Gut microbiota associations with common diseases and prescription medications in a population-based cohort

Lacticaseibacillus rhamnosus Hao9 exerts antidiabetic effects by regulating gut microbiome, glucagon metabolism, and insulin levels in type 2 diabetic mice

Introduction

Type 2 diabetes mellitus (T2DM) is a metabolic disease that has led to a significant global public health burden.

Methods

In this work, we investigated the effects of Lacticaseibacillus rhamnosus Hao9 on T2DM in mice with high-fat diet- and streptozotocin (STZ)-induced diabetes (diabetic mice) and explored the underlying mechanisms.

Results

We found that 10⁹ colony forming units (CFUs) of Hao9 per day significantly reduced fasting blood glucose and insulin levels (p < 0.001) in diabetic mice. Moreover, Hao9 enhanced liver antioxidant capacity and significantly decreased glucose-6-phosphatase and phosphoenolpyruvate carboxykinase expression in the livers of diabetic mice (p < 0.001). Hao9 also reduced the serum concentrations of pro-inflammatory cytokines such as tumor necrosis factor alpha (TNFα), interleukin-1β (IL1β), and IL6 (p < 0.05) and improved intestinal barrier function in diabetic mice. The composition of the gut microbiome was modulated by Hao9, with an increased abundance of Roseburia, Eubacterium, and Lacticaseibacillus, and decreased abundance of Escherichia/Shigella. Notably, Lacticaseibacillus was detected at both weeks 5 and 12 post-treatment, suggesting sustained colonization of the gut by Hao9.

Discussion

The supplementation of Hao9 improved gut microbiota, glucose metabolism, and insulin levels significantly in T2DM mice. That means Hao9 contributes to improving T2DM symptoms with its potential beneficial effects. Therefore, Hao9 is a promising dietary supplement for the treatment of T2DM.

Stable colonization of Akkermansia muciniphila educates host intestinal microecology and immunity to battle against inflammatory intestinal diseases

Gut microbial preparations are widely used in treating intestinal diseases but show mixed success. In this study, we found that the therapeutic efficacy of A. muciniphila for dextran sodium sulfate (DSS)-induced colitis as well as intestinal radiation toxicity was ~50%, and mice experiencing a positive prognosis harbored a high frequency of A. muciniphila in the gastrointestinal (GI) tract. Stable GI colonization of A. muciniphila elicited more profound shifts in the gut microbial community structure of hosts. Coexisting with A. muciniphila facilitated proliferation and reprogrammed the gene expression profile of Lactobacillus murinus, a classic probiotic that overtly responded to A. muciniphila addition in a time-dependent manner. Then, a magnetic-drove, mannose-loaded nanophase material was designed and linked to the surface of A. muciniphila. The modified A. muciniphila exhibited enhancements in inflammation targeting and intestinal colonization under an external magnetic field, elevating the positive-response rate and therapeutic efficacy against intestinal diseases. However, the unlinked cocktail containing A. muciniphila and the delivery system only induced negligible improvement of therapeutic efficacy. Importantly, heat-inactivated A. muciniphila lost therapeutic effects on DSS-induced colitis and was even retained in the GI tract for a long time. Further investigations revealed that the modified A. muciniphila was able to drive M2 macrophage polarization by upregulating the protein level of IL-4 at inflammatory loci. Together, our findings demonstrate that stable colonization of live A. muciniphila at lesion sites is essential for its anti-inflammatory function.

Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation

PURPOSE

The gut microbiota is subject to multiple insults in allogeneic hematopoietic cell transplantation (allo-HCT) recipients. We hypothesized that preparative conditioning regimens contribute to microbiota perturbation in allo-HCT.

EXPERIMENTAL DESIGN

This was a retrospective study that evaluated the relationship between conditioning regimens exposure in 1,188 allo-HCT recipients and the gut microbiome. Stool samples collected from 20 days before transplantation up to 30 days after were profiled using 16S rRNA sequencing. Microbiota injury was quantified by changes in α-diversity.

RESULTS

We identified distinct patterns of microbiota injury that varied by conditioning regimen. Diversity loss was graded into three levels of conditioning-associated microbiota injury (CMBI) in a multivariable model that included antibiotic exposures. High-intensity regimens, such as total body irradiation (TBI)-thiotepa-cyclophosphamide, were associated with the greatest injury (CMBI III). In contrast, the nonmyeloablative regimen fludarabine-cyclophosphamide with low-dose TBI (Flu/Cy/TBI200) had a low-grade injury (CMBI I). The risk of acute GVHD correlated with CMBI degree. Pretransplant microbial compositions were best preserved with Flu/Cy/TBI200, whereas other regimens were associated with loss of commensal bacteria and expansion of Enterococcus.

CONCLUSIONS

Our findings support an interaction between conditioning at the regimen level and the extent of microbiota injury.

Quorum sensing-based interactions among drugs, microbes, and diseases

Many diseases and health conditions are closely related to various microbes, which participate in complex interactions with diverse drugs; nonetheless, the detailed targets of such drugs remain to be elucidated. Many existing studies have reported causal associations among drugs, gut microbes, or diseases, calling for a workflow to reveal their intricate interactions. In this study, we developed a systematic workflow comprising three modules to construct a Quorum Sensing-based Drug-Microbe-Disease (QS-DMD) database ( http://www.qsdmd.lbci.net/ ), which includes diverse interactions for more than 8,000 drugs, 163 microbes, and 42 common diseases. Potential interactions between microbes and more than 8,000 drugs have been systematically studied by targeting microbial QS receptors combined with a docking-based virtual screening technique and in vitro experimental validations. Furthermore, we have constructed a QS-based drug-receptor interaction network, proposed a systematic framework including various drug-receptor-microbe-disease connections, and mapped a paradigmatic circular interaction network based on the QS-DMD, which can provide the underlying QS-based mechanisms for the reported causal associations. The QS-DMD will promote an understanding of personalized medicine and the development of potential therapies for diverse diseases. This work contributes to a paradigm for the construction of a molecule-receptor-microbe-disease interaction network for human health that may form one of the key knowledge maps of precision medicine in the future.

The fecal microbiota of gravidas with fetal growth restriction newborns characterized by metagenomic sequencing

BACKGROUND

Fetal growth restriction (FGR) is a complex obstetric complication with various causes and of great harm. However, the specific pathogenesis of FGR is unclear, which limits its effective treatment. Gut microbiota dysbiosis was found to be important in pathogenesis of various diseases. However, its role in FGR development remains unclear and needs to be clarified.

METHODS

In our case-control study, we recruited eight FGR and eight control female participants and collected their fecal samples in third trimester before delivery. We performed metagenomic sequencing and bioinformatic analysis to compare the gut microbiota composition and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between the two groups.

RESULTS

Our results showed that totally 20 gut microbes were significantly different between two groups (p<0•05), and the correlation analysis found that g__Roseomonas and g__unclassified_f__Propionibacteriaceae were significantly positive correlated with both maternal body mass index (BMI) before delivery, placental weight, and neonatal birth weight (BW) percentile (all p<0•05), while g__Marinisporobacter and g__Sphingomonas were significantly negative correlated with both neonatal BMI and neonatal BW percentile (all p<0•05). Through KEGG pathway analysis, we found that the abundance of the Nitrogen metabolism pathway decreased significantly (p<0•05) whereas the abundance of the Amoebiasis pathway increased significantly in the FGR group (p<0•05).

CONCLUSION

In this study, we demonstrated that the occurrence of FGR is associated with the change of gut microbiota of pregnant women.

Interactions between NSAIDs, opioids and the gut microbiota - Future perspectives in the management of inflammation and pain

The composition of intestinal microbiota is influenced by a number of factors, including medications, which may have a substantial impact on host physiology. Nonsteroidal anti-inflammatory drugs (NSAIDs) and opioid analgesics are among those widely used medications that have been shown to alter microbiota composition in both animals and humans. Although much effort has been devoted to identify microbiota signatures associated with these medications, much less is known about the underlying mechanisms. Mucosal inflammation, changes in intestinal motility, luminal pH and bile acid metabolism, or direct drug-induced inhibitory effect on bacterial growth are all potential contributors to NSAID- and opioid-induced dysbiosis, however, only a few studies have addressed directly these issues. In addition, there is a notable overlap between the microbiota signatures of these drugs and certain diseases in which they are used, such as spondyloarthritis (SpA), rheumatoid arthritis (RA) and neuropathic pain associated with type 2 diabetes (T2D). The aims of the present review are threefold. First, we aim to provide a comprehensive up-to-date summary on the bacterial alterations caused by NSAIDs and opioids. Second, we critically review the available data on the possible underlying mechanisms of dysbiosis. Third, we review the current knowledge on gut dysbiosis associated with SpA, RA and neuropathic pain in T2D, and highlight the similarities between them and those caused by NSAIDs and opioids. We posit that drug-induced dysbiosis may contribute to the persistence of these diseases, and may potentially limit the therapeutic effect of these medications by long-term use. In this context, we will review the available literature data on the effect of probiotic supplementation and fecal microbiota transplantation on the therapeutic efficacy of NSAIDs and opioids in these diseases.

The gut microbiome is a significant risk factor for future chronic lung disease

BACKGROUND

The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults.

OBJECTIVE

We sought to investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD).

METHODS

Shallow metagenomic sequencing was performed for stool samples from a prospective, population-based cohort (FINRISK02; N = 7115 adults) with linked national administrative health register-derived classifications for incident asthma and COPD up to 15 years after baseline. Generalized linear models and Cox regressions were used to assess associations of microbial taxa and diversity with disease occurrence. Predictive models were constructed using machine learning with extreme gradient boosting. Models considered taxa abundances individually and in combination with other risk factors, including sex, age, body mass index, and smoking status.

RESULTS

A total of 695 and 392 statistically significant associations were found between baseline taxonomic groups and incident asthma and COPD, respectively. Gradient boosting decision trees of baseline gut microbiome abundance predicted incident asthma and COPD in the validation data sets with mean area under the curves of 0.608 and 0.780, respectively. Cox analysis showed that the baseline gut microbiome achieved higher predictive performance than individual conventional risk factors, with C-indices of 0.623 for asthma and 0.817 for COPD. The integration of the gut microbiome and conventional risk factors further improved prediction capacities.

CONCLUSIONS

The gut microbiome is a significant risk factor for incident asthma and incident COPD and is largely independent of conventional risk factors.

Pharmacomicrobiomics in Pediatric Oncology: The Complex Interplay between Commonly Used Drugs and Gut Microbiome

The gut microbiome (GM) has emerged in the last few years as a main character in several diseases. In pediatric oncological patients, GM has a role in promoting the disease, modulating the effectiveness of therapies, and determining the clinical outcomes. The therapeutic course for most pediatric cancer influences the GM due to dietary modifications and several administrated drugs, including chemotherapies, antibiotics and immunosuppressants. Interestingly, increasing evidence is uncovering a role of the GM on drug pharmacokinetics and pharmacodynamics, defining a bidirectional relationship. Indeed, the pediatric setting presents some contrasts with respect to the adult, since the GM undergoes a constant multifactorial evolution during childhood following external stimuli (such as diet modification during weaning). In this review, we aim to summarize the available evidence of pharmacomicrobiomics in pediatric oncology.

Microbiota Composition in Diverticular Disease: Implications for Therapy

Gut microbiota (GM) composition and its imbalance are crucial in the pathogenesis of several diseases, mainly those affecting the gastrointestinal tract. Colon diverticulosis and its clinical manifestations (diverticular disease, DD) are among the most common digestive disorders in developed countries. In recent literature, the role of GM imbalance in the onset of the different manifestations within the clinical spectrum of DD has been highlighted. This narrative review aims to summarize and critically analyze the current knowledge on GM dysbiosis in diverticulosis and DD by comparing the available data with those found in inflammatory bowel disease (IBD). The rationale for using probiotics to rebalance dysbiosis in DD is also discussed.

A comparative analysis of gut microbial dysbiosis by select antibiotics and DSS to understand the effects of perturbation on the host immunity and metabolism

AIMS

Balanced gut microbial composition of the host plays a crucial role in maintaining harmony among various physiological processes to maintain physiological homeostasis. Immunity and metabolism are the two physiologies mainly controlled by the gut microbiota. Reports suggested that gut microbial composition and diversity alteration are the leading causes of the host's healthy homeostasis alteration or a diseased state. The extent of gut perturbation depends on the perturbing agents' strength, chemical nature, and mode of action. In the current report, we have studied the effects of different perturbing agents on gut microbial dysbiosis and its impact on host immunity and metabolism.

MATERIALS AND METHODS

We studied the perturbation of gut microbial composition and diversity using next-generation sequencing and further investigated the changes in host immune and metabolic responses.

KEY FINDINGS

Enrichment or abolition of a particular phylum or genus depended on the perturbing agents. In the current study, treatment with neomycin yielded an increase in the Bacteroidetes phylum. Vancomycin treatment caused a significant rise in Verrucomicrobia and Proteobacteria phyla. The treatment with AVNM and DSS caused a substantial increase in the Proteobacteria phylum. The gut microbial diversity was also lowest in AVNM treated group. The altered gut microbial composition ultimately altered the immune responses at localized and systemic levels of the host. Gut dysbiosis also changed the systemic level of SCFAs.

SIGNIFICANCE

This study will help us understand how the enrichment of a particular phylum and genus maintains the host's immune responses and metabolism.

Intestinal microbiota: A promising therapeutic target for hypertension

Hypertension has developed into an escalating serious global public health problem with multiple and unclear pathophysiological mechanisms. Recent studies have identified intestinal microbiota as a key perpetrator of hypertension through a variety of mechanisms. In this review, we highlight the potential roles of the intestinal microbiota and its metabolites in the development of hypertension, as well as the therapeutic potential for targeting intestinal microbiomes. We also shed light on the main limitations and challenges of the current research and suggest directions for future investigations. Finally, we discuss the development of accurate and personalized preventive and therapeutic strategies for hypotension by the modulation of intestinal microbes and metabolites.

Influential factors of saliva microbiota composition

The oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n = 679) of the TwinsUK cohort of adult twins. Alpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: β = -0.16, Q = 0.003, Observed; β = -0.16, Q = 0.002, Shannon; β = -0.16, Q = 0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: β = 0.15, Q = 0.006, Shannon; β = 0.12, Q = 0.003, Simpson; beta diversity: Q = 0.002, Bray Curtis dissimilarity; Q = 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n = 138, periodontal disease n = 66), the association with frailty remained for alpha diversity (Q = 0.002, Observed ASVs; Q = 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet. Of the factors studied, frailty and age emerged as the most influential with regards to saliva microbiota composition. Whilst age and frailty are correlates, the associations were independent of each other, giving precedence to both biological and chronological ageing as processes of potential importance when considering saliva microbiota composition.

Recent advances in modulation of cardiovascular diseases by the gut microbiota

The gut microbiota has recently gained attention due to its association with cardiovascular health, cancers, gastrointestinal disorders, and non-communicable diseases. One critical question is how the composition of the microbiota contributes to cardiovascular diseases (CVDs). Insightful reviews on the gut microbiota, its metabolites and the mechanisms that underlie its contribution to CVD are limited. Hence, the aim of this review was to describe linkages between the composition of the microbiota and CVD, CVD risk factors such as hypertension, diet, ageing, and sex differences. We have also highlighted potential therapies for improving the composition of the gut microbiota, which may result in better cardiovascular health.

Effects of Whey Protein or Its Hydrolysate Supplements Combined with an Energy-Restricted Diet on Weight Loss: A Randomized Controlled Trial in Older Women

An energy-restricted weight-loss approach has limitations when it used in the elderly, especially because of muscle loss. We aimed to assess the effects of whey protein (WP) or WP hydrolysate (WPH) combined with an energy-restricted diet (ERD) on weight reduction and muscle preservation in older women with overweight and obesity. A total of 60 women were randomized to the control (ERD), WP (ERD + 20 g/d WP) or WPH (ERD + 20 g/d WPH) group, using a 1:1:1 allocation ratio. After an 8-week intervention, body composition, gut microbiota, and serum metabolomics changes were compared among the three groups. The reductions in body weight (−1.11 ± 1.11 vs. −2.34 ± 1.35, p < 0.05), BMI (−0.46 ± 0.45 vs. −0.97 ± 0.54, p < 0.05), and body fat (−0.70 ± 0.92 vs. −2.45 ± 1.65, p < 0.01) were higher in the WPH group than in the control group. Body fat (%) was significantly decreased in the two protein groups. Fat-free mass did not significantly change among the three groups. Serum metabolomics showed that the tricarboxylic acid cycle pathway was upregulated in the WPH group. No significant changes in microbiota were observed among the groups. In conclusion, WP or WPH supplementation combined with an energy-restricted diet benefits older women during weight loss. WPH was more effective, possibly due to increased energy metabolism.

Population-level Metagenomics Uncovers Distinct Effects of Multiple Medications on the Human Gut Microbiome

BACKGROUND & AIMS

Medication is a major determinant of human gut microbiome structure, and its overuse increases the risks of morbidity and mortality. However, effects of certain commonly prescribed drugs and multiple medications on the gut microbiome are still underinvestigated.

METHODS

We performed shotgun metagenomic analysis of fecal samples from 4198 individuals in the Japanese 4D (Disease, Drug, Diet, Daily life) microbiome project. A total of 759 drugs were profiled, and other metadata, such as anthropometrics, lifestyles, diets, physical activities, and diseases, were prospectively collected. Second fecal samples were collected from 243 individuals to assess the effects of drug initiation and discontinuation on the microbiome.

RESULTS

We found that numerous drugs across different treatment categories influence the microbiome; more than 70% of the drugs we profiled had not been examined before. Individuals exposed to multiple drugs, polypharmacy, showed distinct gut microbiome structures harboring significantly more abundant upper gastrointestinal species and several nosocomial pathobionts due to additive drug effects. Polypharmacy was also associated with microbial functions, including the reduction of short-chain fatty acid metabolism and increased bacterial stress responses. Even nonantibiotic drugs were significantly correlated with an increased antimicrobial resistance potential through polypharmacy. Notably, a 2-time points dataset revealed the alteration and recovery of the microbiome in response to drug initiation and cessation, corroborating the observed drug-microbe associations in the cross-sectional cohort.

CONCLUSION

Our large-scale metagenomics unravels extensive and disruptive impacts of individual and multiple drug exposures on the human gut microbiome, providing a drug-microbe catalog as a basis for a deeper understanding of the role of the microbiome in drug efficacy and toxicity.

Small molecule modulation of microbiota: a systems pharmacology perspective

BACKGROUND

Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome signatures. However, emerging endeavors in small-molecule microbiome drug discovery continue to follow a conventional "one-drug-one-target-one-disease" process. A systematic pharmacology approach that would suppress multiple interacting pathogenic species in the microbiome, could offer an attractive alternative solution.

RESULTS

We construct a disease-centric signed microbe-microbe interaction network using curated microbe metabolite information and their effects on host. We develop a Signed Random Walk with Restart algorithm for the accurate prediction of effect of microbes on human health and diseases. With a survey on the druggable and evolutionary space of microbe proteins, we find that 8-10% of them can be targeted by existing drugs or drug-like chemicals and that 25% of them have homologs to human proteins. We demonstrate that drugs for diabetes can be the lead compounds for development of microbiota-targeted therapeutics. We further show that the potential drug targets that specifically exist in pathogenic microbes are periplasmic and cellular outer membrane proteins.

CONCLUSION

The systematic studies of the polypharmacological landscape of the microbiome network may open a new avenue for the small-molecule drug discovery of the microbiome. We believe that the application of systematic method on the polypharmacological investigation could lead to the discovery of novel drug therapies.

New research frontiers pertaining to the infant gut microbiota

The human gut microbiota is believed to be responsible for multiple health-impacting host effects. The influence of gut microorganisms on the human host begins immediately after birth, having long-lasting health effects, while the gut microbiota itself continues to develop throughout the host's entire life. The purported health-associated effects of the gut microbiota have fueled extensive and ongoing research efforts. Nonetheless, the precise mode of action of functionalities exerted by microbial colonizers of the infant intestine is still largely unknown. The current perspective intends to illustrate major future investigative directions concerning the human gut microbiota with a specific focus on infant-associated gut microbes.

Modulation of Intestinal Flora by Dietary Polysaccharides: A Novel Approach for the Treatment and Prevention of Metabolic Disorders

Intestinal flora is numerous and diverse, and play a key role in maintaining human health. Dietary polysaccharides are widely present in the daily diet and have a moderating effect on the intestinal flora. Past studies have confirmed that intestinal flora is involved in the metabolic process in the human body, and the change in intestinal flora structure is closely related to the metabolic disorders in the human body. Therefore, regulating intestinal flora through dietary polysaccharides is an effective way to treat and prevent common metabolic diseases and has great research value. However, this area has not received enough attention. In this review, we provide an overview of the modulatory effects of dietary polysaccharides on intestinal flora and the key role of intestinal flora in improving metabolic disorders in humans. In addition, we highlight the therapeutic and preventive effects of intestinal flora modulation through dietary polysaccharides on metabolic disorders, aiming to find new ways to treat metabolic disorders and facilitate future exploration in this field.

Antibiotics enhancing drug-induced liver injury assessed for causality using Roussel Uclaf Causality Assessment Method: Emerging role of gut microbiota dysbiosis

Drug-induced liver injury (DILI) is a disease that remains difficult to predict and prevent from a clinical perspective, as its occurrence is hard to fully explain by the traditional mechanisms. In recent years, the risk of the DILI for microbiota dysbiosis has been recognized as a multifactorial process. Amoxicillin-clavulanate is the most commonly implicated drug in DILI worldwide with high causality gradings based on the use of RUCAM in different populations. Antibiotics directly affect the structure and diversity of gut microbiota (GM) and changes in metabolites. The depletion of probiotics after antibiotics interference can reduce the efficacy of hepatoprotective agents, also manifesting as liver injury. Follow-up with liver function examination is essential during the administration of drugs that affect intestinal microorganisms and their metabolic activities, such as antibiotics, especially in patients on a high-fat diet. In the meantime, altering the GM to reconstruct the hepatotoxicity of drugs by exhausting harmful bacteria and supplementing with probiotics/prebiotics are potential therapeutic approaches. This review will provide an overview of the current evidence between gut microbiota and DILI events, and discuss the potential mechanisms of gut microbiota-mediated drug interactions. Finally, this review also provides insights into the “double-edged sword” effect of antibiotics treatment against DILI and the potential prevention and therapeutic strategies.

Microbiome as an immune regulator in health, disease, and therapeutics

New discoveries in drugs and drug delivery systems are focused on identifying and delivering a pharmacologically effective agent, potentially targeting a specific molecular component. However, current drug discovery and therapeutic delivery approaches do not necessarily exploit the complex regulatory network of an indispensable microbiota that has been engineered through evolutionary processes in humans or has been altered by environmental exposure or diseases. The human microbiome, in all its complexity, plays an integral role in the maintenance of host functions such as metabolism and immunity. However, dysregulation in this intricate ecosystem has been linked with a variety of diseases, ranging from inflammatory bowel disease to cancer. Therapeutics and bacteria have an undeniable effect on each other and understanding the interplay between microbes and drugs could lead to new therapies, or to changes in how existing drugs are delivered. In addition, targeting the human microbiome using engineered therapeutics has the potential to address global health challenges. Here, we present the challenges and cutting-edge developments in microbiome-immune cell interactions and outline novel targeting strategies to advance drug discovery and therapeutics, which are defining a new era of personalized and precision medicine.

Changes in fecal microbiota composition and the cytokine expression profile in school-aged children with depression: A case-control study

Depression in childhood negatively affects the growth and development, school performance, and peer or family relationships of affected children, and may even lead to suicide. Despite this, its etiology and pathophysiology remain largely unknown. Increasing evidence supports that gut microbiota plays a vital role in the development of childhood depression. However, little is known about the underlying mechanisms, as most clinical studies investigating the link between gut microbiota and depression have been undertaken in adult cohorts. In present study, a total of 140 school-aged children (6–12 years) were enrolled, including 92 with depression (male/female: 42/50) and 48 healthy controls (male/female: 22/26) from Lishui, Zhejiang, China. Illumina sequencing of the V3–V4 region of the 16S rRNA gene was used to investigate gut microbiota profiles while Bio-Plex Pro Human Cytokine 27-plex Panel was employed to explore host immune response. We found that, compared with healthy controls, children with depression had greater bacterial richness and altered β-diversity. Pro-inflammatory genera such as Streptococcus were enriched in the depression group, whereas anti-inflammatory genera such as Faecalibacterium were reduced, as determined by linear discriminant analysis effect size. These changes corresponded to altered bacterial functions, especially the production of immunomodulatory metabolites. We also identified the presence of a complex inflammatory condition in children with depression, characterized by increased levels of pro-inflammatory cytokines such as IL-17 and decreased levels of anti-inflammatory cytokines such as IFN-γ. Correlation analysis demonstrated that the differential cytokine abundance was closely linked to changes in gut microbiota of children with depression. In summary, key functional genera, such as Streptococcus and Faecalibacterium, alone or in combination, could serve as novel and powerful non-invasive biomarkers to distinguish between children with depression from healthy ones. This study was the first to demonstrate that, in Chinese children with depression, gut microbiota homeostasis is disrupted, concomitant with the activation of a complex pro-inflammatory response. These findings suggest that gut microbiota might play an important role in the pathogenesis of depression in school-aged children, while key functional bacteria in gut may serve as novel targets for non-invasive diagnosis and patient-tailored early precise intervention in children with depression.

Evaluating the clinical relevance of the enterotypes in the Estonian microbiome cohort

Human gut microbiome is subject to high inter-individual and temporal variability, which complicates building microbiome-based applications, including applications that can be used to improve public health. Categorizing the microbiome profiles into a small number of distinct clusters, such as enterotyping, has been proposed as a solution that can ameliorate these shortcomings. However, the clinical relevance of the enterotypes is poorly characterized despite a few studies marking the potential for using the enterotypes for disease diagnostics and personalized nutrition. To gain a further understanding of the clinical relevance of the enterotypes, we used the Estonian microbiome cohort dataset (n = 2,506) supplemented with diagnoses and drug usage information from electronic health records to assess the possibility of using enterotypes for disease diagnostics, detecting disease subtypes, and evaluating the susceptibility for developing a condition. In addition to the previously established 3-cluster enterotype model, we propose a 5-cluster community type model based on our data, which further separates the samples with extremely high Bacteroides and Prevotella abundances. Collectively, our systematic analysis including 231 phenotypic factors, 62 prevalent diseases, and 33 incident diseases greatly expands the knowledge about the enterotype-specific characteristics; however, the evidence suggesting the practical use of enterotypes in clinical practice remains scarce.

Phytonutrients: Sources, bioavailability, interaction with gut microbiota, and their impacts on human health

Phytonutrients are natural bioactive components present in the daily diet that can exert a positive impact on human health. Studies have shown that phytonutrients may act as antioxidants and improve metabolism after being ingested, which help to regulate physiological processes and prevent metabolic disorders and diseases. However, their efficacy is limited by their low bioavailability. The gut microbiota is symbiotic with humans and its abundance and profile are related to most diseases. Interestingly, studies have shown that the gut microbiota is associated with the metabolism of phytonutrients by converting them into small molecules that can be absorbed by the body, thereby enhancing their bioavailability. Furthermore, phytonutrients can modulate the composition of the gut microbiota, and therefore improve the host's health. Here, we focus on uncovering the mechanisms by which phytonutrients and gut microbiota play roles in health, and the interrelationships between phytonutrients and gut microbiota were summarized. We also reviewed the studies that reported the efficacy of phytonutrients in human health and the future directions.

Bacillus sp. DU-106 ameliorates type 2 diabetes by modulating gut microbiota in high-fat-fed and streptozotocin-induced mice

AIMS

Type 2 diabetes mellitus (T2D) is a chronic disease that manifests as endocrine and metabolic disorders that seriously threatening public health. This study aimed to investigate the effects of Bacillus sp. DU-106 on anti-diabetic effects and gut microbiota in C57BL/6J mice fed a high-fat diet and streptozotocin-induced T2D.

METHODS AND RESULTS

Bacillus sp. DU-106 was administered to model mice for eight consecutive weeks. Oral administration of Bacillus sp. DU-106 decreased food and water intake and alleviated body weight loss. Moreover, Bacillus sp. DU-106 imparted several health benefits to mice, including balanced blood glucose, alleviation of insulin resistance in T2D mice, and an improvement in lipid metabolism. Furthermore, Bacillus sp. DU-106 protected against liver and pancreatic impairment. Additionally, Bacillus sp. DU-106 treatment reshaped intestinal flora by enhancing gut microbial diversity and enriching the abundance of certain functional bacteria.

CONCLUSION

Collectively, these findings suggest that Bacillus sp. DU-106 can ameliorate T2D by regulating the gut microbiota.

SIGNIFICANCE AND IMPACT OF STUDY

Therefore, a novel probiotic, Bacillus sp. DU-106 may be a promising therapeutic agent for improving and alleviating T2D in mice.

Gut microbiota remodeling: A promising therapeutic strategy to confront hyperuricemia and gout

The incidence of hyperuricemia (HUA) and gout continuously increases and has become a major public health problem. The gut microbiota, which colonizes the human intestine, has a mutually beneficial and symbiotic relationship with the host and plays a vital role in the host’s metabolism and immune regulation. Structural changes or imbalance in the gut microbiota could cause metabolic disorders and participate in the synthesis of purine-metabolizing enzymes and the release of inflammatory cytokines, which is closely related to the occurrence and development of the metabolic immune disease HUA and gout. The gut microbiota as an entry point to explore the pathogenesis of HUA and gout has become a new research hotspot. This review summarizes the characteristics of the gut microbiota in patients with HUA and gout. Meanwhile, the influence of different dietary structures on the gut microbiota, the effect of the gut microbiota on purine and uric acid metabolism, and the internal relationship between the gut microbiota and metabolic endotoxemia/inflammatory factors are explored. Moreover, the intervention effects of probiotics, prebiotics, and fecal microbial transplantation on HUA and gout are also systematically reviewed to provide a gut flora solution for the prevention and treatment of related diseases.

Specific gut microbiota alterations in essential tremor and its difference from Parkinson's disease

Essential tremor (ET) is the most common movement disorder and share overlapping symptoms with Parkinson’s disease (PD), making differential diagnosis challenging. Gut dysbiosis is regarded crucial in the pathogenesis of PD. Since ET patients also has comorbidity in gastrointestinal disorders, the relationship between gut microbiota and ET really worth investigating and may help distinguishing ET from PD. Fecal samples from 54 ET, 67 de novo PD and 54 normal controls (NC) were collected for 16S ribosomal RNA gene sequencing and quantitative real-time PCR. ET showed lower species richness (Chao1 index) than NC and PD. ET was with Bacteroides-dominant enterotype, while PD was with Ruminococcus-dominant enterotype. Compared with NC, 7 genera were significantly reduced in ET, 4 of which (Ruminococcus, Romboutsia, Mucispirillum, and Aeromonas) were identified to be distinctive with an area under the curve (AUC) of 0.705. Compared to PD, 26 genera were found significantly different from ET, 4 of which (Bacteroides, Fusobacterium, Phascolarctobacterium, and Lachnospira) were found distinguishable with an AUC of 0.756. Clinical association results indicated that Proteus was associated with disease severity (TETRAS) of ET, while Klebsiella was linked to depression and anxiety in ET. Functional predictions revealed that 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were altered in ET. This study reveals gut dysbiosis in ET and it provides new insight into the pathogenesis of ET and helps distinguishing ET from PD.

Human microbiota colonization and pancreatic ductal carcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a high mortality rate and a poor prognosis. The human microbiota has been confirmed to participate in oncogenesis and may influence the treatment response to both chemotherapy and immunotherapy. Evidence for the association of the microbiota with PDAC risk, tumorigenesis, treatment response, and survival period is rapidly emerging. The oral microbiota and gut microbiota have the potential to be used in early diagnosis and risk stratification. Intratumor microbiota-targeted intervention strategies may be used as adjuvants to current treatments to improve therapeutic efficacy and overall survival. Here, we summarize the effect and association of the oral, gut and intratumor microbiota on the oncogenesis, progression and treatment of PDAC, as well as the potential of the microbiota to serve as a biomarker for the diagnosis and prognosis of PDAC, as well as a therapeutic target.

Reduced gut microbial diversity in familial hypercholesterolemia with no effect of omega-3 polyunsaturated fatty acids intervention - a pilot trial

Individuals with familial hypercholesterolemia (FH) undergo an aggressive treatment with cholesterol-lowering drugs to prevent coronary heart disease. Recent evidence suggests an interplay between the gut microbiota, blood lipid levels and lipid-lowering drugs, but this has yet to be studied in individuals with FH. The objective of the study was to characterize the gut microbiota of individuals with familial hypercholesterolemia and examine if effects of omega-3 polyunsaturated fatty acids (PUFAs) on blood lipids act through modification of the gut microbiome. The gut microbiota composition of individuals with FH (N = 21) and healthy controls (N = 144) was analyzed by extracting DNA from stool samples and sequencing of the V3-V4 region of the 16S rRNA gene. A subgroup (n = 15) of the participants received omega-3 polyunsaturated fatty acids (PUFAs) supplementation or placebo in a crossover manner, and the effect of PUFAs on the gut microbiota was also investigated. Individuals with FH had a different gut microbiota composition compared to healthy controls, characterized by reduced richness (p = .001) and reduction of several genera belonging to Clostridia and Coriobacteriia. Patients using ezetimibe in addition to statins appeared to have lower richness compared to those only using statins (p = .01). Intervention with omega-3 PUFAs had negligible impact on the microbiota composition. Positive effects on blood lipids after intervention with omega-3 PUFA were not associated with baseline gut microbiota composition or gut microbial changes during treatment. Further, patients with FH have an altered gut microbiota compared to healthy controls, possibly driven by the use of ezetimibe.

Metabolic control by the microbiome

The interaction between the metabolic activities of the intestinal microbiome and its host forms an important part of health. The basis of this interaction is in part mediated by the release of microbially-derived metabolites that enter the circulation. These products of microbial metabolism thereby interface with the immune, metabolic, or nervous systems of the host to influence physiology. Here, we review the interactions between the metabolic activities of the microbiome and the systemic metabolism of the host. The concept that the endocrine system includes more than just the eukaryotic host component enables the rational design of exogenous interventions that shape human metabolism. An improved mechanistic understanding of the metabolic microbiome-host interaction may therefore pioneer actionable microbiota-based diagnostics or therapeutics that allow the control of host systemic metabolism via the microbiome.

Human Gut Microbiota and Drug Metabolism

The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.

Gut microbiome: A potential indicator for predicting treatment outcomes in major depressive disorder

The therapeutic outcomes in major depressive disorder (MDD), one of the most common and heterogeneous mental illnesses, are affected by factors that remain unclear and often yield unsatisfactory results. Herein, we characterized the composition and metabolic function of the gut microbiota of patients with MDD during antidepressant treatment, based on 16S rRNA sequencing and metabolomics. The microbial signatures at baseline differed significantly between responder and non-responder groups. The gut microbiota of the non-responder group was mainly characterized by increased relative abundances of the phylum Actinobacteria, families Christensenellaceae and Eggerthellaceae, and genera Adlercreutzia and Christensenellaceae R7 group compared to that of the responder group. Additionally, the gut microbiota composition of the responder and non-responder groups differed significantly before and after treatment, especially at the genus level. Moreover, 20 differential metabolites between the responder and non-responder groups were identified that were mainly involved in lipid metabolism (cholestane steroids and steroid esters). Eggerthellaceae and Adlercreutzia displayed strong co-occurrence relationships with certain metabolites, suggesting alternations in the gut microbiome, and associated metabolites may be potential mediators of successful antidepressant treatment. Overall, our study demonstrates that alterations in gut microbiota composition and metabolic function might be relevant to the response to antidepressants, thereby providing insight into mechanisms responsible for their efficacy.

Age-related diseases, therapies and gut microbiome: A new frontier for healthy aging

The gut microbiome is undoubtedly a key modulator of human health, which can promote or impair homeostasis throughout life. This is even more relevant in old age, when there is a gradual loss of function in multiple organ systems, related to growth, metabolism, and immunity. Several studies have described changes in the gut microbiome across age groups up to the extreme limits of lifespan, including maladaptations that occur in the context of age-related conditions, such as frailty, neurodegenerative diseases, and cardiometabolic diseases. The gut microbiome can also interact bi-directionally with anti-age-related disease therapies, being affected and in turn influencing their efficacy. In this framework, the development of integrated microbiome-based intervention strategies, aimed at favoring a eubiotic configuration and trajectory, could therefore represent an innovative approach for the promotion of healthy aging and the achievement of longevity.

MET-PREVENT: metformin to improve physical performance in older people with sarcopenia and physical prefrailty/frailty - protocol for a double-blind, randomised controlled proof-of-concept trial

INTRODUCTION

Skeletal muscle dysfunction is central to both sarcopenia and physical frailty, which are associated with a wide range of adverse outcomes including falls and fractures, longer hospital stays, dependency and the need for care. Resistance training may prevent and treat sarcopenia and physical frailty, but not everyone can or wants to exercise. Finding alternatives is critical to alleviate the burden of adverse outcomes associated with sarcopenia and physical frailty. This trial will provide proof-of-concept evidence as to whether metformin can improve physical performance in older people with sarcopenia and physical prefrailty or frailty.

METHODS AND ANALYSIS

MET-PREVENT is a parallel group, double-blind, placebo-controlled proof-of-concept trial. Trial participants can participate from their own homes, including completing informed consent and screening assessments. Eligible participants with low grip strength or prolonged sit-to-stand time together with slow walk speed will be randomised to either oral metformin hydrochloride 500 mg tablets or matched placebo, taken three times a day for 4 months. The recruitment target is 80 participants from two secondary care hospitals in Newcastle and Gateshead, UK. Local primary care practices will act as participant identification centres. Randomisation will be performed using a web-based minimisation system with a random element, balancing on sex and baseline walk speed. Participants will be followed up for 4 months post-randomisation, with outcomes collected at baseline and 4 months. The primary outcome measure is the four metre walk speed at the 4-month follow-up visit.

ETHICS AND DISSEMINATION

The trial has been approved by the Liverpool NHS Research Ethics Committee (20/NW/0470), the Medicines and Healthcare Regulatory Authority (EudraCT 2020-004023-16) and the UK Health Research Authority (IRAS 275219). Results will be made available to participants, their families, patients with sarcopenia, the public, regional and national clinical teams, and the international scientific community.

TRIAL REGISTRATION NUMBER

ISRCTN29932357.

Mapping the global research landscape on nutrition and the gut microbiota: Visualization and bibliometric analysis

BACKGROUND

Nutrition is a significant modifiable element that influences the composition of the gastrointestinal microbiota, implying the possibility of therapeutic diet methods that manipulate the composition and diversity of the microbial.

AIM

To overview research papers on nutrition and gut microbiota and determines the hotspots in this field at the global level.

METHODS

Scopus and Reference Citation Analysis were used to construct a bibliometric technique. It was decided to create bibliometric indicators and mapping as in most previous studies. 2012 through 2021 served as the study's timeframe.

RESULTS

A total of 5378 documents from the Scopus database were selected for analysis. Of all retrieved studies, 78.52% were research papers (n = 4223), followed by reviews (n = 820; 15.25%). China ranked first with a total number of articles of 1634 (30.38%), followed by the United States in second place with a total number of articles of 1307 (24.3%). In the last decade, emerging hotspots for gut microbiota and nutrition research included "gut microbiota metabolism and interaction with dietary components", "connection between the gut microbiota and weight gain", and "the influence of high-fat diet and gut microbiota on metabolic disorders".

CONCLUSION

This is the first thorough bibliometric analysis of nutrition and gut microbiota publications conducted on a global level. Investigation of the association between nutrition/diet and the gut microbiota is still in its infancy and will be expanded in the future. However, according to recent trends, the “effect of gut microbiota and high-fat diet on metabolic disorders" will be an increasing concern in the future.

The gut microbiome and melanoma: A review

Disturbances in the microbial ecosystem have been implemented in chronic inflammation, immune evasion and carcinogenesis, with certain microbes associated with the development of specific cancers. In recent times, the gut microbiome has been recognised as a potential novel player in the pathogenesis and treatment of malignant melanoma. It has been shown that the composition of gut microbiota in early-stage melanoma changes from in situ to invasive and then to metastatic disease. The gut bacterial and fungal profile has also been found to be significantly different in melanoma patients compared to controls. Multiple studies of immune checkpoint inhibitor (ICI) therapies have shown that the commensal microbiota may have an impact on anti-tumor immunity and therefore ICI response in cancer patients. When it comes to chemotherapy and radiotherapy treatments, studies demonstrate that gut microbiota are invaluable in the repair of radiation and chemotherapy-induced damage and therapeutic manipulation of gut microbiota can be an effective strategy to deal with side effects. Studies demonstrate the oncogenic and tumor-suppressive properties of the gut microbiome, which may play a role in the pathogenesis of melanoma. Despite this, investigations into specific interactions are still in its infancy, but starting to gain momentum as more significant and clinically relevant effects are emerging.

Intestinal microbiota profile in healthy Saudi children: The bacterial domain

Background

Knowledge of microbiota in health is essential for clinical research on the role of microbiota in disease. We aimed to characterize the intestinal microbiota in healthy Saudi children.

Methods

In this community-based study, stool samples were collected from a randomly selected sample of 20 healthy school children of Saudi origin. The samples were frozen at -80°C till analysis. Bacterial DNA was isolated and libraries were prepared using the Illumina Nextera XT library preparation kit. Unassembled sequencing reads were directly analyzed and quantified for each organism's relative abundance. The abundance for each organism was calculated and expressed as the average relative percentage from phyla to species.

Results

The median age was 11.3 (range 6.8-15.4) years, and 35% of them were males. The three most abundant phyla were Firmicutes, Bacteroidetes, and Actinobacteria accounting for 49%, 26%, and 24%, respectively. The most abundant genera included Bifidobacterium, Bacteroides, and Blautia accounting for 18.9%, 12.8%, and 8.2%, respectively. Finally, the most abundant species included 14 species belonging to the genus Bacteroides and nine species belonging to Bifidobacterium.

Conclusions

The abundance of intestinal microbiome in healthy Saudi children is different from that of other populations. Further studies are needed to understand the causes of variation between populations, which might lead to new preventive methods and treatment strategies of diseases caused by microbial dysbiosis.

Molecular Study of Lactobacilli Species in Patients with Type 2 Diabetes Mellitus

Background:

Diabetes mellitus type 2 (T2DM) is a metabolic disorder of multiple etiologies due to disturbances in carbohydrate, protein, and fat metabolism. Egypt is among the top 10 countries with a high prevalence of T2DM (15.56% of adults). There are studies that show a link between the diversity of the gut microbiota and the development of T2DM. There are species of Lactobacilli that inhabit the gut that might differ in patients with T2DM compared to healthy subjects.

Objective:

The aim of the present research is to study the presence of Lactobacilli species in gut microbiota by multiplex PCR in patients with T2DM compared to healthy controls as a preliminary approach to open the way for future treatment with the help of probiotics or diet modulation.

Methods:

A retrograde case-control study was conducted on 79 patients with T2DM and 100 healthy controls cross-matched with age and sex. All patients were subjected to full clinical examination and laboratory tests, including identification of stool Lactobacillus species by multiplex polymerase chain reaction (PCR).

Results:

Certain species of L. acidophilus, and L. rhamnosus were found to be significantly increased in patients with T2DM (67.1%, 50.6% respectively) compared to control subjects (35%, P=0.001, OR 3.8, 95% CI:2.1-7.1, 25%, P=0.001, OR 3.1, 95% CI:1.64-5.8 respectively). Other species as determined by multiplex PCR, namely, L. gasseri, (70%, P=0.001, OR 0.16, 95% CI: 0.1-0.3), L. reuteri (74%, P=0.001, OR 0.28, 95% CI: 0.5-0.53), and L. plantarum (69%, P=0.003, OR 0.4, 95% CI: 0.073-0.22) were significantly higher in prevalence in control compared to patients with T2DM.

Conclusion:

The present study highlights the significant prevalence of certain species of Lactobacilli in gut as determined by multiplex PCR, namely L. gasseri, L. reuteri and L. plantarum in controls compared to patients with T2DM. These species may have a role in the reduction of certain risk factors associated with the development of T2DM. Moreover, certain species of L. acidophilus, L. delbrueckii and L. rhamnosus were significantly increased in prevalence in patients with T2DM. The findings of this preliminary study need further verification by a larger longitudinal study.

Rethinking healthy eating in light of the gut microbiome

Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.

Host-microbial interactions in metabolic diseases: from diet to immunity

Growing evidence suggests that the gut microbiome is an important contributor to metabolic diseases. Alterations in microbial communities are associated with changes in lipid metabolism, glucose homeostasis, intestinal barrier functions, and chronic inflammation, all of which can lead to metabolic disorders. Therefore, the gut microbiome may represent a novel therapeutic target for obesity, type 2 diabetes, and nonalcoholic fatty liver disease. This review discusses how gut microbes and their products affect metabolic diseases and outlines potential treatment approaches via manipulation of the gut microbiome. Increasing our understanding of the interactions between the gut microbiome and host metabolism may help restore the healthy symbiotic relationship between them.

Chronic Use of Proton Pump Inhibitors Is Associated With an Increased Risk of Immune Checkpoint Inhibitor Colitis in Renal Cell Carcinoma

INTRODUCTION

Immune checkpoint inhibitors (ICIs) have become a standard of care in metastatic renal cell carcinoma (mRCC) but are associated with immune-related adverse events (irAEs) including colitis. Growing evidence suggests proton pump inhibitors (PPIs) increase the risk of inflammatory bowel disease (IBD). Given the pathophysiological overlap between IBD and ICI colitis, we sought to evaluate the relationship between PPI use and ICI colitis in mRCC patients.

PATIENTS AND METHODS

We performed a retrospective study of adult patients who received ICI therapy for mRCC between 2015 and 2018 at University of Texas Southwestern Medical Center affiliated hospitals. Clinical characteristics, oncological outcomes, ICI colitis details, and PPI use details were collected by manual chart review. The diagnosis of ICI colitis was made via biopsy when available, or by clinical criteria (symptoms and response to immunosuppressive therapy) when biopsy specimens were unavailable or inconclusive. Univariable and multivariable logistic regression analyses were conducted to assess the potential contribution of PPIs to ICI colitis.

RESULTS

A total of 176 patients received ICI therapy for mRCC, of which 16 (9.1%) were diagnosed with ICI colitis. Patients with ICI colitis presented with elevated stool lactoferritin and calprotectin and a wide range of endoscopic and histologic findings. There were no significant differences between patients with and without ICI colitis in age, gender, medical comorbidities, RCC history, and overall survival. However, exposure to ipilimumab and PPI use were more frequently observed in patients with ICI colitis than those without. In univariable and multivariable logistic regression analyses, exposure to ipilimumab and chronic use of PPIs > 8 weeks were significantly associated with ICI colitis.

CONCLUSION

In addition to ipilimumab use, chronic use of PPIs may be associated with ICI colitis in patients with mRCC.

The Prebiotic Effect of Australian Seaweeds on Commensal Bacteria and Short Chain Fatty Acid Production in a Simulated Gut Model

Diet is known to affect the composition and metabolite production of the human gut microbial community, which in turn is linked with the health and immune status of the host. Whole seaweeds (WH) and their extracts contain prebiotic components such as polysaccharides (PS) and polyphenols (PP). In this study, the Australian seaweeds, Phyllospora comosa, Ecklonia radiata, Ulva ohnoi, and their PS and PP extracts were assessed for potential prebiotic activities using an in vitro gut model that included fresh human faecal inoculum. 16S rRNA sequencing post gut simulation treatment revealed that the abundance of several taxa of commensal bacteria within the phylum Firmicutes linked with short chain fatty acid (SCFA) production, and gut and immune function, including the lactic acid producing order Lactobacillales and the chief butyrate-producing genera Faecalibacteria, Roseburia, Blautia, and Butyricicoccus were significantly enhanced by the inclusion of WH, PS and PP extracts. After 24 h fermentation, the abundance of total Firmicutes ranged from 57.35−81.55% in the WH, PS and PP samples, which was significantly greater (p ≤ 0.01) than the inulin (INU) polysaccharide control (32.50%) and the epigallocatechingallate (EGCG) polyphenol control (67.13%); with the exception of P. comosa PP (57.35%), which was significantly greater than INU only. However, all WH, PS and PP samples also increased the abundance of the phylum Proteobacteria; while the abundance of the phylum Actinobacteria was decreased by WH and PS samples. After 24 h incubation, the total and individual SCFAs present, including butyric, acetic and propionic acids produced by bacteria fermented with E. radiata and U. ohnoi, were significantly greater than the SCFAs identified in the INU and EGCG controls. Most notably, total SCFAs in the E. radiata PS and U. ohnoi WH samples were 227.53 and 208.68 µmol/mL, respectively, compared to only 71.05 µmol/mL in INU and 7.76 µmol/mL in the EGCG samples. This study demonstrates that whole seaweeds and their extracts have potential as functional food ingredients to support normal gut and immune function.

Gene Rearrangement and Modification of Immunity Factors Are Correlated with the Insertion of Bacteriocin Cassettes in Streptococcus mutans

Bacteriocins have been applied in the food industries and have become promising next-generation antibiotics. Some bacteria produce bacteriocins and possess immunity factors for self-protection. Nisin A, a bacteriocin produced by Lactococcus lactis, shows broad-spectrum activity. However, the evolution and cross-resistance ability of the immunity factors in some species results in reduced susceptibility to bacteriocins. Here, we investigated the elements responsible for nisin A resistance in Streptococcus mutans and their contribution to mutacins (bacteriocins produced by S. mutans) resistance. We classified the nisin A-resistance regions into six types based on the different combinations of 3 immunity factors, mutFEG, nsrX, and mutHIJ, and the presence of mutacin synthesis operon upstream of mutF. Data shows that NsrX effectively acts against nisin A but not mutacins, while the newly identified ABC transporter MutHIJ acts against three mutacins but not nisin A. Three types of MutFEG are identified based on their amino acid sequences: α (in Nsr-types C and D-I), β (in Nsr-types B and d-III), and γ (in Nsr-type E). MutFEG-α strongly contributes to mutacin I resistance, while MutFEG-β and MutFEG-γ strongly contribute to mutacin III, IIIb, and nisin A resistance. Additionally, mutFEG-like structures could be found in various streptococcal species isolated from the oral cavity of humans, chimpanzees, monkeys, bears, and hamsters. Our findings suggest that immunity factors rearrange and adapt in the presence of bacteriocins and could be transferred among closely related species, thus altering the bacterial competition within the microflora.

IMPORTANCEStreptococcus mutans is an important organism of oral microbiota and associated with dental caries and systemic diseases such as stroke and endocarditis. They produce bacteriocins known as mutacins to compete with other oral bacteria and possess immune factors for self-protection. We found that the nisin A and mutacins resistance patterns correlated with the immunity components and MutFEG variants, and the genetic difference was driven by the insertion of mutacin-synthesis cassettes. Our study provides an understanding of the development of bacteriocin resistance among streptococcal species, which may alter the bacterial interaction and ecology within the oral biofilm.

DIet and Health From reGIstered Trials on ClinicalTrials.gov: The DIGIT Study

Background

Clinical trial registration has become a valuable tool that can be used to track the status and nature of trials conducted on a specific topic. This approach has been applied to many areas of research, but less is known about the characteristics and trends over time of clinical trials focused on diet and health. The aim of this study was to analyze diet-related clinical trials registered on the National Institute of Health “ClinicalTrials.gov” web platform in the last 10 years, to list and describe their characteristics, and to identify possible gaps to be filled in the future research.

Methods

A search was performed on the ClinicalTrials.gov database. Intervention studies registered from January 2010 to December 2020, conducted on adults, with a follow-up of ≥2 weeks, evaluating the impact of different diets on all outcomes except those assessed with scales or questionnaires were considered.

Results

At the end of the selection process, a total of 1,016 registered clinical trials were identified and included in the analysis. The most investigated dietary approaches were balanced diets (n = 381 trials), followed by those based on a modification of macronutrients (n = 288) and time-restricted feeding and intermittent fasting diets (n = 140). The main measured outcomes included anthropometric parameters and body composition (57.8%), glycemic control parameters (49.7%), lipid parameters (40.1%), inflammatory markers (29.1%), and blood pressure and/or heart rate (24.5%). A growing body of studies also focused on microbiota and host metabolism (17.8%). Most studies had a duration of less than 12 weeks (~60%), and more than 90% of studies enrolled volunteers with overweight/obesity or other diseases. Regarding aging, only 21 studies focused only on older adults.

Conclusion

The number of studies investigating the relationship between diet and health has increased over the years. Despite the growing interest in the topic, there are some gaps, such as the limited duration of most trials, the underrepresentation of some population groups, and the limited number of studies for some diets that, although popular in the population, lack robust scientific evidence.

Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins

BACKGROUND

Dietary habits have a profound influence on the metabolic activity of gut microorganisms and their influence on health. Concerns have been raised as to whether the consumption of foodstuffs contaminated with pesticides can contribute to the development of chronic disease by affecting the gut microbiome. We performed the first pesticide biomonitoring survey of the British population, and subsequently used the results to perform the first pesticide association study on gut microbiome composition and function from the TwinsUK registry.

METHODS

Dietary exposure of 186 common insecticide, herbicide, or fungicide residues and the faecal microbiome in 65 twin pairs in the UK was investigated. We evaluated if dietary habits, geographic location, or the rural/urban environment, are associated with the excretion of pesticide residues. The composition and metabolic activity of faecal microbiota was evaluated using shotgun metagenomics and metabolomics respectively. We performed a targeted urine metabolomics analysis in order to evaluate whether pesticide urinary excretion was also associated with physiological changes.

RESULTS

Pyrethroid and/or organophosphorus insecticide residues were found in all urine samples, while the herbicide glyphosate was found in 53% of individuals. Food frequency questionnaires showed that residues from organophosphates were higher with increased consumption of fruit and vegetables. A total of 34 associations between pesticide residue concentrations and faecal metabolite concentrations were detected. Glyphosate excretion was positively associated with an overall increased bacterial species richness, as well as to fatty acid metabolites and phosphate levels. The insecticide metabolite Br2CA, reflecting deltamethrin exposure, was positively associated with the phytoestrogens enterodiol and enterolactone, and negatively associated with some N-methyl amino acids. Urine metabolomics performed on a subset of samples did not reveal associations with the excretion of pesticide residues.

CONCLUSIONS

The consumption of conventionally grown fruit and vegetables leads to higher ingestion of pesticides with unknown long-term health consequences. Our results highlight the need for future dietary intervention studies to understand effects of pesticide exposure on the gut microbiome and possible health consequences.

Gut Microbiome in Anesthesiology and Pain Medicine

The gut microbiome plays critical roles in human health and disease. Recent studies suggest it may also be associated with chronic pain and postoperative pain outcomes. In animal models, the composition of the gut microbiome changes after general anesthesia and affects the host response to medications, including anesthetics and opioids. In humans, the gut microbiome is associated with the development of postoperative pain and neurocognitive disorders. Additionally, the composition of the gut microbiome has been associated with pain conditions including visceral pain, nociplastic pain, complex regional pain syndrome, and headaches, partly through altered concentration of circulating bacterial-derived metabolites. Furthermore, animal studies demonstrate the critical role of the gut microbiome in neuropathic pain via immunomodulatory mechanisms. This article reviews basic concepts of the human gut microbiome and its interactions with the host and provide a comprehensive overview of the evidence linking the gut microbiome to anesthesiology, critical care, and pain medicine.

Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets

The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and di-sease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.