Rectal and stool microbiota in cirrhosis, USA

Background: Most studies examining correlations between the gut microbiota and disease states focus on fecal samples due to ease of collection, yet there are distinct differences when compared to samples collected from the colonic mucosa. Although fecal microbiota has been reported to be altered in cirrhosis, correlation with mucosal microbiota characterized via rectal swab has not been previously described in this patient population.</p><p>Methods: We conducted a cross-sectional analysis using 39 stool and 39 rectal swabs from adult patients with cirrhosis of different etiologies and performed shotgun metagenomic sequencing. Bacterial growth studies were performed with Escherichia coli.</p><p>Results: Two asaccharolytic bacterial taxa, Finegoldia magna and Porphyromonas asaccharolytica, were increased in rectal swabs relative to stool (FDR<0.01). Genomic analysis of the microbiome revealed 58 genes and 16 pathways that differed between stool and rectal swabs (FDR<0.05), where rectal swabs were enriched for pathways associated with protein synthesis and cellular proliferation but decreased in carbohydrate metabolism. Although no features in the fecal microbiome differentiated cirrhosis etiologies, the mucosal microbiome revealed decreased abundances of E. coli and Enterobacteriaceae in alcohol-related cirrhosis relative to non-alcohol related cirrhosis (FDR<0.05). In vitro bacterial culture studies showed that physiological concentrations of ethanol and its oxidative metabolites inhibited E. coli growth in a pH- and concentration-dependent manner.</p><p>Conclusions: Characterization of the mucosally-associated gut microbiome via rectal swab revealed findings consistent with amino acid/nitrogen abundance versus carbohydrate limitation in the mucosal microenvironment as well as unique features of alcohol-related cirrhosis possibly consistent with influence of host-derived metabolites on the composition of mucosally-adherent microbiota.

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• body site study.title · “The Mucosally-Adherent Rectal Microbiota Contains Features”
• body site study.description · “correlations between the gut microbiota and disease”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• life stage study.description · “rectal swabs from adult patients with cirrhosis”

84 runs over 84 samples · mean 0.80 Gbp per run (median 1.07 Gbp, total 67.56 Gbp; 84 runs with a base count) · layout PAIRED 84 · platform ILLUMINA 84 · models Illumina HiSeq 2500 (84) · 76% of runs with a Sandpiper profile · first public 2021-09-25

Shen TD first · Daniel SG · Patel S · Kaplan E · Phung L · Lemelle-Thomas K · Chau L · Herman L · Trisolini C · Stonelake A · Toal E · Khungar V · Bittinger K · Reddy KR · Wu GD last

PRJNA766067.csv.gz (3.2 KB) · parquet (74.6 KB) — all 84 samples, every field with route and confidence · PRJNA766067_determinations.csv.gz (6.3 KB) — 866 evidence rows