P073  Analysis of Dysbiosis in Crohn`s Disease by Next-Generation Sequencing: One Size Does NOT Fit All

P073  Analysis of Dysbiosis in Crohn's Disease by Next-Generation Sequencing: One Size Does NOT Fit All

Papoutsis Andreas1, Hazan Sabine1, Daniels Jordan1
1 ProgenaBiome, Ventura, United States

BACKGROUND: Crohn’s Disease (CD) is a debilitating chronic inflammatory process of the gastrointestinal tract which primarily affects children, teens, and young adults, causing severe pain, diarrhea, and other intestinal issues1.  Crohn’s affects nearly 1.4 million individuals in the United States, and is characterized by deep ulcerations, skip lesions, transmural inflammation, fistula and granulomas2.  Some experts suggest that changes in the gut microbiome, like bacteria and viruses, living in the gut may play a role in CD3. Dysbiosis of the enteric microbiota has been demonstrated in CD patients, and it is speculated that this dysbiosis may contribute to the intestinal inflammation observed in those patients4.  This study sought to identify characteristics of dysbiosis in patients with CD to ascertain whether microbiome manipulation is a potential treatment avenue to pursue.

METHODS: Microbiome sequencing results from a subset of eight CD subjects from a larger microbiome study were analyzed in comparison to a first-degree relative (parent, child, or sibling).  To obtain a microbiome profile, DNA was extracted from the fecal samples.  DNA was then quantitated and normalized for downstream library fabrication utilizing shotgun methodology. Prepared and indexed libraries were subsequently pooled and sequenced on the Illumina NextSeq 550 System. Sample FASTQ files were analyzed with a computational tool profiling the microbial communities from metagenomic sequencing data with species level resolution. Finally, individual microbiome profiles were analyzed for Alpha Diversity and relative abundance.

RESULTS: While dysbiosis was found in every subject studied, they each had a unique presentation.  Analysis revealed that Subject 1 had a Shannon Diversity Index of 2.2, compared with the subject’s mother at 3.6.  genus Bacteroides was overrepresented in this subject, representing 74.5% of total reads.  In comparison, Bacteroides represented only 22.4% of the mother’s total reads.  Bifidobacteria, thought to be a beneficial constituent of the microbiome, was markedly decreased (0.089% v 1.5% total reads).  Conversely, Akkermansia, associated with inflammation, was not surprisingly elevated (6.7% v 0.026% of total reads). Contrast this to Subject 4, with a Shannon Diversity Index of 0.6, compared with 3.1 in the subject’s mother.  The dysbiosis in this subject found to be a distinct overgrowth of Enterococcus faecium, which represented 84.95% of the relative abundance. 
While greater similarity was seen between first-degree relatives than the group of CD subjects, the Shannon Diversity Index was a mean of 2.6 in the CD group and 3.65 in the healthy family members.

CONCLUSION(S): Many studies have found potential infectious etiologies for Crohn’s disease.  However, these results vary widely from study to study, and this lack of reproducibility calls the findings into question.  While most authors agree that reduced species diversity and richness can be found in Crohn’s patients, the exact nature of this dysbiosis changes from person to person.  As there is not one single causative agent for Crohn’s disease, the treatment must truly fit the individual.  There is no silver bullet. Rather, the treatment of Crohn’s disease must be guided by next-generation sequencing of the microbiome, to ascertain the nature of the dysbiosis therein.