Cystic fibrosis (CF) results in inflammation, malabsorption of fats and other nutrients, and obstruction in the gastrointestinal (GI) tract, yet the mechanisms linking these disease manifestations to microbiome composition remain largely unexplored. Here we used metagenomic analysis to systematically characterize fecal microbiomes of children with and without CF, demonstrating marked CF-associated taxonomic dysbiosis and functional imbalance. We further showed that these taxonomic and functional shifts were especially pronounced in young children with CF and diminished with age. Importantly, the resulting dysbiotic microbiomes had significantly altered capacities for lipid metabolism, including decreased capacity for overall fatty acid biosynthesis and increased capacity for degrading anti-inflammatory short-chain fatty acids. Notably, these functional differences correlated with fecal measures of fat malabsorption and inflammation. Combined, these results suggest that enteric fat abundance selects for pro-inflammatory GI microbiota in young children with CF, offering novel strategies for improving the health of children with CF-associated fat malabsorption.

Objective Crohn’s disease (CD) is a chronic idiopathic inflammatory intestinal disorder associated with fecal dysbiosis. Fecal Microbial Transplant (FMT) is a potential therapeutic option for individuals with CD based on the hypothesis that changing the fecal dysbiosis could promote less intestinal inflammation. Design Nine patients, ages 12–19 years, with mild to moderate symptoms defined by Pediatric Crohn’s disease activity index (PCDAI of 10–29) were enrolled into a prospective open label study of FMT in CD (FDA IND 14942). Patients received FMT by nasogastric tube with follow up evaluations at 2, 6, and 12 weeks. PCDAI, C-reactive protein (CRP), and fecal calprotectin were evaluated at each study visit. Results All reported adverse events (AE) were graded as mild except for one individual who reported moderate abdominal pain after FMT. All AE were self limiting. Metagenomic evaluation of stool microbiome indicated evidence of FMT engraftment in seven out of nine patients. The mean PCDAI score improved with patients having a baseline of 19.7 ± 7.2, with improvement at 2 weeks to 6.4 ± 6.6, and at 6 weeks to 8.6 ± 4.9. Based upon PCDAI, 7/9 patients were in remission at 2 weeks, and 5/9 patients who did not receive additional medical therapy were in remission at week 6 and 12 weeks. No or modest improvement were seen in the patients who did not engraft or whose microbiome was most similar to their donor. Conclusion This is the first study to demonstrate that FMT for CD may be a possible therapeutic option for Crohn’s disease. Further prospective studies are required to fully assess the safety and efficacy of the FMT in patients with Crohn’s disease.

Most infants with cystic fibrosis (CF) have pancreatic exocrine insufficiency that results in nutrient malabsorption and requires oral pancreatic enzyme replacement. Newborn screening for CF has enabled earlier diagnosis, nutritional intervention, and enzyme replacement for these infants, allowing most infants with CF to achieve their weight goals by 12 months of age 1 . Nevertheless, most infants with CF continue to have poor linear growth during their first year of life 1 . Although this early linear growth failure is associated with worse long-term respiratory function and survival 2 , 3 , the determinants of stature in infants with CF have not been defined. Several characteristics of the CF gastrointestinal (GI) tract, including inflammation, maldigestion and malabsorption, could promote intestinal dysbiosis 4 , 5 . As GI microbiome activities are known to affect endocrine functions 6 , 7 , the intestinal microbiome of infants with CF might also impact growth. We identified an early, progressive fecal dysbiosis that distinguished infants with CF and low length from infants with CF and normal length. This dysbiosis included altered abundances of taxa that perform functions important for GI health, nutrient harvest, and growth hormone signaling, including decreased Bacteroidetes and increased Proteobacteria. Thus, the GI microbiota represent a potential therapeutic target to correct linear growth defects among infants with CF.

SUMMARYMetagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in micro-biological analyses of complex, chronic infection specimens.

Cystic fibrosis (CF) is a multiorgan disease caused by loss of a functional cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel in many epithelia of the body. Here we report the pathology observed in the gastrointestinal organs of juvenile to adult CFTR-knockout ferrets. CF gastrointestinal manifestations included gastric ulceration, intestinal bacterial overgrowth with villous atrophy, and rectal prolapse. Metagenomic phylogenetic analysis of fecal microbiota by deep sequencing revealed considerable genotype-independent microbial diversity between animals, with the majority of taxa overlapping between CF and non-CF pairs. CF hepatic manifestations were variable, but included steatosis, necrosis, biliary hyperplasia, and biliary fibrosis. Gallbladder cystic mucosal hyperplasia was commonly found in 67% of CF animals. The majority of CF animals (85%) had pancreatic abnormalities, including extensive fibrosis, loss of exocrine pancreas, and islet disorganization. Interestingly, 2 of 13 CF animals retained predominantly normal pancreatic histology (84% to 94%) at time of death. Fecal elastase-1 levels from these CF animals were similar to non-CF controls, whereas all other CF animals evaluated were pancreatic insufficient (<2 μg elastase-1 per gram of feces). These findings suggest that genetic factors likely influence the extent of exocrine pancreas disease in CF ferrets and have implications for the etiology of pancreatic sufficiency in CF patients. In summary, these studies demonstrate that the CF ferret model develops gastrointestinal pathology similar to CF patients.