Gut microbiome health and dysbiosis: A clinical primer

A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies

The human gut microbiome plays a vital role in preserving individual health and is intricately involved in essential functions. Imbalances or dysbiosis within the microbiome can significantly impact human health and are associated with many diseases. Several metaproteomics platforms are currently available to study microbial proteins within complex microbial communities. In this study, we attempted to develop an integrated pipeline to provide deeper insights into both the taxonomic and functional aspects of the cultivated human gut microbiomes derived from clinical colon biopsies. We combined a rapid peptide search by MSFragger against the Unified Human Gastrointestinal Protein database and the taxonomic and functional analyses with Unipept Desktop and MetaLab-MAG. Across seven samples, we identified and matched nearly 36,000 unique peptides to approximately 300 species and 11 phyla. Unipept Desktop provided gene ontology, InterPro entries, and enzyme commission number annotations, facilitating the identification of relevant metabolic pathways. MetaLab-MAG contributed functional annotations through Clusters of Orthologous Genes and Non-supervised Orthologous Groups categories. These results unveiled functional similarities and differences among the samples. This integrated pipeline holds the potential to provide deeper insights into the taxonomy and functions of the human gut microbiome for interrogating the intricate connections between microbiome balance and diseases.

The Effect of Microbiome-Modulating Agents (MMAs) on Type 1 Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Gut microbiome-modulating agents (MMAs), including probiotics, prebiotics, postbiotics, and synbiotics, are shown to ameliorate type 1 diabetes (T1D) by restoring the microbiome from dysbiosis. The objective of this systematic review and meta-analysis was to assess the impact of MMAs on hemoglobin A1c (HbA1c) and biomarkers associated with (T1D). A comprehensive search was conducted in PubMed, Web of Science, Embase, Cochrane Library, National Knowledge Infrastructure, WeiPu, and WanFang Data up to 30 November 2023. Ten randomized controlled trials (n = 630) were included, with study quality evaluated using the Cochrane risk-of-bias tool. Random-effect models with standardized mean differences (SMDs) were utilized. MMA supplementation was associated with improvements in HbA1c (SMD = -0.52, 95% CI [-0.83, -0.20]), daily insulin usage (SMD = -0.41, 95% confidence interval (CI) [-0.76, -0.07]), and fasting C-peptide (SMD = 0.99, 95% CI [0.17, 1.81]) but had no effects on FBG, CRP, TNF-α, IL-10, LDL, HDL, and the Shannon index. Subgroup analysis of HbA1c indicated that a long-term intervention (>3 months) might exert a more substantial effect. These findings suggest an association between MMAs and glycemic control in T1D. Further large-scale clinical trials are necessary to confirm these findings with investigations on inflammation and gut microbiota composition while adjusting confounding factors such as diet, physical activity, and the dose and form of MMA intervention.

Gender Differences in the Interplay between Vitamin D and Microbiota in Allergic and Autoimmune Diseases

The synergic role of vitamin D and the intestinal microbiota in the regulation of the immune system has been thoroughly described in the literature. Vitamin D deficiency and intestinal dysbiosis have shown a pathogenetic role in the development of numerous immune-mediated and allergic diseases. The physiological processes underlying aging and sex have proven to be capable of having a negative influence both on vitamin D values and the biodiversity of the microbiome. This leads to a global increase in levels of systemic inflammatory markers, with potential implications for all immune-mediated diseases and allergic conditions. Our review aims to collect and analyze the relationship between vitamin D and the intestinal microbiome with the immune system and the diseases associated with it, emphasizing the effect mediated by sexual hormones and aging.

Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers

Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.

The Variability of Tryptophan Metabolism in Patients with Mixed Type of Irritable Bowel Syndrome

Patients with a mixed type of irritable bowel syndrome (IBS-M) experience constipation and diarrhea, which alternate between weeks or months. The pathogenesis of this syndrome is still little understood. The aim of the study was mainly to evaluate the urinary excretion of selected tryptophan (TRP) metabolites during the constipation and diarrhea periods of this syndrome. In 36 patients with IBS-M and 36 healthy people, serum serotonin level was measured by ELISA and urinary levels of 5-hydroxyindoleacetic acid (5-HIAA), kynurenine (KYN) and indican (3-IS) were determined using the LC-MS/MS method. The levels of all above metabolites were higher in the patient group, and increased significantly during the diarrheal period of IBS-M. In particular, the changes concerned 5-HIAA (3.67 ± 0.86 vs. 4.59 ± 0.95 mg/gCr, p < 0.001) and 3-IS (80.2 ± 17.4 vs. 93.7 ± 25.1 mg/g/Cr, p < 0.001). These changes coexisted with gut microbiome changes, assessed using hydrogen-methane and ammonia breath tests. In conclusion, the variability of TRP metabolism and the gut microbiome may cause the alternation of IBS-M symptoms.

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study

The influence of human gut microbiota on health and disease is now commonly appreciated. Therefore, it is not surprising that microbiome research has found interest in the sports community, hoping to improve health and optimize performance. Comparative studies found new species or pathways that were more enriched in elites than sedentary controls. In addition, sport-specific and performance-level-specific microbiome features have been identified. However, the results remain inconclusive and indicate the need for further assessment. In this case-control study, we tested two athletic populations (i.e. strength athletes, endurance athletes) and a non-athletic, but physically active, control group across two acute exercise bouts, separated by a 2-week period, that measured explosive and high intensity fitness level (repeated 30-s all-out Wingate test (WT)) and cardiorespiratory fitness level (Bruce Treadmill Test). While we did not identify any group differences in alpha and beta diversity or significant differential abundance of microbiome components at baseline, one-third of the species identified were unique to each group. Longitudinal sample (pre- and post-exercise) analysis revealed an abundance of Alistipes communis in the strength group during the WT and 88 species with notable between-group differences during the Bruce Test. SparCC recognized Bifidobacterium longum and Bifidobacterium adolescentis, short-chain fatty acid producers with probiotic properties, species strongly associated with VO2max. Ultimately, we identified several taxa with different baseline abundances and longitudinal changes when comparing individuals based on their VO2max, average power, and maximal power parameters. Our results confirmed that the health status of individuals are consistent with assumptions about microbiome health. Furthermore, our findings indicate that microbiome features are associated with better performance previously identified in elite athletes.

Probiotics, prebiotics, and synbiotics in type 1 diabetes mellitus: A systematic review and meta-analysis of clinical trials

Dysbiosis or imbalance of microbes in the gut has been associated with susceptibility and progression of type 1 diabetes mellitus (T1DM). The present systematic review and meta-analysis examined the effects of probiotics, prebiotics, and synbiotics on fasting blood glucose (FBG), haemoglobin A1c (HbA1c), C-peptide, and insulin requirements in T1DM patients. A systematic search for trials published up to October 2022 was conducted in PubMed, EMBASE, Scopus, Google Scholar, ScienceDirect, Web of Science, and the Central Cochrane Library. Random effect models were used to synthesise quantitative data by STATA14 . After the evaluation of 258 identified entries, five randomised controlled trials (n = 356; mean age = 11.7 years old) were included. The pooled effect size showed that FBG decreased following probiotic supplementation (weighted mean difference = -31.24 mg/dL; 95% confidence interval = -45.65, -16.83; p < 0.001), however, there was no significant improvement in serum HbA1c, C-peptide, and insulin requirements. Probiotic supplementation could be a complementary therapeutic strategy in T1DM. The evidence is limited; therefore, it is crucial to conduct more trials.

Fecal Microbiota, Live-jslm for the Prevention of Recurrent Clostridioides difficile Infection : Subgroup Analysis of PUNCH CD2 and PUNCH CD3

GOALS

To assess fecal microbiota, live-jslm (REBYOTA, abbreviated as RBL, formerly RBX2660) efficacy and safety in participants grouped by recurrent Clostridioides difficile infection (rCDI) risk factors and treatment-related variables.

BACKGROUND

RBL is the first microbiota-based live biotherapeutic approved by the US Food and Drug Administration for the prevention of rCDI in adults after antibiotic treatment for rCDI.

STUDY

Treatment success rates across subgroups for PUNCH CD3 (NCT03244644) were estimated using a Bayesian hierarchical model, borrowing data from PUNCH CD2 (NCT02299570). Treatment-emergent adverse events were summarized for the double-blind treatment period within 8 weeks.

RESULTS

Treatment differences between RBL and placebo at 8 weeks were similar to the total population for most subgroups. Treatment effect sizes were similar between CDI tests, higher for oral vancomycin courses >14 days versus ≤14 days and higher for antibiotic washout periods of 3 days versus ≤2 days. The largest reductions in the rate of rCDI with RBL versus placebo were observed for participants with a 3-day CDI antibiotic washout period and participants with ≥4 previous CDI episodes. Most RBL-treated participants experienced TEAEs that were mild or moderate in severity and related to preexisting conditions.

CONCLUSION

This analysis provides further evidence of RBL efficacy and safety across subgroups, including those at high risk for rCDI.

Higher Bifidobacterium spp. fecal abundance is associated with a lower prevalence of hyperglycemia and cardiovascular risk markers among schoolchildren from Bahia, Brazil

The gut microbiome has recently been the subject of considerable scientific interest due to its essential bodily functions. Several factors can change the composition and function of the gut microbiome, and dietary habits are one of the most important contributors. Despite the recognition of the probiotic effects related to the genus Bifidobacterium spp. (BIF) studies aiming to assess its relationship with metabolic outcomes show conflicting results, particularly in the child population. This cross-sectional study aimed to evaluate the fecal abundance of BIF in a group of schoolchildren from public schools in Bahia, Brazil, and to investigate their relationship with food consumption and laboratory and anthropometric characteristics. A sample of 190 subjects aged 5 to 19y was randomly selected for dietary, laboratory, and anthropometric assessment. Fecal BIF abundance assessment was performed using the Real-Time Polymerase Chain Reaction assay. Fecal BIF abundance was higher among subjects who had lower intakes of meat. The abundance of BIF was also higher among subjects with lower Waist Circumference and Waist-to-Height Ratio (WHtR). Low BIF abundance was associated with a higher prevalence of hyperglycemia (PR 1.04, 95%CI 1.02-1.07, p = 0.001) and high WHtR (PR 1.04, 95%CI 1.01-1, 08, p = 0.015). These findings allow us to conclude that BIF fecal abundance is related to dietary and anthropometric parameters in schoolchildren, and its increase is associated with positive metabolic outcomes.

The value of connections

High proportions of gut bacteria that produce their own food can be an indicator for poor gut health.

The Association between the Gut Microbiome and Development and Progression of Cancer Treatment Adverse Effects

Adverse effects are a common consequence of cytotoxic cancer treatments. Over the last two decades there have been significant advances in exploring the relationship between the gut microbiome and these adverse effects. Changes in the gut microbiome were shown in multiple clinical studies to be associated with the development of acute gastrointestinal adverse effects, including diarrhoea and mucositis. However, more recent studies showed that changes in the gut microbiome may also be associated with the long-term development of psychoneurological changes, cancer cachexia, and fatigue. Therefore, the aim of this review was to examine the literature to identify potential contributions and associations of the gut microbiome with the wide range of adverse effects from cytotoxic cancer treatments.

Review of Major Social Determinants of Health in Schizophrenia-Spectrum Psychotic Disorders: III. Biology

BACKGROUND

Social determinants of health (SDoHs) are nonmedical factors that significantly impact health and longevity. We found no published reviews on the biology of SDoHs in schizophrenia-spectrum psychotic disorders (SSPD).

STUDY DESIGN

We present an overview of pathophysiological mechanisms and neurobiological processes plausibly involved in the effects of major SDoHs on clinical outcomes in SSPD.

STUDY RESULTS

This review of the biology of SDoHs focuses on early-life adversities, poverty, social disconnection, discrimination including racism, migration, disadvantaged neighborhoods, and food insecurity. These factors interact with psychological and biological factors to increase the risk and worsen the course and prognosis of schizophrenia. Published studies on the topic are limited by cross-sectional design, variable clinical and biomarker assessments, heterogeneous methods, and a lack of control for confounding variables. Drawing on preclinical and clinical studies, we propose a biological framework to consider the likely pathogenesis. Putative systemic pathophysiological processes include epigenetics, allostatic load, accelerated aging with inflammation (inflammaging), and the microbiome. These processes affect neural structures, brain function, neurochemistry, and neuroplasticity, impacting the development of psychosis, quality of life, cognitive impairment, physical comorbidities, and premature mortality. Our model provides a framework for research that could lead to developing specific strategies for prevention and treatment of the risk factors and biological processes, thereby improving the quality of life and increasing the longevity of people with SSPD.

CONCLUSIONS

Biology of SDoHs in SSPD is an exciting area of research that points to innovative multidisciplinary team science for improving the course and prognosis of these serious psychiatric disorders.

Auto brewery syndrome from the perspective of the neurologist

BACKGROUND AND PURPOSE

Auto-brewery syndrome (ABS) is a rare condition that causes the digestive system to produce intoxicating amounts of alcohol due to abnormal growth of the gut microbiota. Medicolegal inferences of ABS have two distinct edges. First, malingering in drunk-driving and abusing the syndrome as a factitious disorder may occur. Second, patients suffering from the syndrome may face medicolegal and social problems. Moreover, chronic exposure to alcohol due to undiagnosed ABS might result in cognitive and behavioral disturbances. Here, we present a patient with recurrent encephalopathy episodes and chronic cognitive disturbances, who was diagnosed with the auto-brewery syndrome, to emphasize the neurocognitive consequences of the syndrome.

CASE PRESENTATION

A 58 years old female presented with mild cognitive impairment, behavioral disturbances, and recurrent encephalopathy episodes. The history of hemicolectomy, an odd smell on her breath, and cravings for high carbohydrate meals during the paroxysmal episodes raised the suspicion of ABS. Her blood ethanol concentration reached 315 mg/dL following an oral glucose tolerance test (OGTT), and stool analysis revealed increased colonization with C. krusei and C. parapsilosis. She was free of the acute episodes, cognitive and behavioral disturbances improved, and C. krusei and C. parapsilosis were eliminated from the intestinal flora with dietary recommendations and nystatin treatment.

CONCLUSION

The auto brewery syndrome is a rare disorder of dysbiosis leading to a disturbed gut-brain axis. Being a treatable and relatively benign diagnosis, presentation of the ABS with neurocognitive disturbances necessitates highlighting.

Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics

Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.

Gut microbiome health and dysbiosis: A clinical primer

The gut microbiome has been referred to as the "forgotten organ." Although much about the gut microbiome remains incompletely understood, data on its clinical importance is emerging at rapid speed. Many practicing clinicians may be unaware of the essential role that the microbiome plays in both health and disease. This review aims to improve clinical understanding of the gut microbiome by discussing key terminology and foundational concepts. The role of a healthy microbiome in normal host function is described, as well as the consequences of a disrupted microbiome (i.e., dysbiosis). Management strategies to restore the gut microbiome from a disrupted to a healthy state are also briefly discussed. Lastly, we review emerging areas for therapeutic potential and opportunity to bring determinants of microbiome health from the bench to bedside.