• Topic of the Month
  • B Vitamins
  • Vitamin K
  • Health Functions
  • 2017
  • Disease Risk Reduction

Diet, Nutrition and the Gut Microbiome

Published on

28 September 2017

They may be invisible to us without a microscope, but the billions of microorganisms that make up our own personal microbiome are very important for our health. While microbes are found almost everywhere in our body, it’s the gut microbiome that has the largest concentration of microorganisms (1).

We’ve known for decades that the gut microbiome plays an important role in nutrition. For example, part of our vitamin K requirements is provided by the bacteria in our gut (2). This is the reason why newborn infants receive vitamin K around the time of their birth: their large intestine has not yet been colonized with bacteria capable of providing them with sufficient vitamin K, placing them at risk of vitamin K deficiency (3){Olson, 1987 #4}. Comprehensive investigations of the gut microbiome show that the types of bacteria present are able to produce all eight B-vitamins, and four of these at levels likely to meet a reasonable portion of daily recommendations (4){Magnusdottir, 2015 #5}. Microbes in the gut can also help improve the digestibility of the diet by breaking down polysaccharides that the human body cannot break down itself, making the energy they contain available (5).

Recent research has focused on how we can change the gut microbiota through nutrition to improve our health. The most abundant type of bacterium in the gut is Bacteroides, and other commonly found types are Faecalibacterium, Bifidobacterium (found in many probiotics), Lachnospiraceae and Roseburia (6). Another way of looking at the gut microbiota is to look at the relative amount of Bacteroidetes (a broad group of rod-shaped bacteria) to Firmicutes (bacteria named for their strong cell wall, and includes the Lactobacilli and Clostridia). For example, the gut microbiota shows distinct differences in the obese, and its composition changes during weight loss. When weight is lost, the proportion of common intestinal tract inhabitants named Bacteroides increase, while the relative proportion of Firmicutes decrease (7). It is thought that these changes in the gut microbiome affect feelings of satiety, modify the body’s efficiency in extracting energy from foods, and can change the overall inflammatory load on the body, impacting the health effects of obesity (7). Three main concepts in changing the gut microbiota are considered: probiotics, prebiotics and synbiotics.


When we talk about probiotics and the gut microbiome, we mean the practice of consuming live microorganisms to provide a health benefit (8). Certain bacteria that are used to acidify milk, such as Bifidobacteria or Lactobacilli, are thought to contribute to gut health by maintaining an acidic environment in the large intestine, which promotes its normal function (8). It is also thought that the interaction between gut microbes and our immune system is important for its development. Certain probiotics may be able to assist in the normal development of the immune system by stimulating it without causing disease (9). Several thorough meta-analyses show that probiotics may be effective for several conditions related to gut health or the immune system in general. For example, probiotics may be moderately effective in reducing the incidence of antibiotic-associated diarrhea from meta-analyses conducted in children (10) and adults (11), including Clostridium difficile-associated diarrhea (12). Probiotics may help with abdominal pain in children (13) and adults (14) according to meta-analyses. Another meta-analysis found that probiotics could reduce incidence, duration and medication use associated with upper respiratory tract infections (15). Combinations of different probiotic strains may have a synergistic effect (16).


Prebiotics are a food component consumed with the intention of selectively increasing the proportion of a particular type of microorganism to produce a health benefit. They can be seen as a food for our personal microbes (17). For example, the development of a newborn infant’s normal microbiome is enhanced by the specialized sugars found in human milk, called human milk oligosaccharides (HMOs). HMOs provide “food” for Bifidobacteria and therefore their growth is encouraged by feeding breast milk. Bifidobacteria are considered to have a beneficial effect on infants’ metabolic and immunological systems (17). Other compounds that have been widely studied for their prebiotic effects include the soluble fiber inulin, as well as galactooligosaccharides (GOS) and fructooligosaccharides (FOS), which are made up of short chains of sugar molecules. Consuming these prebiotics causes the proportion of beneficial Bifidobacteria in the gut to increase. Reviews have found beneficial effects on diverse areas of health such as improving satiety, skin moisture, a reduction in constipation, and improvements in the lipid profile (17, 18).


When prebiotics and probiotics are used together, that is supplying certain microbes and their preferred carbohydrate source to the body, we are talking about synbiotics (19). The combination of a probiotic and matching prebiotic means that the probiotic dosed is more likely to thrive in the gut and exert its intended effects. Screening different combinations of pro- and prebiotics helps select synbiotic combinations (20). So far, evidence on synbiotics suggests that it helps stimulate normal bowel function in adults and infants (21, 22), although this area of research is evolving rapidly.

The Future of Gut Microbiome and Nutrition

The human microbiome is incredibly complex and diverse, and there is much that we don’t know about the microorganisms that live within us. One area of microbiota research involves mapping the microbiome using “omics” technologies, which are sophisticated techniques that use state-of-the-art computing systems and software to collectively analyze large amounts of data relating to a particular area of biological science (23). Especially for gut microbiome research, looking at the range of genes that are in the microbiome is of interest (genomics, transcriptomics), as is analyzing how the different compounds formed by the microorganisms in the gut work together (metabolomics, proteomics). These technologies help us better understand the astonishing array of microbes that abound in our digestive tracts.

A second area is the expansion of the concept of prebiotics. In the past, it has been rather narrowly defined as a dietary component that is fermented by a narrow range of gut bacteria to improve health. The dietary components that could be classified as prebiotics are restricted to carbohydrates that we don’t digest ourselves such as dietary fibers. However, it is possible that other components outside of this definition are able to modify the composition of the gut to produce a benefit to health. For example, the B-vitamin riboflavin can stimulate the growth of the “beneficial” bacterium Faecalibacterium prausnitzii in low-oxygen environments such as the large intestine. As the microbiota of people with inflammatory bowel disease is characterized by a lack of Faecalibacterium prausnitzii compared to healthy people, riboflavin supplementation could act as a prebiotic using the newly-proposed broader definition (24).

The complexity of the gut microbiome is incredible, and we are just scratching the surface of understanding how deeply it affects our health. The field of microbiome research is evolving rapidly. The future may see specialized prebiotics, tailored to our particular personal microorganisms (6), that help us to maintain a healthy weight, reduce our risk of cardiovascular disease or keep our blood glucose at a healthy level by modifying the abundance of certain microbes (25). It seems like our tiny friends hold the key to our good health!


  1. Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 2016;14(8):e1002533. doi: 10.1371/journal.pbio.1002533
  2. Karl JP, Fu X, Wang X, Zhao Y, Shen J, Zhang C, Wolfe BE, Saltzman E, Zhao L, Booth SL. Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota-targeted dietary intervention. Am J Clin Nutr 2015;102(1):84-93. doi: 10.3945/ajcn.115.109496
  3. Olson JA. Recommended dietary intakes (RDI) of vitamin K in humans. Am J Clin Nutr 1987;45(4):687-92.
  4.  Magnusdottir S, Ravcheev D, de Crecy-Lagard V, Thiele I. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front Genet 2015;6:148. doi: 10.3389/fgene.2015.00148
  5. Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol 2015;31(1):69-75. doi: 10.1097/MOG.0000000000000139
  6. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, et al. Enterotypes of the human gut microbiome. Nature 2011;473(7346):174-80. doi: 10.1038/nature09944
  7. Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012;489(7415):242-9. doi: 10.1038/nature11552
  8. Hungin AP, Mulligan C, Pot B, Whorwell P, Agreus L, Fracasso P, Lionis C, Mendive J, Philippart de Foy JM, Rubin G, et al. Systematic review: probiotics in the management of lower gastrointestinal symptoms in clinical practice -- an evidence-based international guide. Aliment Pharmacol Ther 2013;38(8):864-86. doi: 10.1111/apt.12460
  9. Amenyogbe N, Kollmann TR, Ben-Othman R. Early-Life Host-Microbiome Interphase: The Key Frontier for Immune Development. Front Pediatr 2017;5:111. doi: 10.3389/fped.2017.00111
  10. Goldenberg JZ, Lytvyn L, Steurich J, Parkin P, Mahant S, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev 2015(12):CD004827. doi: 10.1002/14651858.CD004827.pub4
  11. Hempel S, Newberry SJ, Maher AR, Wang Z, Miles JN, Shanman R, Johnsen B, Shekelle PG. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA 2012;307(18):1959-69. doi: 10.1001/jama.2012.3507
  12. Goldenberg JZ, Ma SS, Saxton JD, Martzen MR, Vandvik PO, Thorlund K, Guyatt GH, Johnston BC. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev 2013(5):CD006095. doi: 10.1002/14651858.CD006095.pub3
  13. Newlove-Delgado TV, Martin AE, Abbott RA, Bethel A, Thompson-Coon J, Whear R, Logan S. Dietary interventions for recurrent abdominal pain in childhood. Cochrane Database Syst Rev 2017;3:CD010972. doi: 10.1002/14651858.CD010972.pub2
  14. Didari T, Mozaffari S, Nikfar S, Abdollahi M. Effectiveness of probiotics in irritable bowel syndrome: Updated systematic review with meta-analysis. World J Gastroenterol 2015;21(10):3072-84. doi: 10.3748/wjg.v21.i10.3072
  15. Hao Q, Dong BR, Wu T. Probiotics for preventing acute upper respiratory tract infections. Cochrane Database Syst Rev 2015(2):CD006895. doi: 10.1002/14651858.CD006895.pub3
  16. Collado MC, Jalonen L, Meriluoto J, Salminen S. Protection mechanism of probiotic combination against human pathogens: in vitro adhesion to human intestinal mucus. Asia Pac J Clin Nutr 2006;15(4):570-5.
  17. Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 2017;14(8):491-502. doi: 10.1038/nrgastro.2017.75
  18. Collins S, Reid G. Distant Site Effects of Ingested Prebiotics. Nutrients 2016;8(9). doi: 10.3390/nu8090523
  19. Collins MD, Gibson GR. Probiotics, prebiotics, and synbiotics: approaches for modulating the microbial ecology of the gut. Am J Clin Nutr 1999;69(5):1052S-7S.
  20. Makelainen H, Saarinen M, Stowell J, Rautonen N, Ouwehand AC. Xylo-oligosaccharides and lactitol promote the growth of Bifidobacterium lactis and Lactobacillus species in pure cultures. Benef Microbes 2010;1(2):139-48. doi: 10.3920/BM2009.0029
  21. Ford AC, Quigley EM, Lacy BE, Lembo AJ, Saito YA, Schiller LR, Soffer EE, Spiegel BM, Moayyedi P. Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis. Am J Gastroenterol 2014;109(10):1547-61; quiz 6, 62. doi: 10.1038/ajg.2014.202
  22. Mugambi MN, Musekiwa A, Lombard M, Young T, Blaauw R. Synbiotics, probiotics or prebiotics in infant formula for full term infants: a systematic review. Nutr J 2012;11:81. doi: 10.1186/1475-2891-11-81
  23. Berger B, Peng J, Singh M. Computational solutions for omics data. Nat Rev Genet 2013;14(5):333-46. doi: 10.1038/nrg3433
  24. Steinert RE, Sadaghian Sadabad M, Harmsen HJ, Weber P. The prebiotic concept and human health: a changing landscape with riboflavin as a novel prebiotic candidate? Eur J Clin Nutr 2016;70(12):1348-53. doi: 10.1038/ejcn.2016.119
  25. Daliri EB, Wei S, Oh DH, Lee BH. The human microbiome and metabolomics: Current concepts and applications. Crit Rev Food Sci Nutr 2017;57(16):3565-76. doi: 10.1080/10408398.2016.1220913

This site uses cookies to store information on your computer.

Learn more