The GIT Microbiome: It's a Party in Your Gut!

Fig. 1: Bacteria improve neonatal immunity

"Gut microbiome." "Probiotics." "Good bacteria." “Kombucha.” “Yogurt.” “Superbug.” “Antibiotic resistance.” These and many other buzz words may pop into your head when you hear about the microbes that live within your body. The gut microbiome is a steadily growing field of understanding, and these buzz words are just highlights of the multifaceted subject the gut microbiome and its implications are. We're discovering many influences the microbes colonizing our guts have, from our behavior to the immune system, to manipulating nutrition and changing our metabolism.

Last year, Salzwedel et al. observed one-year-old children during a resting-state-functional MRI (rsfMRI) to see brain activity (example image, see Fig. 2), specifically in the amygdala, our brain's "emotion center". Scientists also took fecal samples from the babies and analyzed the samples for different species of bacteria. They found an interesting correlation of behavioral patterns coinciding with certain bacterial species, though the children were too young to predict any specifically positive or negative behaviors (Salzwedel et al., 2017). As more study of the symbiotic relationships between microbes and host occur, we are discovering more links between their influence and our behavior. Long-term study of individuals with certain “bacterial profiles” could prove to have interesting results.

Fig. 2: Example amygdala rsfMRI (Baeken et al., 2014)

The immune system was once believed to seek and destroy all microbes; nowadays, we better understand how the "good bacteria" assist the immune system in keeping out the "bad bacteria": competitive inhibition. A breakthrough in treatment against the neonatal sepsis epidemic in India by Dr. Pinaki Panigrahi and his team last year found that the genus of bacteria Lactobacillus, used in fermented foods such as kimchi, sauerkraut, khalpi, helped boost the immune systems of newborn babies when used as a probiotic (Douclef, 2017). Swain et al. further investigated the health benefits of fermented foods as a probiotic source, first assessing the process of food fermentation and how the bacteria alter the nutrient structures, and then linking their activity to many immune system support functions (see Figure 3) (Swain et al., 2014).

Fig. 3: Probiotic benefits (Swain et al., 2014)

You're likely most familiar with how bacteria influence our metabolism. Separate from our innate ability to digest the nutrients in our diet, termed autoenzymatic digestion (digestion via the enzymes we secrete), bacteria, via alloenzymatic digestion (digestion via enzymes not from the host), provide the important functions of synthesizing many important vitamins, complex carbohydrate break down, and short-chain fatty acids (SCFA) formation, molecules integral to the structure and quality of cell membranes. Additionally, bacteria transform complex proteins into essential and non-essential amino acids, providing vital building blocks for life (Cummings and Macfarlane, 1997).

Fig. 4: Unique species in cows (Jami and Mizrahi, 2012)

Theory suggests that colonization is a step-by-step process, similar to the way a forest grows: pioneer species first colonize the area, creating a more accommodating environment for subsequent species to further colonize (Fig. 5 & 6) (Hooper and Gordon, 2001). Microbes colonize all sections of the gastrointestinal tract (GIT), from the foregut/small intestine, to the midgut, to the hindgut/large intestine. Throughout these different areas, scientists have found generally unique groupings. These differences in colonizing species is due to many factors, including pH, or acidity, of the GIT environment, and digesta retention time, or how long digesting food stays in that portion of the gut. In humans, most of our bacterial fermentation happens after our small intestine, where most of the nutrient absorption occurs, so we don't have quite the bacterial diversity or dependency as other animal species. Cows, in comparison, are theorized to host between 5,000 and 7,500 unique species of bacteria (Fig. 4), as they rely heavily on bacterial fermentation in their foregut for their required nutrients (Jami and Mizrahi, 2012).

Fig. 5: Proposed advantage to gut colonization (Hooper et al., 2001)

Beyond the bacteria we know of, scientists have discovered many other organisms: protozoa likely act as the environmental predator to control bacterial populations (Chábe, Lockmer, and Ségurel, 2017); fungi are commensal, and act as additional nutrients in times of nutrient deficiency; yeasts likely contribute to the anaerobic environment of the gut by using the small amounts of oxygen for cellular respiration; and bacteriophages also contribute to bacterial population control.

Beyond humans, we are furthering our knowledge of how the gut microbiome influences our fellow animals, especially in the livestock industry. Providing high quality meat and animal products efficiently and inexpensively, while providing the best quality of life for these hard workers, are constant goals for livestock growers and producers. Improving and refining the gut microbiome is integral to animal welfare, health, and ultimately, production. From egg laying hens and meat chickens, to dairy and beef cattle, to swine and sheep, the gut microbiome influences an animals’ digestion and absorption of nutrients. Creating more efficient animals cuts down on the #1 production cost: feed. Increasing feed conversion efficiency will help make the future of food more sustainable and cost-effective. One way to do this is to better understand what species provide metabolic benefits. Latorre et al. found bacterial colonization can be feed specific, when studying feed and the microbiome in broiler chickens (meat birds). They identified microbes unique to dried distillers grains (DDGs) when compared to birds on other diets (Latorre et al., 2017).

Fig. 6: Step-wise colonization (Hooper et al., 2001)

The future of the gut microbiome is vast. As we continue to learn more about the intricate interactions between the microbes living with us, we will hopefully gain more understanding of how they can further benefit our lives, and help us combat rising issues like antibiotic resistance “superbugs”, obesity and diabetes, and increased nutrient extraction. 


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References:

Advanced Lipids: Healthy Gut Bacteria. c2018. INFAT; [accessed 2018 Feb 02]. http://advancedlipids.com/benefits/healthy-gut-bacteria.

Baeken, C., D. Marinazzo, P. Van Schuerbeek, G. Wu, J. De Mey, R. Luypaert, and R. De Raedt. 2014. Left and Right Amygdala - Mediofrontal Cortical Functional Connectivity Is Differentially Modulated by Harm Avoidance. PLOS ONE. 9(4):1-11. 

Chabé, M., A Lokmer, and L. Ségurel. 2017. Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Trends Parasitol. 33(12):925-934.

Cummings, J.H. and G.T. Macfarlane. 1997. Role of intestinal bacteria in nutrient metabolism. Clinical Nutrition. 16:3-11.

Doucleff, M. 2017. Probiotic Bacteria Could Protect Newborns From Deadly Infection. NPR. https://www.npr.org/sections/goatsandsoda/2017/08/16/543920822/probiotic-bacteria-could-protect-newborns-from-deadly-infection.

Hooper, L.V. and J.I. Gordon. 2001. Commenal host-bacterial relationships in the gut. Science. 292(5519):1115-1118.

Jami, E. and I. Mizrahi. 2012. Composition and Similarity of Bovine Rumen Microbiota across Individual Animals. PLOS ONE. 7(3):1-8.

Latorre, J.D., X. Hernandez-Velasco, J.L. Vicente, R. Wolfenden, B.M. Hargis, and G. Tellez. 2017. Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles. Poult Sci. 96:2728-2735.

Salzwedel, A., G. Wei, A. Carlson, V. Milisavljevic, K. Xia, A. Azcarate-Peril, M. Styner, A. Thompson, X. Geng, B. Goldman, J. Gilmore, and R. Santelli. 2017. Gut Microbiome and Brain Functional Connectivity in Infants: A Preliminary Study Focusing on the Amygdala. Biol Psychiatry 81:S300-S301.

Swain, M.R., M. Anandharaj, R.C. Ray, and R.P. Rani. 2014. Fermented fruit and vegetables of Asia: a potential source of probiotics. BRI. 2014:1-19.