Can the Food We Eat Insert Genes into the Gut Microbiome?
Find out how foods impact our bacterial genes
Have you ever heard the saying, “You are what you eat?” Although the statement is a bit of a stretch, what you eat significantly impacts your metabolism and cellular processes, which in turn, impacts you physically. Within each of us is the microbiome, which is comprised of 300 trillion organisms that live on and in the body. The largest microbiome, with the most variation of organisms, resides in our gut, or gastrointestinal system. The stomach, small intestine, and large intestine are teeming with bacteria, fungi and viruses, all crucial for food processing, synthesis of vitamins, healthy gut function, and overall health.
The microbiome is created and maintained by numerous factors, a major one being our diet. Foods do not just sustain us, they sustain our microbiome. Foods may also do more to the microbiome than simply feed the organisms. All foods have genes, as do humans and the organisms of the microbiome. The genes within the microbiome are influenced by the foods we eat. Not only does diet influence the genetic make-up of our microbiome, but foods may also transfer their genes to the microbiome, resulting in changes inside the organisms. If the changes within organisms are large enough, the person may be impacted positively or negatively, depending on the diet and the resultant microbiome.
Genes and Why They Matter
Every living organism has a genetic code called DNA. Changes to the way the genetic code is read may occur from things outside the DNA, such as our environment—this is considered epigenetics. If proteins or segments of DNA or the structure of DNA can be changed, the overall makeup of the organism changes. If foods can transfer their own genes into organisms, it makes for a profound way that our diet impacts our wellbeing.
What’s so Special About the Microbiome?
Each individual has a special gut microbiome, which impacts their overall health. For example, patients with an imbalance in their gut microbiome can develop a serious infection with the bacterium Clostridium difficile. On the other hand, altering the gut microbiome of patients with certain diseases is very effective. In patients with inflammatory bowel disease, fecal transplant—the transfer of a healthy person’s stool and the associated gut microbiome to the patient—is effective in some cases. In one case report, fecal transplant for C. difficile infection resulted in hair growth in 2 patients with alopecia universalis, although the reasons for the hair regrowth are not clear.
The gut microbiome may affect many different systems in the body including the skin. In regard to the gut-skin axis, maintaining a healthy gut microbiome can positively influence skin conditions like eczema and psoriasis, along with other conditions. Changes in the gut microbiome of an individual may influence overall health. If we know what impacts our microbiome, we can gain more control over our health.
The genes within microbiomes are more mobile than human genes. Because of this additional mobility, the organisms that make up our microbiome have the ability to transfer their genes from one organism to the next, something humans cannot do. Our DNA is much more complex and tightly bound. The transfer of genes from one bacterium to another in the gut microbiome is called horizontal gene transfer. Gut bacteria can transfer genes responsible for antibiotic resistance or factors that make the bacteria more resistant to the immune system.
Plant genes to the gut microbiome
Plants also have more mobile genes than humans. Horizontal gene transfer is possible in plants and has been shown in research. The big question is whether the plants we eat have the ability to transfer their genes to the organisms in the gut. Horizontal gene transfer between different species is rare but exists. Analysis and comparison of the genes in fungi and 6 different plant species showed that plants transferred their genes to fungi long ago. A present-day study showed that plants can transfer genes to bacteria and fungi. Plant-based diets significantly impact the bacteria in our gut. In a large study looking at plant-based diets, researchers found that <400 common compounds found in plants change the expression of genes for specified bacterial proteins. Regardless of gene transfer, gene expression within our microbiome appears to be affected by the foods we eat.
When it comes to foods in the diet, in vitro studies show that bacteria in the gut microbiome, E. coli, and S. gordonii, are able to take up genes in the form of plasmids and free DNA.[15,16] In a study looking at 12 different foods including milk, soy products, tomato, carrot, and orange juice, spinach, and cabbage, the investigators determined that E. coli took up the food DNA in conditions typical of the human body. Another in vitro study showed that the DNA of blood sausage transferred its DNA to S. gordonii. Both of these studies show that foods in our diets are capable of transferring their DNA, It remains to be seen if this happens within the human gut and what impact it may have; therefore, more research is needed.
Plant bacteria genes to the gut microbiome
Although plant genes are not currently known to transfer to the microbiome, the organisms found on certain plants interact with our gut microbiome. Sushi eaters from Japan have a specific bacterium, Bacteroides plebeius (B. plebeius), that developed the ability to breakdown seaweed in sushi by taking up the genes from a bacterium, Zobellia galactanivorans, associated with seaweed.[17,18] The genes are now called the “sushi-genes.” Without the transfer of these genes, B. plebeius in the gut would not be able to metabolize seaweed and Japanese individuals would have a difficult time eating sushi regularly.
Eating Your Way to a New Microbiome
More research is needed to determine if different foods can transfer their genes to our microbes within. Regardless, the microbiome is susceptible to diet the same way individuals are susceptible. Long-term and short-term diets can change the gut microbiome. A plant-based diet with fruits and vegetables results in a very diverse microbiome, while diets high in meat and low in plants results in microbiomes with little diversity. The more diverse and balanced the microbiome, the better and the healthier the individual will be overall. There are well-known foods that harm your microbiome, in the same way, there are good foods to nourish your microbiome. Food harmful to the gut microbiome includes trans fats, high fructose corn syrup, and artificial sweeteners.[20-22] Foods that nourish the gut microbiome include yogurt, high fiber foods, and fruits and vegetables.[23,24] The next time you pick up your favorite food, think about how it may be impacting the organisms living in the gut.
- 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; PMID: 27541692 Link to research.
- Quigley EM. Gut bacteria in health and disease. Gastroenterol Hepatol (N Y).2013;9(9):560-569; PMID: 24729765 Link to research.
- David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature.2014;505(7484):559-563; PMID: 24336217 Link to research.
- Tammen SA, Friso S, Choi SW. Epigenetics: the link between nature and nurture. Mol Aspects Med.2013;34(4):753-764; PMID: 22906839 Link to research.
- Burke KE, Lamont JT. Clostridium difficile infection: a worldwide disease. Gut Liver.2014;8(1):1-6; PMID: 24516694 Link to research.
- Browne AS, Kelly CR. Fecal Transplant in Inflammatory Bowel Disease. Gastroenterol Clin North Am.2017;46(4):825-837; PMID: 29173524 Link to research.
- Rebello D, Wang E, Yen E, et al. Hair Growth in Two Alopecia Patients after Fecal Microbiota Transplant. ACG Case Rep J.2017;4:e107; PMID: 28932754 Link to research.
- Saarialho-Kere U. The gut-skin axis. J Pediatr Gastroenterol Nutr.2004;39 Suppl 3:S734-735; PMID: 15167366 Link to research.
- Brito IL, Yilmaz S, Huang K, et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature.2016;535(7612):435-439; PMID: 27409808 Link to research.
- van Reenen CA, Dicks LM. Horizontal gene transfer amongst probiotic lactic acid bacteria and other intestinal microbiota: what are the possibilities? A review. Arch Microbiol.2011;193(3):157-168; PMID: 21193902 Link to research.
- Gao C, Ren X, Mason AS, et al. Horizontal gene transfer in plants. Funct Integr Genomics.2014;14(1):23-29; PMID: 24132513 Link to research.
- Richards TA, Soanes DM, Foster PG, et al. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell.2009;21(7):1897-1911; PMID: 19584142 Link to research.
- Nikolaidis N, Doran N, Cosgrove DJ. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol Biol Evol.2014;31(2):376-386; PMID: 24150040 Link to research.
- Ni Y, Li J, Panagiotou G. A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. MBio.2015;6(6):e01263-01215; PMID: 26507230 Link to research.
- Bauer F, Hertel C, Hammes WP. Transformation of Escherichia coli in foodstuffs. Syst Appl Microbiol.1999;22(2):161-168; PMID: 10390866 Link to research.
- Kharazmi M, Sczesny S, Blaut M, et al. Marker rescue studies of the transfer of recombinant DNA to Streptococcus gordonii in vitro, in foods and gnotobiotic rats. Appl Environ Microbiol.2003;69(10):6121-6127; PMID: 14532070 Link to research.
- Hehemann JH, Correc G, Barbeyron T, et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature.2010;464(7290):908-912; PMID: 20376150 Link to research.
- Thomas F, Barbeyron T, Tonon T, et al. Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides. Environ Microbiol.2012;14(9):2379-2394; PMID: 22513138 Link to research.
- Jeffery IB, O'Toole PW. Diet-microbiota interactions and their implications for healthy living. Nutrients.2013;5(1):234-252; PMID: 23344252 Link to research.
- Collins KH, Paul HA, Hart DA, et al. A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats. Sci Rep.2016;6:37278; PMID: 27853291 Link to research.
- Payne AN, Chassard C, Lacroix C. Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity. Obes Rev.2012;13(9):799-809; PMID: 22686435 Link to research.
- Nakayama J, Yamamoto A, Palermo-Conde LA, et al. Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island. Front Microbiol.2017;8:197; PMID: 28261164 Link to research.
- De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A.2010;107(33):14691-14696; PMID: 20679230 Link to research.
- Ebner S, Smug LN, Kneifel W, et al. Probiotics in dietary guidelines and clinical recommendations outside the European Union. World J Gastroenterol.2014;20(43):16095-16100; PMID: 25473160 Link to research.