There is evidence suggesting that both lactose and gluten sensitivity may be the result of shifts in the microbiome. In this post I will explore gluten intolerance.
- “The Mayo Clinic reports that intestinal problems such as lactose intolerance may be present long after the parasites are gone.”[src]
Pub Med Studies
- A commensal Bifidobacterium longum strain improves gluten-related immunopathology in mice through expression of a serine protease inhibitor .
- “114 bacterial strains belonging to 32 species were isolated; 85 strains were able to grow in a medium containing gluten as the sole nitrogen source, 31 strains showed extracellular proteolytic activity against gluten protein and 27 strains showed peptidolytic activity towards the 33 mer peptide, an immunogenic peptide for celiac disease patients. ” 
Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease .
- “Candida sp. was detected in 33% of the CoeD group compared 0% of the control group (p = 0.000) and Saccharomyces sp. was detected in 33% of the CoeD group compared to 10% of the control group (p = 0.026).”
- Dysbiosis a risk factor for celiac disease. 
Changes in duodenal tissue-associated microbiota following hookworm infection and consecutivegluten challenges in humans with coeliac disease .
- ” Bacteroidia and Flavobacteriia (class) and Bacteroidales and Flavobacteriales (order) displayed a trend towards increased abundance in Trial subjects “
- “Together, these data suggest that helminth infections and gluten exposure can significantly alter the composition of the tissue-resident and faecal microbiota, which has implications for the purported therapeutic efficacy of helminths in inflammatory disease.”
Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study. 
- ” The comparison between CD subjects and Control group revealed an alteration in the intestinal microbial composition of coeliacs mainly characterized by a reduction of the Firmicutes/Bacteroidetes ratio, of Actinobacteria and Euryarchaeota. Regarding the effects of the probiotic, an increase of Actinobacteria was found as well as a re-establishment of the physiological Firmicutes/Bacteroidetes ratio. Therefore, a three-month administration of B. breve strains helps in restoring the healthy percentage of main microbial components.”
- “Conclusion. The probiotic formula[5 g of VSL#3 twice daily] when taken orally over the 12-week period did not significantly alter the microbiota measured in this population. ” 
The Overlap between Irritable Bowel Syndrome and Non-Celiac Gluten Sensitivity: A Clinical Dilemma .
- “While the treatment of non-celiac gluten sensitivity is exclusion of gluten from the diet, some, but not all, of the patients with IBS also improve on a gluten-free diet. “
Intestinal microbiota modulates gluten-induced immunopathology in humanized mice.
- ” Antibiotic treatment, leading to Proteobacteria expansion, further enhanced gluten-induced immunopathology in conventional SPF mice. Protection against gluten-induced immunopathology in clean SPF mice was reversed after supplementation with a member of the Proteobacteria phylum, an enteroadherent Escherichia coli isolated from a CD patient. The intestinal microbiota can both positively and negatively modulate gluten-induced immunopathology in mice. In subjects with moderate genetic susceptibility, intestinal microbiota changes may be a factor that increases CD risk.”
Novel players in coeliac disease pathogenesis: role of the gut microbiota .
- “Several studies point towards alteration in gut microbiota composition and function in coeliac disease, some of which can precede the onset of disease and/or persist when patients are on a gluten-free diet. Evidence also exists that the gut microbiota might promote or reduce coeliac-disease-associated immunopathology. “
- “Approximately 30% of the general population carry the HLA-DQ2/8 coeliac disease susceptibility genes; however, only 2–5% of these individuals will go on to develop coeliac disease, suggesting that additional environmental factors contribute to disease development. “
- “Specifically, changes in the abundance of Firmicutes and Proteobacteria have been detected in children and adults with active coeliac disease.42,43 Other studies have reported decreases in the proportion of protective, anti-inflammatory bacteria such as Bifidobacterium, and increases in the proportion of Gram-negative bacteria such as Bacteroides and E. coli, in patients with active coeliac disease.44–46 Increases in the number of Staphylococcus44,46 and Clostridium,44,47 and decreases in Lactobacillus spp.46,48,49 have also been reported in children with coeliac disease.” 
EFFECTS OF PROBIOTIC INTAKE ON INTESTINAL BIFIDOBACTERIA OF CELIAC PATIENTS.
- “Faecal bifidobacteria concentration before probiotic consumption was significantly higher in healthy individuals (2.3×108±6.3×107 CFU/g) when compared to celiac patients (1.0×107±1.7×107 CFU/g). “
- “The probiotic supplementation significantly increased the number of bifidobacteria in the feces of celiac patients, although it was not sufficient to reach the concentration found in healthy individuals prior to its consumption.”
The DNA risk of gluten sensitivity may exist in 30% of the population, however developing gluten sensitivity may be an epigentic event triggered by a shift in bacteria in the microbiome.
You have not become gluten/lactose sensitive — your microbiome has become gluten/lactose sensitive.
Correction of the microbiome shift appears likely to reverse the gluten sensitivity even with a DNA risk factor. We see studies suggesting that some bifidobacteria have a positive effect. Lactobacillus containing VSL#3 does not appear to be effective. We do not know which families or strains are the problem (too high or too low is unclear).
The Dilemma: Going on a Gluten free diet does alter the microbiome. Does this change make it easier or harder to return to a healthy microbiome? Yes, it helps with symptom relief … but…
- “A number of taxon-specific differences were seen during the gluten-free diet: the most striking shift was seen for the family Veillonellaceae (class Clostridia), which was significantly reduced during the intervention (p = 2.81 × 10(-05)). Seven other taxa also showed significant changes; the majority of them are known to play a role in starch metabolism. We saw stronger differences in pathway activities: 21 predicted pathway activity scores showed significant association to the change in diet. ”