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Background: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested., Results: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort., Conclusions: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.

The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. By using nondirected 16S rRNA gene amplicon sequencing, the fecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated with the overall microbial composition, with a decrease in the abundance of Faecalibacterium being observed in older patients. We observed the emergence of a potential Escherichia-Shigella -dominated enterotype in a subset of patients, and this enterotype was predicted to be more proinflammatory than the other common enterotypes, with the latter being dominated by Bacteroides or Faecalibacterium The increased abundance of Escherichia-Shigella did not appear to be associated with infection with an agent of a similar sequence similarity. Stool color and consistency were associated with the diversity and composition of the microbiome, with deviations from the norm (not brown and solid) showing increases in the abundances of bacteria such as Escherichia-Shigella and Veillonella Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases, including Treponema , Proteus , Capnocytophaga , Arcobacter , Campylobacter , Haemophilus , Aeromonas , and Pseudomonas Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in stool color and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified by using routine diagnostic tests, suggesting that in the future, microbiome analyses may be utilized to improve diagnostics., (Copyright © 2018 American Society for Microbiology.)

Culture-independent molecular techniques have demonstrated that the majority of the gut microbiota is uncultivable. Application of these molecular techniques to more accurately identify the indigenous gut microbiome has moved with great pace over recent years, leading to a substantial increase in understanding of gut microbial communities in both health and a number of disorders, including irritable bowel syndrome (IBS). Use of culture-independent molecular techniques already employed to characterise faecal and, to a lesser extent, colonic mucosal microbial populations in IBS, without reliance on insensitive, traditional microbiological culture techniques, has the potential to more accurately determine microbial composition in the small intestine of patients with this disorder, at least that occurring proximally and within reach of sampling. Current data concerning culture-based and culture-independent analyses of the small intestinal microbiome in IBS are considered here.

Purpose of Review: To review recently published studies investigating any association between gut flora and symptoms of irritable bowel syndrome., Recent Findings: Experimental studies demonstrate associations between gut flora, gut motility, mucosal inflammation and visceral hypersensitivity. Scientific bases for possible benefits of selected probiotics on irritable bowel symptoms have been identified. Disturbances in viable counts of fecal flora have been demonstrated in patients with irritable bowel syndrome. Results of studies based on breath tests are conflicting as to whether the prevalence of small intestinal bacterial overgrowth is increased in this group. Nonetheless, a longitudinal analysis based on bacteriological assessments of serial small intestinal aspirates suggests that this entity should be considered in patients with irritable bowel symptoms, especially in the setting of predisposition to bacterial overgrowth. Clinical trials of probiotic treatment for irritable bowel syndrome have yielded conflicting results., Summary: Recent studies provide increasing support for the concept that disturbances in gut flora occur in patients with irritable bowel syndrome and that such abnormalities may contribute to irritable bowel syndrome-type symptoms. The relative importance of disturbed gut flora to symptom pathogenesis, along with the therapeutic potential of modulation of the gut flora for amelioration of irritable bowel syndrome symptoms, however, remains to be fully defined.

OBJECTIVES: The aims of this study were 1) to document the sensitivity, specificity, and predictive values of the rice breath hydrogen test for small intestinal bacterial over-growth; 2) to determine the possible influence of concurrent gastric bacterial overgrowth and gastroduodenal pH on the efficacy of this test; and 3) to investigate whether reliability is limited by an inability of small intestinal luminal flora to ferment rice or its product of hydrolysis, maltose. METHODS: Twenty adult subjects were investigated with microbiological culture of proximal small intestinal aspirate and a 3-g/kg rice breath hydrogen test. Gastroduodenal pH, the presence or absence of gastric bacterial overgrowth, and the in vitro capability of small intestinal luminal flora to ferment rice and maltose, its product of hydrolysis, were determined. RESULTS: Sensitivity of the rice breath hydrogen test for small intestinal bacterial overgrowth was 33% and remained low even when subjects with small intestinal overgrowth with oropharyngeal-type (38%) and colonic-type flora (20%) and those with concurrent small intestinal and gastric bacterial overgrowth (40%) were considered separately. Sensitivity remained suboptimal despite favorable gastroduodenal luminal pH and documented ability of bacterial isolates to ferment rice and maltose in vitro. Specificity of the rice breath hydrogen test for small intestinal bacterial over-growth was 91%. Positive predictive value, negative predictive value, and predictive accuracy were 75%, 63%, and 65%, respectively. CONCLUSIONS: Clinical value of the rice breath hydrogen test for detecting small intestinal bacterial overgrowth is limited. The rice breath hydrogen test is not a suitable alternative to small intestinal intubation and culture of secretions for the detection of small intestinal bacterial overgrowth. [ABSTRACT FROM AUTHOR]

Objective: Some rodent strains with experimental small intestinal bacterial overgrowth (SIBO) unrelated to jejunoileal bypass are susceptible to hepatic damage, possibly because of increased small intestinal permeability to proinflammatory bacterial polymers. However, data on the prevalence of hepatic damage in human subjects with SIBO in this setting are lacking. This study addressed this issue. Methods: Seventy adult subjects were investigated for possible SIBO and hepatic damage with bacteriological analysis of small intestinal aspirates and measurement of serum concentrations of alkaline phosphatase, gamma-glutamyl transpeptidase, aspartate aminotransferase, and alanine aminotransferase. Nutritional indices (serum albumin and anthropometry) and the urinary lactulose/mannitol ratio, an index of small intestinal permeability, were measured in all subjects with SIBO and liver damage. Results: SIBO was present in 40 of 70 subjects (57.1%). Overgrowth flora included salivary-type bacteria alone in 11 subjects and colonic-type bacteria in 29 subjects (facultative anaerobes [En-terobacteriaceae] alone in 21 subjects and both facultative and obligate anaerobes [Enterobacteriaceae and Bacteroides spp] in eight subjects). Biochemical evidence of liver damage was found in zero of 30 subjects without SIBO, zero of 11 subjects with SIBO with salivary-type bacteria alone, zero of 21 subjects with SIBO with facultative but not obligate anaerobic colonic-type bacteria, and in one of eight subjects (12.5%) with SIBO with obligate anaerobic colonic-type bacteria, in whom serum alkaline phosphatase and gamma-glutamyl transpeptidase levels were elevated. Nutritional indices were normal in this patient. Small intestinal permeability was increased and, along with liver enzyme abnormalities, normalized after eradication of SIBO. Small intestinal permeability was also increased in three of six patients (50.0%) with SIBO with obligate anaerobic colonic-type bacteria who had no... [ABSTRACT FROM AUTHOR]

Objectives: 1) To determine the prevalence of small intestinal overgrowth with colonic-type bacteria in symptomatic elderly subjects, particularly those without important "clues" such as clinically apparent predisposition or vitamin B12 deficiency, and 2) to investigate defense mechanisms such as gastric acidity, small intestinal motility, and luminal IgA in this setting. Methods: Fifty-two symptomatic subjects without vitamin B12 deficiency or clinically apparent predisposition to bacterial overgrowth or disturbed mucosal immunity, including 22 subjects ≥ 75 yr old, underwent culture of small intestinal luminal secretions. Indicator paper was used to measure fasting gastric pH. The presence of bacteria of confirmed nonsalivary origin in small intestinal secretions served as an index of small intestinal dysmotility. Small intestinal luminal IgA concentrations were measured by radial immunodiffusion. Results: Small intestinal overgrowth with colonic-type flora was not present in any subject investigated for dyspepsia, irrespective of age. In subjects with chronic diarrhea, anorexia, or nausea, overgrowth with colonic-type flora (Enterobacteriaceae) was present in 0/12 (0%), 1/10 (10.0%), and 9/14 (64.3%) subjects aged < 50 yr, 50-74 yr, and ≥ 75 yr, respectively. Enterobacteriaceae were not concurrently recovered from saliva of any subject ≥ 75 yr old with small intestinal overgrowth with these bacteria. Fasting hypochlorhydria was present in only 1/9 (11.1%) such subjects. Luminal IgA concentrations were significantly greater in subjects ≥ 75 yr old with bacterial overgrowth than in culture-negative subjects (p ≤ 0.003). Conclusions: Small intestinal overgrowth with colonic-type bacteria should be considered in subjects ≥ 75 yr old with chronic diarrhea, anorexia, or nausea, even in the absence of clues such as clinically apparent predisposition or vitamin B12 deficiency. Small... [ABSTRACT FROM AUTHOR]

Objectives: To document the sensitivity of the 1-g 14C-D-xylose breath test for bacterial overgrowth and to investigate luminal and nonluminal factors that may influence breath 14CO2 levels and impact on the clinical utility of this test. Methods: Thirty-five adult subjects were investigated for bacterial overgrowth by culture of gastric and small intestinal aspirates and by a 1-g 14C-D-xylose breath test. Body weight, gastroduodenal pH and the in vitro capability of overgrowth flora to ferment D-xylose were assessed. Serial breath 14CO12 levels were also recorded before and after the resolution of malabsorption in a subject with celiac disease to determine the importance of postabsorptive metabolism of this substrate. Results: Gastric and small intestinal bacterial overgrowth were present in 19/35 (54.3%) and 21/35 (60.0%) subjects, respectively. The positivity rate of culture of aspirate exceeded that of the 1-g 14C-D-xylose breath test. Endogenous CO2 production independently influenced breath 14CO2 levels. After excluding this influence, sensitivity of the 1-g 14C-D-xyose breath test for gastric bacterial overgrowth or small intestinal bacterial overgrowth was poor, even when overgrowth with specific "marker organisms" was considered. Poor sensitivity could not be explained by unfavorable luminal pH. Overgrowth flora were proven capable of in vitro D-xylose fermentation in 81.8% of subjects. Systemic and/or colonic metabolism of 1-g 14C-D-xylose appear to be important factors influencing results of the 1-g 14C-D-xylose breath test, especially in partial gastrectomy subjects. Conclusions: The 1-g 14C-D-xylose breath test is not a suitable alternative to culture of aspirate for the investigation of subjects for bacterial overgrowth. [ABSTRACT FROM AUTHOR]