Gut Microbiota Inside Us

Have you ever heard that the human body has more bacteria compared to human cells? Well, that statement is actually true! The National Institute of Health (2012) stated that our body contains trillions of microorganisms, which outnumber human cells by 10 to 1! These microorganisms include bacteria, fungi, archaea, viruses, and protozoans.

But, don’t worry! Because the majority of these bacteria are non-pathogenic, therefore they would not harm us. In fact, some of them are able to co-habit with our human cells in a symbiotic relationship. These non-pathogenic, and possibly beneficial, microorganisms are known as normal microbiota! The majority of them live on the skin, in the saliva and oral mucosa, and in the gastrointestinal tract (Clemente et al., 2012; Jandhyala, 2015). In this article, we are going to discuss deeper into the normal microorganisms residing in the gastrointestinal tract, commonly called the gut microbiota!

---

About Gut Microbiota

Gut microbiota lives along our gastrointestinal tract, from the esophagus to the rectum, with the most dominant genera of Bacteroides, Clostridium, and Bifidobacterium (Rajilić-Stojanović & de Vos, 2014). Interestingly, this biome of microorganisms has been suggested to become its own organ system of the human body! This is mainly because the gut microbiota have their own metabolic capability and substantial functional plasticity, and they are able to gain their nutrients from the host’s dietary components (Sonnenburg et al., 2005).

Is Gut Microbiota Beneficial?

Yes! Gut microbiota can perform a symbiotic relationship with the human body, helping us with different tasks ranging from our metabolism to our immune system! Let’s discuss them in more detail below.

Nutrient metabolism

Several gut microorganisms, such as Bacteroides, Roseburia, and Enterobacteria, aid in the fermentation of carbohydrates in the colon, producing short-chain fatty acids (SCFA) which are rich in energy for the host to use (Macfarlane & Macfarlane, 2003). Other gut microorganisms also give a positive impact on lipid metabolism, as well as help the synthesis of vitamin K and components of vitamin B (Feitoza et al., 2008).

Antimicrobial protection

The gut microbiota helps the mucosal immune system to prevent the overgrowth of resident pathogens. One of the mechanisms is by inducing local immunoglobulins, which are plasma proteins that are able to bind to antigens of the resident pathogens, aiming them for destruction. In addition, some gut microorganisms are able to induce the synthesis of antimicrobial proteins (AMP), which helps in eliminating pathogenic microorganisms (He et al., 2007).

​Vocabulary Builder 👨‍🔧

Resident pathogens: microorganisms that occupy a certain body site for a long time, generally having an important role

​Vocabulary Builder 👨‍🔧

Immunoglobulins: serum proteins and cells of the immune system, acting as antibodies

Immunomodulation

Immunomodulation is any changes in the human immune system, including its activation or suppression. In this role, the gut microbiota works with parts of the immune system, including the gut-associated lymphoid tissues (GALT), T cells, B cells, macrophages, and dendritic cells.

Protect the gastrointestinal tract barrier and structural integrity

Some gut microorganisms help to produce substances that protect the gastrointestinal tract barrier and structure. One of them is Bacteroides thetaiotaomicron, which increases the expression of small proline-rich protein 2A (sprr2A) for the maintenance of desmosomes of the epithelial villi (Lutgendorff et al., 2008). Another example is the bacterium Lactobacillus rhamnosus, which produces soluble proteins (p40 and p75) which prevent apoptosis of the intestinal epithelial cells (Yan et al., 2011).

​Vocabulary Builder 👨‍🔧

Desmosomes: adhesive, intracellular junction that attaches adjacent cells together

​Vocabulary Builder 👨‍🔧

Apoptosis: programmed cell death, usually as a part of the organism's growth and development

Factors Affecting the Diversity of Gut Microbiota

Gut microbiota varies from person to person. This is because there are several factors that help in shaping the gut microbiome, including:

Birth delivery method

Past research has found that the microbiota profile is largely impacted by the method of delivery, which includes vaginal or cesarean delivery. In infants born vaginally, the intestines are colonized by microorganisms found in the maternal vagina, generally from the genera Lactobacillus and Prevotella (Mackie et al., 1999). On the other hand, the intestines of infants born through cesarean delivery are observed to be colonized by microorganisms found in the maternal skin, such as Streptococcus, Corynebacterium, and Propionibacterium (Dominguez-Bello et al., 2010).

Age

Studies have found that the variations of gut microbiota differ significantly between children-adolescents and adults, especially in the proportions of Bacteroides and Bifidobacterium (Agans et al., 2011; Ringel-Kulka et al., 2013).

Diet during infancy

Interestingly, the type of milk fed to infants also affects the composition of their gut microbiota. Formula-fed infants’ gut microbiota is mainly composed of anaerobic/facultative anaerobic bacteria, such as Enterococcus, Enterobacteria, Bacteroides, Clostridia, and other anaerobic Streptococcus. Meanwhile, the gut microbiota in breastfed infants is dominated by Bifidobacterium and Lactobacillus. This is because of the different compounds contained in each type of milk, especially the indigestible glycans called human milk oligosaccharides (HMO) in breast milk, which are easily broken down by Bifidobacterium and Lactobacillus (Groer et al., 2014; Sherman et al., 2014).

Diet during adulthood

Not only diet during infancy, but diet during adulthood also plays a role in gut microbiota diversity. Research has shown that high consumption of fibers, fruits, and vegetables is associated with a higher number of carbohydrate-metabolizing microorganisms of the phylum Firmicutes, such as Ruminococcus bromii, Roseburia, and Eubacterium rectale (Walker et al., 2010). Meanwhile, an animal-based diet results in a decrease in microorganisms of the Firmicutes phylum, and an increase in bile-tolerant microorganisms, such as Alistipes sp. and Bacteroides sp (David et al., 2013).

Use of antibiotics or antibiotics-like molecules

Lastly, the use of antibiotics and their analogs have important effects on the ecology of the gut microbiota. It has been proven that the use of antibiotics increases the number of multi-drug-resistant bacterial genes (Kersten et al., 2011). In addition, some taxa of the gut microbiome were observed to not recover even months after the treatment, causing a long-term decrease in gut microbiota diversity (Sommer et al., 2009).

---

And now that you know the importance of gut microbiota, let’s not forget to take care of it just like we care about our other organs. You can do this by maintaining a healthy lifestyle, eating your vegetables, and avoiding the use of antibiotics. And without you knowing, these microbes are actually helping our systems work inside our bodies!

---

References

• Agans, R., Rigsbee, L., Kenche, H., Michail, S., Khamis, H. J., & Paliy, O. (2011). Distal gut microbiota of adolescent children is different from that of adults. FEMS Microbiology Ecology, 77(2), 404–412. https://doi.org/10.1111/j.1574-6941.2011.01120.x

• Clemente, J., Ursell, L., Parfrey, L., & Knight, R. (2012). The Impact of the Gut Microbiota on Human Health: An Integrative View. Cell, 148(6), 1258–1270. https://doi.org/10.1016/j.cell.2012.01.035

• David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2013). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559–563. https://doi.org/10.1038/nature12820

• Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971–11975. https://doi.org/10.1073/pnas.1002601107

• Feitoza, A. B., Pereira, A. F., de Costa, N. F., & Ribeiro, B. G. (2008). Conjugated linoleic acid (CLA): effect modulation of body composition and lipid profile. Nutr Hosp., 24(4), Article 422–8.

• Groer, M. W., Luciano, A. A., Dishaw, L. J., Ashmeade, T. L., Miller, E., & Gilbert, J. A. (2014). Development of the preterm infant gut microbiome: a research priority. Microbiome, 2(1). https://doi.org/10.1186/2049-2618-2-38

• He, B., Xu, W., Santini, P. A., Polydorides, A. D., Chiu, A., Estrella, J., Shan, M., Chadburn, A., Villanacci, V., Plebani, A., Knowles, D. M., Rescigno, M., & Cerutti, A. (2007). Intestinal Bacteria Trigger T Cell-Independent Immunoglobulin A2 Class Switching by Inducing Epithelial-Cell Secretion of the Cytokine APRIL. Immunity, 26(6), 812–826. https://doi.org/10.1016/j.immuni.2007.04.014

• Jandhyala, S. M. (2015). Role of the normal gut microbiota. World Journal of Gastroenterology, 21(29), 8787. https://doi.org/10.3748/wjg.v21.i29.8787

• Kersten, R. D., Yang, Y. L., Xu, Y., Cimermancic, P., Nam, S. J., Fenical, W., Fischbach, M. A., Moore, B. S., & Dorrestein, P. C. (2011). A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nature Chemical Biology, 7(11), 794–802. https://doi.org/10.1038/nchembio.684

• Lutgendorff, F., Akkermans, L., & Soderholm, J. (2008). The Role of Microbiota and Probiotics in Stress-Induced Gastrointestinal Damage. Current Molecular Medicine, 8(4), 282–298. https://doi.org/10.2174/156652408784533779

• Macfarlane, S., & Macfarlane, G. T. (2003). Regulation of short-chain fatty acid production. Proceedings of the Nutrition Society, 62(1), 67–72. https://doi.org/10.1079/pns2002207

• Mackie, R. I., Sghir, A., & Gaskins, H. R. (1999). Developmental microbial ecology of the neonatal gastrointestinal tract. The American Journal of Clinical Nutrition, 69(5), 1035s–1045s. https://doi.org/10.1093/ajcn/69.5.1035s

• National Institute of Health. (2012). National Institutes of Health. Retrieved September 7, 2022, from https://www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body#:%7E:text=The%20human%20body%20contains%20trillions,vital%20role%20in%20human%20health

• Rajilić-Stojanović, M., & de Vos, W. M. (2014). The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiology Reviews, 38(5), 996–1047. https://doi.org/10.1111/1574-6976.12075

• Ringel-Kulka, T., Cheng, J., Ringel, Y., Salojärvi, J., Carroll, I., Palva, A., de Vos, W. M., & Satokari, R. (2013). Intestinal Microbiota in Healthy U.S. Young Children and Adults—A High Throughput Microarray Analysis. PLoS ONE, 8(5), e64315. https://doi.org/10.1371/journal.pone.0064315

• Sherman, M. P., Zaghouani, H., & Niklas, V. (2014). Gut microbiota, the immune system, and diet influence the neonatal gut–brain axis. Pediatric Research, 77(1–2), 127–135. https://doi.org/10.1038/pr.2014.161

• Sommer, M. O. A., Dantas, G., & Church, G. M. (2009). Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora. Science, 325(5944), 1128–1131. https://doi.org/10.1126/science.1176950

• Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C. H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005). Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont. Science, 307(5717), 1955–1959. https://doi.org/10.1126/science.1109051

• Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., Louis, P., McIntosh, F., Johnstone, A. M., Lobley, G. E., Parkhill, J., & Flint, H. J. (2010). Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME Journal, 5(2), 220–230. https://doi.org/10.1038/ismej.2010.118

• Yan, F., Cao, H., Cover, T. L., Washington, M. K., Shi, Y., Liu, L., Chaturvedi, R., Peek, R. M., Wilson, K. T., & Polk, D. B. (2011). Colon-specific delivery of a probiotic-derived soluble protein ameliorates intestinal inflammation in mice through an EGFR-dependent mechanism. Journal of Clinical Investigation, 121(6), 2242–2253. https://doi.org/10.1172/jci44031