Monday, June 10, 2013

Biodiversity in Human Gut Microbiome

Biodiversity in Human Gut Microbiome

by Tak Wan Kim

            When we take a trip to the forest, we see various plants, insects, and animals. By considering more about where they live and how they live, we can figure out that the lives which interact with each other form a community to give and take food sources and other necessary sources to live. The community in the forest is structured by biological factors, and it is called ecosystem. An ecosystem consists of the biological community that occurs in a specific area and the physical and chemical factors that make up its non-living or abiotic environment. Interestingly, we can see various ecosystems in human body. The ecosystems in human body do not consist of other species such as animals and plants, but are comprised of microorganisms. The microbes interact with human body; they are provided energy sources and habitats, and they provide services to human body, such as helping digestion in the gut by metabolizing with ingested food. In this article, I will tell a story about the microorganisms in human gut: how human gut microbes form ecosystem and make biodiversity, how they interact with human body and diet, and furthermore, strategies for keeping a healthy gut microbiome.

Ecosystem and biodiversity of Human Gut Microbiome

Figure 1. Microorganisms in human gut (Image Credit: Juan Gaertner / Shutterstock)
            Ecosystems are formed depending on environmental factors because the species that can live in a specific area depend on food sources and interactive communication with members in the area. In terms of human gut microbial ecosystem, the human gastrointestinal tract is divided into sections which have different pH condition, allowing digestion and nutrient absorption in the proximal region to be separated from the vast microbial populations in the large intestine. This reduces conflict between host and microbes. In the distinct habitats of the gut, environmental filtering and competitive exclusion between microbes are the driving factors shaping microbial diversity (1). Depending on environmental factors in the gut, such as pH, microbes structure their own ecosystem among stomach, small intestine, and large intestine. The stomach retains the food and provides the acidic pH for the host’s proteases to be active. Additional enzymes such as proteases, lipases, and amylase are added from the pancreas and liver via the biliary ducts in the small intestine. Food components that are degradable by the digestive enzymes are broken down to simple sugars, amino acids, and fatty acids, which are absorbed in the SI. Food components that escape digestion (fiber, resistant starch, some peptides and lipids) are passed into the large intestine (2). The environmental factors composed by ingested food and pH are different among sections of gut, and these differences make microbes in gut form a specific ecosystem. The species comprising ecosystems in each stomach, small intestine, and large intestine are given in Fig 2.

Figure 2. Microbial inhabitants in major habitats of human gastrointestinal tract (The Human Gut Microbiome: Ecology and Recent Evolutionary Changes)

In the article “Microbial ecology of the gastrointestinal tract”, Savage, intestinal microbiologist, studied microbial communities in the gastrointestinal tract. Based on observation about microbiomes in mice gut, Savage suggested that microbial communities in the gastrointestinal tract contain autochthonous and allochthonous members, and these categories provide a useful framework for understanding patterns of diversity and stability in the human gastrointestinal tract (3). The autochthonous members occupy physical spaces (niches) and form stable populations over long periods; on the other hand, the allochthonous microbes lack specific niches, and although they may be found in any given habitat in significant numbers, they contribute little to the economy of the ecosystem (3).

            Like I said above, biodiversity of microbiome in human gut is decided by specific condition of each section of gastrointestinal tract. However the compositions of microbial community are different among people because the environmental conditions of guts are distinct depending on body condition, diet, and lifestyle. Therefore, both in terms of their age, geography and cultural traditions, features of gut microbiomes are unique to different locations and lifestyles (4). Dr. Nanette Steinle of the University of Maryland’s School of Medicine and Dr. Emmanuel Mongodin of the University of Maryland Institute of Genome Sciences investigated effect of diet on the composition of microbes in human gut. They provided food of Mediterranean diet to participants and got blood samples from them for the analysis of fasting lipids and stool samples to determine the present microbes. Each individual appears to have a unique microbiome signature, like a fingerprint (5). As a result, ecosystem constructed by microbes in the human gut essentially depends on gastrointestinal tract’s condition like pH; however, it is unique among people because they have differences in lifestyle, diet profile, body conditions, etc.

How to make healthy gut microbiome:

            The microbiome in human gastrointestinal tract greatly influences human health, especially digestion. This is because the gut microbiome is essentially a massive chemical factory performing many metabolic functions, and the chemicals produced by metabolisms are able to affect the human health. The microbes produce massive amounts of antigens, regulating innate signaling mechanisms that affect metabolic and circadian rhythms (6). To know what effects human gastrointestinal tract get from the gut microbiome, we should know normal type of gut microbes. They are represented by 6 main phyla: Bacteroides, Firmicutes (including Clostridia, Lactobacilli and Streptococci), Actinobacteria (including Bifidobacteria), Proteobacteria (including Enterobacteria), Fusobacteria, and Verucomicrobia, that is given in Fig 3. 

Figure 3. Global phylogenetic tree comparing the intestinal microbiomes of healthy children (interior ring, light red) with those of children with IBS (interior ring, light green). From Rajilic-Stojanovic M, et al. Gastroenterology. 2011; 141: 1792-1801

The Fig 3 shows phylogenetic tree comparing the intestinal microbes of healthy children with those of children with IBS (6). Considering the roles played by Lactobacilli and Bifidobacteria, we can figure out why one child’s gut is healthy, while another child has disease. The two bacteria are quite different. In general, lactobacilli tend to have more immunostimulatory effects because they are strong inducers of IL-12, TNF-α and IFN-β. Bifidobacteria are, broadly speaking, anti-inflammatory because they are weak cytokine inducers. Bifidobacteria can actually down-regulate the immunostimulating effects of lactobacilli (7). Therefore, the gut flora's net influence on immune system function is greatly influenced by the relationship between populations of Lactobacilli and Bifidobacteria. As you can see above, the health of gut can be determined by the gut microbiome and their relationship with each other. The composition of human gut microbiome is influenced by what food we ingest. Therefore, a strategy that we can easily do by ourselves is to control diet to make healthy ecosystem of the gut microbiome.


Work Cited
  1. Walter, J., & Ley, R. (January 01, 2011). The human gut microbiome: ecology and recent evolutionary changes. Annual Review of Microbiology, 65, 411-29.
  2. GrabitskeHA, Slavin JL. 2008. Low-digestible carbohydrates in practice. J. Am.Dietetic Assoc. 108:1677–81.
  3. Savage DC. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107–33.
  4. Yatsunenko, T., Rey, F. E., Gordon, J. I., Manary, M. J., Trehan, I., Warner, B., Dominguez-Bello, M. G., ... Caporaso, J. G. (June 14, 2012). Human gut microbiome viewed across age and geography. Nature, 486, 7402, 222-227.
  5. Your Gut’s Microbiome Has A Unique Bacterial Signature: http://www.redorbit.com/news/health/1112829683/microbiome-has-unique-bacteria-signature-042413/
  6. Strategies for Establishing a Healthy Gut Microbiome: http://holisticprimarycare.net/topics/topics-a-g/digestive-health/1333-strategies-for-establishing-a-healthy-gut-microbiome
  7. Weiss G, et al. Cytokine. 2011 Nov;56(2):520-30.
  8. Global phylogenetic tree comparing the intestinal microbiomes of healthy children (interior ring, light red) with those of children with IBS (interior ring, light green). From Rajilic-Stojanovic M, et al. Gastroenterology. 2011; 141: 1792-1801

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