The influence of a short-term gluten-free diet on the human gut microbiome

The interplay between diet and the gut microbiome: implications for health and disease

Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies.

Microbiota, natural products, and human health: exploring interactions for therapeutic insights

The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.

How the Microbiota May Affect Celiac Disease and What We Can Do

Celiac disease (CeD) is an autoimmune disease with a strong association with human leukocyte antigen (HLA), characterized by the production of specific autoantibodies and immune-mediated enterocyte killing. CeD is a unique autoimmune condition, as it is the only one in which the environmental trigger is known: gluten, a storage protein present in wheat, barley, and rye. How and when the loss of tolerance of the intestinal mucosa to gluten occurs is still unknown. This event, through the activation of adaptive immune responses, enhances epithelial cell death, increases the permeability of the epithelial barrier, and induces secretion of pro-inflammatory cytokines, resulting in the transition from genetic predisposition to the actual onset of the disease. While the role of gastrointestinal infections as a possible trigger has been considered on the basis of a possible mechanism of antigen mimicry, a more likely alternative mechanism appears to involve a complex disruption of the gastrointestinal microbiota ecosystem triggered by infections, rather than the specific effect of a single pathogen on intestinal mucosal homeostasis. Several lines of evidence show the existence of intestinal dysbiosis that precedes the onset of CeD in genetically at-risk subjects, characterized by the loss of protective bacterial elements that both epigenetically and functionally can influence the response of the intestinal epithelium leading to the loss of gluten tolerance. We have conducted a literature review in order to summarize the current knowledge about the complex and in part still unraveled dysbiosis that precedes and accompanies CeD and present some exciting new data on how this dysbiosis might be prevented and/or counteracted. The literature search was conducted on PubMed.gov in the time frame 2010 to March 2024 utilizing the terms "celiac disease and microbiota", "celiac disease and microbiome", and "celiac disease and probiotics" and restricting the search to the following article types: Clinical Trials, Meta-Analysis, Review, and Systematic Review. A total of 364 papers were identified and reviewed. The main conclusions of this review can be outlined as follows: (1) quantitative and qualitative changes in gut microbiota have been clearly documented in CeD patients; (2) intestinal microbiota's extensive and variable interactions with enterocytes, viral and bacterial pathogens and even gluten combine to impact the inflammatory immune response to gluten and the loss of gluten tolerance, ultimately affecting the pathogenesis, progression, and clinical expression of CeD; (3) gluten-free diet fails to restore the eubiosis of the digestive tract in CeD patients, and also negatively affects microbial homeostasis; (4) new tools allowing targeted microbiota therapy, such as the use of probiotics (a good example being precision probiotics like the novel strain of B. vulgatus (20220303-A2) begin to show exciting potential applications.

Interplay Between Drug-Induced Liver Injury and Gut Microbiota: A Comprehensive Overview

Drug-induced liver injury is a prevalent severe adverse event in clinical settings, leading to increased medical burdens for patients and presenting challenges for the development and commercialization of novel pharmaceuticals. Research has revealed a close association between gut microbiota and drug-induced liver injury in recent years. However, there has yet to be a consensus on the specific mechanism by which gut microbiota is involved in drug-induced liver injury. Gut microbiota may contribute to drug-induced liver injury by increasing intestinal permeability, disrupting intestinal metabolite homeostasis, and promoting inflammation and oxidative stress. Alterations in gut microbiota were found in drug-induced liver injury caused by antibiotics, psychotropic drugs, acetaminophen, antituberculosis drugs, and antithyroid drugs. Specific gut microbiota and their abundance are associated closely with the severity of drug-induced liver injury. Therefore, gut microbiota is expected to be a new target for the treatment of drug-induced liver injury. This review focuses on the association of gut microbiota with common hepatotoxic drugs and the potential mechanisms by which gut microbiota may contribute to the pathogenesis of drug-induced liver injury, providing a more comprehensive reference for the interaction between drug-induced liver injury and gut microbiota.

Maternal dietary intervention during lactation impacts the maternal faecal and human milk microbiota

AIMS

To determine the effect of a two-week reduced fat and sugar and increased fibre maternal dietary intervention on the maternal faecal and human milk (HM) microbiomes.

METHODS AND RESULTS

Faecal swabs and HM samples were collected from mothers (n = 11) immediately pre-intervention, immediately post-intervention, and 4 and 8 weeks post-intervention, and were analysed using full-length 16S rRNA gene sequencing. Maternal macronutrient intake was assessed at baseline and during the intervention. Maternal fat and sugar intake during the intervention were significantly lower than pre-intervention (P = <0.001, 0.005, respectively). Significant changes in the bacterial composition of maternal faeces were detected after the dietary intervention, with decreases in the relative abundance of Bacteroides caccae (P = <0.001) and increases in the relative abundance of Faecalibacillus intestinalis (P = 0.006). In HM, the diet resulted in a significant increase in Cutibacterium acnes (P = 0.001) and a decrease in Haemophilus parainfluenzae (P = <0.001). The effect of the diet continued after the intervention, with faecal swabs and HM samples taken 4 and 8 weeks after the diet showing significant differences compared to baseline.

CONCLUSION

This pilot study demonstrates that short-term changes in maternal diet during lactation can alter the bacterial composition of the maternal faeces and HM.

Gluten-Free Diet Alters the Gut Microbiome in Women with Autoimmune Thyroiditis

The gut microbiome may contribute to the development of autoimmune diseases, such as autoimmune thyroiditis (AIT). Diet has a critical impact on the gut microbiome, and it has been shown that a gluten-free diet can negatively affect its composition. A gluten-free diet is popular among patients, and therefore the aim of this study was to check whether it affects thyroid function and gut microbiome composition in AIT. Thirty-one women with AIT complied with a gluten-free diet for 8 weeks. After the first 4 weeks, participants were divided into two groups: the first group received gluten in capsules and the other one-rice starch (placebo). Blood and stool samples were examined before diet (T0), after 4 weeks (T1) and after 8 weeks of diet (T2). The only significant difference in blood parameters was observed between T1 and T2 in the placebo group for the thyroid peroxidase antibody level. After the first 4 weeks, a significant increase in Desulfobacterota, Proteobacteria, Prevotella and Parasutterella and a significant decrease in Actinobacteriota, Coriobacteriaceae and Bifidobacterium were observed. The detected microbiome alterations may indicate increasing inflammation; however, further research is required, and for now, a gluten-free diet should be used cautiously in AIT.

Precision Nutrition Unveiled: Gene-Nutrient Interactions, Microbiota Dynamics, and Lifestyle Factors in Obesity Management

BACKGROUND

Obesity is a complex metabolic disorder that is associated with several diseases. Recently, precision nutrition (PN) has emerged as a tailored approach to provide individualised dietary recommendations.

AIM

This review discusses the major intrinsic and extrinsic components considered when applying PN during the management of obesity and common associated chronic conditions.

RESULTS

The review identified three main PN components: gene-nutrient interactions, intestinal microbiota, and lifestyle factors. Genetic makeup significantly contributes to inter-individual variations in dietary behaviours, with advanced genome sequencing and population genetics aiding in detecting gene variants associated with obesity. Additionally, PN-based host-microbiota evaluation emerges as an advanced therapeutic tool, impacting disease control and prevention. The gut microbiome's composition regulates diverse responses to nutritional recommendations. Several studies highlight PN's effectiveness in improving diet quality and enhancing adherence to physical activity among obese patients. PN is a key strategy for addressing obesity-related risk factors, encompassing dietary patterns, body weight, fat, blood lipids, glucose levels, and insulin resistance.

CONCLUSION

PN stands out as a feasible tool for effectively managing obesity, considering its ability to integrate genetic and lifestyle factors. The application of PN-based approaches not only improves current obesity conditions but also holds promise for preventing obesity and its associated complications in the long term.

The impact of intermittent fasting on gut microbiota: a systematic review of human studies

Background

Intermittent fasting (IF) has gained popularity in interventions targeting overweight, obesity and metabolic syndrome. IF may affect the gut microbiome composition and therefore have various effects on gut microbiome mediated functions in humans. Research on the effects of IF on human gut microbiome is limited. Therefore, the objective of this systematic review was to determine how different types of IF affect the human gut microbiome.

Methods

A literature search was conducted for studies investigating the association of different types of IF and gut microbiota richness, alpha and beta diversity, and composition in human subjects. Databases included Cochrane Library (RRID:SCR_013000), PubMed (RRID:SCR_004846), Scopus (RRID:SCR_022559) and Web of Science (RRID:SCR_022706). A total of 1,332 studies were retrieved, of which 940 remained after removing duplicates. Ultimately, a total of 8 studies were included in the review. The included studies were randomized controlled trials, quasi-experimental studies and pilot studies implementing an IF intervention (time-restricted eating, alternate day fasting or 5:2 diet) in healthy subjects or subjects with any disease.

Results

Most studies found an association between IF and gut microbiota richness, diversity and compositional changes. There was heterogeneity in the results, and bacteria which were found to be statistically significantly affected by IF varied widely depending on the study.

Conclusion

The findings in this systematic review suggest that IF influences gut microbiota. It seems possible that IF can improve richness and alpha diversity. Due to the substantial heterogeneity of the results, more research is required to validate these findings and clarify whether the compositional changes might be beneficial to human health.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42021241619.

Major depressive disorder: hypothesis, mechanism, prevention and treatment

Worldwide, the incidence of major depressive disorder (MDD) is increasing annually, resulting in greater economic and social burdens. Moreover, the pathological mechanisms of MDD and the mechanisms underlying the effects of pharmacological treatments for MDD are complex and unclear, and additional diagnostic and therapeutic strategies for MDD still are needed. The currently widely accepted theories of MDD pathogenesis include the neurotransmitter and receptor hypothesis, hypothalamic-pituitary-adrenal (HPA) axis hypothesis, cytokine hypothesis, neuroplasticity hypothesis and systemic influence hypothesis, but these hypothesis cannot completely explain the pathological mechanism of MDD. Even it is still hard to adopt only one hypothesis to completely reveal the pathogenesis of MDD, thus in recent years, great progress has been made in elucidating the roles of multiple organ interactions in the pathogenesis MDD and identifying novel therapeutic approaches and multitarget modulatory strategies, further revealing the disease features of MDD. Furthermore, some newly discovered potential pharmacological targets and newly studied antidepressants have attracted widespread attention, some reagents have even been approved for clinical treatment and some novel therapeutic methods such as phototherapy and acupuncture have been discovered to have effective improvement for the depressive symptoms. In this work, we comprehensively summarize the latest research on the pathogenesis and diagnosis of MDD, preventive approaches and therapeutic medicines, as well as the related clinical trials.

Novel functional insights into ischemic stroke biology provided by the first genome-wide association study of stroke in indigenous Africans

BACKGROUND

African ancestry populations have the highest burden of stroke worldwide, yet the genetic basis of stroke in these populations is obscure. The Stroke Investigative Research and Educational Network (SIREN) is a multicenter study involving 16 sites in West Africa. We conducted the first-ever genome-wide association study (GWAS) of stroke in indigenous Africans.

METHODS

Cases were consecutively recruited consenting adults (aged > 18 years) with neuroimaging-confirmed ischemic stroke. Stroke-free controls were ascertained using a locally validated Questionnaire for Verifying Stroke-Free Status. DNA genotyping with the H3Africa array was performed, and following initial quality control, GWAS datasets were imputed into the NIH Trans-Omics for Precision Medicine (TOPMed) release2 from BioData Catalyst. Furthermore, we performed fine-mapping, trans-ethnic meta-analysis, and in silico functional characterization to identify likely causal variants with a functional interpretation.

RESULTS

We observed genome-wide significant (P-value < 5.0E-8) SNPs associations near AADACL2 and miRNA (MIR5186) genes in chromosome 3 after adjusting for hypertension, diabetes, dyslipidemia, and cardiac status in the base model as covariates. SNPs near the miRNA (MIR4458) gene in chromosome 5 were also associated with stroke (P-value < 1.0E-6). The putative genes near AADACL2, MIR5186, and MIR4458 genes were protective and novel. SNPs associations with stroke in chromosome 2 were more than 77 kb from the closest gene LINC01854 and SNPs in chromosome 7 were more than 116 kb to the closest gene LINC01446 (P-value < 1.0E-6). In addition, we observed SNPs in genes STXBP5-AS1 (chromosome 6), GALTN9 (chromosome 12), FANCA (chromosome 16), and DLGAP1 (chromosome 18) (P-value < 1.0E-6). Both genomic regions near genes AADACL2 and MIR4458 remained significant following fine mapping.

CONCLUSIONS

Our findings identify potential roles of regulatory miRNA, intergenic non-coding DNA, and intronic non-coding RNA in the biology of ischemic stroke. These findings reveal new molecular targets that promise to help close the current gaps in accurate African ancestry-based genetic stroke's risk prediction and development of new targeted interventions to prevent or treat stroke.

Co-Administration of Proton Pump Inhibitors May Negatively Affect the Outcome in Inflammatory Bowel Disease Treated with Vedolizumab

Concomitant medications may alter the effect of biological therapy in inflammatory bowel disease. The aim was to investigate the effect of proton pump inhibitors on remission rates in patients with inflammatory bowel disease treated with the gut-selective vedolizumab. Patients from the Hungarian nationwide, multicenter vedolizumab cohort were selected for post hoc analysis. Primary outcomes were the assessment of clinical response and endoscopic and clinical remission at weeks 14 and 54. Secondary outcomes were the evaluation of the combined effect of concomitant steroid therapy and other factors, such as smoking, on remission. A total of 108 patients were identified with proton pump inhibitor data from 240 patients in the original cohort. Patients on steroids without proton pump inhibitors were more likely to have a clinical response at week 14 than patients on concomitant PPI (95% vs. 67%, p = 0.005). Non-smokers with IBD treated with VDZ were more likely to develop a clinical response at week 14 than smokers, particularly those not receiving PPI compared with patients on co-administered PPI therapy (81% vs. 53%, p = 0.041, and 92% vs. 74%, p = 0.029, respectively). We found that the use of PPIs in patients treated with VDZ may impair the achievement of response in certain subgroups. Unnecessary PPI prescriptions should be avoided.

Diet-microbiota associations in gastrointestinal research: a systematic review

Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet-microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.

Comparison of yeast-derived commercial feed additives on Salmonella Enteritidis survival and microbiota populations in rooster cecal in vitro incubations

Yeast-derived products have become more of an interest in the poultry industry as of late because of their use in modulating the gastrointestinal tract (GIT) microbiome to both improve production parameters and prevent infection. This study aimed to evaluate the effects of various yeast-derived products on Salmonella enterica inoculation in un in vitro rooster cecal incubations and associated effects on the cecal microbiome. Cecal contents were obtained from 53-wk old White Leghorn H & N Nick Chick roosters (n = 3) fed a wheat-based, commercial-type basal diet. Cecal contents were diluted 1:3000 in anaerobic dilution solution (ADS) in an anaerobic chamber, with 20 mL aliquoted to each serum bottle. There were three controls (n = 3): basal diet only, diluted cecal contents only, and basal diet and diluted cecal contents; and five treatments containing the basal diet and diluted cecal contents (n = 3): Citristim® (ADM), ImmunoWall® (ICC), Maxi-Gen Plus® (CBS Bio Platforms), Hilyses® (ICC), and Original XPC® (Diamond V). All treatments were applied at a rate of 2.5 kg/tonne or less. All groups were inoculated with a nalidixic acid-resistant strain of Salmonella Enteritidis at 10^7 CFU/mL and incubated at 37 deg C. Samples were collected at 0, 24, and 48 h for S. Enteritidis enumeration and 16S rDNA microbial sequencing. Salmonella data were log-transformed and analyzed in a two-way ANOVA with means separated using Tukey's HSD (P≤0.05). Genomic DNA was extracted, and resulting libraries were prepared and sequenced using an Illumina MiSeq. Sequencing data were analyzed in QIIME2 (2021.4) with diversity metrics (alpha and beta), and an analysis of the composition of microbiomes (ANCOM) was performed. Main effects were considered significant at P≤0.05, with pairwise differences considered significant at Q≤0.05. There was an interaction of treatment and time on the enumeration of Salmonella where treatments of Citristim, Immunowall, Hilyses, and XPC reduced Salmonella by 1 log CFU/mL compared to the controls. At 48 h, each yeast product treatment reduced Salmonella by 3 log CFU/mL compared to the controls. There was no main effect of treatment on the alpha diversity metrics, richness, or evenness (P > 0.05). Treatment affected the beta diversity, abundance, and phylogenetic differences, but there were no pairwise differences (P>0.05, Q>0.05). Using ANCOM at the genus level, the taxa Synergistes, Alloprevotella, Sutterella, and Megasphaera abundance were significantly different (W = 154,147,145,140, respectively). These results demonstrate the potential of these yeast-derived products to reduce foodborne pathogens, such as Salmonella Enteriditis, in vitro, without negatively disrupting the cecal microbiome.

Association of intestinal bacteria with immune activation in a cohort of healthy adults

IMPORTANCE

Chronic inflammation may develop over time in healthy adults as a result of a variety of factors, such as poor diet directly affecting the composition of the intestinal microbiome, or by causing obesity, which may also affect the intestinal microbiome. These effects may trigger the activation of an immune response that could eventually lead to an inflammation-related disease, such as colon cancer. Before disease develops it may be possible to identify subclinical inflammation or immune activation attributable to specific intestinal bacteria normally found in the gut that could result in future adverse health impacts. In the present study, we examined a group of healthy men and women across a wide age range with and without obesity to determine which bacteria were associated with particular types of immune activation to identify potential preclinical markers of inflammatory disease risk. Several associations were found that may help develop dietary interventions to lower disease risk.

Impact of Gluten-free Diet on Anthropometric Indicators in Individuals With and Without Celiac Disease: A Systematic Review and Meta-analysis

PURPOSE

Previous studies have found that a gluten-free diet (GFD) may have improve obesity-related factors. For this reason, we conducted a systematic review and meta-analysis to investigate the effect of a GFD on anthropometric indicators.

METHODS

We performed a systematic search in databases from inception until July 12, 2022. We included all relevant articles that evaluate efficacy of a GFD on anthropometric indicators in patients with and without celiac disease (CD). Random-effects models were applied to combine the data. The main outcomes were then analyzed using weight mean differences (WMDs) and 95% CIs.

FINDINGS

A total of 27 articles met the eligible criteria and were included. Pooled results from the random-effects model indicated that the GFD has no significant effect on any of the factors of anthropometry, including weight (WMD, 1.20 kg; 95% CI, -1.16 to 3.55 kg; P = 0.319), body mass index (WMD, 0.70 kg/m2; 95% CI, -0.45 to 1.84 kg/m2; P = 0.233), waist circumference (WMD, 0.92 cm; 95% CI, -1.34 to 3.17 cm; P = 0.497), and body fat (WMD, 1.02%; 95% CI, -0.38% to 2.42%; P = 0.153). The subgroup results indicated that after implementation of a GFD significant increased weight and body fat occurred in patients with compared with without CD. In addition, the effect of this diet on the increase of BMI and body fat in the intervention of more than 48 weeks was significantly higher.

IMPLICATIONS

The results of the present study indicate that a GFD can have a significant and beneficial effect on weight and body fat in patients with CD.

Changes in the fecal gut microbiome of home healthcare patients with disabilities through consumption of malted rice amazake

The aim of the present study was to investigate changes in the gut microbiome both during and after consumption of malted rice amazake (MR-Amazake), a fermented food from Japan, in-home healthcare patients with disabilities, including patients with severe motor and intellectual disabilities. We monitored 12 patients who consumed MR-Amazake for 6 wk and investigated them before and after the intervention as well as 6 wk after the end of intake to compare their physical condition, diet, type of their medication, constipation assessment scale, and analysis of their comprehensive fecal microbiome using 16S rRNA sequencing. Their constipation symptoms were significantly alleviated, and principal coordinate analysis revealed that 30% of patients showed significant changes in the gut microbiome after MR-Amazake ingestion. Furthermore, Bifidobacterium was strongly associated with these changes. These changes were observed only during MR-Amazake intake; the original gut microbiome was restored when MR-Amazake intake was discontinued. These results suggest that 6 wk is a reasonable period of time for MR-Amazake to change the human gut microbiome and that continuous consumption of MR-Amazake is required to sustain such changes.NEW & NOTEWORTHY The consumption of malted rice amazake (MR-Amazake) showed significant changes in the gut microbiome according to principal coordinate analysis in some home healthcare patients with disabilities, including those with severe motor and intellectual disabilities. After discontinuation of intake, the gut microbiome returned to its original state. This is the first pilot study to examine both the changes in the gut microbiome and their sustainability after MR-Amazake intake.

Drug-microbiota interactions: an emerging priority for precision medicine

Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.

Is there a role for microbiome-based approach in common variable immunodeficiency?

Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by low levels of serum immunoglobulins and increased susceptibility to infections, autoimmune disorders and cancer. CVID embraces a plethora of heterogeneous manifestations linked to complex immune dysregulation. While CVID is thought to be due to genetic defects, the exact cause of this immune disorder is unknown in the large majority of cases. Compelling evidences support a linkage between the gut microbiome and the CVID pathogenesis, therefore a potential for microbiome-based treatments to be a therapeutic pathway for this disorder. Here we discuss the potential of treating CVID patients by developing a gut microbiome-based personalized approach, including diet, prebiotics, probiotics, postbiotics and fecal microbiota transplantation. We also highlight the need for a better understanding of microbiota-host interactions in CVID patients to prime the development of improved preventive strategies and specific therapeutic targets.

Celiac-the lone horse? An autoimmune condition without signals of microbiota dysbiosis

Accumulating evidence supports the role of microbiota in autoimmune processes, but research regarding the role of the gut microbiota in celiac disease (CD) is still emerging, and a consistent CD-associated dysbiosis pattern has not yet been defined. Here, we characterized the microbiota of children newly diagnosed with CD, with their unaffected family members as a healthy control group to reduce confounding factors including genetic background, hygiene, dietary habits, and environment, and followed children with CD over 1 year of dietary intervention (exclusion of gluten) to understand if the microbiota is associated with CD and its mediation. We did not find differences in the microbiota of siblings with and without CD, despite a wealth of evidence in the literature supporting CD-specific microbiota. CD is common among first-degree relatives, so this could suggest that unaffected family members in this study may be living in a pre-CD state, currently below clinical detection. Interestingly, despite the effectiveness of diet in CD control, we did not observe diet-mediated microbiota changes, except for short-term increase in Akkermansia muciniphila. This lack of effect could suggest a very strong CD microbial signature even when controlled or could be a technical shortcoming. Expanded future studies with both related and unrelated controls and diet interventions in both the CD and control arms can provide further context to our findings. IMPORTANCE The microbiota is the community of microbes that live in and on us. These microbes are essential to our health and everyday function. Disruption of the community is associated with diseases ranging from metabolic syndrome to autoimmune diseases to mental disorders. In the case of celiac disease (CD), research remains inconclusive regarding implications of the microbiota in etiology. Here, we compared microbiota of children with CD to those of their unaffected family members and found very few differences in microbiota profiles. We next examined how gluten elimination in CD patients affects the microbiota. Surprisingly, despite diet adherence, microbiota shifts were minimal, with only a short-term increase in Akkermansia muciniphila. Previous studies suggest that family members of CD patients may be living in a pre-CD state, which could explain their microbial similarity. A larger study with unrelated controls and increased microbiota monitoring during diet intervention should give our findings more perspective.

Effect of gluten-free diet on autoimmune thyroiditis progression in patients with no symptoms or histology of celiac disease: a meta-analysis

Background

Hashimoto's thyroiditis (HT) is the most common autoimmune disease. HT may be associated with nonthyroidal autoimmune diseases, including celiac disease (CD) or other gluten-related conditions (GRC). In the last years, interest about gluten-free diet (GFD) has increased for its supposed extraintestinal anti-inflammatory effect; thus, many patients with HT initiate GFD on their own.

Objectives

The aim of this meta-analysis is to examine all available data in literature about the effect of a GFD on TgAb, TPOAb, TSH, FT4, and FT3 levels in patients with HT and no symptoms or histology of CD.

Methods

The study was conducted according to MOOSE (Meta-analysis Of Observational Studies in Epidemiology). The search was performed on databases PubMed and Scopus. The last search was performed on 7 February 2023. Quality assessment was performed. Meta-analyses were performed using the random-effect model. Hedges' g was used to measure the effect size (ES). Statistical analyses were performed using StataSE 17.

Results

The online search retrieved 409 articles, and 4 studies with a total of 87 patients were finally included for quantitative analysis. The risk of bias was generally low. The mean period of GFD was almost 6 months. The meta-analyses showed reduction in antibody levels with ES: -0.39 for TgAb (95% CI: -0.81 to +0.02; p = 0.06; I² = 46.98%) and -0.40 for TPOAb (95% CI: -0.82 to +0.03; p = 0.07; I² = 47.58%). TSH showed a reduction with ES: -0.35 (95% CI: -0.64 to -0.05; p = 0.02; I² = 0%) and FT4 showed an increase with ES: +0.35% (95% CI: 0.06 to 0.64; p = 0.02; I² = 0%). FT3 did not display variations (ES: 0.05; 95% CI: -0.38 to +0.48; p = 0.82; I² = 51%). The heterogeneity of TgAb, TPOAb, and FT3 data was solved performing sub-analyses between patients with or without GRC (TgAb p = 0.02; TPOAb p = 0.02; FT3 p = 0.04) and only for FT3, performing a sub-analysis between patients taking and not taking LT4 (p = 0.03).

Conclusion

This is the first meta-analysis investigating the effect of GFD on HT. Our results seem to indicate a positive effect of the gluten deprivation on thyroid function and its inflammation, particularly in patients with HT and GRC. However, current lines of evidence are not yet sufficient to recommend this dietary approach to all patients with a diagnosis of HT.

The Relationship between the Source of Dietary Animal Fats and Proteins and the Gut Microbiota Condition and Obesity in Humans

The relationship between gut microbiota and obesity is well documented in humans and animal models. Dietary factors can change the intestinal microbiota composition and influence obesity development. However, knowledge of how diet, metabolism, and intestinal microbiota interact and modulate energy metabolism and obesity development is still limited. Epidemiological studies show a link between consuming dietary proteins and fats from specific sources and obesity. Animal studies confirm that proteins and fats of different origins differ in their ability to prevent or induce obesity. Protein sources, such as meat, dairy products, vegetables, pulses, and seafood, vary in their amino acid composition. In addition, the type and level of other factors, such as fatty acids or persistent organic pollutants, vary depending on the source of dietary protein. All these factors can modulate the intestinal microbiota composition and, thus, may influence obesity development. This review summarizes selected evidence of how proteins and fats of different origins affect energy efficiency, obesity development, and intestinal microbiota, linking protein and fat-dependent changes in the intestinal microbiota with obesity.

Effects of FODMAPs and Gluten on Gut Microbiota and Their Association with the Metabolome in Irritable Bowel Syndrome: A Double-Blind, Randomized, Cross-Over Intervention Study

BACKGROUND

A mechanistic understanding of the effects of dietary treatment in irritable bowel syndrome (IBS) is lacking. Our aim was therefore to investigate how fermentable oligo- di-, monosaccharides, and polyols (FODMAPs) and gluten affected gut microbiota and circulating metabolite profiles, as well as to investigate potential links between gut microbiota, metabolites, and IBS symptoms.

METHODS

We used data from a double-blind, randomized, crossover study with week-long provocations of FODMAPs, gluten, and placebo in participants with IBS. To study the effects of the provocations on fecal microbiota, fecal and plasma short-chain fatty acids, the untargeted plasma metabolome, and IBS symptoms, we used Random Forest, linear mixed model and Spearman correlation analysis.

RESULTS

FODMAPs increased fecal saccharolytic bacteria, plasma phenolic-derived metabolites, 3-indolepropionate, and decreased isobutyrate and bile acids. Gluten decreased fecal isovalerate and altered carnitine derivatives, CoA, and fatty acids in plasma. For FODMAPs, modest correlations were observed between microbiota and phenolic-derived metabolites and 3-indolepropionate, previously associated with improved metabolic health, and reduced inflammation. Correlations between molecular data and IBS symptoms were weak.

CONCLUSIONS

FODMAPs, but not gluten, altered microbiota composition and correlated with phenolic-derived metabolites and 3-indolepropionate, with only weak associations with IBS symptoms. Thus, the minor effect of FODMAPs on IBS symptoms must be weighed against the effect on microbiota and metabolites related to positive health factors.

Two-Sample Mendelian Randomization detects bidirectional causality between gut microbiota and celiac disease in individuals with high genetic risk

Background

Celiac Disease (CeD) is an autoimmune disorder triggered by gluten intake in genetically susceptible individuals. Highest risk individuals are homozygous for the Human Leucocyte Antigen (HLA) DQ2.5 haplotype or DQ2.5/DQ2.2 heterozygous. Both the HLA-DQ2-positive high genetic risk individuals and those that have developed the disease have altered intestinal microbiota, but it remains unclear whether these alterations are a cause or a consequence of CeD.

Objective

To investigate a potential bidirectional causality between gut microbiota (GM) and CeD in HLA-DQ2 high genetic risk individuals.

Materials and Methods

We performed a bidirectional Two-Sample Mendelian Randomization (2SMR) test using summary statistics from the largest publicly available Genome-Wide Association Study (GWAS) of GM and the summary statistics of the Immunochip CeD study of those individuals with the HLA-DQ2 high-risk haplotype. To test whether changes in GM composition were causally linked to CeD, GM data were used as exposure and CeD data as outcome; to test for reverse causation, the exposure and outcome datasets were inverted.

Results

We identified several bacteria from Ruminococcaceae and Lachnospiraceae families of the Firmicutes phylum as potentially causal in both directions. In addition, our results suggest that changes in the abundance of Veillonellaceae family might be causal in the development of CeD, while alterations in Pasteurellaceae family might be a consequence of the disease itself.

Conclusion

Our results suggest that the relationship between GM and HLA-DQ2 high risk individuals is highly complex and bidirectional.

Diets, Gut Microbiota and Metabolites

The gut microbiota refers to the gross collection of microorganisms, estimated trillions of them, which reside within the gut and play crucial roles in the absorption and digestion of dietary nutrients. In the past decades, the new generation 'omics' (metagenomics, transcriptomics, proteomics, and metabolomics) technologies made it possible to precisely identify microbiota and metabolites and describe their variability between individuals, populations and even different time points within the same subjects. With massive efforts made, it is now generally accepted that the gut microbiota is a dynamically changing population, whose composition is influenced by the hosts' health conditions and lifestyles. Diet is one of the major contributors to shaping the gut microbiota. The components in the diets vary in different countries, religions, and populations. Some special diets have been adopted by people for hundreds of years aiming for better health, while the underlying mechanisms remain largely unknown. Recent studies based on volunteers or diet-treated animals demonstrated that diets can greatly and rapidly change the gut microbiota. The unique pattern of the nutrients from the diets and their metabolites produced by the gut microbiota has been linked with the occurrence of diseases, including obesity, diabetes, nonalcoholic fatty liver disease, cardiovascular disease, neural diseases, and more. This review will summarize the recent progress and current understanding of the effects of different dietary patterns on the composition of gut microbiota, bacterial metabolites, and their effects on the host's metabolism.

Mechanistic Insights into Immune-Microbiota Interactions and Preventive Role of Probiotics Against Autoimmune Diabetes Mellitus

Recent studies on genetically susceptible individuals and animal models revealed the potential role of the intestinal microbiota in the pathogenesis of type 1 diabetes (T1D) through complex interactions with the immune system. T1D incidence has been increasing exponentially with modern lifestyle altering normal microbiota composition, causing dysbiosis characterized by an imbalance in the gut microbial community. Dysbiosis has been suggested to be a potential contributing factor in T1D. Moreover, several studies have shown the potential role of probiotics in regulating T1D through various mechanisms. Current T1D therapies target curative measures; however, preventive therapeutics are yet to be proven. This review highlights immune microbiota interaction and the immense role of probiotics and postbiotics as important immunological interventions for reducing the risk of T1D.

Analysis of Circulating Food Antigen-Specific T-Cells in Celiac Disease and Inflammatory Bowel Disease

To demonstrate and analyze the specific T-cell response following barrier disruption and antigen translocation, circulating food antigen-specific effector T-cells isolated from peripheral blood were analyzed in patients suffering from celiac disease (CeD) as well as inflammatory bowel disease (IBD). We applied the antigen-reactive T-cell enrichment (ARTE) technique allowing for phenotypical and functional flow cytometric analyses of rare nutritional antigen-specific T-cells, including the celiac disease-causing gliadin (gluten). For CeD, patient groups, including treatment-refractory cases, differ significantly from healthy controls. Even symptom-free patients on a gluten-free diet were distinguishable from healthy controls, without being previously challenged with gluten. Moreover, frequency and phenotype of nutritional antigen-specific T-cells of IBD patients directly correlated to the presence of small intestinal inflammation. Specifically, the frequency of antigen specific T-cells as well as pro-inflammatory cytokines was increased in patients with active CeD or Crohn's disease, respectively. These results suggest active small intestinal inflammation as key for the development of a peripheral food antigen-specific T-cell response in Crohn's disease and celiac disease.

Current evidence for dietary therapies in irritable bowel syndrome

PURPOSE OF REVIEW

Diet appears to trigger symptoms in the majority of individuals with irritable bowel syndrome (IBS) and is associated with a reduced quality of life. There has been a recent focus on the role of dietary therapies to manage individuals with IBS. The aim of this review is to discuss the utility of traditional dietary advice (TDA), low-FODMAP diet (LFD) and gluten-free diet (GFD) in IBS.

RECENT FINDINGS

Several recent randomized controlled trials (RCTs) have been published demonstrating the efficacy of the LFD and GFD in IBS, with the evidence base for TDA being predominantly based on clinical experience, with emerging RCTs evaluating TDA. Only one RCT has been published to date comparing TDA, LFD and GFD head to head, with no difference noted between diets in terms of efficacy. However, TDA has been noted to be more patient-friendly and is commonly implemented as a first-line dietary therapy.

SUMMARY

Dietary therapies have been demonstrated to improve symptoms in patients with IBS. In view of insufficient evidence to recommend one diet over another currently, specialist dietetic input in conjunction with patient preference is required to determine implementation of dietary therapies. Novel methods of dietetic delivery are required in view of the lack of dietetic provision to deliver these therapies.

Comedications with Immune Checkpoint Inhibitors: Involvement of the Microbiota, Impact on Efficacy and Practical Implications

Immune checkpoint inhibitors (ICIs) have been a major breakthrough in solid oncology over the past decade. The immune system and the gut microbiota are involved in their complex mechanisms of action. However, drug interactions have been suspected of disrupting the fine equilibrium necessary for optimal ICI efficacy. Thus, clinicians are facing a great deal of sometimes contradictory information on comedications with ICIs and must at times oppose conflicting objectives between oncological response and comorbidities or complications. We compiled in this review published data on the role of the microbiota in ICI efficacy and the impact of comedications. We found mostly concordant results on detrimental action of concurrent corticosteroids, antibiotics, and proton pump inhibitors. The timeframe seems to be an important variable each time to preserve an initial immune priming at ICIs initiation. Other molecules have been associated with improved or impaired ICIs outcomes in pre-clinical models with discordant conclusions in retrospective clinical studies. We gathered the results of the main studies concerning metformin, aspirin, and non-steroidal anti-inflammatory drugs, beta blockers, renin-angiotensin-aldosterone system inhibitors, opioids, and statins. In conclusion, one should always assess the necessity of concomitant treatment according to evidence-based recommendations and discuss the possibility of postponing ICI initiation or switching strategies to preserve the critical window.

How Do Diet Patterns, Single Foods, Prebiotics and Probiotics Impact Gut Microbiota?

The human gastrointestinal tract hosts a complex and dynamic population of commensal bacterial species, which have coevolved with the host, generating a symbiotic relationship. Some compounds present in foods, such as polyols, prebiotic fibers, or phenolic compounds, are poorly metabolized and absorbed by the host before the transformation guided by the colonic microbiota. By influencing gut microbiota, diet plays a fundamental role in understanding the beneficial effects of the gut microbiota on the host, including its long-term metabolism. The idea that probiotics can act not only by influencing the colonizing microbiota opens the door to a wider range of probiotic possibilities, encouraging innovation in the field. Furthermore, it has been shown both that some probiotics increase phagocytosis or the activity of natural killer cells. Current prebiotics are mainly based on carbohydrates, but other substances, such as polyphenols and polyunsaturated fatty acids, could exert prebiotic effects. A prebiotic substance has been defined as ‘a substrate that is selectively used by host microorganisms that confer a health benefit’, and so can interact with the gut microbiota through competition for nutrients, antagonism, cross-feeding, and support for microbiota stability. Influencing its composition in terms of richness and diversity, food components have a key impact on the intestinal microbiota. Eating habits can strongly influence the composition of the intestinal microbiota. A healthy intestinal microbiota is essential for maintaining general health, and diet is one of the major modulators of this fascinating world of microorganisms. This must give us one more reason to adopt a healthy lifestyle.

Interactions Between Antidepressants and Intestinal Microbiota

The microbiota-gut-brain axis has been shown to influence human health and diseases, including depression. The interactions between drugs and intestinal microbiota are complex and highly relevant to treat diseases. Studies have shown an interaction between antidepressants and intestinal microbiota. Antidepressants may alter the abundance and composition of intestinal microbiota, which are closely related to the treatment outcomes of depression. Intestinal microbiota can influence the metabolism of antidepressants to change their availability (e.g., tryptophan can be metabolized to kynurenine by intestinal microbiota) and regulate their absorption by affecting intestinal permeability. In addition, the permeability of the blood-brain barrier can be altered by intestinal microbiota, influencing antidepressants to reach the central nervous system. Bioaccumulation is also a type of drug-microbiota interaction, which means bacteria accumulate drugs without biotransformation. These findings imply that it is important to consider intestinal microbiota when evaluating antidepressant therapy regimens and that intestinal microbiota can be a potential target for depression treatment.

In Vitro Digestion and Fecal Fermentation of Low-Gluten Rice and Its Effect on the Gut Microbiota

Low-gluten rice is part of a special diet for chronic kidney disease patients, but its digestive mechanism in the gastrointestinal tract is unclear. In this study, low-gluten rice (LGR), common rice (CR), and rice starch (RS) were used as experimental samples, and their digestion and bacterial fermentation were simulated using an in vitro gastrointestinal reactor to investigate the mechanism of the effect of LGR on human health. The starch digestibility of CR was higher than that of LGR, with statistically significant differences. LGR has growth-promoting and metabolic effects on Akkermansia muciniphila. Among the beneficial metabolites, the concentration of short-chain fatty acids (SCFAs) from LGR reached 104.85 mmol/L, an increase of 44.94% (versus RS) and 25.33% (versus CR). Moreover, the concentration of lactic acid reached 18.19 mmol/L, an increase of 60.55% (versus RS) and 25.28% (versus CR). Among the harmful metabolites, the concentration of branched-chain fatty acids (BCFAs) in LGR was 0.29 mmol/L and the concentration of ammonia was 2.60 mmol/L, which was 79.31% and 16.15% lower than CR, respectively. A significant increase in the concentration of the beneficial intestinal bacteria Bacteroides and Bifidobacterium occurred from LGR. The 16s rDNA sequencing showed that the abundance of the Bacteroidetes and Firmicutes increased and the abundance of the Proteobacteria and Fusobacteria decreased. Thus, LGR has positive effects on digestion and gut microbiota structure and metabolism in humans.

The role of diet in shaping human gut microbiota

Gut microbiota plays a fundamental role within human health, and exerts key functions within the human body. Diet is one of the most powerful modulators of gut microbiota functions and composition. This complex interplay involves also the immune system and the intestinal barrier, highlighting the central role of diet in the pathogenesis and treatment of multiple diseases. In this review article we will paint the landscape of the effects of specific dietary nutrients, and of the detrimental or beneficial outcomes of different dietary patterns, on the composition of human gut microbiota. Moreover, we will discuss the potential application of diet as a therapeutic modulator of gut microbiota, including cutting-edge ways of exploitation, including the use of dietary components as adjuvants to promote microbial engraftment after fecal microbiota transplantation, or personalized nutritional approaches, targeted to the patient microbiome.

The gut microbiome in Alzheimer's disease: what we know and what remains to be explored

Alzheimer's disease (AD), the most common cause of dementia, results in a sustained decline in cognition. There are currently few effective disease modifying therapies for AD, but insights into the mechanisms that mediate the onset and progression of disease may lead to new, effective therapeutic strategies. Amyloid beta oligomers and plaques, tau aggregates, and neuroinflammation play a critical role in neurodegeneration and impact clinical AD progression. The upstream modulators of these pathological features have not been fully clarified, but recent evidence indicates that the gut microbiome (GMB) may have an influence on these features and therefore may influence AD progression in human patients. In this review, we summarize studies that have identified alterations in the GMB that correlate with pathophysiology in AD patients and AD mouse models. Additionally, we discuss findings with GMB manipulations in AD models and potential GMB-targeted therapeutics for AD. Lastly, we discuss diet, sleep, and exercise as potential modifiers of the relationship between the GMB and AD and conclude with future directions and recommendations for further studies of this topic.

Changes in the gut bacteriome upon gluten-free diet intervention do not mediate beta cell preservation

AIMS/HYPOTHESIS

We previously detected indications that beta cell function is protected by gluten-free diet (GFD) introduced shortly after the onset of childhood type 1 diabetes. The present aim was to assess whether GFD was associated with changes in the gut bacteriome composition and in its functional capacity, and whether such changes mediated the observed effects of GFD on beta cell function.

METHODS

Forty-five children (aged 10.2 ± 3.3 years) were recruited into a self-selected intervention trial primarily focused on determining the role of GFD on beta cell preservation ( ClinicalTrials.gov NCT02867436). Stool samples were collected prior to the dietary intervention and then at 3-month intervals. A total of 128 samples from the GFD group and 112 from the control group were analysed for bacteriome 16S rDNA community profiles, the bacteriome functional capacity was predicted using PICRUSt2 and actual gut metabolome profiles measured using NMR. Intestinal permeability was assessed using serum zonulin concentrations at 1, 6 and 12 months and lactulose/mannitol tests at the end of intervention. Dietary questionnaires were used to ensure that the dietary intervention did not result in differences in energy or nutrient intake.

RESULTS

The bacteriome community composition changed during the intervention with GFD: of abundant genera, a 3.3-fold decrease was noted for Bifidobacterium genus (adjusted p=1.4 × 10^-4 in a DESeq2 model, p=0.026 in generalised estimating equations model), whereas a 2.4-fold increase was observed in Roseburia (adjusted p=0.02 in DESeq2 model, p=0.002 in generalised estimating equations model). The within-sample (alpha) diversity did not change, and there was no statistically significant clustering of GFD samples in the ordination graphs of beta diversity. Neither of the genera changes upon GFD intervention showed any association with the pace of beta cell loss (p>0.50), but of the remaining taxa, several genera of Bacteroidaceae family yielded suggestive signals. The faecal metabolome profile ordination correlated with that of bacteriomes but did not associate with GFD or categories of beta cell preservation. There was no indication of changes in gut permeability.

CONCLUSIONS/INTERPRETATION

The bacteriome reacted to GFD, but the changes were unrelated to the pace of beta cell capacity loss. The previously observed moderately protective effect of GFD is therefore mediated through other pathways.

The effects of esketamine on the intestinal microenvironment and intestinal microbiota in mice

OBJECTIVE

This study aimed to investigate the impact of esketamine on the intestinal flora and microenvironment in mice using mRNA transcriptome sequencing and 16S rRNA sequencing.

METHODS

Ten female mice were randomly assigned to two groups. One group received daily intramuscular injections of sterile water, while the other group received esketamine. After 24 days, the mice were sacrificed, and their intestinal tissues and contents were collected for 16S rRNA sequencing and mRNA transcriptome sequencing. The intergroup differences in the mouse intestinal flora were analyzed. Differentially expressed genes were utilized to construct ceRNA networks and transcription factor regulatory networks to assess the effects of esketamine on the intestinal flora and intestinal tissue genes.

RESULTS

Esketamine significantly altered the abundance of intestinal microbiota, including Adlercreutzia equolifaciens and Akkermansia muciniphila. Differential expression analysis revealed 301 significantly upregulated genes and 106 significantly downregulated genes. The ceRNA regulatory network consisted of 6 lncRNAs, 44 miRNAs, and 113 mRNAs, while the regulatory factor network included 13 transcription factors and 53 target genes. Gene Ontology enrichment analysis indicated that the differentially expressed genes were primarily associated with immunity, including B-cell activation and humoral immune response mediation. The biological processes in the ceRNA regulatory network primarily involved transport, such as organic anion transport and monocarboxylic acid transport. The functional annotation of target genes in the TF network was mainly related to epithelial cells, including epithelial cell proliferation and regulation.

CONCLUSION

Esketamine induces changes in gut microbiota and the intestinal microenvironment, impacting the immune environment and transport modes.

Dynamics impacts of oxytetracycline on growth performance, intestinal health and antibiotic residue of grouper in exposure and withdrawal treatment

Little is known about the effects of oxytetracycline (OTC) on marine fish. Using juvenile pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), we investigated the effects of 56 days dietary oxytetracycline (OTC; OTCD) exposure (80 mg/kg body weight/day) on fish growth performance, intestinal health and antibiotic residue. Meanwhile, the alteration of intestinal health status and antibiotic residue after 7 (O7) or 14 days (O14) OTC withdrawal treatment were explored. We also assessed the potential human health risks based on target hazard quotient (THQ). The results showed that OTC exposure had no effects on growth rate parameters but caused liver and intestine atrophy. OTC exposure impaired the intestinal health by distorting intestinal morphological features, inducing oxidative stress, repressing immune function, triggering NF-κB-mediated inflammatory response and apoptosis, while 7 days OTC withdrawal treatment improved intestinal health status and 14 days OTC withdrawal treatment further improved it. In addition, the order of OTC residue in tested tissues after OTC exposure was: liver > kidney > spleen > muscle > intestine. OTC residue was significantly decreased in all tissues along with the increasing of withdrawal treatment period. Adults and children consuming the edible tissues (muscle) of OTC-treated or withdrawal-treated pearl gentian grouper would not experience any previous health risk as the THQ < 1 in all group.

Artificial intelligence-driven prediction of multiple drug interactions

When a drug is administered to exert its efficacy, it will encounter multiple barriers and go through multiple interactions. Predicting the drug-related multiple interactions is critical for drug development and safety monitoring because it provides foundations for practical, safe compatibility and rational use of multiple drugs. With the progress of artificial intelligence (AI) technology, a variety of novel prediction methods for single interaction have emerged and shown great advantages compared to the traditional, expensive and time-consuming laboratory research. To promote the comprehensive and simultaneous predictions of multiple interactions, we systematically reviewed the application of AI in drug-drug, drug-food (excipients) and drug-microbiome interactions. We began by outlining the model methods, evaluation indicators, algorithms and databases commonly used to build models for three types of drug interactions. The models based on the metabolic enzyme P450, drug similarity and drug targets have empathized among the machine learning models of drug-drug interactions. In particular, we discussed the limitations of current approaches and identified potential areas for future research. It is anticipated the in-depth review will be helpful for the development of the next-generation of systematic prediction models for simultaneous multiple interactions.

A comprehensive map of microbial biomarkers along the gastrointestinal tract for celiac disease patients

Dysbiosis of the microbiome has been related to Celiac disease (CeD) progress, an autoimmune disease characterized by gluten intolerance developed in genetically susceptible individuals under certain environmental factors. The microbiome contributes to CeD pathophysiology, modulating the immune response by the action of short-chain fatty acids (SCFA), affecting gut barrier integrity allowing the entrance of gluten-derived proteins, and degrading immunogenic peptides of gluten through endoprolyl peptidase enzymes. Despite the evidence suggesting the implication of gut microbiome over CeD pathogenesis, there is no consensus about the specific microbial changes observed in this pathology. Here, we compiled the largest dataset of 16S prokaryotic ribosomal RNA gene high-throughput sequencing for consensus profiling. We present for the first time an integrative analysis of metataxonomic data from patients with CeD, including samples from different body sites (saliva, pharynx, duodenum, and stool). We found the presence of coordinated changes through the gastrointestinal tract (GIT) characterized by an increase in Actinobacteria species in the upper GIT (pharynx and duodenum) and an increase in Proteobacteria in the lower GIT (duodenum and stool), as well as site-specific changes evidencing a dysbiosis in patients with CeD' microbiota. Moreover, we described the effect of adherence to a gluten-free diet (GFD) evidenced by an increase in beneficial bacteria and a decrease in some Betaproteobacteriales but not fully restoring CeD-related dysbiosis. Finally, we built a Random Forest model to classify patients based on the lower GIT composition achieving good performance.

The gut microbiota and celiac disease: Pathophysiology, current perspective and new therapeutic approaches

Celiac disease (CD) as a chronic gluten-sensitive intestinal condition, mainly affects genetically susceptible hosts. The primary determinants of CD have been identified as environmental and genetic variables. The development of CD is significantly influenced by environmental factors, including the gut microbiome. Therefore, gut microbiome re-programming-based therapies using probiotics, prebiotics, postbiotics, gluten-free diet, and fecal microbiota transplantation have shown promising results in the modification of the gut microbiome. Due to the importance and paucity of information regarding the CD pathophysiology, in this review, we have covered the association between CD development and gut microbiota, the effects of infectious agents, particularly the recent Covid-19 infection in CD patients, and the efficacy of potential therapeutic approaches in the CD have been discussed. Hence, scientific literature indicates that the diverse biological functions of the gut microbiota against immunomodulatory responses have made microbiome-based therapy an alternative therapeutic paradigm to ameliorate the symptoms of CD and quality of life. However, the exact potential of microbiota-based techniques that aims to quantitatively and qualitatively alter the gut microbiota to be used in the treatment and ameliorate the symptoms of CD will be determined with further research in the future.

Diet and irritable bowel syndrome: an update from a UK consensus meeting

There has been a renewed interest in the role of dietary therapies to manage irritable bowel syndrome (IBS), with diet high on the agenda for patients. Currently, interest has focussed on the use of traditional dietary advice (TDA), a gluten-free diet (GFD) and the low FODMAP diet (LFD). A consensus meeting was held to assess the role of these dietary therapies in IBS, in Sheffield, United Kingdom.Evidence for TDA is from case control studies and clinical experience. Randomised controlled trials (RCT) have demonstrated the benefit of soluble fibre in IBS. No studies have assessed TDA in comparison to a habitual or sham diet. There have been a number of RCTs demonstrating the efficacy of a GFD at short-term follow-up, with a lack of long-term outcomes. Whilst gluten may lead to symptom generation in IBS, other components of wheat may also play an important role, with recent interest in the role of fructans, wheat germ agglutinins, as well as alpha amylase trypsin inhibitors. There is good evidence for the use of a LFD at short-term follow-up, with emerging evidence demonstrating its efficacy at long-term follow-up. There is overlap between the LFD and GFD with IBS patients self-initiating gluten or wheat reduction as part of their LFD. Currently, there is a lack of evidence to suggest superiority of one diet over another, although TDA is more acceptable to patients.In view of this evidence, our consensus group recommends that dietary therapies for IBS should be offered by dietitians who first assess dietary triggers and then tailor the intervention according to patient choice. Given the lack of dietetic services, novel approaches such as employing group clinics and online webinars may maximise capacity and accessibility for patients. Further research is also required to assess the comparative efficacy of dietary therapies to other management strategies available to manage IBS.

Reshaping the Gut Microbiota Through Lifestyle Interventions in Women with PCOS: A Review

Polycystic ovary syndrome (PCOS) is an endocrine disorder evolving as a global threat to women's health. However, its multifactorial etiology causes difficulty in eliminating it. The interrelation between the gut microbiota and metabolic disorders has been trending recently, giving rise to new opportunities on the etiology and pathogenesis of PCOS. Lifestyle interventions such as healthy diet, physical exercises, and behavioral interventions such as regulation of stress and sleep cycles have been identified to improve the symptoms of PCOS across the endocrinological, metabolic and psychological scales and are recommended as the first line of treatment for PCOS. The impact of the unhealthy lifestyle factors on intestinal dysbiosis that cause PCOS is summarized in this review. This review also provides an insight on the therapeutic approaches that primarily target the gut microbiota and offers novel gut microflora-associated treatment strategies for PCOS. Further, this survey also highlights the need for the implementation of lifestyle management strategies and strongly recommends a healthy and stress-free lifestyle to promote gut health and manage PCOS.

Developing and Piloting a Novel Ranking System to Assess Popular Dietary Patterns and Healthy Eating Principles

A multitude of weight loss diets exist. However, no one diet has been proven to be superior, despite their claims. Resultingly, this creates confusion amongst consumers and conflicting nutrition messages. The aim of the ranking system was to evaluate a range of dietary pattern’s nutrition profile and financial costs, as well as their potential long-term sustainability and associated adverse effects. Nutrition profile is typically the focal point of weight loss diets with less attention focused towards other factors that may affect their suitability. Five popular diets (Keto, Paleo, Intermittent Fasting, Optifast, and 8 Weeks to Wow) and two energy restricted healthy eating principles (Australian Guide to Healthy Eating and the Mediterranean Diet) were compared for diet quality, cost, adverse effects, and support for behaviour change. In general, healthy eating principles scored more favourably compared to popular weight loss diets in all categories. Lower carbohydrate diets tended to score lower for diet quality due to restricting multiple food groups, had more associated adverse effects and did not encourage behaviour change compared to the other weight loss diets. Optifast was the only weight loss diet to receive a negative score for cost. There should be considerations when undertaking a change to dietary patterns beyond nutrition profile. Diets indeed vary in terms of diet quality, and in addition can be costly, incur adverse effects, and disregard behaviour change which is important for sustainable weight loss and maintenance. This ranking system could create a reference point for future comparisons of diets.

Influence of Gut Microbiota and Trimethylamine N-Oxide in Patients with Coronary Heart Disease

In the current study, the gut microbiota of patients with and without coronary heart disease was compared and the relationship between gut microbiota distribution, intending to reveal the role of gut microbiota in the coronary atherosclerosis process, was investigated.This study included 50 patients diagnosed with coronary heart disease (CHD) who received conventional coronary angiography or computed tomography angiography and 50 patients with CHD at Changshu No. 2 People's Hospital, Suzhou, China, from May 2020 to January 2021. Trimethylamine N-oxide (TMAO) level was tested and feces were collected, the DNA of the gut microbiota was extracted, and the distribution by 16SrRNA gene sequencing was obtained from the two groups of patients.Plasma TMAO concentrations were significantly higher in patients with CHD (P < 0.001). In the CHD group, 22 patients with multivessel disease had a higher level of TMAO compared with the 28 patients who had the single-vessel disease (P < 0.001). No difference in the gut microbiota diversity was noted between the two groups (P < 0.001). Patients with CHD had a significantly lower proportion of Bacteroidetes phyla and more proportion of Epsilonbacteraeota phyla. At the genus level, patients with CHD had an increased abundance of Enterococcus, whereas healthy controls had significantly higher levels of Streptococcus. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 analysis found that, in the KEGG ORTHOLOGY, the level of choline trimethylamine-lyase gene expression correlated with TMAO production was higher in the fecal microbiome of the CHD group (P < 0.05).Gut microbiota and its product were expected to become a diagnostic marker and a new target for preventing CHD.

How Metabolomics Provides Novel Insights on Celiac Disease and Gluten-Free Diet: A Narrative Review

Celiac disease (CD) is an inflammatory autoimmune disorder triggered by the ingestion of gluten from wheat and other cereals. Nowadays, its positive diagnosis is based on invasive approaches such as the histological examination of intestinal biopsies and positive serology screening of antibodies. After proven diagnosis, the only admissible treatment for CD individuals is strict life-long adherence to gluten-free diet (GFD), although it is not a conclusive therapy. Acting by different mechanisms and with different etiologies, both CD and GFD have a great impact on gut microbiota that result in a different taxa composition. Altered production of specific metabolites reflects these microbiota changes. In this light, the currently available literature reports some suggestions about the possible use of specific metabolites, detected by meta-omics analyses, as potential biomarkers for a CD non-invasive diagnosis. To highlight insights about metabolomics application in CD study, we conducted a narrative dissertation of selected original articles published in the last decade. By applying a systematic search, it clearly emerged how the metabolomic signature appears to be contradictory, as well as poorly investigated.

How Diet and Physical Activity Modulate Gut Microbiota: Evidence, and Perspectives

Gut microbiota plays a significant role in the maintenance of physiological homeostasis, contributing to human health. Nevertheless, some factors (sex, age, lifestyle, physical activity, drug-based therapies, diet, etc.) affect its composition and functionality, linked to pathologies and immunological diseases. Concerning diet, it interacts with microorganisms, leading to beneficial or detrimental outcomes for the health of host. On the other hand, physical activity is known to be useful for preventing and, sometimes, treating several diseases of cardiovascular, neuroendocrine, respiratory, and muscular systems. This paper focuses on diet and physical activity presenting the current knowledge about how different diets (Western, ketogenic, vegan, gluten free, Mediterranean) as well as different types of exercise (intensive, endurance, aerobic) could shape gut microbiota.

Consumption of Tritordeum Bread Reduces Immunogenic Gluten Intake without Altering the Gut Microbiota

Gluten proteins are responsible for the wheat breadmaking quality. However, gluten is also related to human pathologies for which the only treatment is a gluten-free diet (GFD). GFD has gained popularity among individuals who want to reduce their gluten intake. Tritordeum is a cereal species that originated after crossing durum wheat with wild barley and differs from bread wheat in its gluten composition. In this work, we have characterized the immunogenic epitopes of tritordeum bread and results from a four-phase study with healthy adults for preferences of bread and alterations in the gut microbiota after consuming wheat bread, gluten-free bread, and tritordeum bread are reported. Tritordeum presented fewer peptides related to gluten proteins, CD-epitopes, and IgE binding sites than bread wheat. Participants rated tritordeum bread higher than gluten-free bread. Gut microbiota analysis revealed that the adherence to a strict GFD involves some minor changes, especially altering the species producing short-chain fatty acids. However, the short-term consumption of tritordeum bread does not induce significant changes in the diversity or community composition of the intestinal microbiota in healthy individuals. Therefore, tritordeum bread could be an alternative for healthy individuals without wheat-related pathologies who want to reduce their gluten consumption without harming their gut health.

What about TSH and Anti-Thyroid Antibodies in Patients with Autoimmune Thyroiditis and Celiac Disease Using a Gluten-Free Diet? A Systematic Review

The prevalence of celiac disease (CD) in patients with chronic autoimmune thyroiditis (CAIT) is estimated to be between 2 and 7.8%. A gluten-free diet (GFD) in patients with CD is suggested to have a beneficial effect on CAIT. Thus, the present systematic review was undertaken to achieve more robust evidence about the change in thyroid stimulating hormone (TSH) and thyroid-specific antibodies (T-Ab) levels obtained in CD patients following a GFD. A specific search strategy was planned. The last search was performed on March 2022. The following data were mainly searched for in order to be extracted: sample size, mean and/or median with standard deviation (SD), and error (SE), individually, of thyroid hormones and T-Ab at baseline and after GFD, and the duration of the study. The initial search retrieved 297 records and 6 articles met the inclusion criteria. In total, 50 patients with both CD and CAIT and 45 controls were reported. The effects of a GFD on the thyroid hormonal and immunological profile could be extracted only in a part of the studies. Two studies were case reports. A low risk of bias was observed. These findings advise further studies, ideally randomized, in order to better investigate the potential relationship between GFD and thyroid homeostasis. The level of evidence is not still sufficient to recommend GFD to patients with CAIT.

Dietary Patterns and Gut Microbiota: The Crucial Actors in Inflammatory Bowel Disease

It is widely believed that diet and the gut microbiota are strongly related to the occurrence and progression of inflammatory bowel disease (IBD), but the effects of the interaction between dietary patterns and the gut microbiota on IBD have not been well elucidated. In this article, we aim to explore the complex relation between dietary patterns, gut microbiota, and IBD. We first comprehensively summarized the dietary patterns associated with IBD and found that dietary patterns can modulate the occurrence and progression of IBD through various signaling pathways, including mammalian target of rapamycin (mTOR), mitogen-activated protein kinases (MAPKs), signal transducer and activator of transcription 3 (STAT3), and NF-κB. Besides, the gut microbiota performs a vital role in the progression of IBD, which can affect the expression of IBD susceptibility genes, such as dual oxidase 2 (DUOX2) and APOA-1 , the intestinal barrier (in particular, the expression of tight junction proteins), immune function (especially the homeostasis between effector and regulatory T cells) and the physiological metabolism, in particular, SCFAs, bile acids (BAs), and tryptophan metabolism. Finally, we reviewed the current knowledge on the interaction between dietary patterns and the gut microbiota in IBD and found that dietary patterns modulate the onset and progression of IBD, which is partly attributed to the regulation of the gut microbiota (especially SCFAs-producing bacteria and Escherichia coli). Faecalibacteria as "microbiomarkers" of IBD could be used as a target for dietary interventions to alleviate IBD. A comprehensive understanding of the interplay between dietary intake, gut microbiota, and IBD will facilitate the development of personalized dietary strategies based on the regulation of the gut microbiota in IBD and expedite the era of precision nutritional interventions for IBD.

Impact of long-term dietary habits on the human gut resistome in the Dutch population

The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.