. bromii, acarbose only affects pullulan but not starch potato. The experiment on R. bromii just makes me more confused. Sus seems not necessary to acarbose, because R. bromii doesn’t have Sus proteins, but acarbose inhibits and only inhibits pullulan in R. bromii. So, does R. bromii have different starch digestion protein that looks like Sus, how does acarbose act on Sus, and how does acarbose act on the proteins in R. bromii? But anyway, what can be confirmed is acarbose doesn’t inhibit monosaccharides and disaccharides in all the organisms studied in the article.

    • R. bromii does have a different system to digest starches (not the Sus). Acarbose had a limited effect on R. bromii growth, so the inhibition was minimal. As for the mechanism of action of acarbose on Sus proteins, that is an active area of research and a question that the authors aim to answer in a future paper. I believe it is still unclear exactly how acarbose acts on the proteins of R. bromii, which cause that small amount of inhibition.

  • For the patient’s who are genetically at risk for diabetes, besides a familial history, it may be important to know what (if anything) leads to a bloom in bacteria, an event that the authors report to precede stages of autoimmunity associated with type I diabetes. In evaluating the concentration dependence on the selective inhibition of potato starch metabolism by Bf, what is the reason that the ability of Bf to metabolize pullulan remains unaffected? Finally, what are some applications of utilizing these techniques to alter the metabolism of polysaccharides in the human gut?

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