Gut microbiome and obesity in late adolescence: A case-control study in "Children of 1997" birth cohort

PURPOSE

Although the gut microbiome is important in human health, its relation to adolescent obesity remains unclear. Here we assessed the associations of the gut microbiome with adolescent obesity in a case-control study.

METHODS

In the "Children of 1997" birth cohort, participants with and without obesity at ∼17.4 years were 1:1 matched on sex, physical activity, parental education and occupation (n = 312). Fecal gut microbiome composition and pathways were assessed via shotgun metagenomic sequencing. The association of microbiota species with obesity was evaluated using conditional logistic regression. We explored the association of the obesity-relevant species with adolescent metabolomics using multivariable linear regression, and causal relationships with type 2 diabetes using Mendelian randomization analysis.

RESULTS

Gut microbiota in the adolescents with obesity exhibited lower richness (p = 0.031) and evenness (p = 0.014) compared to controls. Beta diversity revealed differences in the microbiome composition in two groups (p = 0.034). Lower relative abundance of Clostridium spiroforme, Clostridium phoceensis and Bacteroides uniformis were associated with higher obesity risk (q<0.15). Lower Bacteroides uniformis was associated with higher branched-chain amino acid, potentially contributing to higher type 2 diabetes risk.

CONCLUSION

Adolescents with obesity had a distinct gut microbiota profile compared to the controls, possibly linked to metabolic pertubation and related diseases.

Role of the Microbiome and Diet for Response to Cancer Checkpoint Immunotherapy: A Narrative Review of Clinical Trials

PURPOSE OF REVIEW

The advent of checkpoint immunotherapy has dramatically changed the outcomes for patients with cancer. However, a considerable number of patients have little or no response to therapy. We review recent findings on the connection between the gut microbiota and the immune system, exploring whether this link could enhance the effectiveness of immunotherapy.

RECENT FINDINGS

Clinical studies have reported specific types of bacteria in larger quantities at baseline in responders than in non-responders, especially Akkermansia mucinifila, Ruminococcaceae, Faecalibacterium, and Lachnospiraceae. Following the consumption of a high-fiber diet, bacteria in the gut ferment dietary fiber to short-chain fatty acids (SCFAs), like acetate, propionate, and butyrate. Some of the SCFAs nurture intestinal epithelial cells, and some enter the bloodstream. Here SCFAs can activate DC8 + cytotoxic T-cells to induce cancer cell death. High fiber intake in the diet was associated with a reduced risk of progression or death during checkpoint immunotherapy. Recent findings demonstrate that high-fiber plant-based diets such as the Mediterranean Diet positively influence the gut microbiota whereas antibiotics and proton pump inhibitors can negatively influence outcomes of cancer immunotherapy by changing the gut microbiota. This narrative review provides evidence of an association between types of bacteria and their metabolites and favorable responses to checkpoint immunotherapy. Prospective clinical trials are needed to determine if diet interventions can improve treatment outcomes.

Chronic arsenic exposure-provoked biotoxicity involved in liver-microbiota-gut axis disruption in chickens based on multi-omics technologies

INTRODUCTION

Arsenic has been ranked as the most hazardous substance by the U.S. Agency for Toxic Substances and Disease Registry. Environmental arsenic exposure-evoked health risks have become a vital public health concern worldwide owing to the widespread existence of arsenic. Multi-omics is a revolutionary technique to data analysis providing an integrated view of bioinformation for comprehensively and systematically understanding the elaborate mechanism of diseases.

OBJECTIVES

This study aimed at uncovering the potential contribution of liver-microbiota-gut axis in chronic inorganic arsenic exposure-triggered biotoxicity in chickens based on multi-omics technologies.

METHODS

Forty Hy-Line W-80 laying hens were chronically exposed to sodium arsenite with a dose-dependent manner (administered with drinking water containing 10, 20, or 30 mg/L arsenic, respectively) for 42 d, followed by transcriptomics, serum non-targeted metabolome, and 16S ribosomal RNA gene sequencing accordingly.

RESULTS

Arsenic intervention induced a serious of chicken liver dysfunction, especially severe liver fibrosis, simultaneously altered ileal microbiota populations, impaired chicken intestinal barrier, further drove enterogenous lipopolysaccharides translocation via portal vein circulation aggravating liver damage. Furtherly, the injured liver disturbed bile acids (BAs) homoeostasis through strongly up-regulating the BAs synthesis key rate-limiting enzyme CYP7A1, inducing excessive serum total BAs accumulation, accompanied by the massive synthesis of primary BA-chenodeoxycholic acid. Moreover, the concentrations of secondary BAs-ursodeoxycholic acid and lithocholic acid were markedly repressed, which might involve in the repressed dehydroxylation of Ruminococcaceae and Lachnospiraceae families. Abnormal BAs metabolism in turn promoted intestinal injury, ultimately perpetuating pernicious circle in chickens. Notably, obvious depletion in the abundance of four profitable microbiota, Christensenellaceae, Ruminococcaceae, Muribaculaceae, and Faecalibacterium, were correlated tightly with this hepato-intestinal circulation process in chickens exposed to arsenic.

CONCLUSION

Our study demonstrates that chronic inorganic arsenic exposure evokes liver-microbiota-gut axis disruption in chickens and establishes a scientific basis for evaluating health risk induced by environmental pollutant arsenic.

Akkermansia muciniphila: A Potential Target for the Prevention of Diabetes

Akkermansia muciniphila, a Gram-negative anaerobic bacterium colonizing the intestinal mucus layer, is regarded as a promising "next-generation probiotic". There is mounting evidence that diabetes and its complications are associated with disorders of A. muciniphila abundance. Thus, A. muciniphil and its components, including the outer membrane protein Amuc_1100, A. muciniphila-derived extracellular vesicles (AmEVs), and the secreted proteins P9 and Amuc_1409, are systematically summarized with respect to mechanisms of action in diabetes mellitus. Diabetes treatments that rely on altering changes in A. muciniphila abundance are also reviewed, including the identification of A. muciniphila active ingredients, and dietary and pharmacological interventions for A. mucinihila abundance. The potential and challenges of using A. muciniphila are also highlighted, and it is anticipated that this work will serve as a reference for more in-depth studies on A. muciniphila and diabetes development, as well as the creation of new therapeutic targets by colleagues domestically and internationally.

FAAHcilitating recovery in malnourished kids

The molecular underpinnings behind the diet-microbiome-host health relationship are largely undescribed. In a recent issue of Science, Cheng et al.1 uncovered one piece of the puzzle by describing a novel fatty acid amide hydrolase (FAAH) derived from a Faecalibacterium prausnitzii strain that correlated with improved malnutrition recovery. This emphasized the microbiome's role in supporting recovery from malnutrition.

Cold-pressed extraction of perilla seed oil enriched with alpha-linolenic acid mitigates tumour progression and restores gut microbial homeostasis in the AOM/DSS mice model of colitis-associated colorectal cancer

The present investigation explores into the influence of dietary nutrients, particularly alpha-linolenic acid (ALA), a plant-derived omega-3 fatty acid abundant in perilla seed oil (PSO), on the development of colitis-associated colorectal cancer (CRC). The study employs a mouse model to scrutinize the effects of ALA-rich PSO in the context of inflammation-driven CRC. Perilla seeds were subjected to oil extraction, and the nutritional composition of the obtained oil was analysed. Male ICR mice, initiated at four weeks of age, were subjected to diets comprising 5%, 10%, or 20% PSO, 10% fish oil, or 5% soybean oil. All groups, with the exception of the control group (5% soybean oil), underwent induction with azoxymethane (AOM) and dextran sulphate sodium (DSS) to instigate CRC. Disease development, colon samples, preneoplastic lesions, dysplasia, and biomarkers were meticulously evaluated. Furthermore, gut microbiota composition was elucidated through 16S rRNA sequencing. The analysis revealed that PSO contained 61.32% ALA and 783.90 mg/kg tocopherols. Mice subjected to diets comprising 5% soybean or 10% fish oil exhibited higher tumour incidence, burden, multiplicity, and aberrant crypt counts. Remarkably, these parameters were significantly reduced in mice fed a 5% PSO diet. Additionally, 5% PSO-fed mice displayed reduced proliferative and pro-inflammatory markers in colon tissues, coupled with an alleviation of AOM/DSS-induced gut dysbiosis. Notably, PSO demonstrated inhibitory effects on colitis-associated CRC in the AOM/DSS mice model, achieved through the suppression of proliferative and pro-inflammatory protein levels, and mitigation of gut dysbiosis, with discernible efficacy observed at a 5% dietary concentration.

In ovo sodium butyrate administration differentially impacts growth performance, intestinal barrier function, immune response, and gut microbiota characteristics in low and high hatch-weight broilers

BACKGROUND

Hatch weight (HW) affects broiler growth and low HW (LHW) often leads to suboptimal performance. Sodium butyrate (SB) has been shown to promote growth through enhanced intestinal health. This study investigated how broilers with different HW responded to in ovo SB injection and whether SB could enhance gut health and performance in LHW chicks. Ross 308 broiler eggs were injected on incubation d 12 with physiological saline (control) or SB at 0.1% (SB1), 0.3% (SB3), or 0.5% (SB5). Post-hatch, male chicks from each treatment were categorized as high HW (HHW) or LHW and assigned to 8 groups in a 4 × 2 factorial design. Production parameters were recorded periodically. Intestinal weight, length, and gene expression related to gut barrier function and immune response were examined on d 14 and 42. Cecal microbiota dynamics and predicted functionality were analyzed using 16S rRNA gene sequencing.

RESULTS

SB treatments did not affect hatchability. HHW-control group exhibited consistently better weight gain and FCR than LHW-control group. SB dose-dependently influenced performance and gut health in both HW categories, with greater effects in LHW broilers at 0.3%. LHW-SB3 group attained highest body weight on d 42, exceeding controls but not significantly differing from HHW-SB3 group. LHW-SB3 group showed upregulation of gut-barrier genes CLDN1 in ileum, TJP1 in jejunum and anti-inflammatory cytokine IL-10 in both jejunum and ileum on d 14. Additionally, LHW-SB3 group upregulated mucin-producing MUC6 gene in ileum, while HHW-SB5 group increased pro-inflammatory IL-12p40 cytokine in caecum on d 42. LHW-SB3 group demonstrated shorter relative intestinal lengths, while HHW-SB5 had longer lengths. HHW-control group had higher bacterial diversity and growth-promoting bacteria while LHW-control group harbored the potential pathogen Helicobacter. SB reshaped gut microbiota biodiversity, composition, and predicted metabolic pathways in both HW categories. The LHW-SB3 group exhibited highest alpha diversity on d 14 and most beneficial bacteria at all timepoints. HHW-SB5 group presented increased pathogenic Escherichia-Shigella and Campylobacter on d 42.

CONCLUSIONS

HW significantly affects subsequent performance and SB has differential effects based on HW. LHW chicks benefited more from 0.3% SB, showing improvements in growth, intestinal development, health, and gut microbiota characteristics.

Arsenotrophic Achromobacter aegrifaciens strains isolated from arsenic contaminated tubewell water and soil sources shared similar genomic potentials

BACKGROUND

Arsenic (As), found in diverse ecosystems, poses major public health risks in various parts of the world. Arsenotrophic bacteria in contaminated environments help reduce toxicity by converting arsenite (AsIII) to less harmful arsenate (AsV). We assumed that Achromobacter aegrifaciens strains from As-contaminated tubewell water and soil would share similar genomic characteristics associated with arsenic detoxification and bioremediation. To investigate this, we employed both culture-dependent and culture-independent viz. whole genome sequencing (WGS) methods to thoroughly elucidate the phenotypic and genotypic features of two A. aegrifaciens strains isolated from As-contaminated tubewell water (BAW48) and soil (BAS32) samples collected in the Bogura district of Bangladesh.

RESULTS

Both BAW48 and BAS32 isolates demonstrated As(III) oxidation in the KMNO4 test, which was corroborated by molecular analysis confirming the presence of aioA and arsB genes in both strains. These strains were found to be phylogenetically related to many strains of Achromobacter spp., isolated from biological inorganic reactors, environmental soils, sediments and human clinical samples across diverse geographical regions. Moreover, both strains possessed distinct heavy metal resistance genes conferring resistance to Co, Zn, Cu, Cd, Hg, As, and Cr. Three As gene clusters such as As(III) oxidizing aioBA, As(III) reducing arsRCDAB and the MMA(III) oxidizing ars resistance gene (arsHCsO) cluster were predicted in both genomes of A. aegrifaciens. Further genomic analyses revealed similar profiles in both strains, with mobile genetic elements, antimicrobials and heavy metal resistance genes, virulence genes, and metabolic features. Pangenome and synteny analysis showed that the two genomes are evolutionary distinct from other strains, but closely related to one another.

CONCLUSION

The genomic data confirmed that A. aegrifaciens strains can oxidize As(III) and detoxify heavy metals like As, suggesting their potential for As detoxification and bioremediation. These findings align with our assumption and provide a basis for developing sustainable solutions for bioremediation efforts in As-contaminated environments.

Short-sighted evolution of virulence for invasive gut microbes: From hypothesis to tests

Why microbes harm their hosts is a fundamental question in evolutionary biology with broad relevance to our understanding of infectious diseases. Several hypotheses have been proposed to explain this "evolution of virulence." In this perspective, we reexamine one of these hypotheses in the specific context of the human gut microbiome, namely short-sighted evolution. According to the short-sighted evolution hypothesis, virulence is a product of niche expansion within a colonized host, whereby variants of commensal microbes establish populations in tissues and sites where the infection causes morbidity or mortality. This evolution is short-sighted in that the evolved variants that infect those tissues and sites are not transmitted to other hosts. The specific hypothesis that we propose is that some bacteria responsible for invasive infections and disease are the products of the short-sighted evolution of commensal bacteria residing in the gut microbiota. We present observations in support of this hypothesis and discuss the challenges inherent in assessing its general application to infections and diseases associated with specific members of the gut microbiota. We then describe how this hypothesis can be tested using genomic data and animal model experiments and outline how such studies will serve to provide fundamental information about both the evolution and genetic basis of virulence, and the bacteria of intensively studied yet poorly understood habitats including the gut microbiomes of humans and other mammals.

Akkermansia muciniphila: A promising probiotic against inflammation and metabolic disorders

Metabolic disease is a worldwide epidemic that has become a public health problem. Gut microbiota is considered to be one of the important factors that maintain human health by regulating host metabolism. As an abundant bacterium in the host gut, A. muciniphila regulates metabolic and immune functions, and protects gut health. Multiple studies have indicated that alterations in the abundance of A. muciniphila are associated with various diseases, including intestinal inflammatory diseases, obesity, type 2 diabetes mellitus, and even parasitic diseases. Beneficial effects were observed not only in live A. muciniphila, but also in pasteurized A. muciniphila, A. muciniphila-derived extracellular vesicles, outer membrane, and secreted proteins. Although numerous studies have only proven the simple correlation between multiple diseases and A. muciniphila, an increasing number of studies in animal models and preclinical models have demonstrated that the beneficial impacts shifted from correlations to in-depth mechanisms. In this review, we provide a comprehensive view of the beneficial effects of A. muciniphila on different diseases and summarize the potential mechanisms of action of A. muciniphila in the treatment of diseases. We provide a comprehensive understanding of A. muciniphila for improving host health and discuss the perspectives of A. muciniphila in the future studies.

The role of gut microbiota involved in prostate microenvironment and symptoms improvement in chronic prostatitis/chronic pelvic pain syndrome patients treated with low-intensity extracorporeal shock wave

BACKGROUND

Low-intensity extracorporeal shockwave therapy (Li-ESWT) is emerging as a promising and safe treatment for Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this study, we aimed to investigate the role of the gut microbiota involved in the prostate microenvironment and symptom improvement during the Li-ESWT for CP/CPPS patients.

METHODS

CP/CPPS patients not taking antibiotics or other treatments were included. NIH-Chronic Prostatitis Symptom Index (NIH-CPSI), International Prostate Symptom Score (IPSS), and International Index of Erectile Function (IIEF-5) were used to evaluate the effectiveness of Li-ESWT at the end of treatment. Visual analogue scale/score was used to evaluate the pain during procedure. Stool and semen samples were collected before and after Li-ESWT. Shotgun metagenomics analyzed gut microbiota, while ELISA and other diagnostic kits detected biochemical changes in seminal plasma.

RESULT

Of the 60 enrolled patients, 52 completed treatment. Li-ESWT response rate was 78.8% (41/52) at end of treatment. Among responders, the subitems of the NIH-CPSI; IPSS; and IIEF-5 scores improved significantly, and the seminal plasma analysis showed decreased TNF-a and MDA levels and increased SOD and Zn2+ levels posttreatment. Gut microbiome analysis indicated that posttreatment, both α and β diversity increased, and the abundance of certain specific species significantly increased. Fifty-eight pathways significantly enriched posttreatment, notably in branched-chain amino acid synthesis and butyrate synthesis. The abundance of several specific species was found to be significantly higher in non-responders than responders. Among responders, at the species level, some bacteria associated with NIH-CPSI and its subscales, IPSS, IIEF-5, and prostate microenvironment markers (TNF-a, MDA, Zn2+, and SOD) were identified.

CONCLUSIONS

Our study demonstrates for the first time that Li-ESWT improves the prostate microenvironment and gut microbiota in CP/CPPS patients. Treatment nonresponse may be associated with a high abundance of specific pathogens before treatment. The gut microbiota could have a significant impact on Li-ESWT response and the prostate microenvironment.

Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma

Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.

Role of folic acid in regulating gut microbiota and short-chain fatty acids based on an in vitro fermentation model

Folic acid deficiency is common worldwide and is linked to an imbalance in gut microbiota. However, based on model animals used to study the utilization of folic acid by gut microbes, there are challenges of reproducibility and individual differences. In this study, an in vitro fecal slurry culture model of folic acid deficiency was established to investigate the effects of supplementation with 5-methyltetrahydrofolate (MTHF) and non-reduced folic acid (FA) on the modulation of gut microbiota. 16S rRNA sequencing results revealed that both FA (29.7%) and MTHF (27.9%) supplementation significantly reduced the relative abundance of Bacteroidetes compared with control case (34.3%). MTHF supplementation significantly improved the relative abundance of Firmicutes by 4.49%. Notably, compared with the control case, FA and MTHF supplementation promoted an increase in fecal levels of Lactobacillus, Bifidobacterium, and Pediococcus. Short-chain fatty acid (SCFA) analysis showed that folic acid supplementation decreased acetate levels and increased fermentative production of isobutyric acid. The in vitro fecal slurry culture model developed in this study can be utilized as a model of folic acid deficiency in humans to study the gut microbiota and demonstrate that exogenous folic acid affects the composition of the gut microbiota and the level of SCFAs. KEY POINTS: • Establishment of folic acid deficiency in an in vitro culture model. • Folic acid supplementation regulates intestinal microbes and SCFAs. • Connections between microbes and SCFAs after adding folic acid are built.

Exploring the relationship between Faecalibacterium duncaniae and Escherichia coli in inflammatory bowel disease (IBD): Insights and implications

Inflammatory bowel disease (IBD) is a group of disorders characterized by an inflammation of the gastrointestinal tract (GIT) and represents a major social and economic burden. Despite ongoing research into the etiology and pathophysiology of this multifactorial disease, treatment options remain limited. From this perspective, the gut microbiota has emerged as a potential player in the pathogenesis of IBD, and animal and human studies support this hypothesis. Indeed, the human gut is one of the most complex ecological communities (composed of 1013-1014 microorganisms) that plays a critical role in human health by influencing normal physiology and disease susceptibility through its collective metabolic activities and host interactions. In addition, live probiotic bacteria present in some food products (which transit through the GIT) have been shown to interact with the host immune system and confer several health benefits. The aim of this review is to provide an overview of the link between Faecalibacterium duncaniae and Escherichia coli and IBD, highlighting the main areas of research in this field. An ecological perspective on the gut microbiota may offer new insights for the development of clinical therapies targeting this bacterial community to improve human health.

Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries

Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.

Gut microbiota, physical activity and/or metabolic markers in healthy individuals - towards new biomarkers of health

Background

The global prevalence of the metabolic disease Type 2 Diabetes (T2D) is increasing. Risk factors contributing to the development of T2D include overweight and obesity, lack of physical activity (PA), and an unhealthy diet. In addition, the gut microbiota has been shown to affect metabolic regulation. Since T2D is preventable, efforts should be put into the discovery of new biomarkers for early detection of individuals at risk of developing the disease.

Objective

The objective of the cross-sectional study was to explore the relationship between gut microbiota and physical activity (PA) and/or metabolic markers such as selected amino acids (AA), markers of glycaemic regulation and lipid metabolism and anthropometric measures.

Design

Healthy adults (18 and 65 years) with BMI between 18.5 and 27.5 kg/m2 originally recruited to a randomised controlled trial (RCT) (n = 17: six males, eleven females), were included in this exploratory cross-sectional study. Physical activity data was calculated based on a 3-days registration, and blood metabolome, gut microbiota analyses and anthropometric measures from one visit of the intervention were used in this cross-sectional study.

Results

Of the 47 gut bacteria analysed, there were a total of 87 significant correlations with AA, PA, body composition and/or metabolic markers. Several of the gut bacteria correlated with both PA, metabolic or anthropometric markers.

Conclusion

In this study, we demonstrate associations between gut bacteria and PA and/or metabolic markers including AA in healthy individuals. The results may guide future studies aiming at identifying new and early biomarkers of metabolic health and diseases.

Microbiome of Xiphinema elongatum (Nematoda, Longidoridae), isolated from water berry

The soil microbiome is crucial for the environment and significantly impacts the ecosystem. Understanding the microbiome and its interaction with soil microorganisms is essential for improving ecological and environmental strategies. In this study, Xiphinema elongatum nematodes were collected from water berry in Sovenga Hills, Limpopo Province, South Africa, and were analyzed their associated bacterial communities using metabarcoding analysis. The findings revealed that X. elongatum forms associations with a wide range of bacterial species. Among the most abundant species identified, we found Sphingomonas sp., a bacterial species commonly found in various habitats and primarily beneficial to plants, and Candidatus Xiphinematobacter, a bacterial species commonly found in nematode species of Xiphinema as an endosymbiont. The analysis using principal component analysis (PCA) revealed that the abundance of X. elongatum in the soil is inversely correlated with clay content (r = -0.52) and soil pH levels (r = -0.98), and directly correlated with soil sand content (r = 0.88). This study provides valuable insights into the bacterial species associated with plant-parasitic nematodes in trees in South Africa. It underscores the presence of various potentially detrimental and beneficial nematode-associated bacteria. The results could potentially influence the overall quality of the soil, leading to implications for the productivity and yield of fruit crops. Additionally, the results help us understand the interaction between bacteria and X. elongatum.

Effect of Postbiotic Bifidobacterium longum CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study

OBJECTIVES

A randomised, double-blind, placebo-controlled pilot trial was conducted to assess the effect of heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in healthy adults with mild to moderate digestive symptoms. A total of 60 participants were recruited and received either HT-ES1 or an identical placebo for 8 weeks with a further follow-up at week 10.

METHODS

This study monitored changes in the total Gastrointestinal Symptom Rating Scale for IBS score (GSRS-IBS), Irritable Bowel Syndrome Symptom Severity Scale (IBS-SSS), IBS Quality of Life index (IBS-QoL), gut microbiome using 16S rRNA sequencing, and the Visceral Sensitivity Index, as well as a range of biochemical markers, anthropometric parameters, and adverse events.

RESULTS

While minimal changes were observed in gastrointestinal (GI) symptoms, the HT-ES1 group showed a significant decrease in total and non-HDL cholesterol compared to the placebo. The intervention group also exhibited a significant increase in the abundance of the genera Faecalibacterium and Anaerobutyricum, both of which were positively correlated with butyrate concentrations. Faecal calprotectin significantly increased over time in the placebo group but remained stable in the HT-ES1 group.

CONCLUSIONS

Overall, these findings suggest that HT-ES1 may promote gut health by increasing butyrate-producing bacteria in the gut, maintaining normal levels of faecal calprotectin and reducing serum cholesterol.

Mucosal immunization with the lung Lactobacillus-derived amphiphilic exopolysaccharide adjuvanted recombinant vaccine improved protection against P. aeruginosa infection

Respiratory infections caused by Pseudomonas aeruginosa are a major health problem globally. Current treatment for P. aeruginosa infections relies solely on antibiotics, but the rise of antibiotic-resistant strains necessitates an urgent need for a protective vaccine. Traditional parenteral vaccines, despite employing potent adjuvants aimed at serotype-dependent immunity, often fail to elicit the desired mucosal immune response. Thus, developing vaccines that target both localized mucosal and systemic immune responses represents a promising direction for future research on P. aeruginosa vaccination. In this study, we explored EPS301, the exopolysaccharide derived from the lung microbiota strain Lactobacillus plantarum WXD301, which exhibits excellent self-assembly properties, enabling the formation of homogeneous nanoparticles when encapsulating recombinant PcrV of P. aeruginosa, designated as EPS301@rPcrV. Notably, the EPS301 vector effectively enhanced antigen adhesion to the nasal and pulmonary mucosal tissues and prolonged antigen retention. Moreover, EPS301@rPcrV provided effective and sustained protection against P. aeruginosa pneumonia, surpassing the durability achieved with the "gold standard" cholera toxin adjuvant. The EPS301-adjuvanted vaccine formulation elicited robust mucosal IgA and Th17/γδ17 T cell responses, which exceeded those induced by the CTB-adjuvanted vaccination and were sustained for over 112 days. Additionally, Th 17 and γδ 17 resident memory T cells induced by EPS301@rPcrV were crucial for protection against P. aeruginosa challenge. Intriguingly, IL-17A knockout mice exhibited lower survival rates, impaired bacterial clearance ability, and exacerbated lung tissue damage upon EPS301 adjuvanted vaccination against P. aeruginosa-induced pneumonia, indicating an IL-17A-dependent protective mechanism. In conclusion, our findings provided direct evidence that EPS301@rPcrV mucosal vaccine is a promising candidate for future clinical application against P. aeruginosa-induced pulmonary infection.

Changes in the Composition and Diversity of the Intestinal Microbiota Associated with Carbohydrate Consumption in Type 2 Diabetes Mellitus Patients

Type 2 diabetes mellitus (T2DM) is a multifactorial disease, influenced by dietary and environmental factors that can modify the intestinal microbiota. The aim of this study was to evaluate changes in the composition and diversity of the intestinal microbiota associated with carbohydrate (CHO) consumption in T2DM patients. Forty patients participated, with and without T2DM. Fecal samples were collected for the characterization of microbial diversity from the massive sequencing of the 16S rRNA gene. Carbohydrate consumption was quantified using the Frequency Consumption Foods questionnaire (FCF), the groups were categorized according to Body Mass Index (BMI) and BMI + CHO consumption. The group without T2DM showed normal biochemical and anthropometric parameters, although they had a high carbohydrate consumption compared to the group with T2DM. At the phylum level, there were differences in relative abundance; the control overweight group (CL-OW > CHO) and T2DM-Normal Weight > CHO patients had increased Bacteroides and decreased Firmicutes. In contrast, the CL-OW > CHO and T2DM-OW < CHO patients, showed reduced Bacteroidetes and an elevated amount of Firmicutes. At the genus level, the differences were in the relative abundance of Roseburia, Clostridium_IV, Prevotella, and Sporobacter, associated with the consumption of carbohydrates. The groups that consumed high amounts of carbohydrates, regardless of whether they had diabetes mellitus or were overweight, had a significantly reduced proportion of Faecalibacterium, an altered proportion of Bacteroides. The high consumption of carbohydrates showed considerable modifications in the composition and diversity of the bacterial communities.

Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy

BACKGROUND AND AIMS

The gut microbiota contributes to aberrant inflammation in inflammatory bowel disease, but the bacterial factors causing or exacerbating inflammation are not fully understood. Further, the predictive or prognostic value of gut microbial biomarkers for remission in response to biologic therapy is unclear.

METHODS

We perform whole metagenomic sequencing of 550 stool samples from 287 ulcerative colitis patients from a large, phase 3, head-to-head study of infliximab and etrolizumab.

RESULTS

We identify several bacterial species in baseline and/or post-treatment samples that associate with clinical remission. These include previously described associations [Faecalibacterium prausnitzii_F] as well as new associations with remission to biologic therapy [Flavonifractor plautii]. We build multivariate models and find that gut microbial species are better predictors for remission than clinical variables alone. Finally, we describe patient groups that differ in microbiome composition and remission rate after induction therapy, suggesting the potential utility of microbiome-based endotyping.

CONCLUSIONS

In this large study of ulcerative colitis patients, we show that few individual species associate strongly with clinical remission, but multivariate models including microbiome can predict clinical remission and have better predictive power compared with clinical data alone.

Increasing degree of substitution inhibits acetate while promotes butyrate production during in vitro fermentation of citric acid-modified rice starch

Citric acid-modified starch functions as a resistant starch, while the combined effects of its fine molecular structure and degree of substitution on gut microbiota are not well understood. To this end, citric acid-modified starches with varying degrees of substitution were synthesized from rice starches with distinct molecular structures and their impact on gut microbiota composition and short-chain fatty acid (SCFA) production was analyzed. Notably, rice starch with a higher degree of substitution significantly reduced acetate production, while promoted butyrate production. Correlation analysis further suggested that amylopectin chains with 12 < DP ≤ 36 and amylose chains with 100 < DP ≤ 500 alter the growth of Faecalibacterium_prausnitzii and Bacteroides_vulgatus, consequentially determining the production of SCFAs. Collectively, these findings indicate that citric acid-modified rice starch with different degrees of substitution can target specific gut bacteria and SCFA production, thus conferring beneficial impact on human health.

Dietary Dihydromyricetin Zinc Chelate Supplementation Improves the Intestinal Health of Magang Geese

To fulfill the nutritional requirements of poultry, effective Zn supplementation is required due to Zn deficiency in basic feed. In this study, we investigated the effects of DMY-Zn (dihydromyricetin zinc chelate) on the growth performance, morphology, and biochemical indices; the expression of intestinal barrier-related genes; the intestinal microflora; and the cecum metabolome of Magang geese. A total of 300 14-day-old Magang geese (equal number of males and females) with an average body weight of 0.82 ± 0.08 kg were randomly divided into five groups and fed a basal diet; these groups were given DMY-Zn (low, medium, or high level of DMY-Zn with 30, 55, or 80 mg/kg Zn added to the basal diet) or ZnSO4 (80 mg/kg Zn added) for 4 weeks. Our results revealed that DMY-Zn significantly impacts growth and biochemical indices and plays a significant role in regulating the intestinal barrier and microflora. DMY-Zn is involved in the upregulation of intestinal barrier gene (ZO1 and MUC2) expression, as well as upregulated Zn-related gene expression (ZIP5). On the other hand, a low concentration of DMY-Zn increased the ɑ diversity index and the abundance of Lactobacillus and Faecalibacterium. Additionally, a cecal metabolomics study showed that the main metabolic pathways affected by DMY-Zn were the pentose phosphate pathway, the biosynthesis of different alkaloids, and the metabolism of sphingolipids. In conclusion, DMY-Zn can reduce feed intake, increase the expression of intestinal barrier-related genes, help maintain the intestinal microflora balance, and increase the abundance of beneficial bacteria in the intestine to improve intestinal immunity.

Adherent-invasive Escherichia coli LF82 disrupts the tight junctions of Caco-2 monolayers

BACKGROUND AND STUDY AIMS

Adherent invasive Escherichia coli (AIEC) are enriched in IBD (inflammatory bowel disease) patients, but the role and mechanism of AIEC in the intestinal epithelial barrier is poorly defined. We evaluated the role of the AIEC strain E. coli LF82 in vitro and investigated the role of Th17 in this process.

MATERIAL AND METHODS

After coincubation with AIEC, the epithelial barrier integrity was monitored by epithelial resistance measurements. The permeability of the barrier was evaluated by TEER (trans-epithelial electrical resistance) and mucosal-to-serosal flux rate. The presence of interepithelial tight junction proteins ZO-1 and Claudin-1 were determined by immunofluorescence and western blot analysis. Cytokines in the cell culture supernatant were assayed by enzyme-linked immunosorbent assay (ELISA).

RESULTS

AIEC infection decreased TEER and increased the mucosal-to-serosal flux rate of Lucifer yellow in the intestinal barrier model in a time- and dose-dependent manner. AIEC infection decreased the expression and changed the distribution of ZO-1 and claudin-1. It also induced the secretion of cytokines such as TNF-α and IL-17.

CONCLUSION

AIEC strain E. coli LF82 increased the permeability and disrupted the tight junctions of the intestinal epithelial barrier, revealing that AIEC plays an aggravative role in the inflammatory response.

Short-Term Cocoa Supplementation Influences Microbiota Composition and Serum Markers of Lipid Metabolism in Elite Male Soccer Players

OBJECTIVES

Dietary strategies to improve arachidonic acid:eicosapentaenoic acid (AA:EPA) ratios are of interest due to potential reductions in inflammation and oxidative stress following exercise. The aim of this study was to investigate the impact of a novel dietary intervention, that is, the ingestion of 30 g of dark chocolate, on blood lipid profiles and gut microbiota composition in elite male soccer players.

METHODS

Professional male soccer players were randomly assigned to the experimental group (DC) provided with 30 g of dark chocolate or to the control group (WC), provided with 30 g of white chocolate, for 30 days. Before and after intervention, blood, fecal sample, and anthropometry data were collected. For each outcome, two-way repeated-measure analysis of variance was used to identify differences between baseline and endpoint (Week 4), considering treatment (dark chocolate, white chocolate) as intersubjects' factors. Metagenomic analysis was performed following the general guidelines, which relies on the bioBakery computational environment.

RESULTS

DC group showed increased plasma polyphenols (from 154.7 ± 18.6 μg gallic acid equivalents/ml to 185.11 ± 57.6 μg gallic acid equivalents/ml, Δ pre vs. post = +30.41 ± 21.50) and significant improvements in lipid profiles: total cholesterol (Δ -32.47 ± 17.18 mg/dl DC vs. Δ -2.84 ± 6.25 mg/dl WC, Time × Treatment interaction p < .001), triglycerides (Δ -6.32 ± 4.96 mg/dl DC vs. Δ -0.42 ± 6.47 mg/dl WC, Time × Treatment interaction p < .001), low-density lipoprotein (Δ -18.42 ± 17.13 mg/dl vs. Δ -2.05 ± 5.19 mg/dl WC, Time × Treatment interaction p < .001), AA/EPA ratio (Δ -5.26 ± 2.35; -54.1% DC vs. Δ -0.47 ± 0.73, -6.41% WC, Time × Treatment interaction p < .001) compared with WC group. In addition, 4 weeks of intervention showed a significant increase in high-density lipoprotein concentration in DC group (Δ + 3.26 ± 4.49 mg/dl DC vs. Δ -0.79 ± 5.12 mg/dl WC). Microbial communities in the DC group maintained a slightly higher microbial stability over time (exhibiting lower within-subject community dissimilarity).

CONCLUSION

Ingesting 30 g of dark chocolate over 4 weeks positively improved AA:EPA ratio and maintained gut microbial stability. Dark chocolate ingestion represents an effective nutritional strategy to improve blood lipid profiles in professional soccer players. What Are the Findings? Ingesting 30 g of dark chocolate for 4 weeks positively influences blood lipid AA: EPA ratio while maintaining gut microbial stability. What This Study Adds? Dietary intake of specific foods such as dark chocolate represents an alternative strategy to support the health and recovery of elite soccer players. What Impact Might This Have on Clinical Practice in the Future? From a clinical and translational perspective, dark chocolate ingestion positively modulates favorable blood lipid profiles and polyunsaturated fatty acid metabolism while maintaining gut microbial stability. Dark chocolate ingestion may be considered as an effective nutritional strategy in elite sport environments during periods of high-intensity training and congested competitions. Further research is required to determine functional outcomes associated with the observed improvements in blood lipid profiles.

Dysbiosis of the gut microbiota is associated with in-hospital mortality in patients with antibiotic-associated diarrhoea: A metagenomic analysis

BACKGROUND

The increasing incidence of antibiotic-associated diarrhoea (AAD) is a serious health care problem. Dysbiosis of the gut microbiota is suspected to play a role in the pathogenesis of AAD, but its impact on the clinical outcomes of patients remains unclear.

METHODS

Between May and October 2022, 210 patients with AAD admitted to a university hospital and 100 healthy controls were recruited. DNA extraction from stool specimens and shotgun sequencing were performed. Machine learning was conducted to assess profiling at different taxonomic levels and to select variables for multivariable analyses.

RESULTS

Patients were classified into two groups: Clostridioides difficile infection (CDI, n = 39) and non-CDI AAD (n = 171). The in-hospital mortality rate for the patients was 20.0%, but the presence of C. difficile in the gut microbiota was not associated with mortality. Machine learning showed that taxonomic profiling at the genus level best reflected patient prognosis. The in-hospital mortality of patients was associated with the relative abundance of specific gut microbial genera rather than alpha-diversity: each of the five genera correlated either positively (Enterococcus, Klebsiella, Corynebacterium, Pseudomonas, and Anaerofustis) or negatively (Bifidobacterium, Bacteroides, Streptococcus, Faecalibacterium, and Dorea). Genes for vancomycin resistance were significantly associated with in-hospital mortality in patients with AAD (adjusted hazard ratios, 2.45; 95% CI, 1.20-4.99).

CONCLUSION

This study demonstrates the potential utility of metagenomic studies of the gut microbial community as a biomarker for prognosis prediction in AAD patients.

In vitro fecal microbiota modulation properties of pectin and xyloglucan from hazelnut (Corylus avellana L.) skin, an industrial byproduct, and their incorporation into biscuit formula

The aim of this study was to extract water-soluble dietary fibers (WSDFskin), pectin (PECskin), and xyloglucan (XGskin) from hazelnut skin and to determine their impacts on colonic microbiota and metabolic function. WSDFskin, PECskin, and XGskin were extracted by water, acid, and alkali treatments, respectively. Monosaccharide analysis revealed WSDFskin and PECskin were dominated by uronic acids, while the XGskin was found to contain xyloglucan- and pectin-associated sugars. In vitro fecal fermentation analysis showed that WSDFskin, PECskin, and XGskin are fermented to different microbial short-chain fatty acid profiles by identical microbiota. 16S rRNA sequencing demonstrated that PECskin promoted Faecalibacterium prausnitzii and Lachnospiraceae related operational taxonomic units (OTUs), which are recognized as beneficial members of the human gut, whereas WSDFskin and XGskin stimulated Bacteroides OTUs. Interestingly, increased abundances of F. prausnitzii and Lachnospiraceae OTUs in PECskin were higher than those in commercially available pectin. Finally, PECskin and XGskin were tested in a biscuit model and the results showed that either PECskin or XGskin can be incorporated into biscuit formulations without impacting physical, textural, and sensory properties of the final product. Overall, our results demonstrated that hazelnut skin, an industrial byproduct, can be utilized for the production of functional dietary fibers, especially pectin, to improve colonic health.

The landscape of new therapeutic opportunities for IBD

This chapter presents an overview of the emerging strategies to address the unmet needs in the management of inflammatory bowel diseases (IBD). IBD poses significant challenges, as over half of patients experience disease progression despite interventions, leading to irreversible complications, and a substantial proportion do not respond to existing therapies, such as biologics. To overcome these limitations, we describe a diverse array of novel therapeutic approaches. In the area of immune homeostasis restoration, the focus is on targeting cytokine networks, leukocyte trafficking, novel immune pathways, and cell therapies involving regulatory T cells and mesenchymal stem cells (MSC). Recognizing the critical role of impaired intestinal barrier integrity in IBD, we highlight therapies aimed at restoring barrier function and promoting mucosal healing, such as those targeting cell proliferation, tight junctions, and lipid mediators. Addressing the challenges posed by fibrosis and fistulas, we describe emerging targets for reversing fibrosis like kinase and cytokine inhibitors and nuclear receptor agonists, as well as the potential of MSC for fistulas. The restoration of a healthy gut microbiome, through strategies like fecal microbiota transplantation, rationally defined bacterial consortia, and targeted antimicrobials, is also highlighted. We also describe innovative approaches to gut-targeted drug delivery to enhance efficacy and minimize side effects. Reinforcing these advancements is the critical role of precision medicine, which emphasizes the use of multiomics analysis for the discovery of biomarkers to enable personalized IBD care. Overall, the emerging landscape of therapeutic opportunities for IBD holds great potential to surpass the therapeutic ceiling of current treatments.

Proteomic approach to identify host cell attachment proteins provides protective Pseudomonas aeruginosa vaccine antigen FtsZ

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes severe nosocomial infections in susceptible individuals due to the emergence of multidrug-resistant strains. There are no approved vaccines against P. aeruginosa infections nor candidates in active clinical development, highlighting the need for novel candidates and strategies. Using a cell-blot proteomic approach, we reproducibly identified 49 proteins involved in interactions with human lung epithelial cells across four P. aeruginosa strains. Among these were cell division protein FtsZ and outer membrane protein OpmH. Escherichia coli BL21 cells overexpressing recombinant FtsZ or rOpmH showed a 66- and 15-fold increased ability to attach to 16HBE14o- cells, further supporting their involvement in host cell attachment. Both antigens led to proliferation of NK and CD8+ cytotoxic T cells, significant increases in the production of IFN-γ, IL-17A, TNF and IL-4 in immunised mice and elicited strong antigen-specific serological IgG1 and IgG2c responses. Immunisation with FtsZ significantly reduced bacterial burden in the lungs by 1.9-log CFU and dissemination to spleen by 1.8-log CFU. The protective antigen candidate, FtsZ, would not have been identified by traditional approaches relying on either virulence mechanisms or sequence-based predictions, opening new avenues in the development of an anti-P. aeruginosa vaccine.

Microbial biomarker discovery in Parkinson's disease through a network-based approach

Associations between the gut microbiota and Parkinson's disease (PD) have been widely investigated. However, the replicable biomarkers for PD diagnosis across multiple populations remain elusive. Herein, we performed a meta-analysis to investigate the pivotal role of the gut microbiome in PD and its potential diagnostic implications. Six 16S rRNA gene amplicon sequence datasets from five independent studies were integrated, encompassing 550 PD and 456 healthy control samples. The analysis revealed significant alterations in microbial composition and alpha and beta diversity, emphasizing altered gut microbiota in PD. Specific microbial taxa, including Faecalibacterium, Roseburia, and Coprococcus_2, known as butyrate producers, were notably diminished in PD, potentially contributing to intestinal inflammation. Conversely, genera such as Akkermansia and Bilophila exhibited increased relative abundances. A network-based algorithm called NetMoss was utilized to identify potential biomarkers of PD. Afterwards, a classification model incorporating 11 optimized genera demonstrated high performance. Further functional analyses indicated enrichment in pathways related to neurodegeneration and metabolic pathways. These findings illuminate the intricate relationship between the gut microbiota and PD, offering insights into potential therapeutic interventions and personalized diagnostic strategies.

Host-pathobiont interactions in Crohn's disease

The mammalian intestine is colonized by trillions of microorganisms that are collectively referred to as the gut microbiota. The majority of symbionts have co-evolved with their host in a mutualistic relationship that benefits both. Under certain conditions, such as in Crohn's disease, a subtype of inflammatory bowel disease, some symbionts bloom to cause disease in genetically susceptible hosts. Although the identity and function of disease-causing microorganisms or pathobionts in Crohn's disease remain largely unknown, mounting evidence from animal models suggests that pathobionts triggering Crohn's disease-like colitis inhabit certain niches and penetrate the intestinal tissue to trigger inflammation. In this Review, we discuss the distinct niches occupied by intestinal symbionts and the evidence that pathobionts triggering Crohn's disease live in the mucus layer or near the intestinal epithelium. We also discuss how Crohn's disease-associated mutations in the host disrupt intestinal homeostasis by promoting the penetration and accumulation of pathobionts in the intestinal tissue. Finally, we discuss the potential role of microbiome-based interventions in precision therapeutic strategies for the treatment of Crohn's disease.

Xylanase enhances gut microbiota-derived butyrate to exert immune-protective effects in a histone deacetylase-dependent manner

BACKGROUND

Commensal bacteria in the intestine release enzymes to degrade and ferment dietary components, producing beneficial metabolites. However, the regulatory effects of microbial-derived enzymes on the intestinal microbiota composition and the influence on host health remain elusive. Xylanase can degrade xylan into oligosaccharides, showing wide application in feed industry.

RESULTS

To validate the immune-protective effects of xylanase, Nile tilapia was used as the model and fed with xylanase. The results showed that dietary xylanase improved the survival rate of Nile tilapia when they were challenged with Aeromonas hydrophila. The transcriptome analysis showed significant enrichment of genes related to interleukin-17d (il-17d) signaling pathway in the xylanase treatment group. High-throughput sequencing revealed that dietary xylanase altered the composition of the intestinal microbiota and directly promoted the proliferation of Allobaculum stercoricanis which could produce butyrate in vitro. Consequently, dietary xylanase supplementation increased the butyrate level in fish gut. Further experiment verified that butyrate supplementation enhanced the expression of il-17d and regenerating islet-derived 3 gamma (reg3g) in the gut. The knockdown experiment of il-17d confirmed that il-17d is necessary for butyrate to protect Nile tilapia from pathogen resistance. Flow cytometry analysis indicated that butyrate increased the abundance of IL-17D+ intestinal epithelial cells in fish. Mechanistically, butyrate functions as an HDAC3 inhibitor, enhancing il-17d expression and playing a crucial role in pathogen resistance.

CONCLUSION

Dietary xylanase significantly altered the composition of intestinal microbiota and increased the content of butyrate in the intestine. Butyrate activated the transcription of il-17d in intestinal epithelial cells by inhibiting histone deacetylase 3, thereby protecting the Nile tilapia from pathogen infection. This study elucidated how microbial-derived xylanase regulates host immune function, providing a theoretical basis for the development and application of functional enzymes. Video Abstract.

Gastrointestinal, Behaviour and Anxiety Outcomes in Autistic Children Following an Open Label, Randomised Pilot Study of Synbiotics vs Synbiotics and Gut-Directed Hypnotherapy

Alterations of the microbiome-gut-brain (MGB) axis have been associated with autism spectrum disorder (ASD) and disorders of gut-brain interaction (DGBI). DGBI are highly prevalent in autistic children and are associated with worsening behaviour and anxiety. Treatments such as probiotics, prebiotics and gut-directed hypnotherapy (GDH) have shown efficacy in improving gut symptoms in children. The primary objective of the study was to compare changes in gastrointestinal (GI) scores following a 12-week intervention of synbiotics (prebiotic + probiotic) +/- GDH with a follow-up at 24 weeks. Secondary objectives included changes in behavioural and anxiety symptoms, while changes in gut microbiome composition were assessed as an exploratory objective. Children diagnosed with ASD aged 5.00-10.99 years (n = 40) were recruited and randomised (1:1) to a 12-week intervention of either synbiotics (SYN group) or synbiotics + GDH (COM group). Both the SYN and COM group experienced significant reductions in total GI scores post-intervention and at follow-up (p < 0.001), with no superiority of the COM treatment over the SYN treatment. The COM group showed beneficial reductions in anxiety scores (p = 0.002) and irritability behaviours (p < 0.001) which were not present in the SYN group. At follow-up, only those in the COM group maintained significant reductions in GI pain scores (p < 0.001). There were significant changes in gut microbiota such as increases in Bifidobacterium animalis and Dialister in both groups over time. In conclusion, synbiotics with or without GDH may help support standard care for autistic children who suffer comorbid DGBI. The trial was prospectively registered at clinicialtrials.gov on 16 November 2020 (NCTO4639141).

Colorectal Cancer in Inflammatory Bowel Disease: A Review of the Role of Gut Microbiota and Bacterial Biofilms in Disease Pathogenesis

The risk of colorectal cancer [CRC] is increased in patients with inflammatory bowel disease [IBD], particularly in extensive ulcerative colitis [UC] and Crohn's colitis. Gut microbiota have been implicated in the pathogenesis of CRC via multiple mechanisms, including the release of reactive oxygen species and genotoxins, and induction of inflammation, as well as activation of the immune response. Gut microbiota can enhance their carcinogenic and proinflammatory properties by organising into biofilms, potentially making them more resistant to the host's immune system and to antibiotics. Colonic biofilms have the capacity to invade colonic tissue and accelerate tumorigenesis in tumour-prone models of mice. In the context of IBD, the prevalence of biofilms has been estimated to be up to 95%. Although the relationship between chronic inflammation and molecular mediators that contribute to IBD-associated CRC is well established, the role of gut microbiota and biofilms in this sequence is not fully understood. Because CRC can still arise in the absence of histological inflammation, there is a growing interest in identifying chemopreventive agents against IBD-associated CRC. Commonly used in the treatment of UC, 5-aminosalicylates have antimicrobial and anticarcinogenic properties that might have a role in the chemoprevention of CRC via the inhibition or modulation of carcinogenic gut microbiota and potentially of biofilm formation. Whether biologics and other IBD-targeted therapies can decrease the progression towards dysplasia and CRC, via mechanisms independent of inflammation, is still unknown. Further research is warranted to identify potential new microbial targets in therapy for chemoprevention of dysplasia and CRC in IBD.

Therapeutic and Immunologic Effects of Short-Chain Fatty Acids in Inflammatory Bowel Disease: A Systematic Review

Inflammatory bowel disease is a chronic condition characterized by recurrent intestinal inflammation. Its etiopathogenesis is driven by a series of events that disrupt the mucosal barrier, alter the healthy balance of intestinal microbiota, and abnormally stimulate intestinal immune responses. Therefore, numerous studies suggest the use of short-chain fatty acids and their immunomodulatory effects as a therapeutic approach in this disease. The objective of this systematic review was to synthesize previous evidence on the relevance and therapeutic use of short-chain fatty acids, particularly butyrate, in the immune regulation of inflammatory bowel disease. This systematic review of articles linking inflammatory bowel disease with short-chain fatty acids was conducted according to the PRISMA-2020 guidelines. The Medline and the Web of Science databases were searched in August 2024. The risk of bias was assessed using the Joanna Briggs Institute checklists. A total of 1460 articles were reviewed, of which, 29 met the inclusion criteria. Short-chain fatty acids, particularly butyrate, play a critical role in the regulation of intestinal inflammation and can be used as a strategy to increase the levels of short-chain fatty acid-producing bacteria for use in therapeutic approaches.

Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population

Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.

The hidden threat: Comprehensive assessment of antibiotic and disinfectant resistance in commercial pig slaughterhouses

The presence of antibiotic resistance genes (ARGs), disinfectant resistance genes (DRGs), and pathogens in animal food processing environments (FAPE) poses a significant risk to human health. However, knowledge of the contamination and risk profiles of a typical commercial pig slaughterhouse with periodic disinfectant applications is limited. By creating the overall metagenomics-based behavior and risk profiles of ARGs, DRGs, and microbiomes in a nine-section pig slaughterhouse, an important FAPE in China. A total of 454 ARGs and 84 DRGs were detected in the slaughterhouse with resistance genes for aminoglycosides and quaternary ammonium compounds, respectively. The entire slaughtering chain is a hotspot for pathogens, including 83 human pathogenic bacteria (HPB), with 47 core HPB. In addition, 68 high-risk ARGs were significantly correlated with 55 HPB, 30 of which were recognized as potential bacteria co-resistant to antibiotics and disinfectants, confirm a three-fold risk of ARGs, DRGs, and pathogens prevailing throughout the chain. Pre-slaughter pig house (PSPH) was the major risk source for ARGs, DRGs, and HPB. Moreover, 75 Escherichia coli and 47 Proteus mirabilis isolates showed sensitivity to potassium monopersulfate and sodium hypochlorite, suggesting that slaughterhouses should use such related disinfectants. By using whole genome multi-locus sequence typing and single nucleotide polymorphism analyses, genetically closely related bacteria were identified across distinct slaughter sections, suggesting bacterial transmission across the slaughter chain. Overall, this study underscores the critical role of the PSPH section as a major source of HPB, ARGs, and DRGs contamination in commercial pig slaughterhouses. Moreover, it highlights the importance of addressing clonal transmission and cross-contamination of antibiotic- and disinfectant-resistant bacteria within and between slaughter sections. These issues are primarily attributed to the microbial load carried by animals before slaughter, carcass handling, and content exposure during visceral treatment. Our findings provide valuable insights for One Health-oriented slaughterhouse management practices.

Rapid species-level metagenome profiling and containment estimation with sylph

Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph's ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph took <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.

Gut bacteria: an etiological agent in human pathological conditions

Through complex interactions with the host's immune and physiological systems, gut bacteria play a critical role as etiological agents in a variety of human diseases, having an impact that extends beyond their mere presence and affects the onset, progression, and severity of the disease. Gaining a comprehensive understanding of these microbial interactions is crucial to improving our understanding of disease pathogenesis and creating tailored treatment methods. Correcting microbial imbalances may open new avenues for disease prevention and treatment approaches, according to preliminary data. The gut microbiota exerts an integral part in the pathogenesis of numerous health conditions, including metabolic, neurological, renal, cardiovascular, and gastrointestinal problems as well as COVID-19, according to recent studies. The crucial significance of the microbiome in disease pathogenesis is highlighted by this role, which is comparable to that of hereditary variables. This review investigates the etiological contributions of the gut microbiome to human diseases, its interactions with the host, and the development of prospective therapeutic approaches. To fully harness the benefits of gut microbiome dynamics for improving human health, future research should address existing methodological challenges and deepen our knowledge of microbial interactions.

Description of Faecalibacterium wellingii sp. nov. and two Faecalibacterium taiwanense strains, aiding to the reclassification of Faecalibacterium species

OBJECTIVES

The genus Faecalibacterium is one of the most important butyrate producers in the human intestinal tract and has been widely linked to health. Recently, several different species have been described, but still more phylogroups have been identified, suggesting that additional species may exist. Four strains HTF-FT, HTF-128, HTF-75H and HTF-76H, representing two different phylogenetic clusters, are evaluated in this study.

METHODS

Phylogenomic analysis was performed using whole-genome sequences and 16S rRNA gene sequences. Chemotaxonomic analysis was done based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Physiological and phenotypical characteristics of these strains were also determined. All characteristics of these strains were compared with other validly published species within the genus Faecalibacterium.

RESULTS

On a genomic level, the strains HTF-FT and HTF-128 shared an average nucleotide identity (ANI) of <95.0 % and digital DNA-DNA hybridization (dDDH) of <70.0 with other Faecalibacterium species, while between HTF-FT and HTF-128 the ANI-value was 97.18 % and the dDDH was 76.8 %. HTF-75H and HTF-76H had an ANI and dDDH value of 100 % (99.96 %) and 100 % (99.99 %) respectively. Both HTF-75H and HTF-76H were closely related to Faecalibacterium taiwanense HLW78T. 16S rRNA gene and chemotaxonomic analysis were in accordance with the genomic data, confirming that HTF-FT and HTF-128 represent a novel Faecalibacterium species and HTF-75H and HTF-76H belong to F. taiwanense.

CONCLUSIONS

Faecalibacterium strains HTF-FT (=DSM 117771T = NCIMB 15531T) and HTF-128 represent a novel species. The name Faecalibacterium wellingii with HTF-FT as type strain is proposed. Two novel isolates HTF-75H (=DSM 17770 = NCIMB 15530) and HTF-76H are described in this study and belong to the recently described Faecalibacterium taiwanense.

Host-diet-microbiota interplay in intestinal nutrition and health

The intestine is populated by a complex and dynamic assortment of microbes, collectively called gut microbiota, that interact with the host and contribute to its metabolism and physiology. Diet is considered a key regulator of intestinal microbiota, as ingested nutrients interact with and shape the resident microbiota composition. Furthermore, recent studies underscore the interplay of dietary and microbiota-derived nutrients, which directly impinge on intestinal stem cells regulating their turnover to ensure a healthy gut barrier. Although advanced sequencing methodologies have allowed the characterization of the human gut microbiome, mechanistic studies assessing diet-microbiota-host interactions depend on the use of genetically tractable models, such as Drosophila melanogaster. In this review, we first discuss the similarities between the human and fly intestines and then we focus on the effects of diet and microbiota on nutrient-sensing signaling cascades controlling intestinal stem cell self-renewal and differentiation, as well as disease. Finally, we underline the use of the Drosophila model in assessing the role of microbiota in gut-related pathologies and in understanding the mechanisms that mediate different whole-body manifestations of gut dysfunction.

Escherichia coli on colorectal cancer: A two-edged sword

Escherichia coli (E. coli) is a ubiquitous symbiotic bacterium in the gut, and the diversity of E. coli genes determines the diversity of its functions. In this review, the two-edged sword theory was innovatively proposed. For the question 'how can we harness the ambivalent nature of E. coli to screen and treat CRC?', in terms of CRC screening, the variations in the abundance and subtypes of E. coli across different populations present an opportunity to utilise it as a biomarker, while in terms of CRC treatment, the natural beneficial effect of E. coli on CRC may be limited, and engineered E. coli, particularly certain subtypes with probiotic potential, can indeed play a significant role in CRC treatment. It seems that the favourable role of E. coli as a genetic tool lies not in its direct impact on CRC but its potential as a research platform that can be integrated with various technologies such as nanoparticles, imaging methods, and synthetic biology modification. The relationship between gut microflora and CRC remains unclear due to the complex diversity and interaction of gut microflora. Therefore, the application of E. coli should be based on the 'One Health' view and take the interactions between E. coli and other microorganisms, host, and environmental factors, as well as its own changes into account. In this paper, the two-edged sword role of E. coli in CRC is emphasised to realise the great potential of E. coli in CRC screening and treatment.

Impact of a legumes diet on the human gut microbiome articulated with fecal and plasma metabolomes: A pilot study

BACKGROUND & AIMS

Legumes intake is known to be associated with several health benefits the origins of which is still a matter of debate. This paper addresses a pilot small cohort to probe for metabolic aspects of the interplay between legumes intake, human metabolism and gut microbiota.

METHODS

Untargeted nuclear magnetic resonance (NMR) metabolomics of blood plasma and fecal extracts was carried out, in tandem with qPCR analysis of feces, to assess the impact of an 8-week pilot legumes diet intervention on the fecal and plasma metabolomes and gut microbiota of 19 subjects.

RESULTS

While the high inter-individual variability hindered the detection of statistically significant changes in the gut microbiome, increased fecal glucose and decreased threonine levels were noted. Correlation analysis between the microbiome and fecal metabolome lead to putative hypotheses regarding the metabolic activities of prevalent bacteria groups (Clostridium leptum subgroup, Roseburia spp., and Faecalibacterium prausnitzii). These included elevated fecal glucose as a preferential energy source, the involvement of valerate/isovalerate and reduced protein degradation in gut microbiota. Plasma metabolomics advanced mannose and betaine as potential markers of legume intake and unveiled a decrease in formate and ketone bodies, the latter suggesting improved energy utilization through legume carbohydrates. Amino acid metabolism was also apparently affected, as suggested by lowered urea, histidine and threonine levels.

CONCLUSIONS

Despite the high inter-individual gut microbiome variability characterizing the small cohort addressed, combination of microbiological measurements and untargeted metabolomics unveiled several metabolic effects putatively related to legumes intake. If confirmed in larger cohorts, our findings will support the inclusion of legumes in diets and contribute valuable new insight into the origins of associated health benefits.

Disclosing α-lactalbumin impact on the intestinal and vaginal microbiota of women suffering from polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is one of the most widespread endocrinopathy affecting women of reproductive age with detrimental effects on life quality and health. Among several mechanisms involved in its aetiopathogenesis, recent studies have also postulated the involvement of the vaginal and intestinal microbiota in the development of this disorder. In this study, an accurate insight into the microbial changes associated with PCOS was performed through a pooled-analysis highlighting that this syndrome is characterized by intestinal and vaginal dysbiosis with a reduction of beneficial microorganisms and a higher proportion of potential pathogens. Based on this observation, we evaluated the ability of a milk-derived protein exerting positive outcomes in the management of PCOS, that is, α-lactalbumin (α-LA), to recover PCOS-related dysbiosis. In vitro experiments revealed that this protein improved the growth performances of members of two health-promoting bacterial genera, that is, Bifidobacterium and Lactobacillus, depleted in both intestinal and vaginal microbiota of PCOS-affected women. In addition, α-LA modulated the taxonomic composition and growth performances of the microbial players of the complex intestinal and vaginal microbiota. Finally, an in vivo pilot study further corroborated these observations. The oral administration of α-LA for 30 days to women with PCOS revealed that this protein may have a role in favouring the growth of health-promoting bacteria yet limiting the proliferation of potential pathogens. Overall, our results could pave the way to the use of α-LA as a valid compound with 'prebiotic effects' to limit/restore the PCOS-related intestinal and vaginal dysbiosis.

The emerging role of the gut microbiota and its application in inflammatory bowel disease

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of the gut microbiome has been found to play a role in IBD etiology, including exacerbated immune responses and defective intestinal barrier integrity. The gut microbiome can also be a potential biomarker for several diseases, including IBD. Currently, conventional treatments targeting pro-inflammatory cytokines and pathways in IBD-associated dysbiosis do not yield effective results. Other therapies that directly target the dysbiotic microbiome for effective outcomes are emerging. We review the role of the gut microbiome in health and IBD and its potential as a diagnostic, prognostic, and therapeutic target for IBD. This review also explores emerging therapeutic advancements that target gut microbiome-associated alterations in IBD, such as nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), gut proteins, and herbal formulas.

Outer membrane barrier impairment by envC deletion reduces gut colonization of Crohn's disease pathobiont Escherichia coli

Adherent-invasive Escherichia coli (AIEC) has been implicated in the aetiology of Crohn's disease (CD), a chronic inflammatory disorder of the gastrointestinal tract. The presence of Enterobacteriaceae, including AIEC, is heightened in the intestines of CD patients. Therefore, inhibiting AIEC colonization in the gastrointestinal tract could be a promising therapeutic intervention for CD. This study aims to assess the potential of EnvC as a novel therapeutic target, examining how disrupting EnvC activity through the deletion of the envC gene decreases AIEC gut colonization levels. EnvC serves as a catalyst for peptidoglycan (also called murein) amidases, facilitating bacterial cell division. An AIEC mutant lacking the envC gene exhibited impaired cell division. Furthermore, envC deletion led to a diminished outer membrane barrier, as seen in our finding that the envC mutant became susceptible to vancomycin. Finally, we found that the envC mutant is impaired in competitive gut colonization in a dysbiotic mouse model. The colonization defects might be attributable to reduced resistance to colonic bile acids, as evidenced by our finding that increased colonic levels of bile acids inhibited the colonization of the gastrointestinal tract by AIEC strains. The present findings suggest that targeting bacterial cell division through the inhibition of EnvC activity could represent a promising intervention for CD.

Gut microbiota, serum metabolites, and lipids related to blood glucose control and type 1 diabetes

BACKGROUND

The composition and function of gut microbiota, lipids, and metabolites in patients with type 1 diabetes (T1D) or its association with glycemic control remains unknown. We aimed to use multi-omics sequencing technology and machine learning (ML) approaches to investigate potential function and relationships among the gut microbiota, lipids, and metabolites in T1D patients at varied glycemic levels.

METHODS

We conducted a multi-omics analysis of the gut microbiome from fecal samples, metabolites, and lipids obtained from serum samples, collected from a cohort of 72 T1D patients. The patients were divided into two groups based on their hemoglobin A1c (HbA1c) levels. 16S rRNA sequencing, and metabolomics methods were applied to analyze changes in composition and function of gut microbiota, metabolites, and lipids.

RESULTS

The linear discriminant analysis, Shapley additive explanations (SHAP) algorithm, and ML algorithms revealed the enrichment of Bacteroides_nordii, Bacteroides_cellulosilyticus in the glycemic control (GC) group, while Bacteroides_coprocola and Sutterella_wadsworthensis were enriched in the poor glycemic control (PGC) group. Several metabolic enrichment sets like fatty acid biosynthesis and glycerol phosphate shuttle metabolism were different between two groups. Bacteroides_nordii exhibited a negative association with D-fructose, a component involved in the starch and sucrose metabolism pathway, as well as with monoglycerides (16:0) involved in the glycerolipid metabolism pathway.

CONCLUSIONS

We identified distinct characteristics of gut microbiota, metabolites, and lipids in T1D patients exhibiting different levels of glycemic control. Through comprehensive analysis, microbiota (Bacteroides_nordii, Bacteroides_coprocola), metabolites (D-fructose), and lipids (Monoglycerides) may serve as potential mediators that communicated the interaction between the gut, circulatory systems, and glucose fluctuations in T1D patients.

The JAK inhibitor, Tofacitinib, Corrects the Overexpression of CEACAM6 and Limits Susceptibility to AIEC Caused by Reduced Activity of the IBD Associated Gene, PTPN2

Background and Aims

A cohort of patients with inflammatory bowel disease (IBD) exhibit expansion of the gut pathobiont, adherent-invasive E. coli (AIEC). Loss of activity of the IBD susceptibility gene, protein tyrosine phosphatase type 2 (PTPN2), results in dysbiosis of the gut microbiota both in human subjects and mice. Further, constitutive Ptpn2 knock-out (Ptpn2-KO) mice display expansion of AIEC compared to wildtype littermates. CEACAM6, a host cell surface glycoprotein, is exploited by AIEC to attach to and enter intestinal epithelial cells (IECs). Here, we investigate the role of IEC-specific PTPN2 in restricting AIEC invasion.

Methods

Biopsies from IBD patients heterozygous (CT) or homozygous (CC) for the PTPN2 SNP (single nucleotide polymorphism) rs1893217 were processed for immunohistochemistry. HT-29 intestinal epithelial cells (IEC) were transfected with control shRNA (PTPN2-CTL), or a shRNA targeted towards PTPN2 (PTPN2-KD). The rs1893217 SNP was inserted (PTPN2-KI), or a complete knock-out of PTPN2 (PTPN2-KO) was generated, with CRISPR-Cas9 gene editing of Caco-2BBe IEC lines. Adherence and invasion assays were performed with either the human IBD AIEC isolate, LF82, or a novel fluorescent-tagged mouse adherent-invasive E. coli (mAIECred) at multiplicity of infection (MOI) of 10. IL-6 and the pan-JAK inhibitor tofacitinib were administered to interrogate JAK-STAT signaling. Protein expression was determined by western blotting and densitometry.

Results

CEACAM6 expression was elevated (colon and ileum) in IBD patients carrying the PTPN2 rs1893217 SNP (CT, CC) compared to wildtype (TT) IBD patients. HT-29 and Caco-2BBe cell lines deficient in PTPN2 expressed significantly higher levels of CEACAM6. Further, PTPN2-KI and PTPN2-KO cell lines also displayed greater adherence and invasion by AIEC LF82 and higher mAIECred invasion. CEACAM6 expression was further elevated after administration of IL-6 in PTPN2-deficient cell lines compared to untreated controls. Silencing of STAT1 and 3 partially reduced CEACAM6 protein expression. Tofacitinib significantly reduced the elevated CEACAM6 protein expression and the higher AIEC adherence and invasion in PTPN2-KI and PTPN2-KO cell lines compared to DMSO controls.

Conclusion

Our findings highlight a crucial role for PTPN2 in restricting pathobiont entry into host cells. Our study also describes a role for the FDA-approved drug, tofacitinib (Xeljanz) in correcting the JAK-STAT-mediated over-expression of CEACAM6, used by pathobionts as an entry portal into host cells. These findings suggest a role for JAK-inhibitors in mitigating AIEC colonization in IBD-susceptible hosts.

Gut microbiota and interstitial cystitis: exploring the gut-bladder axis through mendelian randomization, biological annotation and bulk RNA sequencing

Background

Several observational studies have indicated an association between interstitial cystitis and the composition of the gut microbiota; however, the causality and underlying mechanisms remain unclear. Understanding the link between gut microbiota and interstitial cystitis could inform strategies for prevention and treatment.

Methods

A two-sample Mendelian randomization analysis was conducted using published genome-wide association study summary statistics. We employed inverse variance weighted, weighted mode, MR-Egger, weighted median, simple mode, and cML-MA methods to investigate the causal relationship between gut microbiota and interstitial cystitis. Sensitivity analysis was performed to validate the results. Relevant gut microbiota was examined through reverse MR. Single nucleotide polymorphisms were annotated using FUMA to identify genes associated with these genetic variants, thereby revealing potential host gene-microbiota associations in interstitial cystitis patients.

Results

Eight bacterial taxa were identified in our analysis as associated with interstitial cystitis. Among these, Butyricimonas, Coprococcus, Lactobacillales, Lentisphaerae, and Bilophila wadsworthia were positively correlated with interstitial cystitis risk, while taxa such as Desulfovibrio piger, Oscillibacter unclassified and Ruminococcus lactaris exhibited protective effects against interstitial cystitis. The robustness of these associations was confirmed through sensitivity analyses. Reverse MR analysis did not reveal evidence of reverse causality. Single nucleotide polymorphisms were annotated using FUMA and subjected to biological analysis. Seven hub genes (SPTBN1, PSME4, CHAC2, ERLEC1, ASB3, STAT5A, and STAT3) were identified as differentially expressed between interstitial cystitis patients and healthy individuals, representing potential therapeutic targets.

Conclusion

Our two-sample Mendelian randomization study established a causal relationship between gut microbiota and interstitial cystitis. Furthermore, our identification of a host gene-microbiota association offers a new avenue for investigating the potential pathogenesis of interstitial cystitis and suggests avenues for the development of personalized treatment strategies.

Towards geospatially-resolved public-health surveillance via wastewater sequencing

Wastewater is a geospatially- and temporally-linked microbial fingerprint of a given population, making it a potentially valuable tool for tracking public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (N = 2238 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County, USA, from 2020-2022. We used targeted amplicon sequencing to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with positive PCR tests from University students and Miami-Dade hospital patients. Additionally, in bulk metatranscriptomic data, we demonstrate that the bacterial content of different wastewater sampling locations serving small population sizes can be used to detect putative, host-derived microorganisms that themselves have known associations with human health and diet. We also detect multiple enteric pathogens (e.g., Norovirus) and characterize viral diversity across sites. Moreover, we observed an enrichment of antimicrobial resistance genes (ARGs) in hospital wastewater; antibiotic-specific ARGs correlated to total prescriptions of those same antibiotics (e.g Ampicillin, Gentamicin). Overall, this effort lays the groundwork for systematic characterization of wastewater that can potentially influence public health decision-making.