Gut flora adapt to the food nutrients that are prevalent in different parts of the world. Bacteria able to digest unusual nutrients, such as the sulfated porphyrans found in seaweed eaten in Japanese cuisine, are also consumed along with algae. Formation of bacterial biofilms triggers the exchange of genes among gut bacteria and the acquisition of new polysaccharide-degrading enzyme activities.
Gut Flora Adapts to Diet
The million or so genes of the thousands of bacterial species found in the guts of humans around the world are adapted to the diet of each of those individuals. Each individual gut harbors a couple of hundred different bacterial species and those different types of bacteria increase or decrease in number in response to the composition of each meal.
Diversity of Plant Polysaccharides Provides Digestion Challenge
Plants provide the greatest challenge for digestion, because plants differ the most in their carbohydrate (sugars, oligosaccharides, polysaccharides) composition. Some of those carbs, such as sucrose, starch or the components of the plant cell walls, pectins, arabinogalactans and xyloglucans, are present in all vegetables. Whereas other polysaccharides, such as the sulfated porphyrans from red algae of the same name (Porphyra) are restricted to particular plants. Each different linkage and sugar requires a different digestive enzyme.
Gut Bacteria of Algae Eaters Have Algae-Degrading Enzymes
A recent report (see ref.) traced genes from marine bacteria that digest marine algae/seaweed, to gut bacteria of people who routinely eat seaweed. Researchers studying marine bacteria identified genes coding for new enzymes, porphyranases, that hydrolyzed porphyrans. When they checked gene databases for other porphyranase genes, they found that some gut bacteria had previously unassigned genes that were apparently, based on their nucleotide sequences, porphyranases. Curiously, these genes were only present in gut bacteria isolated from Japanese sources, i.e. from people who traditionally ate seaweed. In some of these bacteria there were more than 260 genes for degrading a huge variety of different plant polysaccharides.
Marine Bacteria on Seaweed Release DNA Incorporated into Gut Bacteria
Bacteria recognize that other bacteria are around by a process called quorum sensing. This signaling system triggers the production of matrix polysaccharides produced by the bacteria to hold the bacteria together in complex communities. Quorum sensing also mobilizes the release of copies of the bacterium’s genes, which is coordinated with uptake of DNA from the surrounding environment. [Note that the proteins that take in foreign DNA have basic amino acids arranged in the same heparin-binding domains that are also used by growth factors and their receptors or the numerous proteins that bind to nucleic acids in the nucleus or in ribosomes.] Thus, biofilm formation is accompanied by enhanced lateral gene exchange that would also enhance the incorporation of porphyranase genes from ingested marine bacteria.
Gut Bacteria Are Made in Guts and Shaped by Diet
Species of gut bacteria are defined in the micro lab by their ability to grow in Petri dishes of agar containing particular combinations of sugar, polysaccharides, etc. The sugars that different bacteria are able to metabolize for growth reflect sugars available as niches in different parts of the gut. Thus species are defined in part by the sugars and polysaccharides they can metabolize, i.e. by the enzymes they can produce.
In each human gut, however, bacteria of the species filling a particular niche will have many other additional genes than those that define the species. These atypical genes are present as a consequence of serendipitous encounters with genes from other bacteria (lateral gene transfer) and may reflect peculiarities of individual diets. Different regional cuisines also shape the regional gut flora. Persistent diet components would be expected to provide selective advantage for bacteria with genes capable of metabolizing new nutrients. Access to a rich diversity of bacterial genes to augment typical gut flora genomes will facilitate adaptation. Food processing to refine and simplify nutrient diversity, and hygiene to eliminate bacterial diversity in food, will reduce diversity in gut flora and minimize adaptation to novel foods. Antibiotics, especially persistent use, can permanently disrupt gut flora. Decreased diversity in gut flora may eliminate species of gut bacteria that are essential for normal physiological functioning of the gut and associated immune system, and may be major contributors to degenerative and autoimmune disease.
Sources of Personal Gut Flora:
- Exposure to Mother, Breast Milk
- Pathogens from Others
- Pets, Farm Animals
- Environmental Sources
- Ingested with Food
- Appendix Reservoir of Gut Flora
Selection Pressures on Gut Flora:
- Breast Milk Normalizes Flora Development
- Formula Disrupts Flora
- Food Nutrients
- Food Phytochemicals (herbs and spices)
- Gut Secretions
- Secretory Antibodies
- Bacteriophages, Bacteriocins
- Lateral Gene Transfer
Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010 Apr 8;464(7290):908-12.