I think they are saying just that. Other studies suggest stable enterotype over time, too. For example:
Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Comparison of long-term and short-term dietary data showed that only the long-term diet was correlated with enterotype clustering in the cross-sectional study. In the interventional study, changes were significant and rapid, but the magnitude of the changes was modest and not sufficient to switch individuals between the enterotype clusters associated with protein/fat and carbohydrates. Thus, our data indicate that long-term diet is particularly strongly associated with enterotype partitioning.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368382/
However, that's not the whole story:
The human gut microbiome: are we our enterotypes?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819005/This study indicates the existence of a limited number of well‐balanced host–microbial symbiotic states in human faeces that presumably reflect the microbial composition in the large intestine. Perhaps it would have been wiser to call these ‘faecotypes’ than ‘enterotypes’, since it is well known that the microbial abundance and composition changes dramatically throughout the GIT. It remains to be seen whether such stable and universal microbial consortia are also found in the small intestine where the genera Streptococcus, Clostridium and Veillonella are dominant (Booijink etal., 2007; 2010a,b; van den Bogert etal., 2011).
If you look at research on SIBO (just diving into this area), it really can wreak havoc downstream, so to speak.
In treating SIBO, I found one study that said:
SIBO is often misdiagnosed and generally underdiagnosed. Clinical symptoms might be non-specific (dyspepsia, bloating, abdominal discomfort). Nevertheless, SIBO can cause severe malabsorption, serious malnutrition and deficiency syndromes.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890937/In several patients, it is necessary to exclude lactose from the diet, to reduce other simple sugars, to increase coverage of energy needs by fat and to administer MCT oils (medium-chain triacylglyceroles).
Does that kind of diet sound familiar? Maybe some of us do better on a more Paleo-type diet since we have SIBO problems (I was diagnosed with IBS a few years ago and know immediately if I add too much of certain types of carbs, primarily resistant starches). Maybe more of us have SIBO problems than we realize, and with more research we might better understand the impact of diet and microbiota "types" related to a healthy small intestine, too.
Would love to see more studies on effects of microbiome and diet on lipid profiles and inflammation markers. Now wouldn't that be useful!!! Throw in APOE and I'd be practically giddy.