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Gut bacteria are what we eat

Gut microbes, which help humans degrade otherwise indigestible plant material, acquire some crucial digestive enzyme genes from the bacteria in the food we eat, according to a study published this week in Nature. This new finding provides an example of horizontal gene transfer by which diet can influence the genetic diversity and functionality of the human gut microbiome. Image: Wikimedia commons, Alessandro Scotti"It's a fascinating story," said microbiologist linkurl:Jeffrey Gordon;http://gor

By | April 7, 2010

Gut microbes, which help humans degrade otherwise indigestible plant material, acquire some crucial digestive enzyme genes from the bacteria in the food we eat, according to a study published this week in Nature. This new finding provides an example of horizontal gene transfer by which diet can influence the genetic diversity and functionality of the human gut microbiome.
Image: Wikimedia commons,
Alessandro Scotti
"It's a fascinating story," said microbiologist linkurl:Jeffrey Gordon;http://gordonlab.wustl.edu/ of Washington University School of Medicine in St. Louis, who did not participate in the study. "It shows that there's a dimension to human evolution that's occurring at the level of our gut microbiome." "This is an exciting development," agreed microbiologist linkurl:Justin Sonnenburg;http://med.stanford.edu/profiles/microimmuno/researcher/Justin_Sonnenburg/ of Stanford University School of Medicine, who also was not involved in the research. "I think we're at the tip of the iceberg here. Human diet is so diverse, I think that we're just getting an initial glimpse of what's likely to be really huge area of variation that differentiates populations of humans." The human digestive tract harbors trillions of bacteria, many of which establish lifetime, symbiotic relationships with their hosts. The food we eat nourishes our gut flora, and those bacteria feed us with the products and byproducts of their own digestive activities. Consequently, the gut microbiome has evolved to encode a variety of digestive enzymes, for example, those that break down hard-to-digest polysaccharides in food plants, such as celery, broccoli, and other vegetables. As a PhD student at the linkurl:Station Biologique de Roscoff;http://www.sb-roscoff.fr/ in France, biochemist and co-author on the Nature paper Jan-Hendrik Hehemann was interested in a different type of enzymes -- bacterial catalysts that break down polysaccharides in marine algae, which contain sulfates not found in typical food plants. Hehemann and his colleagues identified several genes that they suspected to code for those specialized enzymes in a recently sequenced marine bacteria genome and tested their activity on red algae extracts. Their results revealed that the enzymes encoded by two of the genes represent a whole new class of carbohydrate-digesting proteins, capable of degrading porphyrans -- a unique component of marine plant polysaccharides. Mining the databases for other marine bacteria that might also contain these so-called porphyranases, Hehemann instead stumbled upon a gut bacterium found in human populations inhabiting Japan (but not North America). The similarities between the genomes of the two bacteria suggested that gut microbe had somehow obtained those genes directly from the marine species. "I was really blown away by this result," he recalled. Japanese people regularly consume sushi wrapped in seaweed, which carries with it marine bacteria that produce porphyranases. "It was directly obvious for us that this was horizontal gene transfer from the ocean to the Japanese gut," Hehemann said. "As far as I know, there has not before been an example of horizontal gene transfer between different ecosystems." In a commentary accompanying the study, Sonnenburg compared the gene transfer event to giving human gut bacteria a "new set of utensils" -- likely providing them the ability to digest specific foods prevalent in different regional diets. "I think there's a good bet that you'll see diet match microbiota functionality over and over and over again," he said. "That's exactly what we see in this study." But the food purification and sterilization techniques commonly used throughout the industrialized world might affect the environmental tuning of the human gut biome function suggested by the study, Sonnenburg added. Removing many harmful bacteria from foods has dramatically reduced food-borne diseases in recent decades, he said, "but I think there's a likely cost -- the loss of microbes that are not harmful." Such microbes may transfer seemingly beneficial genes to the gut biome, increasing its ability to adapt to changes in diet, as well as fine-tune the immune system, such that "if you begin to eradicate microbes with which we have coevolved, that has the potential [to disrupt] homeostasis," Sonnenburg said. "It shows how we rely on biodiversity that is surrounding us," Hehemann agreed. "Maybe that's the natural way -- that there is a frequent update of our gut microbiome [through] gene transfer to increase gene diversity. Obviously when we eat these highly processed foods, that's not going to happen." How exactly this gene transfer helps the host, however, is still unclear, said Hehemann, who is currently looking into the benefits porphyranase genes provide gut bacteria in his new lab at the University of Victoria in British Columbia, Canada. It's possible that when the bacteria break down marine algae polysaccharides, it benefits the host through the production of short chain fatty acids, the end product of bacterial metabolism, which can be taken up by the host in the form of calories, Sonnenburg said. "Those are calories that, in the absence of this capability, go totally unrealized."
**__Related stories:__***linkurl:Gut harbors antibiotic resistance;http://www.the-scientist.com/blog/display/55928/
[27th August 2009]*linkurl:Diversity in the gut;http://www.the-scientist.com/article/display/53643/
[October 2007]*linkurl:Commensal bacteria damage host DNA;http://www.the-scientist.com/news/display/24285/
[10th August 2006]
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Comments

Avatar of: anonymous poster

anonymous poster

Posts: 2

April 7, 2010

Necessary bacteria can is on a surface of berries and fruit.\n
Avatar of: John Dos Santos

John Dos Santos

Posts: 9

April 7, 2010

Could this information shed light on a possible etiology for Inflammatory Bowel Disease or Irritable Bowel Syndrome?\nOften people with IBD or IBS develop food intolerances. Could it be that certain people, who eat primarily processed/pasteurized foods, become deficient in these bacterial enzymes and develop these illnesses since they are not able to digest food effectively?\nAnecdotally, I've heard that certain probiotics help to alleviate symptoms of these illnesses. Could the probiotics be restoring enzymatic activities, thus reducing the presence of inflammatory agents in the food?
Avatar of: Oron Zachar

Oron Zachar

Posts: 9

April 7, 2010

There is no "dimension to human evolution that's occurring at the level of our gut microbiome", Since what ever happens in our gut does not get into the germline.
Avatar of: anonymous poster

anonymous poster

Posts: 2

April 7, 2010

Very interesting on a lot of levels. Refined foods and obesity, health and immunity.\n\nWe have evolved with bacteria, most of which are benign, useful or highly beneficial, yet we treat all bacteria the same. Re-education is needed in the community.

April 8, 2010

The article here is fabulous from various points of view:\n1. It may explain (in part) the increasing epidemic of allergic disease: the more "civilized" a country is, the more sterile its food (when did you last eat an apple directly plucked from a tree? Or at least directly in the market?). The more sterile its food, the less variation in the intestinal flora and less chances for immune system regulation. This flora is then passed on to the newborn child (either via the birth canal, or during nursing) and God forbid it's a pathogenic, changed flora.\n2. It should be food for thought regarding the GM foods with new genes introduced. For example, we might one day select for a bacteria with resistance to Bt toxin and we might ingest it one day and then this gene may be given to our intestinal flora. In my opinion, it's more a question of "when" rather than "if".\n\n@John Dos Santos:\nOften people with IBD or IBS develop food intolerances.\n\nI guess it's "always" rather than "often". IBS is, in fact, a reaction to various foods. Eliminating those foods from the diet leads to a certain improvement. (Atkinson 2004, PMID 15361495).\n\n\nAnecdotally, I've heard that certain probiotics help to alleviate symptoms of these illnesses. Could the probiotics be restoring enzymatic activities, thus reducing the presence of inflammatory agents in the food?\n\nWell, it's not only anecdotally and there's a good reason for these results. Work from various authors (Mazmanian recounts his "trace" in this article: the-scientist.com/article/display/55864/) shows that various surface antigens from probiotic bacteria play a very important role in regulation of the immune system. And this immune system is extremely well represented in the gut, there's a lot of "training" happening in the Peyer patches. So it's not about "removing inflammatory agents" from the food/gut, but actually telling the immune system to take it more easy and not overreact to some harmless apple proteins, or whatever else.\n\nIntestinal flora does not play a role only in IBS/IBD (Mazmanian, NRI 2009, doi:10.1038/nri2515), but also in other, seemingly unrelated disorders like obesity or "metabolic syndrome" (Vijay-Kumar 2010, doi:10.1126/science.1179721)\n\nSecond good reason for the beneficial effect probiotics have, is that they keep the "bad" flora in check. One very simple explanation is that the "good" flora (regardless whether it's intestinal or vaginal) produces lactic acid and lowers the pH to values which are not very friendly for many other bacteria. There are, however, more sophisticated reasons, like stimulating IL production and differentiation to Th17 (Ivanov, Cell 2009, PMID: 19836068). {There's also a good reason why stopping the probiotic treatment leads to reappearance of the symptoms: the ingested probiotics have no free ecologic niche where they could establish themselves, unless we prepare one for them.}\n(references given here just to substantiate the statements, which otherwise may sound a bit "spooky"; I did not mean to make an exhaustive review)

April 8, 2010

By some accounts we are more "microbiome" than "genome": the number of different genes in our guts is one two two orders of magnitude larger than the number of our own genes. \nWe do, indeed, pass these genes to our progeny. Like I mentioned before, mothers pass gut bacteria to their child at birth: the way a natural birth takes place, the child comes with its mouth to the anus of the mother, so he gets a good dose of bacteria from both the vaginal and digestive tract. Even if the flora is not stable from day 1, this "innoculation" has a rather serious influence on the final outcome.\n\nAnd we are what our microbiome is, from metabolic syndrome to allergy to drug metabolization. Call it "epigenetics" if you wish (it's not quite, though), call it whatever, but it's there and we pass it on to our progeny.
Avatar of: anonymous poster

anonymous poster

Posts: 12

April 8, 2010

This info fits well with recent research on gut microbes and their differing abilities to digest (and extract calories from) different foods. Obese people (and mice) have different gut microbes than skinny ones, and those microbes can extract calories from certain foods more efficiently. This lead many people to suggest that if we could get the gut microbes to be less efficient in extracting calories from our food we wouldn?t be so fat. Sounds like the modern practice of sterilizing our food (and reducing the ability of our gut microbes to extract calories from our food) should help us be skinnier instead of fatter. So I?m not sure how this study could explain the obesity epidemic that another commenter suggested. I do see how this could affect our gut immune system though.\n\nLey RE. (2010) ?Obesity and the human microbiome?. Curr Opin Gastroenterol. 26(1):5-11
Avatar of: harsh rao

harsh rao

Posts: 6

April 8, 2010

Well if horizontal gene transfer is found out then it would more interesting and challenging to find mechanism and the changes that take place during this mechanism.

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