The duodenal microbiome is altered in small intestinal bacterial overgrowth

• Published in: PloS one Vol. 15; no. 7; p. e0234906
• Main Authors: Leite, Gabriela, Morales, Walter, Weitsman, Stacy, Celly, Shreya, Parodi, Gonzalo, Mathur, Ruchi, Barlow, Gillian M., Sedighi, Rashin, Millan, Maria Jesus Villanueva, Rezaie, Ali, Pimentel, Mark
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 09.07.2020; Public Library of Science (PLoS)
• Subjects: Abdomen; Abundance; Antibiotics; Biology and Life Sciences; Breath tests; Catheters; Colon; Comparative analysis; Constipation; Correlation; Development and progression; Duodenum; Dysbiosis; Endoscopy; Gammaproteobacteria; Gastrointestinal diseases; Gastrointestinal system; Gastrointestinal tract; Gene sequencing; Health aspects; Hydrogen; Intestine; Irritable bowel syndrome; Lactulose; Liver diseases; Medicine and Health Sciences; Methods; Microbiomes; Microbiota; Microbiota (Symbiotic organisms); Physical Sciences; Physiological aspects; Proteobacteria; Questionnaires; Relative abundance; Research and Analysis Methods; rRNA 16S; Signs and symptoms; Small intestine; United States; Los Angeles California; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0234906

Small intestinal bacterial overgrowth (SIBO) is highly prevalent and is associated with numerous gastrointestinal disorders, but the microbes involved remain poorly defined. Moreover, existing studies of microbiome alterations in SIBO have utilized stool samples, which are not representative of the entire gastrointestinal tract. Therefore, we aimed to determine and compare the duodenal microbiome composition in SIBO and non-SIBO subjects, using duodenal aspirates from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Using the recently-redefined cutoff for SIBO of >10.sup.3 colony forming units per milliliter (CFU/mL), 42 SIBO and 98 non-SIBO subjects were identified. Duodenal samples from SIBO subjects had 4x10.sup.3 -fold higher counts than non-SIBO subjects when plated on MacConkey agar (P<0.0001), and 3.8-fold higher counts when plated on blood agar (P<0.0001). Twenty subjects had also undergone lactulose hydrogen breath tests (LHBTs), of whom 7/20 had SIBO. At the 90-minute timepoint, 4/7 SIBO subjects had positive LHBTs (rise in hydrogen (H.sub.2) [greater than or equal to] 20 ppm above baseline), as compared to 2/13 non-SIBO subjects. 16S ribosomal RNA (rRNA) sequencing revealed that SIBO subjects had 4.31-fold higher relative abundance of Proteobacteria (FDR P<0.0001) and 1.64-fold lower Firmicutes (P<0.0003) than non-SIBO subjects. This increased relative abundance of Proteobacteria correlated with decreased [alpha]-diversity in SIBO subjects (Spearman R = 0.4866, P<0.0001) Specific increases in class Gammaproteobacteria correlated with the area-under-the-curve for H.sub.2 for 0-90 mins during LHBT (R = 0.630, P = 0.002). Increases in Gammaproteobacteria resulted primarily from higher relative abundances of the family Enterobacteriaceae (FDR P10.sup.3 CFU/mL cutoff for the definition of SIBO, and also reveal specific overgrowth of Proteobacteria in SIBO vs. non-SIBO subjects, coupled with an altered Proteobacterial profile that correlates with symptom severity. Future research may elucidate host-microbiome interactions underlying these symptoms in SIBO patients.