In answer to the question posed in the title of this post: "A GFD [gluten-free diet] changes the gut microbiome composition and alters the activity of microbial pathways."
So said the findings reported by Marc Jan Bonder and colleagues  (open-access) who presented results based on the "changes in the gut microbiomes of 21 healthy volunteers who followed a GFD for four weeks." Said research volunteers (12 women and 9 men) initially followed a GFD for 4 weeks following some baseline assessments that was followed by "a “wash-out” period of five weeks." At various time points along the study, they supplied blood samples and er, 'fecal samples' that alongside some food diary information, were analysed and processed. Outside the use of "454 pyrosequencing" to see what was living in said poo(p) samples, researchers also looked at a panel of various 'biomarkers' in those blood samples including some old friends - the cytokines.
Results: bearing in mind 3-day food diaries are not without their methodological issues, the authors reported some group differences between use of a GFD and a habitual diet (not GFD) but nothing that came up as statistically significant in terms of energy, protein, carbohydrates or fats. They concluded that: "dietary macronutrient composition was not significantly changed by following a GFD." I might add that other research from other areas has suggested that when it comes to things like vegetable and fruit intake and corresponding nutrient intake, the horror that is a GFD as part of a gluten-free, casein-free (GFCF) strategy might actually not be so horrible...
Next: "Inter-individual variation in the gut microbiota remained stable during this short-term GFD intervention." Allowing for the fact that the GFD was only in place for 4 weeks, the authors reported that adoption of such a dietary change did not seem to significantly affect the bacterial diversity noted in poo(p) samples. But... they did note that certain types of bacteria seemed to be affected by the implementation of a GFD: "On a taxonomic level we identified eight bacteria that change significantly in abundance on GFD: Veillonellaceae, Ruminococcus bromii, and Roseburia faecis decreased on GFD, and Victivallaceae, Clostridiaceae, ML615J-28, Slackia, and Coriobacteriaceae increased on GFD. The strongest effect was seen in the decrease of Veillonellaceae during GFD, Gram-negative bacteria known for lactate fermentation."
Here's where it also gets a little bit interesting. "This is the first time that the Veillonellaceae family has been associated to a dietary intervention, but it was recently shown to be decreased in autistic patients." The citation in question covering that previous research is that from Kang et al  that has also been discussed on this blog (see here). Kang and colleagues did include some participants (a quarter) who were on a GFCF diet at the time of sampling suggesting the "the importance of including dietary information in analyses of microbiota in relation to diseases." I might add that I don't readily accept that autism is a 'disease' but can see the point the authors are trying to make about diet affecting the gut microbiome and what that might mean for research into various labels.
Further on: "Veillonellaceae is considered to be a pro-inflammatory family of bacteria; an increase in Veillonellaceae abundance was consistently reported in IBD, IBS, and cirrhosis patients. It is conceivable that a decrease in Veillonellaceae abundance might be one of the mediators of the GFD’s beneficial effect observed in patients with IBS and gluten-related disorders." This is an interesting observation. Allowing for the fact that there is some blurring when it comes to binary notions of pro-inflammatory and anti-inflammatory actions of various compounds and so one has to be a little careful, the idea that the GFD might significantly affect the the presence of something like Veillonellaceae is deserving of quite a bit more research attention. On my previous 'wish-list' entry about the use of a GFD with autism in mind (see here) I did suggest that the gut microbiome might be an important part of future studies in this area...
There is quite a bit more data included in the Bonder paper (including the conclusion that: "a GFD and its downstream effects on the microbiome do not cause major inflammatory or metabolic changes in gut function in healthy participants") and I would encourage readers to take some time over the findings. Keep in mind the short time-scale for dietary intervention and relatively small participants numbers however but don't lose sight of the idea that what we eat (or don't eat) might have quite a few 'effects' on the trillions of wee beasties that call us home.
 Bonder MJ. et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Medicine. 2016;8:45.
 Kang DW. et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One. 2013 Jul 3;8(7):e68322.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, & Zhernakova A (2016). The influence of a short-term gluten-free diet on the human gut microbiome. Genome medicine, 8 (1) PMID: 27102333