OBJECTIVE: To compare colonic microbial composition in systemic sclerosis (SSc) 
patients and healthy controls and to determine whether certain microbial genera 
are associated with gastrointestinal (GI) tract symptoms in patients with SSc.
METHODS: Healthy controls were age- and sex-matched (1:1) with adult SSc 
patients. Cecum and sigmoid mucosal lavage samples were obtained during 
colonoscopy. The microbiota in these samples were determined by Illumina HiSeq 
2000 16S sequencing, and operational taxonomic units were selected. Linear 
discriminant analysis effect size was used to identify the genera that showed 
differential expression in SSc patients versus controls. Differential expression 
analysis for sequence count data was used to identify specific genera associated 
with GI tract symptoms.
RESULTS: Among 17 patients with SSc (88% female; median age 52.1 years), the 
mean ± SD total GI Tract 2.0 score was 0.7 ± 0.6. Principal coordinate analysis 
illustrated significant differences in microbial communities in the cecum and 
sigmoid regions in SSc patients versus healthy controls (both P = 0.001). 
Similar to the findings in inflammatory disease states, SSc patients had 
decreased levels of commensal bacteria, such as Faecalibacterium and 
Clostridium, and increased levels of pathobiont bacteria, such as Fusobacterium 
and γ-Proteobacteria, compared with healthy controls. Bifidobacterium and 
Lactobacillus, which are typically reduced under conditions of inflammation, 
were also increased in abundance in patients with SSc. In SSc patients with 
moderate/severe GI tract symptoms, the abundance of Bacteroides fragilis was 
decreased, and that of Fusobacterium was increased, compared with patients who 
had no or mild symptoms.
CONCLUSION: This study demonstrates a distinct colonic microbial signature in 
SSc patients compared with healthy controls. This unique ecologic change may 
perpetuate immunologic aberrations and contribute to clinical manifestations of 
SSc.