Relationship between our microbiome and personalized nutrition

Question

Recently, it has been asked whether there are 'metabolic types' between humans that can benefit from a sort of personalized nutrition. One answer suggested that one discerning factor could be the human microbiome. It is known that host–microbial symbiotic states might respond differently to diet and drug intake, but whether this can be useful for personalized nutrition is less clear to me. I wonder:

does the microbiome affect food metabolism? (useful for personalized nutrition)

OR

is the food that we eat affecting the microbiome? (less useful for personalized nutrition)

I know the answer is probably both, but there are examples causally demonstrating one branch and excluding the other?

Answer 1

does the microbiome affect food metabolism?

Most definitely (and not surprisingly). The Arumugam paper [1] notes that

The drivers of [enterotype 1] seem to derive energy primarily from carbohydrates and proteins through fermentation, … because genes encoding enzymes involved in the degradation of these substrates (galactosidases, hexosaminidases, proteases) along with glycolysis and pentose phosphate pathways are enriched in this enterotype […]

Enterotype 2 … is enriched in Prevotella … and the co-occurring Desulfovibrio, which can act in synergy to degrade mucin glycoproteins present in the mucosal layer of the gut […]

Enterotype 3 is […] enriched in membrane transporters, mostly of sugars, indicating the efficient binding of mucin and its subsequent hydrolysis as well as uptake of the resulting simple sugars by these genera. […]

The enriched genera indicate that enterotypes use different routes to generate energy from fermentable substrates available in the colon, reminiscent of a potential specialization in ecological niches or guilds. In addition to the conversion of complex carbohydrates into absorbable substrates, the gut microbiota is also beneficial to the human host by producing vitamins. Although all the vitamin metabolism pathways are represented in all samples, enterotypes 1 and 2 were enriched in biosynthesis of different vitamins […]

[All emphasis mine.]

is the food that we eat affecting the microbiome?

Yes, just as certainly. I don’t have a publication handy but it should be obvious that our food influences our gut microbiome – in the extreme case, it can kill it (consider antibiotics side effects).

[1] Manimozhiyan Arumuga, Jeroen Raes & al., Enterotypes of the human gut microbiome, Nature 473, 174–180, May 2011.

Answer 2

Yes, the microbiome affects food metabolism and the diet affects the composition of the microbiome. +1 to Konrad for his response. This is an area of research in which I and colleagues are engaged. Frankly, it is easier to assess the changes to the microbiome based on diet rather than looking at the fecal material to determine (unused) metabolic energy or potential given a certain input (i.e, from a controlled diet).

Recently, we've fed humans a high number of servings of whole grains. The response is highly individualistic with some declines and others increases in Firmicutes, for example. Typically, Bacteroidetes numbers move opposite to Firmicutes, but not in all individuals. These observations are also seen by others in this growing field of research.

The "enterotypes" paper Konrad cites is beginning to see some resistance in the field in that the three enterotypes defined by those authors are not really so cleanly defined when one takes a closer look at more individuals. Time will tell how well one view or the other holds.