Food and Our Bacterial Mix – Can we really change them both?
A few weeks ago (June 2012), a paper in Nature by a group of researchers suggested that despite the vast geographical and nutritional differences in the human population, that just three predominant bacterial clusters (referred to as enterotypes hereafter) could explain all of our gastric microbial mixes. This they suggest indicates the existence of a limited number of well-balanced host–microbial symbiotic states that might respond differently to diet and drug intake.
Each of these three enterotypes are identifiable by the variation in the levels of one of three genera: Bacteroides (enterotype 1), Prevotella (enterotype 2) and Ruminococcus (enterotype 3). These enterotypes are not as sharply delimited as, for example, human blood groups; they are, in contrast, densely populated areas in a multidimensional space of community composition. They are nevertheless likely to characterise individuals, in line with previous reports that gut microbiota are quite stable in individuals and can even be restored after perturbation.
More surprisingly, these enterotypes were independent not just of sex and body mass index but also of nationality, despite the profound differences in long-term dietary habits between western nations and east Asian countries.
The authors recognise the limitations in their work stating:
As our current data do not reveal which environmental or even genetic factors are causing the clustering, and as faecal samples are not representative of the entire intestine, we anticipate that the enterotypes introduced here will be refined with deeper and broader analysis of individuals’ microbiomes.
A second paper in Science suggests that long term dietary patterns do influence microbial enterotypes. Here the author’s state:
Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fibre or low-fat/high-fibre diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
These findings are in agreement with a previous study comparing children from Italy and Burkina-Faso, which showed that the African children, who have practically no animal fat and protein in their diets, are colonized by members of Prevotella (or Xylanibacter, a closely related genus), whereas their European counterparts have high Bacteroides levels. Profound changes in diet and lifestyle conditions began with the so-called “Neolithic revolution” with the introduction of agriculture and animal husbandry ≈10,000 y ago. After that time, food resources became more abundant and constant, the concentration of large populations in limited areas created selective pressure that favoured pathogens specialised in colonising human hosts and probably produced the first wave of emerging human diseases.
Thus, enterotypes appear to reflect long-term nutritional habits, and altering them may require a more prolonged dietary intervention, unless it is preceded by antibiotic treatment, which is usually undesirable. Although the enterotypes represent a useful framework for the study of the gut microbiota, the clinical value of knowing one’s enterotype remains to be determined. The role of diet and supplementation with probiotics, or faecal transfer will continue to represent low risk to benefit options and as we learn more, the gut will increasingly be defined as a therapeutic tube, ripe for medical manipulation through traditional food selection and specialised bacterial repopulation.
 Arumugam M et al. Enterotypes of the human gut microbiome. Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20. View Abstract
 Vanhoutte, T., Huys, G., Brandt, E., d & Swings, J. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol. Ecol. 48, 437–446 (2004) View Abstract
 Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7;334(6052):105-8. Epub 2011 Sep 1. View Full Paper
 De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P.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 Aug 17;107(33):14691-6. Epub 2010 Aug 2. View Full Paper
 Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, O’Keefe JH, Brand-Miller J. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005 Feb;81(2):341-54. Review. View Full Paper
 Nesse RM, Williams GC. Why we get sick. The new science of Darwinian medicine. New York: Times Books, 1994.
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