Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic.

Although fecal microbiota composition is considered to preserve relevant and representative information for distal colonic content, it is evident that it does not represent microbial communities inhabiting the small intestine. Nevertheless, studies investigating the human small intestinal microbiome and its response to dietary intervention are still scarce. The current study investigated the spatio-temporal dynamics of the small intestinal microbiome within a day and over 20 days, as well as its responses to a 14-day synbiotic or placebo control supplementation in 20 healthy subjects. Microbial composition and metabolome of luminal content of duodenum, jejunum, proximal ileum and feces differed significantly from each other. Additionally, differences in microbiota composition along the small intestine were most pronounced in the morning after overnight fasting, whereas differences in composition were not always measurable around noon or in the afternoon. Although overall small intestinal microbiota composition did not change significantly within 1 day and during 20 days, remarkable, individual-specific temporal dynamics were observed in individual subjects. In response to the synbiotic supplementation, only the microbial diversity in jejunum changed significantly. Increased metabolic activity of probiotic strains during intestinal passage, as assessed by metatranscriptome analysis, was not observed. Nevertheless, synbiotic supplementation led to a short-term spike in the relative abundance of genera included in the product in the small intestine approximately 2 hours post-ingestion. Collectively, small intestinal microbiota are highly dynamic. Ingested probiotic bacteria could lead to a transient spike in the relative abundance of corresponding genera and ASVs, suggesting their passage through the entire gastrointestinal tract. This study was registered to http://www.clinicaltrials.gov, NCT02018900.

A non-invasive tool to collect small intestine content in post weaning pigs: validation study.

The Capsule for Sampling (CapSa) is an ingestible capsule that collects small intestine content while transiting through the natural digestive pathway. In this study, 14 Swiss Large White pigs weighing less than 12 kg (Category < 12 kg) and 12 weighing between 12 and 20 kg (Category [12-20 kg]) were given two CapSas and monitored for three days. The animals were euthanized for post-mortem sampling, allowing us to directly obtain gut microbiota samples from the gastrointestinal tract. This post-mortem approach enabled a direct comparison between the microbial content from the gut and the samples collected via the CapSas, and it also facilitated precise identification of the CapSas' sampling sites within the gastrointestinal tract. For the category under 12 kg, only 2.3% of the administered CapSas were recovered from the feces. In contrast, in the 12-20 kg category, 62.5% of the CapSas were successfully retrieved from the feces within 48 h. Of these recovered CapSas, 73.3%-equating to 11 capsules from eight pigs-had a pH > 5.5 and were therefore selected for microbiome analysis. Bacterial composition of the CapSas was compared with that of the three segments of the small intestine, the large intestine and feces of the corresponding pig. The results were tested using a PERMANOVA model (Adonis) including sample type as a factor, and then pairwise comparisons were made. The bacterial composition found in the CapSas differed from that of the large intestine and feces (P < 0.01), while it did not differ from the first segment of the small intestine (P > 0.10). This study provides evidence that the CapSa effectively samples the intestinal microbiota from the upper section of the small intestine in post-weaning pigs. Furthermore, it was found that the collection of CapSas could only be successfully achieved in pigs classified within the heavier weight category.

LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model.

Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.

Small Intestine Bacterial Overgrowth is associated with increased Campylobacter and epithelial injury in duodenal biopsies of Bangladeshi children.

Small intestine bacterial overgrowth (SIBO) has been associated with enteric inflammation, linear growth stunting, and neurodevelopmental delays in children from low-income countries. Little is known about the histologic changes or epithelial adherent microbiota associated with SIBO. We sought to describe these relationships in a cohort of impoverished Bangladeshi children. Undernourished 12-18-month-old children underwent both glucose hydrogen breath testing for SIBO and duodenoscopy with biopsy. Biopsy samples were subject to both histological scoring and 16s rRNA sequencing. 118 children were enrolled with 16s sequencing data available on 53. Of 11 histological features, we found that SIBO was associated with one, enterocyte injury in the second part of the duodenum (R = 0.21, p = 0.02). SIBO was also associated with a significant increase in Campylobacter by 16s rRNA analysis (Log 2-fold change of 4.43; adjusted p = 1.9 x 10-6). These findings support the growing body of literature showing an association between SIBO and enteric inflammation and enterocyte injury and further delineate the subgroup of children with environmental enteric dysfunction who have SIBO. Further, they show a novel association between SIBO and Campylobacter. Mechanistic work is needed to understand the relationship between SIBO, enterocyte injury, and Campylobacter.

Microbiome changes under enteral deprivation are dynamic and dependent on intestinal location.

BACKGROUND: The microbiome has a pivotal role in intestinal health, and nutrition has a major role shaping its structure. Enteral deprivation, in which no oral/enteral nutrition is administered, is common in hospitalized/gastrointestinal patients. The dynamics that enteral deprivation exerts on the microbial community, specifically in the small intestine, are not well understood. METHODS: Enteral deprivation was modeled with exclusive parenteral nutrition (EPN) mice. Mice were allocated to receive either EPN or saline and chow (control) and euthanized after 0, 2, 4, or 6 days. DNA was extracted from jejunum, ileum, and colon content. 16S sequencing was used to compare changes in microbial communities between groups. Functional pathways were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS: EPN-treated mice showed community changes throughout the intestine. Beta diversity in colon showed clear separation between the groups (Bray-Curtis, P < 0.001). Time-dependent dynamics were seen in ileal but not jejunal samples. Alpha diversity was lower in the colon of EPN mice compared with control/baseline mice (Chao1, P < 0.01) but not in ileum/jejunum. Progressive loss of single-taxon domination was seen, most notably in the small intestine. This was accompanied by increases/decreases in specific taxa. A clear separation was seen in the functional capacity of the community between fed and enterally deprived mice at the ileum and colon, which was observed early on. CONCLUSIONS: Enteral deprivation disturbs the microbial community in a spatial and dynamic manner. There should be further focus on studying the effect of these changes on the host.

Probiotics and Prebiotics in Subclinical Hypothyroidism of Pregnancy with Small Intestinal Bacterial Overgrowth.

Evaluating efficacy of probiotics combined with prebiotics in small intestinal bacterial overgrowth (SIBO) in subclinical hypothyroidism (SCH) in the second trimester. We collected data from 78 pregnant women with SCH (SCH group) and 74 normal pregnant women (control group) in second trimester, compare the differences in high sensitivity C-reactive protein (hsCRP), result of lactulose methane-hydrogen breath test and gastrointestinal symptoms assessed by GSRS scale between two groups. In SCH group, 32 patients with SIBO were selected as intervention group. Treatment with probiotics + prebiotics for 21 days; The differences of lipid metabolism, hsCRP, thyroid function level, methane-hydrogen breath test results and GSRS scores before and after treatment were compared to evaluate the therapeutic effect. (1) The positive rate of SIBO and methane, hsCRP levels in SCH group were higher than those in control group (P < 0.05), the total score of GSRS scale, mean score of indigestion syndrome, and constipation syndrome in SCH group were higher (P < 0.05). (2) The mean abundance of hydrogen and methane were higher in SCH group. (3) After treatment, serum levels of thyrotropin(TSH), total cholesterol(TC), triglyceride(TG), low-density lipoprotein (LDL), and hsCRP in intervention group were decreased, and high-density lipoprotein (HDL) was increased compared with before treatment (P < 0.05). (4) After treatment, methane positive rate, total score of GSRS scale, mean score of diarrhea syndrome, dyspepsia syndrome, and constipation syndrome were decreased (P < 0.05). (5) The average abundance of methane and hydrogen were lower. Probiotics combined with prebiotics are effective in the treatment of SIBO in pregnant SCH patients.Clinical Trial Registration Number: ChiCTR1900026326.

Comparison of jejunal aspirate culture and methane and hydrogen breath test in the diagnosis of small intestinal bacterial overgrowth.

BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is still difficult to diagnose. Quantitative culture of small intestine aspirate is recommended to be the gold standard. The methane and hydrogen breath tests are easily repeatable, sufficiently sensitive and highly specific for SIBO diagnosis. Our goal is to contrast the diagnostic value of the breath tests with jejunal aspiration cultures. METHODS: 40 adult outpatients (age < 60) were enrolled in our study. Randomly, within 2 days, both the methane and the hydrogen breath test and jejunal aspiration culture were performed on each patient and the results of both tests were evaluated and contrasted. RESULTS: The jejunal culture was positive (105CFU / mL) in 14/40(35%) subjects, the lactulose breath test (LBT) was positive in 18/40 (45%) subjects, and the glucose breath test (GBT) was positive in 12/40 (30%). The GBT showed good agreement (κ = 0.659) and LBT showed poor agreement (κ = 0.588) with the jejunal aspirate culture. The sensitivity, specificity, positive and negative predictive values of LBT/GBT were 85.7/71.4%,76.9/92.3%, 66.6/83.3% and 90.9/85.7%, respectively. CONCLUSIONS: 35% of patients with suspected SIBO are identified using jejunal aspirate cultures. For the identification of SIBO, GBT is more specific than LBT, but has a lower sensitivity. In individuals with suspected SIBO, the breath test should be initially due to its good agreement with the jejunal aspirate culture.

The prevalence and impact of small intestine bacterial overgrowth in biliary atresia patients.

BACKGROUND: Acute cholangitis is an ominous complication in biliary atresia (BA) patients. We investigated the prevalence of small intestine bacterial overgrowth (SIBO) in BA patients and its role in predicting acute cholangitis. METHODS: There are 69 BA patients with native liver recruited into this study prospectively. They received hydrogen and methane-based breath testing (HMBT) to detect SIBO after recruitment and were followed prospectively in our institute. RESULTS: There are 16 (23.19%) subjects detected to have SIBO by HMBT. BA subjects with SIBO were noted to have higher serum alanine aminotransferase levels than others without SIBO (P = 0.03). The risk of acute cholangitis is significantly higher in BA patients with SIBO than in others without SIBO (62.50% vs. 15.09%, P < 0.001). The logistic regression analysis demonstrated that BA subjects with SIBO have a higher risk of acute cholangitis than others without SIBO (odds ratio = 9.38, P = 0.001). Cox's proportional hazard analysis further confirmed the phenomena in survival analysis (hazard ratio = 6.43, P < 0.001). CONCLUSIONS: The prevalence of SIBO in BA patients is 23.19% in this study. The presence of SIBO is associated with the occurrence of acute cholangitis in BA patients. IMPACT: What is the key message of your article? Acute cholangitis is common in BA, and is associated with SIBO after hepatoportoenterostomy in this study. What does it add to the existing literature? This study demonstrated that SIBO is common in BA after hepatoportoenterostomy, and is predictive of acute cholangitis and elevated serum ALT levels in BA. What is the impact? This prospective cohort study provides data regarding the significance of SIBO on the risk of acute cholangitis in BA patients.

Incidence of Small Intestinal Bacterial Overgrowth and Symptoms After 7 Days of Proton Pump Inhibitor Use: A Study on Healthy Volunteers.

INTRODUCTION: Proton pump inhibitors (PPIs) are commonly prescribed drugs. Chronic PPI use has recently been associated with the risk for developing small intestinal bacterial overgrowth (SIBO). It is not known whether the short-term prescription of a PPI can trigger SIBO. Therefore, the aim of the present study was to evaluate the incidence of SIBO and gastrointestinal symptoms after 7 days of PPI use. MATERIALS AND METHODS: A prospective, pilot, open-label study was conducted on asymptomatic healthy volunteers. The incidence of SIBO was evaluated at the baseline and after administration of 40 mg of pantoprazole once a day for 7 days, through a glucose breath test. In addition, the presence of gastrointestinal symptoms, the number of bowel movements, and the consistency of stools, according to the Bristol scale, were assessed. RESULTS: Thirty-eight healthy subjects (71.1% women, mean age 25.18 ± 6.5 years) were analyzed. The incidence of SIBO after 7 days of PPI administration was 7.8% (95% CI 1.6-21.3%). The patients that developed SIBO had a greater prevalence of bloating (p = 0.0002) and flatulence (p = 0.004) after 7 days of treatment. CONCLUSIONS: Our study showed that a short-term 7-day PPI course produced SIBO in 7.8% of healthy subjects. Although, inappropriate use of PPIs should be discouraged, but since more than 90% of subjects who received PPIs for one week did not develop SIBO, the advantages of PPI administration seem to outweigh the disadvantages.

Helicobacter pylori infection and small intestinal bacterial overgrowth: a systematic review and meta-analysis.

BACKGROUND: There is a link between Helicobacter pylori (HP) infection and small intestinal bacterial overgrowth (SIBO) with nonspecific digestive symptoms. Nonetheless, whether HP infection is associated with SIBO in adults remains unclear. Based on a meta-analysis, we evaluated this relationship. RESULTS: Observational studies relevant to our research were identified by searching PubMed, Embase, the Cochrane Library, and the Web of Science. We evaluated between-study heterogeneity using the Cochrane Q test and estimated the I2 statistic. Random-effects models were used when significant heterogeneity was observed; otherwise, fixed-effects models were used. Ten datasets from eight studies, including 874 patients, were involved in the meta-analysis. It was shown that HP infection was related to a higher odds of SIBO (odds ratio [OR]: 1.82, 95% confidence interval: 1.29 to 2.58, p < 0.001) with mild heterogeneity (p for Cochrane Q test = 0.11, I2 = 7%). Subgroup analyses showed that HP infection was related to SIBO in young patients (mean age < 48 years, OR: 2.68, 95% CI: 1.67 to 4.28, p < 0.001; I2 = 15%) but not in older patients (mean age ≥ 48 years, OR: 1.15, 95% CI: 0.69 to 1.92, p < 0.60; I2 = 1%; p for subgroup difference = 0.02). Subgroup analyses further indicated that the association was not significantly affected by the country of study, comorbidities, exposure to proton pump inhibitors, or methods of evaluating HP infection and SIBO. CONCLUSIONS: HP infection may be related to SIBO in adults, which supports the detection of SIBO in patients with digestive symptoms and HP infection.

Plasma levels of intestinal fatty-acid binding protein (I-FABP), abdominal distension and hydrogen concentration after lactitol small intestinal bacterial overgrowth (SIBO) test / Niveles plasmáticos de intestino proteína fijadora de ácidos grasos (I-FABP), distensión abdominal y concentración de hidrógeno después del lactitol intestino delgado prueba de sobrecrecimiento bacteriano (SIBO)

Breath tests with glucose, lactulose or lactitol are useful for diagnosis of small intestinal bacterial overgrowth (SIBO). Nevertheless, they have suboptimal sensitivity and specificity and, indeed, are positive in a considerable number of patients with irritable bowel syndrome (IBS). The complexity in the management of patients with functional intestinal disorders and the availability of these tests are leading to frequent diagnoses of SIBO. Intestinal Fatty-Acid Binding protein (I-FABP) is a protein present in the cytosol of intestinal epithelial cells. Its plasmatic levels have been related to different enteropathies and, therefore, could be a marker of early intestinal damage with unconfirmed clinical utility. Hence, we have studied the plasmatic I-FABP level of patients who are requested a lactitol test to confirm SIBO and related it to clinical and laboratory characteristics and SIBO test results.(AU)

[Single hydrogen-methane breath test for the diagnosis of small intestinal bacterial growth].

Objective: To investigate the diagnostic value of a single hydrogen-methane breath test (SHMBT) for small intestinal bacterial overgrowth (SIBO). Method: The current investigation was a cross-sectional study. Questionnaires and SHMBTs were administered to 162 patients with gastrointestinal symptoms (case group) and 69 healthy volunteers (control group). Differences in SHMBT results between the two groups were assessed,and cut-off values of CH4 (methane) and H2 (hydrogen) were analyzed via receiver operating characteristic (ROC) curves. Lastly,archived SHMBT data from 2 655 patients with gastrointestinal symptoms (validation set) were used to evaluate the diagnostic value of the SHMBT with respect to SIBO. The Chi-square test,the Mann-Whitney U test,Spearman's Rank correlation analysis,and the Z test were used for statistical analysis. Results: Based on the international recommended diagnostic criteria for SIBO,which are fasting CH4 ≥10 ppm (parts per million) or H2 ≥20 ppm,the SHMBT-positive rate in the case group was significantly higher than that of control group (35.2% vs. 21.7%, χ2=4.08, P=0.043). Levels of CH4 and H2 were higher in the case group than in the control group [CH4: 3(2,7) vs. 3(1,3) ppm, H2: 11(4,22) vs. 10(5,15) ppm],and the difference in CH4 levels was statistically significant (Z=6.22,P=0.001). ROC curves were generated based on whether the subjects had gastrointestinal symptoms. The areas under the ROC curves were 0.633 for CH4 alone,0.531 for H2 alone, and 0.620 for CH4 combined with H2. The cut-off values were fasting CH4≥4 ppm,fasting H2≥13 ppm,and fasting CH4 ≥5 ppm (or CH4≥4 ppm and H2≥24 ppm),respectively. Measuring CH4 alone and CH4 combined with H2 was effective for determining the presence of gastrointestinal symptoms (P<0.05). When CH4 alone or CH4 combined with H2 were used as diagnostic indicators of SIBO, the respective SHMBT-positive rates in the validation set were 34.2% and 30.4%. These rates did not significantly differ from the SIBO-positive rate of 32.0% obtained via the international recommended diagnostic criteria (P>0.05). The specificity of CH4 alone was 79.9%,and the accuracy of CH4 alone was 68.8%. The specificity of CH4 combined with H2 was 85.0%,and the accuracy of CH4 combined with H2 was 71.7%. Conclusion: Rapid one-time determination of CH4 and H2 in exhaled breath may a viable diagnostic method for SIBO, and using CH4 combined with H2 (i.e.,fasting CH4≥5 ppm, or CH4 ≥4 ppm and H2 ≥24 ppm) as cutoff values may be feasible.

Small intestinal bacterial overgrowth: current update.

PURPOSE OF REVIEW: This article aims to provide an up-to-date review of small intestinal bacterial overgrowth (SIBO), including etiology and risk factors, clinical manifestations, diagnostic evaluation for suspected SIBO, and therapeutic options. RECENT FINDINGS: Recent advances in breath testing, capsule and urine-based testing have opened new avenues and improved diagnostic yield of SIBO. Nonantibiotic-based treatment strategies have shown promising results in initial trials. SUMMARY: Small intestinal bacterial overgrowth (SIBO) is a condition defined by the excess bacteria or changes in bacterial composition of the small intestine. These are associated with various gastrointestinal (GI) symptoms such as bloating, abdominal distension, diarrhea, nutrient deficiencies, and even frank weight loss. Small bowel jejunal aspirate of >10 5 CFU/ml has traditionally been considered the gold standard for diagnosis. Glucose and lactulose breath testing have become more common in clinical practice as they are noninvasive, easily accessible, and have lower cost. Treatment focuses on the eradication of excess bacteria in the small bowel and is traditionally done with the use of oral antibiotics. Other emerging therapies may include probiotics, diet manipulation, and prokinetic agents.

Low dietary fiber intake impairs small intestinal Th17 and intraepithelial T cell development over generations.

Dietary fiber strongly impacts the microbiota. Here, we show that a low-fiber diet changes the small intestinal (SI) microbiota and impairs SI Th17, TCRαß+CD8αß+ and TCRαß+CD8αα+ intraepithelial T cell development. We restore T cell development with dietary fiber supplementation, but this defect becomes persistent over generations with constant low-fiber diets. Offspring of low-fiber diet-fed mice have reduced SI T cells even after receiving a fiber-rich diet due to loss of bacteria important for T cell development. In these mice, only a microbiota transplant from a fiber-rich diet-fed mouse and a fiber-rich diet can restore T cell development. Low-fiber diets reduce segmented filamentous bacteria (SFB) abundance, impairing its vertical transmission. SFB colonization and a fiber-rich diet partially restore T cell development. Finally, we observe that low-fiber diet-induced T cell defects render mice more susceptible to Citrobacter rodentium infection. Together, these results demonstrate the importance of fiber to microbiota vertical transmission and host immune system development.

Coronavirus Disease 2019 (COVID-19) Pandemic Lifestyle Changes May Have Influenced Small Bowel Microbial Composition and Microbial Resistance.

BACKGROUND: The coronavirus disease 2019 (COVID-19) global pandemic necessitated many severe lifestyle changes, including lockdowns, social distancing, altered food consumption and exercise patterns, and extensive hygiene practices. These extensive changes may have affected the human gut microbiome, which is highly influenced by lifestyle. AIMS: To examine the potential effects of pandemic-related lifestyle changes on the metabolically relevant small bowel microbiome. METHODS: Adult subjects presenting for upper endoscopy without colonoscopy were identified and divided into two matched groups: pre-pandemic (February 2019-March 2020) and intra-pandemic (April 2021-September 2021, all COVID-19 negative). Duodenal aspirates and blood samples were collected. Duodenal microbiomes were analyzed by 16S rRNA sequencing. Serum cytokine levels were analyzed by Luminex FlexMap3D. RESULTS: Fifty-six pre-pandemic and 38 COVID-negative intra-pandemic subjects were included. There were no significant changes in duodenal microbial alpha diversity in the intra-pandemic vs. pre-pandemic group, but beta diversity was significantly different. The relative abundance (RA) of phylum Deinococcus-Thermus and family Thermaceae, which are resistant extremophiles, was significantly higher in the intra-pandemic vs. pre-pandemic group. The RA of several Gram-negative taxa including Bacteroidaceae (phylum Bacteroidetes) and the Proteobacteria families Enterobacteriaceae and Pseudomonadaceae, and the RA of potential disruptor genera Escherichia-Shigella and Rothia, were significantly lower in the intra-pandemic vs. pre-pandemic group. Circulating levels of interleukin-18 were also lower in the intra-pandemic group. CONCLUSIONS: These findings suggest the small bowel microbiome underwent significant changes during the pandemic, in COVID-19-negative individuals. Given the key roles of the small bowel microbiota in host physiology, this may have implications for human health.

ARF1 maintains intestinal homeostasis by modulating gut microbiota and stem cell function.

AIMS: The small GTPase protein ARF1 has been shown to be involved in the lipolysis pathway and to selectively kill stem cells in Drosophila melanogaster. However, the role of ARF1 in mammalian intestinal homeostasis remains elusive. This study aimed to explore the role of ARF1 in intestinal epithelial cells (IECs) and reveal the possible mechanism. MATERIALS AND METHODS: IEC-specific ARF1 deletion mouse model was used to evaluate the role of ARF1 in intestine. Immunohistochemistry and immunofluorescence analyses were performed to detect specific cell type markers, and intestinal organoids were cultured to assess intestinal stem cell (ISC) proliferation and differentiation. Fluorescence in situ hybridization, 16S rRNA-seq analysis, and antibiotic treatments were conducted to elucidate the role of gut microbes in ARF1-mediated intestinal function and the underlying mechanism. Colitis was induced in control and ARF1-deficient mice by dextran sulfate sodium (DSS). RNA-seq was performed to elucidate the transcriptomic changes after ARF1 deletion. KEY FINDINGS: ARF1 was essential for ISC proliferation and differentiation. Loss of ARF1 increased susceptibility to DSS-induced colitis and gut microbial dysbiosis. Gut microbiota depletion by antibiotics could rescue the intestinal abnormalities to a certain extent. Furthermore, RNA-seq analysis revealed alterations in multiple metabolic pathways. SIGNIFICANCE: This work is the first to elucidate the essential role of ARF1 in regulating gut homeostasis, and provides novel insights into the pathogenesis of intestinal diseases and potential therapeutic targets.

Clinical Presentation of Small Intestinal Bacterial Overgrowth from Aerodigestive Tract Bacteria Versus Colonic-Type Bacteria: A Comparison Study.

BACKGROUND: Small Intestinal Bacterial Overgrowth (SIBO) is a heterogenous syndrome from excessive bacteria in the small intestine lumen. It is unknown if differences in type of bacterial overgrowth lead to differences in symptoms. METHODS: Patients with suspected SIBO were recruited prospectively. Exclusion criteria were probiotics, antibiotics, or bowel prep in preceding 30 days. Clinical characteristics, risk factors, and labs were collected. Proximal jejunal aspiration via upper enteroscopy was performed. Aerodigestive tract (ADT) SIBO was defined as > 105 CFU/mL of oropharyngeal and respiratory bacteria. Colonic-type SIBO was defined as > 104 CFU/mL of distal small bowel and colon bacteria. Aims were to compare symptom profiles, clinical complications, labs, and underlying risk factors between ADT and colonic-type SIBO. KEY RESULTS: We consented 166 subjects. Aspiration was not obtained in 22 and SIBO was found in 69 (49%) of 144 subjects. Daily abdominal distention trended towards more prevalent in ADT SIBO versus colonic-type SIBO (65.2% vs 39.1%, p = 0.09). Patient symptom scores were similar. Iron deficiency was more prevalent in ADT SIBO (33.3% vs 10.3%, p = 0.04). Subjects with colonic-type SIBO were more likely to have a risk factor for colonic bacteria colonization (60.9% vs 17.4%, p = 0.0006). Subjects with ADT SIBO were more likely to have a risk factor for diminished gastric acid (91.3% vs 67.4%, p = 0.02). CONCLUSIONS & INFERENCES: We found differences in iron deficiency and underlying risk factors between ADT and colonic-type SIBO. However, distinct clinical profiles remained elusive. Future research is needed to develop validated symptom assessment tools and distinguish cause from correlation.

Gut Microbiota Modulation of Short Bowel Syndrome and the Gut-Brain Axis.

Short bowel syndrome (SBS) is a condition that results from a reduction in the length of the intestine or its functional capacity. SBS patients can have significant side effects and complications, the etiology of which remains ill-defined. Thus, facilitating intestinal adaptation in SBS remains a major research focus. Emerging data supports the role of the gut microbiome in modulating disease progression. There has been ongoing debate on defining a "healthy" gut microbiome, which has led to many studies analyzing the bacterial composition and shifts that occur in gastrointestinal disease states such as SBS and the resulting systemic effects. In SBS, it has also been found that microbial shifts are highly variable and dependent on many factors, including the anatomical location of bowel resection, length, and structure of the remnant bowel, as well as associated small intestinal bacterial overgrowth (SIBO). Recent data also notes a bidirectional communication that occurs between enteric and central nervous systems called the gut-brain axis (GBA), which is regulated by the gut microbes. Ultimately, the role of the microbiome in disease states such as SBS have many clinical implications and warrant further investigation. The focus of this review is to characterize the role of the gut microbiota in short bowel syndrome and its impact on the GBA, as well as the therapeutic potential of altering the microbiome.

The small intestine: dining table of host-microbiota meetings.

Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo, and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical, and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.

Evaluation of small intestinal bacterial overgrowth.

INTRODUCTION: There has been phenomenal interest concerning gut microbiota dysbiosis including small intestinal bacterial overgrowth (SIBO). However, the diagnostic methods for SIBO are still unsatisfactory. AREAS COVERED: The current review covers the different invasive and noninvasive tests to diagnose SIBO, their methodology, interpretation, sensitivity, specificity, and limitations based on the selected articles from literature search using searchterms 'small intestinal bacterial overgrowth' AND 'digestive diseases' OR'diagnosis' OR 'hydrogen breath test' in PubMed in December 2022. The current review will cover some potential methods for diagnosis of SIBO that may be of clinical utility in the future. EXPERT OPINION: SIBO was conventionally defined as a total bacterial count >105 colony forming units (CFU) per mL on quantitative culture of upper gut aspirate. The threshold for the diagnosis of SIBO has been reduced to >103CFU per mL of aspirate recently. Considering the invasiveness of collecting upper gut aspirate, need for laboratory infrastructure and manpower to culture it, noninvasive hydrogen breath tests (HBT) became popular. However, due to the poor sensitivity and specificity of HBT to diagnose SIBO, their utility is being challenged. A new technology of measuring intra-luminal hydrogen gas has a potential to bring a paradigm shift in the diagnostic tests for SIBO.