The duodenal microbiome is altered in small intestinal bacterial overgrowth

Leite, Gabriela; Morales, Walter; Weitsman, Stacy; Celly, Shreya; Parodi, Gonzalo; Mathur, Ruchi; Barlow, Gillian; Sedighi, Rashin; Millan, Maria Jesus Villanueva; Rezaie, Ali; Pimentel, Mark

doi:10.1371/journal.pone.0234906

Cited by 75 publications

(80 citation statements)

References 48 publications

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“…A reduction in alpha diversity in the microbiome may indicate a loss of microbial species in response to different environmental factors (i.e., antibiotics) or a presence of microbial players that may be driving the reduction in diversity. For example, there was increased abundance in Klebsiella and Escherichia/Shigella in small intestinal bacterial overgrowth and a reduced duodenal microbiome diversity (31). Consistent with IBS-A, IBS-C, and Crohn’s disease studies, we found lower relative abundances of the anti-inflammatory microbe F. prasunitzii in individuals with IBS than the healthy cohort (29, 32–35).…”

Section: Discussionmentioning

confidence: 99%

Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation

Phan

Nair

Jain

et al. 2021

Preprint

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Background. Irritable bowel syndrome (IBS) is characterized by abdominal discomfort and irregular bowel movements and stool consistency. Because there are different symptoms associated with IBS, it is difficult to diagnose the role of the microbiome in IBS. Objective. Here, we present a study that includes metagenomic sequencing of stool samples from subjects with the predominant subtypes of IBS and a healthy cohort. We collected longitudinal samples from individuals with IBS who took daily made-to-order precision probiotic and prebiotic supplementation throughout the study. Materials and Methods. This study includes a population of 489 individuals with IBS and 122 healthy controls. All stool samples were subjected to shotgun metagenomic sequencing. Precision probiotics and prebiotics were formulated for all subjects with longitudinal timepoints. Results. There was significant variation explained in the microbiome between the healthy and IBS cohorts. Individuals with IBS had a lower gut microbiome diversity and reduced anti-inflammatory microbes compared to the healthy controls. Eubacterium rectale and Faecalibacterium prausnitzii were associated with healthy microbiomes while Shigella species were associated with IBS. Pathway analysis indicated a functional imbalance of short chain fatty acids, vitamins, and a microbial component of Gram-negative bacteria in IBS compared to healthy controls. In the longitudinal dataset, there was a significant difference in microbiome composition between timepoints 1 and 3. There was also a significant increase in the overall microbiome score and relative abundances of probiotic species used to target the symptoms associated with IBS. Conclusions. We identified microbes and pathways that differentiate healthy and IBS microbiomes. In response to precision probiotic supplementation, we identified a significant improvement in the overall microbiome score in individuals with IBS. These results suggest an important role for probiotics in managing IBS symptoms and modulation of the microbiome as a potential management strategy.

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Section: Discussionmentioning

confidence: 99%

Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation

Phan

Nair

Jain

et al. 2021

Preprint

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“…Only a few studies have attempted to characterize the small bowel microbiome in subjects with SIBO and IBS. A North American study found that SIBO subjects had a 7-8-fold increase in Klebsiella and Escherichia/Shigella compared to non SIBO patients (40). One Indian study, on jejunal aspirate of SIBO and IBS subjects, found that 40% of subjects had Pseudomonas aeruginosa, 6.7% had Acinetobacter baumannii, 13.3% had Acinetobacter lwoffii, 13.3% had Staphylococcus spp, 6.7% had Enterococcus faecalis, 20% had Escherichia coli, 6.7% had Enterococcus faecium, 13.3% had Klebsiella pneumoniae, and 6.7% had Streptococcus spp.…”

Section: Prevalence Of Sibo In Ibsmentioning

confidence: 99%

Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome – An Update

Takakura

Pimentel

2020

Front. Psychiatry

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Small intestinal bacterial overgrowth (SIBO) is one manifestation of gut microbiome dysbiosis and is highly prevalent in IBS (Irritable Bowel Syndrome). SIBO can be diagnosed either by a small bowel aspirate culture showing ≥10 3 colony-forming units (CFU) per mL of aspirate, or a positive hydrogen lactulose or glucose breath test. Numerous pathogenic organisms have been shown to be increased in subjects with SIBO and IBS, including but not limited to Enterococcus, Escherichia coli, and Klebsiella. In addition, Methanobrevibacter smithii, the causal organism in a positive methane breath test, has been linked to constipation predominant irritable bowel syndrome (IBS-C). As M. smithii is an archaeon and can overgrow in areas outside of the small intestine, it was recently proposed that the term intestinal methanogen overgrowth (IMO) is more appropriate for the overgrowth of these organisms. Due to gut microbiome dysbiosis, patients with IBS may have increased intestinal permeability, dysmotility, chronic inflammation, autoimmunity, decreased absorption of bile salts, and even altered enteral and central neuronal activity. As a consequence, SIBO and IBS share a myriad of symptoms including abdominal pain, distention, diarrhea, and bloating. Furthermore, gut microbiome dysbiosis may be associated with select neuropsychological symptoms, although more research is needed to confirm this connection. This review will focus on the role of the gut microbiome and SIBO in IBS, as well as novel innovations that may help better characterize intestinal overgrowth and microbial dysbiosis.

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“…IBS is a complicated disease that display comorbidities of both impairment of GI motility and CNS symptoms. The cause of SIBO in IBS is incompletely understood although several studies demonstrated that some of the indole producing bacteria like Escherichia coli exhibit high abundance in the small intestine of SIBO associated IBS patients (Ghoshal et al, 2014, Leite et al, 2020, Avelar Rodriguez et al, 2019. Our findings raise the possibility that SIBO leads to an increase of microbial tryptophan metabolite production in the small intestine, which then activates Trpa1+EECs to increases intestinal motility and modulate CNS activity through the vagal nerve, resulting in the complex comorbidities of intestinal and psychiatric disorders in IBS.…”

Section: Trpa1+eecs Are Frontline Intestinal Sensorsmentioning

confidence: 77%

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

Bae

Cassilly

et al. 2020

Preprint

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The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EECs). EECs can communicate nutritional information to the nervous system, but similar mechanisms for microbial information are unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda specifically activates EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increases intestinal motility in an EEC-dependent manner. Microbial, pharmacological, or optogenetic activation of Trpa1 + EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons through 5-HT. We identified a distinct subset of indole derivatives of tryptophan catabolites produced by E. tarda that potently activate zebrafish EEC Trpa1 signaling and also directly activate human and mouse Trpa1. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to specific microbial signals.

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The duodenal microbiome is altered in small intestinal bacterial overgrowth

Cited by 75 publications

References 48 publications

Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation

Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation

Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome – An Update

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

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