Interaction between microbiota and immunity in health and disease

The involvement of the microbiota-gut-brain axis in the pathophysiology of mood disorders and therapeutic implications

INTRODUCTION

There is a growing body of evidence implicating gut-brain axis dysfunction in the pathophysiology of mood disorders. Accordingly, gut microbiota has become a promising target for the development of biomarkers and novel therapeutics for bipolar and depressive disorders.

AREAS COVERED

We describe the observed changes in the gut microbiota of patients with mood disorders and discuss the available studies assessing microbiota-based strategies for their treatment.

EXPERT OPINION

Microbiota-targeted interventions, such as symbiotics, prebiotics, paraprobiotics, and fecal microbiota transplants seem to attenuate the severity of depressive symptoms. The available results must be seen as preliminary and need to be replicated and/or confirmed in larger and independent studies, also considering the pathophysiological and clinical heterogeneity of mood disorders.

Advances in bio-polymer coatings for probiotic microencapsulation: chitosan and beyond for enhanced stability and controlled release

This review paper analyzes recent advancements in bio-polymer coatings for probiotic microencapsulation, with a particular emphasis on chitosan and its synergistic combinations with other materials. Probiotic microencapsulation is essential for protecting probiotics from environmental stresses, enhancing their stability, and ensuring effective delivery to the gut. The review begins with an overview of probiotic microencapsulation, highlighting its significance in safeguarding probiotics through processing, storage, and gastrointestinal transit. Advances in chitosan-based encapsulation are explored, including the integration of chitosan with other bio-polymers such as alginate, gelatin, and pectin, as well as the application of nanotechnology and innovative encapsulation techniques like spray drying and layer-by-layer assembly. Detailed mechanistic insights are integrated, illustrating how chitosan influences gut microbiota by promoting beneficial bacteria and suppressing pathogens, thus enhancing its role as a prebiotic or synbiotic. Furthermore, the review delves into chitosan's immunomodulatory effects, particularly in the context of inflammatory bowel disease (IBD) and autoimmune diseases, describing the immune signaling pathways influenced by chitosan and linking gut microbiota changes to improvements in systemic immunity. Recent clinical trials and human studies assessing the efficacy of chitosan-coated probiotics are presented, alongside a discussion of practical applications and a comparison of in vitro and in vivo findings to highlight real-world relevance. The sustainability of chitosan sources and their environmental impact are addressed, along with the novel concept of chitosan's role in the gut-brain axis. Finally, the review emphasizes future research needs, including the development of personalized probiotic therapies and the exploration of novel bio-polymers and encapsulation techniques.

Spatiotemporal dynamics of the oropharyngeal microbiome in a cohort of Ivorian school children

The respiratory tract harbours microorganisms of the normal host microbiota which are also capable of causing invasive disease. Among these, Neisseria meningitidis a commensal bacterium of the oropharynx can cause meningitis, a disease with epidemic potential. The oral microbiome plays a crucial role in maintaining respiratory health. An imbalance in its composition is associated with increased risk of invasive disease. The main objective of this study was to evaluate changes in the spatio-temporal dynamics of the oropharyngeal microbiota considering meningococcal carriage in a cohort of 8-12-year-old school children within (Korhogo) and outside (Abidjan) of the meningitis belt of Côte d'Ivoire. A significant geographic difference in the oropharyngeal microbiome was identified between the two study sites in terms of bacterial abundance and diversity (p < 0.001), with greater diversity in children in Abidjan than in Korhogo. Meningococcal carriage was low in the cohort with eight Neisseria carriers identified in Korhogo (3.64%) including one Neisseria meningitidis (0.45%). No Neisseria were detected in Abidjan indicating geographical differences in carriage (p = 0.006). Negative correlations were also found between Neisseria abundance and humidity. Meningococcal carriage was very low during the study; however, Neisseria carriage differed between the two study areas, with a higher frequency in children in Korhogo. Analysis of the oropharyngeal microbiome showed significant differences between children followed in Abidjan and Korhogo with higher microbial diversity in Abidjan, which is generally associated with better health status. Significant correlations between Neisseria or other pathogens carriage and climatic variables (Temperature, Relative humidity, and Wind speed) were also demonstrated, indicating an important role of climate in the carriage of these bacteria; an important element to note in the current context of climate change.

The Gut-Kidney Axis in Chronic Kidney Diseases

The gut-kidney axis represents the complex interactions between the gut microbiota and kidney, which significantly impact the progression of chronic kidney disease (CKD) and overall patient health. In CKD patients, imbalances in the gut microbiota promote the production of uremic toxins, such as indoxyl sulfate and p-cresyl sulfate, which impair renal function and contribute to systemic inflammation. Mechanisms like endotoxemia, immune activation and oxidative stress worsen renal damage by activating pro-inflammatory and oxidative pathways. Insights into these mechanisms highlight the impact of gut-derived metabolites, bacterial translocation, and immune response changes on kidney health, suggesting new potential approaches for CKD treatment. Clinical applications, such as dietary interventions, prebiotics, probiotics and fecal microbiota transplantation, are promising in adjusting the gut microbiota to alleviate CKD symptoms and slow disease progression. Current research highlights the clinical relevance of the gut-kidney axis, but further study is essential to clarify these mechanisms' diagnostic biomarkers and optimize therapeutic interventions. This review emphasizes the importance of an integrated approach to CKD management, focusing on the gut microbiota as a therapeutic target to limit kidney injury.

Nutrient colimitation is a quantitative, dynamic property of microbial populations

Resource availability dictates how fast and how much microbial populations grow. Quantifying the relationship between microbial growth and resource concentrations makes it possible to promote, inhibit, and predict microbial activity. Microbes require many resources, including macronutrients (e.g., carbon and nitrogen), micronutrients (e.g., metals), and complex nutrients like vitamins and amino acids. When multiple resources are scarce, as frequently occurs in nature, microbes may experience resource colimitation in which more than one resource simultaneously limits growth. Despite growing evidence for colimitation, the data are difficult to interpret and compare due to a lack of quantitative measures of colimitation and systematic tests of resource conditions. We hypothesize that microbes experience a continuum of nutrient limitation states and that nutrient colimitation is common in the laboratory and in nature. To address this, we develop a quantitative theory of resource colimitation that captures the range of possible limitation states and describes how they can change dynamically with resource conditions. We apply this approach to clonal populations of Escherichia coli to show that colimitation occurs in common laboratory conditions. We also show that growth rate and growth yield are colimited differently, reflecting the different underlying biology of these traits. Finally, we analyze environmental data to provide intuition for the continuum of limitation and colimitation conditions in nature. Altogether our results provide a quantitative framework for understanding and quantifying colimitation of microbes in biogeochemical, biotechnology, and human health contexts.

Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup

Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.

Microbial and proteomic signatures of type 2 diabetes in an Arab population

BACKGROUND

The rising prevalence of Type 2 diabetes mellitus (T2D) in the Qatari population presents a significant public health challenge, highlighting the need for innovative approaches to early detection and management. While most efforts are centered on using blood samples for biomarker discovery, the use of saliva remains underexplored.

METHODS

Using noninvasive saliva samples from 2974 Qatari subjects, we analyzed the microbial communities from diabetic, pre-diabetic, and non-diabetic participants based on their HbA1C levels. The salivary microbiota was assessed in all subjects by sequencing the V1-V3 regions of 16S rRNA gene. For the proteomics profiling, we randomly selected 50 gender and age-matched non-diabetic and diabetic subjects and compared their proteome with SOMAscan. Microbiota and proteome profiles were then integrated to reveal candidate biomarkers for T2D.

RESULTS

Our results indicate that the salivary microbiota of pre-diabetic and diabetic individuals differs significantly from that of non-diabetic subjects. Specifically, a significant increase in the abundance of Campylobacter, Dorea, and Bacteroidales was observed in the diabetic subjects compared to their non-diabetic controls. Metabolic pathway prediction analysis for these bacteria revealed a significant overrepresentation of genes associated with fatty acid and lipid biosynthesis, as well as aromatic amino acid metabolism in the diabetic group. Additionally, we observed distinct differences in salivary proteomic profiles between diabetic and non-diabetic subjects. Notably, levels of Haptoglobin, Plexin-C1, and MCL-1 were elevated, while Osteopontin (SPP1), Histone1H3A (HIST3H2A), and Histone H1.2 were reduced in diabetic individuals. Furthermore, integrated correlation analysis of salivary proteome and microbiota data demonstrated a strong positive correlation between HIST1H3A and HIST3H2A with Porphyromonas sp., all of which were decreased in the diabetic group.

CONCLUSION

This is the first study to assess the salivary microbiota in T2D patients from a large cohort of the Qatari population. We found significant differences in the salivary microbiota of pre-diabetic and diabetic individuals compared to non-diabetic controls. Our study is also the first to assess the salivary proteome using SOMAScan in diabetic and non-diabetic subjects. Integration of the microbiota and proteome profiles revealed a unique signature for T2D that can be used as potential T2D biomarkers.

The cow GUTBIOME CY study: investigating the composition of the cattle gut microbiome in health and infectious disease transmission in cyprus

BACKGROUND

Recent evidence suggests that the lower gut microbiome of ruminants presents roles in their health and environment, including the development of the mucosal immune system, milk production efficiency and quality and subsequent methane emissions. However, there are proportionately fewer studies on this complex microbial community in cattle and region-focus studies are non- existent.

METHODS

Herein, we present the research protocol of the GUTBIOME CY project pertaining to determine the composition of the lower gut microbiome in dairy cows situated in 37 farms across five districts of the island of Cyprus. Detailed questionnaires on animal husbandry and farming practices will be gathered from each farm. Faecal, milk (individual and bulk) and water samples will also be collected from cows and their offspring. Samples will be analysed using a combination of molecular biology and bioinformatics pipelines to define microbiome profiles and antimicrobial resistance (AMR). Information collected from the questionnaires will be used to test for associations between animal husbandry or farming practices and microbiome components and AMR.

DISCUSSION

Collected samples will establish the first dairy cattle biobank in the country for contributing substantially towards scientific advancements in microbiome research and providing insights to all stakeholders, tailored to the unique agricultural context of Cyprus.

The exometabolome as a hidden driver of bacterial virulence and pathogenesis

The traditional view of metabolism as merely supplying energy and biosynthetic precursors is undergoing a paradigm shift. Metabolic dynamics not only regulates gene expression but also orchestrates cellular processes with remarkable precision. Most bacterial pathogens exhibit exceptional metabolic plasticity, enabling them to adapt to diverse environments, including hostile conditions within a host. While the role of intracellular bacterial metabolism in pathogen-host interactions has been extensively studied, the contributions of the extracellularly released or secreted bacterial metabolites (referred to here as the bacterial 'exometabolome') to metabolic adaptations and disease pathogenesis remain largely unexplored. In this review, we highlight the significant and intriguing roles of bacterial exometabolomes in drug tolerance, immune suppression, and disease pathogenesis, opening a new frontier in our understanding of bacterial-host interactions.

Etiology-Dependent Microbiome Differences in Hepatocellular Carcinoma Development

Chronic liver disease is characterised by persistent inflammation, tissue damage, and regeneration, which leads to steatosis, fibrosis, and, lastly, cirrhosis and hepatocellular carcinoma (HCC). HCC, the most prevalent form of primary liver cancer, is one of the leading causes of cancer-related mortality worldwide. The gut microbiota plays a fundamental role in human physiology, and disturbances in its critical balance are widely recognised as contributors to various pathological conditions, including chronic liver diseases, both infectious and non-infectious in nature. Growing interest in microbiota research has recently shifted the focus towards the study of intratumoural microbiota, referred to as the "oncobiome", which can significantly impact the development and progression of HCC. In this review, we discuss existing research and provide an overview of the microbiota influence on viral hepatitis, particularly in shaping the progression of liver disease caused by the hepatitis B and hepatitis C viruses. We also explore microbial dysbiosis and its contribution to the silent and dangerous progression of non-alcoholic fatty liver disease. Additionally, we address the impact of alcohol on the liver and its interaction with the microbiota, tracing the pathway from inflammation to cirrhosis and cancer. The review emphasises the most common etiologies of hepatocellular carcinoma.

Modelling the influence of vitamin D and probiotic supplementation on the microbiome and immune response

The intestinal microbiota play a critical role in human health and disease, maintaining metabolic and immune/inflammatory health, synthesizing essential vitamins and amino acids and maintaining intestinal barrier integrity. The aim of this paper is to develop a mathematical model to describe the complex interactions between the microbiota, vitamin D/vitamin D receptor (VDR) pathway, epithelial barrier and immune response in order to understand better the effects of supplementation with probiotics and vitamin D. This is motivated by emerging data indicating the beneficial effects of vitamin D and probiotics individually and when combined. We propose a system of ordinary differential equations determining the time evolution of intestinal bacterial populations, concentration of the VDR:1,25(OH)$_{2}$D complex in epithelial and immune cells, the epithelial barrier and the immune response. The model shows that administration of probiotics and/or vitamin D upregulates the VDR complex, which enhances barrier function and protects against intestinal inflammation. The model also suggests co-supplementation to be superior to individual supplements. We explore the effects of inflammation on the populations of commensal and pathogenic bacteria and the vitamin D/VDR pathway and discuss the value of gathering additional experimental data motivated by the modelling insights.

Exploring the causal relationship of gut microbiota in nonunion: a Mendelian randomization analysis mediated by immune cell

Background

Emerging research indicates that gut microbiota (GM) are pivotal in the regulation of immune-mediated bone diseases. Nonunion, a bone metabolic disorder, has an unclear causal relationship with GM and immune cells. This study aims to elucidate the causal relationship between GM and nonunion using Mendelian Randomization (MR) and to explore the mediating role of immune cells.

Methods

Using a two-step, two-sample Mendelian randomization approach, this study explores the causal link between GM and nonunion, as well as the mediating role of immune cells in this relationship. Data were sourced from multiple cohorts and consortiums, including the MiBioGen consortium. GM data were derived from a recently published dataset of 473 gut microbiota, and nonunion data were obtained from genome-wide association studies (GWAS).

Results

MR analysis identified 12 bacterial genera with protective effects against nonunion and seven bacterial genera associated with a higher risk of nonunion, including Agathobacter sp000434275, Aureimonas, Clostridium M, Lachnospirales, Megamonas funiformis, and Peptoccia. Reverse MR analysis indicated that nonunion does not influence GM. Additionally, MR analysis identified 12 immune cell types positively associated with nonunion and 14 immune cell types negatively associated with nonunion. Building on these findings, we conducted mediation MR analysis to identify 24 crucial GM and immune cell-mediated relationships affecting nonunion. Notably, Campylobacter D, Megamonas funiformis, Agathobacter sp000434275, Lachnospirales, Clostridium E sporosphaeroides, and Clostridium M significantly regulated nonunion through multiple immune cell characteristics.

Conclusions

To our knowledge, our research results are the first to emphasize a causal relationship between the gut microbiome and nonunion, potentially mediated by immune cells. The correlations and mediation effects identified in our study provide valuable insights into potential therapeutic strategies targeting the gut microbiome, informing global action plans.

The costs and benefits of a dynamic host microbiome

All species host a rich community of microbes. This microbiome is dynamic, and displays seasonal, daily, and even hourly changes, but also needs to be resilient to fulfill important roles for the host. In evolutionary ecology, the focus of microbiome dynamism has been on how it can facilitate host adaptation to novel environments. However, an hitherto largely overlooked issue is that the host needs to keep its microbiome in check, which is costly and leads to trade-offs with investing in other fitness-related traits. Investigating these trade-offs in natural vertebrate systems by collecting longitudinal data will lead to deeper insight into the evolutionary mechanisms that shape host-microbiome interactions.

New insights into methods to measure biological age: a literature review

Biological age is a concept that reflects the physiological state of an individual rather than the chronological time since birth. It can help assess the risk of age-related diseases and mortality and the effects of interventions to slow down or reverse aging. However, there is no consensus on measuring biological age best, and different methods may yield different results. In this paper, which includes 140 relevant pieces of literature, out of 33,000, we review some new methods to measure biological age based on recent advances in biotechnology and data science. We discussed some novel biomarkers and algorithms that can capture the dynamic and multidimensional aspects of aging at different levels. We evaluate their performance and validity using various datasets and criteria and compare them with existing methods. We also discuss their potential applications and implications for aging research and clinical practice. We conclude that the new methods offer more accurate and reliable estimates of biological age and open new avenues for understanding and modulating the aging process.

Gut microbiota as a modulator of type 1 diabetes: A molecular perspective

Type 1 diabetes (T1D) is defined as an autoimmune metabolic disorder, characterized by destruction of pancreatic β-cells and high blood sugar levels. If left untreated, T1D results in severe health complications, including cardiovascular and kidney disease, as well as nerve damage, with ultimately grave consequences. Besides the role of genetic and certain environmental factors in T1D development, in the last decade, one new player emerged to affect T1D pathology as well, and that is a gut microbiota. Dysbiosis of gut bacteria can contribute to T1D by gut barrier disruption and the activation of autoimmune response, leading to the destruction of insulin producing cells, causing the development and aggravation of T1D symptoms. The relationship between gut microbiota and diabetes is complex and varies between individuals and additional research is needed to fully understand the effects of gut microbiome alternations in T1D pathogenesis. Therefore, the goal of this review is to understand the current knowledge in underlying molecular mechanism of gut microbiota effects, which leads to the new approaches for further studies in the prevention and treatment of T1D.

Chitosan and its derivatives: A novel approach to gut microbiota modulation and immune system enhancement

Chitosan, a biopolymer derived from the deacetylation of chitin found in crustacean shells and certain fungi, has attracted considerable attention for its promising health benefits, particularly in gut microbiota maintenance and immune system modulation. This review critically examines chitosan's multifaceted role in supporting gut health and enhancing immunity, beginning with a comprehensive overview of its sources, chemical structure, and its dual function as a dietary supplement and biomaterial. Chitosan's prebiotic effects are highlighted, with a focus on its ability to selectively stimulate beneficial gut bacteria, such as Bifidobacteria and Lactobacillus, while enhancing gut barrier integrity and inhibiting the growth of pathogenic microorganisms. The review delves deeply into chitosan's immunomodulatory mechanisms, including its impact on antigen-presenting cells, cytokine profiles, and systemic immune responses. A detailed comparative analysis assesses chitosan's efficacy relative to other prebiotics and immunomodulatory agents, examining challenges related to bioavailability and metabolic activity. Beyond its role in gut health, this review explores chitosan's potential as a dual-action agent that not only supports gut microbiota but also fortifies immune resilience. It introduces emerging research on novel chitosan derivatives, such as chitooligosaccharides, and evaluates their enhanced bioactivity for functional food applications. Special attention is given to sustainability, with an exploration of alternative, plant-based sources of chitosan and their implications for both health and environmental stewardship. Also, the review identifies new research avenues, such as the growing interest in chitosan's role in the gut-brain axis and its potential mental health benefits through microbial interactions. By addressing these innovative areas, the review aims to shift the focus from basic health effects to chitosan's broader impact on public health. The findings encourage further exploration, particularly through human trials, and emphasize chitosan's untapped potential in revolutionizing health and disease management.

Intestinal Microbiota and Aging in People with HIV-What We Know and What We Don't

PURPOSE OF REVIEW

People with HIV (PWH) experience premature aging and an elevated risk of age-related comorbidities, even with viral suppression through antiretroviral therapy (ART). We examine gastrointestinal disruptions, specifically impaired intestinal barrier integrity and microbial dysbiosis, as contributors to these comorbidities.

RECENT FINDINGS

HIV infection compromises the intestinal epithelial barrier, increasing permeability and microbial translocation, which trigger inflammation and cellular stress. ART does not fully restore gut barrier integrity, leading to persistent inflammation and cellular stress. Additionally, HIV-associated microbial dysbiosis favors pro-inflammatory bacteria, intensifying inflammation and tissue damage, which may contribute to premature aging in PWH. Understanding the interactions between intestinal microbiota, chronic inflammation, cellular stress, and aging is essential to developing therapies aimed at reducing inflammation and slowing age-related diseases in PWH. In this review, we discuss critical knowledge gaps and highlight the therapeutic potential of microbiota-targeted interventions to mitigate inflammation and delay age-associated pathologies in PWH.

A Snapshot of Cytokine Dynamics: A Fine Balance Between Health and Disease

Health and disease are intricately intertwined and often determined by the delicate balance of biological processes. Cytokines, a family of small signalling molecules, are pivotal in maintaining this balance, ensuring the body's immune system functions optimally. In a healthy condition, cytokines act as potent mediators of immune responses. They orchestrate the activities of immune cells, coordinating their proliferation, differentiation, and migration. This intricate role of cytokine signalling enables the body to effectively combat infections, repair damaged tissues, and regulate inflammation. However, the delicate equilibrium of cytokine production is susceptible to disruption. Excessive or abnormal cytokine levels can lead to a cascade of pathological conditions, including autoimmune diseases, chronic inflammation, infections, allergies, and even cancer. Interestingly, from the bunch of cytokines, few cytokines play an essential role in maintaining the balance between normal physiological status and diseases. In this review, we have appraised key cytokines' potential role and feedback loops in augmenting the imbalances in the body's biological functions, presenting a critical link between inflammation and disease pathology. Moreover, we have also highlighted the significance of cytokines and their molecular interplay, particularly in the recent viral pandemic COVID-19 disease. Hence, understandings regarding the interplay between viral infection and cytokine responses are essential and fascinating for developing effective therapeutic strategies.

Gut Microbiome Signatures During Acute Infection Predict Long COVID

Long COVID (LC), manifests in 10-30% of non-hospitalized individuals post-SARS-CoV-2 infection leading to significant morbidity. The predictive role of gut microbiome composition during acute infection in the development of LC is not well understood, partly due to the heterogeneous nature of disease. We conducted a longitudinal study of 799 outpatients tested for SARS-CoV-2 (380 positive, 419 negative) and found that individuals who later developed LC harbored distinct gut microbiome compositions during acute infection, compared with both SARS-CoV-2-positive individuals who did not develop LC and negative controls with similar symptomatology. However, the temporal changes in gut microbiome composition between the infectious (0-1 month) and post-infectious (1-2 months) phases was not different between study groups. Using machine learning, we showed that microbiome composition alone more accurately predicted LC than clinical variables. Including clinical data only marginally enhanced this prediction, suggesting that microbiome profiles during acute infection may reflect underlying health status and immune responses thus, help predicting individuals at risk for LC. Finally, we identified four LC symptom clusters, with gastrointestinal and fatigue-only groups most strongly linked to gut microbiome alterations.

Study of Microbiota Associated to Early Tumors Can Shed Light on Colon Carcinogenesis

An increasingly important role for gut microbiota in the initiation and progression of colorectal cancer (CRC) has been described. Even in the early stages of transformation, i.e., colorectal adenomas, changes in gut microbiota composition have been observed, and several bacterial species, such as pks+Escherichia coli and enterotoxigenic Bacteroides fragilis, have been proposed to drive colon tumorigenesis. In recent years, several strategies have been developed to study mucosa-associated microbiota (MAM), which is more closely associated with CRC development than lumen-associated microbiota (LAM) derived from fecal samples. This review summarizes the state of the art about the oncogenic actions of gut bacteria and compares the different sampling strategies to collect intestinal microbiota (feces, biopsies, swabs, brushes, and washing aspirates). In particular, this article recapitulates the current knowledge on MAM in colorectal adenomas and serrated polyps, since studying the intestinal microbiota associated with early-stage tumors can elucidate the molecular mechanisms underpinning CRC carcinogenesis.

Oral Pathogens' Substantial Burden on Cancer, Cardiovascular Diseases, Alzheimer's, Diabetes, and Other Systemic Diseases: A Public Health Crisis-A Comprehensive Review

This review synthesizes the findings from 252 studies to explore the relationship between the oral pathogens associated with periodontitis, dental caries, and systemic diseases. Individuals with oral diseases, such as periodontitis, are between 1.7 and 7.5 times (average 3.3 times) more likely to develop systemic diseases or suffer adverse pregnancy outcomes, underscoring the critical connection between dental and overall health. Oral conditions such as periodontitis and dental caries represent a significant health burden, affecting 26-47% of Americans. The most important oral pathogens, ranked by publication frequency, include the herpes virus, C. albicans, S. mutans, P. gingivalis, F. nucleatum, A. actinomycetemcomitans, P. intermedia, T. denticola, and T. forsythia. The systemic diseases and disorders linked to oral infections, ranked similarly, include cancer, respiratory, liver, bowel, fever, kidney, complications in pregnancy, cardiovascular bacteremia, diabetes, arthritis, autoimmune, bladder, dementia, lupus, and Alzheimer's diseases. Evidence supports the efficacy of dental and periodontal treatments in eliminating oral infections and reducing the severity of systemic diseases. The substantial burden that oral pathogens have on cancer, cardiovascular diseases, Alzheimer's, diabetes, and other systemic diseases poses a significant public health crisis.

Lycium ruthenicum Murray anthocyanin-driven neuroprotection modulates the gut microbiome and metabolome of MPTP-treated mice

Emerging evidence suggests that Parkinson's disease (PD) is strongly associated with altered gut microbiota. The present study investigated the prophylactic effects of anthocyanins (ACNs) from Lycium ruthenicum Murray on Parkinson's disease based on microbiomics and metabolomics. In this study, sixty-six adult male C57BL/6J mice were randomized into the control group, model group, positive drug (Madopar) group, and low-, medium- and high-dose ACN groups. Behavioral experiments were conducted and pathological indicators were determined. Fresh feces were collected for microbiomic analysis using 16S rRNA sequencing. Urine and serum were analyzed by the UPLC-MS method for untargeted metabolomics. The results demonstrated that ACNs ameliorated 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced motor deficits, dopamine neuron death, and glial cell activation, while 100 mg kg-1 and 200 mg kg-1 ACNs were more neuroprotective than 50 mg kg-1. Mice with PD-like phenotypes have an altered gut microbiota composition, and ACNs may regulate this disorder by causing an increase in Firmicutes/Bacteroidota ratio and abundance of norank_f__Eubacterium_coprostanoligenes_group and a decrease in the abundance of norank_f__Muribaculaceae, Coriobacteriaceae_UCG-002 and Parvibacter. Furthermore, ACNs increased 14 urinary key metabolites such as DIMBOA-Glc and tauroursodeoxycholic acid, decreased N,N-dimethyllysine, and increased 12 serum key metabolites such as 1-methylguanine and 1-nitro-5-glutathionyl-6-hydroxy-5,6-dihydronaphthalene, and decreased lamivudine-monophosphate and 5-butyl-2- methylpyridine. The present study reveals that ACNs are protective against MPTP-induced PD in mice by modulating anti-inflammatory flora in the gut and endogenous metabolites in serum/urine, and the key mechanisms may be related to Coriobacteriaceae_UCG-002 and glycerophospholipid metabolic pathways. Our findings provide new insights into the pathogenesis and potential treatment of Parkinson's disease.

Gut microbiota has important roles in the obstructive sleep apnea-induced inflammation and consequent neurocognitive impairment

Obstructive sleep apnea (OSA) is a state of sleep disorder, characterized by repetitive episodes of apnea and chronic intermittent hypoxia. OSA has an extremely high prevalence worldwide and represents a serious challenge to public health, yet its severity is frequently underestimated. It is now well established that neurocognitive dysfunction, manifested as deficits in attention, memory, and executive functions, is a common complication observed in patients with OSA, whereas the specific pathogenesis remains poorly understood, despite the likelihood of involvement of inflammation. Here, we provide an overview of the current state of the art, demonstrating the intimacy of OSA with inflammation and cognitive impairment. Subsequently, we present the recent findings on the investigation of gut microbiota alteration in the OSA conditions, based on both patients-based clinical studies and animal models of OSA. We present an insightful discussion on the role of changes in the abundance of specific gut microbial members, including short-chain fatty acid (SCFA)-producers and/or microbes with pathogenic potential, in the pathogenesis of inflammation and further cognitive dysfunction. The transplantation of fecal microbiota from the mouse model of OSA can elicit inflammation and neurobehavioral disorders in naïve mice, thereby validating the causal relationship to inflammation and cognitive abnormality. This work calls for greater attention on OSA and the associated inflammation, which require timely and effective therapy to protect the brain from irreversible damage. This work also suggests that modification of the gut microbiota using prebiotics, probiotics or fecal microbiota transplantation may represent a potential adjuvant therapy for OSA.

Plasticity and Tumor Microenvironment in Pancreatic Cancer: Genetic, Metabolic, and Immune Perspectives

Cancer has long been believed to be a genetic disease caused by the accumulation of mutations in key genes involved in cellular processes. However, recent advances in sequencing technology have demonstrated that cells with cancer driver mutations are also present in normal tissues in response to aging, environmental damage, and chronic inflammation, suggesting that not only intrinsic factors within cancer cells, but also environmental alterations are important key factors in cancer development and progression. Pancreatic cancer tissue is mostly comprised of stromal cells and immune cells. The desmoplasmic microenvironment characteristic of pancreatic cancer is hypoxic and hypotrophic. Pancreatic cancer cells may adapt to this environment by rewiring their metabolism through epigenomic changes, enhancing intrinsic plasticity, creating an acidic and immunosuppressive tumor microenvironment, and inducing noncancerous cells to become tumor-promoting. In addition, pancreatic cancer has often metastasized to local and distant sites by the time of diagnosis, suggesting that a similar mechanism is operating from the precancerous stage. Here, we review key recent findings on how pancreatic cancers acquire plasticity, undergo metabolic reprogramming, and promote immunosuppressive microenvironment formation during their evolution. Furthermore, we present the following two signaling pathways that we have identified: one based on the small G-protein ARF6 driven by KRAS/TP53 mutations, and the other based on the RNA-binding protein Arid5a mediated by inflammatory cytokines, which promote both metabolic reprogramming and immune evasion in pancreatic cancer. Finally, the striking diversity among pancreatic cancers in the relative importance of mutational burden and the tumor microenvironment, their clinical relevance, and the potential for novel therapeutic strategies will be discussed.

Emerging Role of Gut Microbiota in Breast Cancer Development and Its Implications in Treatment

Background: The human digestive system contains approximately 100 trillion bacteria. The gut microbiota is an emerging field of research that is associated with specific biological processes in many diseases, including cardiovascular disease, obesity, diabetes, brain disease, rheumatoid arthritis, and cancer. Emerging evidence indicates that the gut microbiota affects the response to anticancer therapies by modulating the host immune system. Recent studies have explained a high correlation between the gut microbiota and breast cancer: dysbiosis in breast cancer may regulate the systemic inflammatory response, hormone metabolism, immune response, and the tumor microenvironment. Some of the gut bacteria are related to estrogen metabolism, which may increase or decrease the risk of breast cancer by changing the number of hormones. Further, the gut microbiota has been seen to modulate the immune system in respect of its ability to protect against and treat cancers, with a specific focus on hormone receptor-positive breast cancer. Probiotics and other therapies claiming to control the gut microbiome by bacterial means might be useful in the prevention, or even in the treatment, of breast cancer. Conclusions: The present review underlines the various aspects of gut microbiota in breast cancer risk and its clinical application, warranting research on individualized microbiome-modulated therapeutic approaches to breast cancer treatment.

"Pleiotropic" Effects of Antibiotics: New Modulators in Human Diseases

Antibiotics, widely used medications that have significantly increased life expectancy, possess a broad range of effects beyond their primary antibacterial activity. While some are recognized as adverse events, others have demonstrated unexpected benefits. These adjunctive effects, which have been defined as "pleiotropic" in the case of other pharmacological classes, include immunomodulatory properties and the modulation of the microbiota. Specifically, macrolides, tetracyclines, and fluoroquinolones have been shown to modulate the immune system in both acute and chronic conditions, including autoimmune disorders (e.g., rheumatoid arthritis, spondyloarthritis) and chronic inflammatory pulmonary diseases (e.g., asthma, chronic obstructive pulmonary disease). Azithromycin, in particular, is recommended for the long-term treatment of chronic inflammatory pulmonary diseases due to its well-established immunomodulatory effects. Furthermore, antibiotics influence the human microbiota. Rifaximin, for example, exerts a eubiotic effect that enhances the balance between the gut microbiota and the host immune cells and epithelial cells. These pleiotropic effects offer new therapeutic opportunities by interacting with human cells, signaling molecules, and bacteria involved in non-infectious diseases like spondyloarthritis and inflammatory bowel diseases. The aim of this review is to explore the pleiotropic potential of antibiotics, from molecular and cellular evidence to their clinical application, in order to optimize their use. Understanding these effects is essential to ensure careful use, particularly in consideration of the threat of antimicrobial resistance.

Nanomechanical detection to empower robust monitoring of sepsis and microbial adaptive immune system-mediated proinflammatory disease

The correlation between circulating microbes and sepsis as well as proinflammatory diseases is increasingly gaining recognition. However, the detection of microbes' cell-free DNA (cfDNA), which exist at concentrations of a billion times lower than blood proteins, poses a significant challenge for early disease detection. Here, we present Nano mechanics combined with highly sensitive readout sequences to address the challenges of ultralow counts of disease biomarkers, thus enabling robust quantitative monitoring of chronic medical conditions at different stages of human disease progression. To showcase the effectiveness of our approach, we employ fragments of cfDNA and human cell secretory proteins as models with predictive capabilities for human diseases. Notably, our method reveals a reliable representation over an impressive three to four orders of magnitude in the detection limit and dynamic range, surpassing commercially available quantitative polymerase chain reaction (qPCR) commonly used in routine clinical practice. This concept underpins a highly sensitive and selective medical device designed for the early detection of circulating microbes in patients undergoing intensive cancer therapy. This will help pinpoint individuals at risk of complications, including damage to the intestinal barrier and development of neutropenic fever/Sirsa/Sepsis. Moreover, this approach introduces new avenues for stratifying antibiotic prophylaxis in proinflammatory diseases.

Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting

There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analyzed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures, but not with birth mode or antibiotic exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.

The oral-gut microbiome axis in health and disease

The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.

Christensenellaceae minuta modulates epithelial healing via PI3K-AKT pathway and macrophage differentiation in the colitis

Ulcerative colitis (UC) is a chronic inflammatory disorder with an unsatisfactory cure rate and mucosal healing is a key treatment objective. Christensenellaceae minuta (C. minuta) has emerged as a next-generation of probiotic for maintaining intestinal health. We investigated the therapeutic efficacy of C. minuta in dextran sulfate sodium (DSS)-induced colitis, focusing on mucosal healing and the underlying mechanisms. C. minuta effectively alleviated colitis and promoted the regeneration of intestinal epithelial cells (IECs). Using 16S rRNA sequencing and metabolomics, we found that C. minuta administration increased beneficial bacteria, decreased pathogenic bacteria, and significantly elevated propionic acid levels. Additionally, C. minuta activated the PI3K-AKT pathway by upregulating systemic and local IGF-1 expression. Inhibiting the PI3K-AKT pathway reduced the therapeutic effects of C. minuta and impaired IEC regeneration. Furthermore, C. minuta promoted macrophage differentiation into the M2 phenotype and decreased proinflammatory factors. We propose that C. minuta alleviates colitis by regulating the gut microbiota, modulating macrophage differentiation, and enhancing mucosal healing by activating the PI3K-AKT pathway via IGF-1 secretion induced by short-chain fatty acids. Our findings provide evidence from animal experiments to support future clinical trials and the therapeutic translation of C. minuta.

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.

Advancing vaccine technology through the manipulation of pathogenic and commensal bacteria

Advancements in vaccine technology are increasingly focused on leveraging the unique properties of both pathogenic and commensal bacteria. This revolutionary approach harnesses the diverse immune modulatory mechanisms and bacterial biology inherent in different bacterial species enhancing vaccine efficacy and safety. Pathogenic bacteria, known for their ability to induce robust immune responses, are being studied for their potential to be engineered into safe, attenuated vectors that can target specific diseases with high precision. Concurrently, commensal bacteria, which coexist harmlessly with their hosts and contribute to immune system regulation, are also being explored as novel delivery systems and in microbiome-based therapy. These bacteria can modulate immune responses, offering a promising avenue for developing effective and personalized vaccines. Integrating the distinctive characteristics of pathogenic and commensal bacteria with advanced bacterial engineering techniques paves the way for innovative vaccine and therapeutic platforms that could address a wide range of infectious diseases and potentially non-infectious conditions. This holistic approach signifies a paradigm shift in vaccine development and immunotherapy, emphasizing the intricate interplay between the bacteria and the immune systems to achieve optimal immunological outcomes.

GEMimp: An Accurate and Robust Imputation Method for Microbiome Data Using Graph Embedding Neural Network

Microbiome research has increasingly underscored the profound link between microbial compositions and human health, with numerous studies establishing a strong correlation between microbiome characteristics and various diseases. However, the analysis of microbiome data is frequently compromised by inherent sparsity issues, characterized by a substantial presence of observed zeros. These zeros not only skew the abundance distribution of microbial species but also undermine the reliability of scientific conclusions drawn from such data. Addressing this challenge, we introduce GEMimp, an innovative imputation method designed to infuse robustness into microbiome data analysis. GEMimp leverages the node2vec algorithm, which incorporates both Breadth-First Search (BFS) and Depth-First Search (DFS) strategies in its random walks sampling process. This approach enables GEMimp to learn nuanced, low-dimensional representations of each taxonomic unit, facilitating the reconstruction of their similarity networks with unprecedented accuracy. Our comparative analysis pits GEMimp against state-of-the-art imputation methods including SAVER, MAGIC and mbImpute. The results unequivocally demonstrate that GEMimp outperforms its counterparts by achieving the highest Pearson correlation coefficient when compared to the original raw dataset. Furthermore, GEMimp shows notable proficiency in identifying significant taxa, enhancing the detection of disease-related taxa and effectively mitigating the impact of sparsity on both simulated and real-world datasets, such as those pertaining to Type 2 Diabetes (T2D) and Colorectal Cancer (CRC). These findings collectively highlight the strong effectiveness of GEMimp, allowing for better analysis on microbial data. With alleviation of sparsity issues, it could be greatly facilitated in downstream analyses and even in the field of microbiology.

Butyricimonas paravirosa bacteremia associated with acute terminal ileitis: Case report and literature review

We present the first described case of bacteremia due to Butyricimonas paravirosa, a commensal gram-negative anaerobic bacterium identified by whole-genome sequencing in an elderly patient with acute terminal ileitis, who was successfully treated with ceftriaxone and metronidazole. We reviewed eleven previous cases of infection due to other Butyricimonas spp, which can cause a range of diseases but may be treated conservatively with a short antimicrobial course in the appropriate clinical setting. Additionally, while most Butyricimonas spp are susceptible to empiric anaerobic therapy, drug resistance has been reported in some cases.

Impact of gluten intake on clinical outcomes in patients with chronic inflammatory diseases initiating biologics: Secondary analysis of the prospective multicentre BELIEVE cohort study

Chronic inflammatory diseases (CIDs) pose a growing healthcare challenge, with a substantial proportion of patients showing inadequate response to biological treatment. There is renewed interest in dietary changes to optimize treatment regimens, with a growing body of evidence suggesting beneficial effects with adherence to a gluten-free diet. This study compared the likelihood of achieving clinical response to biological treatment after 14-16 weeks in patients with CID with high versus low-to-medium gluten intake. Secondary outcomes of interest included changes in disease activity, health-related quality of life and C-reactive protein. The study was a multicentre prospective cohort of 193 participants with a CID diagnosis (i.e. Crohn's Disease, Ulcerative Colitis, Rheumatoid Arthritis, Axial Spondyloarthritis, Psoriatic Arthritis or Psoriasis) who initiated biological treatment between 2017 and 2020. Participants were stratified based on their habitual gluten intake: the upper 33.3% (high gluten intake) and the remaining 66.6% (low-to-medium gluten intake). The proportion of patients achieving clinical response to biological treatment after 14-16 weeks was compared using logistic regression models. The median gluten intake differed significantly between groups (12.5 g/day vs. 5.9 g/day, standardized mean difference = 1.399). In total, 108 (56%) achieved clinical response to treatment, with no difference between 35 (55%) in the high gluten group and 73 (57%) in the medium-to-low gluten group (OR = 0.96 [0.51-1.79], p = 0.897). No differences were found with secondary outcomes. In conclusion, this study found no association between gluten intake and response to biological treatment in patients with CID.

FMT Restores Colonic Protein Biosynthesis and Cell Proliferation in Patients with Recurrent Clostridioides difficile Disease

Recurrent C. difficile infection (CDI) is a major health threat with significant mortality and financial costs. Fecal Microbiota Transplantation (FMT) is an effective therapy, however the mechanisms by which it acts, particularly on the host, are poorly understood. Here we enrolled a prospective cohort of human patients with recurrent CDI (n=16) undergoing FMT therapy. Colonic biopsies were collected and bulk RNA sequencing was performed to compare changes in host gene expression pre- and two months post-FMT. Transcriptional profiles were significantly altered after FMT therapy, with many differentially expressed genes (~15% of annotated genes detected). Enrichment analysis determined that these changes were reflective of increased protein production post-FMT, with enrichment of pathways such as Ribosome Biogenesis, Protein Processing, and signaling pathways (Myc, mTORc1, E2F) associated with cell proliferation and protein biosynthesis. Histology of H&E-stained biopsies identified a significant increase in colonic crypt length post-FMT, suggesting that this treatment promotes cell proliferation. Crypt length was significantly correlated with enriched Myc and mTOR signaling pathways as well as genes associated with polyamine biosynthesis, providing a potential mechanism through which this may occur. Finally, signaling pathways upstream of Myc and mTOR, notably IL-33 Signaling and EGFR ligands, were significantly upregulated, suggesting that FMT may utilize these signals to promote cell proliferation and restoration of the intestine.

Combined effects of polyvinyl chloride or polypropylene microplastics with cadmium on the intestine of zebrafish at environmentally relevant concentrations

Cadmium (Cd) is a common additive in polyvinyl chloride (PVC) and polypropylene (PP) plastics. Aquatic organisms were inevitably co-exposed to PVC/PP microplastics (MPs) and Cd, but their combined toxicity is still unknown. In this study, adult zebrafish were exposed to 200 μg/L MPs (PVC or PP) and 10 μg/L Cd alone or in combination for 28 days to investigate their toxicity and mechanisms. Results showed that combined exposure with PVC/PP enhanced the Cd accumulation in the zebrafish intestine. Subsequently, toxicology analyses showed that both PVC and PP possessed synergistic toxicity with Cd, manifested by the exfoliation and necrosis of intestinal epithelial cells, and increased levels of interleukin-1β (IL-1β), superoxide dismutase (SOD) and malondialdehyde (MDA). PP exhibited a stronger synergistic effect than PVC. Integration of non-targeted metabolomics and 16S rRNA gene sequencing revealed that combined exposure to PVC and Cd induced intestine toxicity mainly through bile acid (BA) biosynthesis, fructose (Fru) and mannose (Man) metabolism, and pentose phosphate pathway (PPP). The combined exposure of PP and Cd induced toxicity through the arginine (Arg) and glutathione (GSH) metabolisms. Meanwhile, combined exposure of PVC/PP and Cd increased the abundance of intestinal Proteobacteria and pathogen Vibrio, and decreased the abundance of Gemmobacter. These changes indrectly promoted the synergistic toxicity of PVC/PP and Cd through metabolites, such as indole-3-pyruvate (IPyA), chenodeoxycholic acid (CDCA), and cholic acid (CA). These findings highlighted that more attention should be paid to the toxicity of chemicals at environmentally relevant concentrations, particularly those co-existing with MPs.

The importance of gut microbiome in the perinatal period

This narrative review describes the settlement of the neonatal microbiome during the perinatal period and its importance on human health in the long term. Delivery methods, maternal diet, antibiotic exposure, feeding practices, and early infant contact significantly shape microbial colonization, influencing the infant's immune system, metabolism, and neurodevelopment. By summarizing two decades of research, this review highlights the microbiome's role in disease predisposition and explores interventions like maternal vaginal seeding and probiotic and prebiotic supplementation that may influence microbiome development.

CONCLUSION

The perinatal period is a pivotal phase for the formation and growth of the neonatal microbiome, profoundly impacting long-term health outcomes.

WHAT IS KNOWN

• The perinatal period is a critical phase for the development of the neonatal microbiome, with factors such as mode of delivery, maternal diet, antibiotic exposure, and feeding practices influencing its composition and diversity, which has significant implications for long-term health. • The neonatal microbiome plays a vital role in shaping the immune system, metabolism, and neurodevelopment of infants.

WHAT IS NEW

• Recent studies have highlighted the potential of targeted interventions, such as probiotic and prebiotic supplementation, and innovative practices like maternal vaginal seeding, to optimize microbiome development during the perinatal period. • Emerging evidence suggests that specific bacterial genera and species within the neonatal microbiome are associated with reduced risks of developing chronic conditions, indicating new avenues for promoting long-term health starting from early life.

Cross-talk between adipose tissue and microbiota-gut-brain-axis in brain development and neurological disorder

The gut microbiota is an important factor responsible for the physiological processes as well as pathogenesis of host. The communication between central nervous system (CNS) and microbiota occurs by different pathways i.e., chemical, neural, immune, and endocrine. Alteration in gut microbiota i.e., gut dysbiosis causes alteration in the bidirectional communication between CNS and gut microbiota and linked to the pathogenesis of neurological and neurodevelopmental disorder. Therefore, now-a-days microbiota-gut-brain-axis (MGBA) has emerged as therapeutic target for the treatment of metabolic disorder. But, experimental data available on MGBA from basic research has limited application in clinical study. In present study we first summarized molecular mechanism of microbiota interaction with brain physiology and pathogenesis via collecting data from different sources i.e., PubMed, Scopus, Web of Science. Furthermore, evidence shows that adipose tissue (AT) is active during metabolic activities and may also interact with MGBA. Hence, in present study we have focused on the relationship among MGBA, brown adipose tissue, and white adipose tissue. Along with this, we have also studied functional specificity of AT, and understanding heterogeneity among MGBA and different types of AT. Therefore, molecular interaction among them may provide therapeutic target for the treatment of neurological disorder.

Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4+CD8αα+ intraepithelial T cells

The impact of dietary fiber on intestinal T cell development is poorly understood. Here we show that a low fiber diet reduces MHC-II antigen presentation by small intestinal epithelial cells (IECs) and consequently impairs development of CD4+CD8αα+ intraepithelial lymphocytes (DP IELs) through changes to the microbiota. Dietary fiber supports colonization by Segmented Filamentous Bacteria (SFB), which induces the secretion of IFNγ by type 1 innate lymphoid cells (ILC1s) that lead to MHC-II upregulation on IECs. IEC MHC-II expression caused either by SFB colonization or exogenous IFNγ administration induced differentiation of DP IELs. Finally, we show that a low fiber diet promotes overgrowth of Bifidobacterium pseudolongum, and that oral administration of B. pseudolongum reduces SFB abundance in the small intestine. Collectively we highlight the importance of dietary fiber in maintaining the balance among microbiota members that allow IEC MHC-II antigen presentation and define a mechanism of microbiota-ILC-IEC interactions participating in the development of intestinal intraepithelial T cells.

Molecular patterns of microbial and metabolic interactions in septic patients with persistent lymphopenia

BACKGROUND

Persistent lymphopenia can be regarded as an important index of acquired immune dysfunction in sepsis. Whether the specific immune factor changes in septic patients with lymphopenia and the correlation to gut microbiota and metabolites remain unclear.

METHODS

This single-center prospective observation conducted lymphocyte subgroup analysis of blood samples and 16S rRNA gene amplicons sequencing and untargeted metabolomics analysis of fecal samples from 36 subjects with the persistent (≥3d) (n = 21) and non-persistent lymphopenia (<3d) (n = 15).

RESULTS

The persistent lymphopenia showed higher the 28d mortality and 90d mortality, while significantly lower CD3+T/LY, CD3+T cells, CD3+CD4+T cells, CD3+CD8+T cells, Th1 cells, Th2 cells, CD45RA + Treg cells. The 16S rRNA results showed that Staphylococcus, Peptostreptococcus, Bulleidia, Leuconostoc were significant enriched in the persistent lymphopenia. The metabolomics analysis showed that α-Ketoisovaleric acid was increased and 7-DHCA, α-MCA, β-MCA, HCA, LCA-3S, CA, UCA and Citramalic acid were decreased in the persistent lymphopenia.

CONCLUSION

In the process of interaction between host receptors and gut microbiota in patients with persistent lymphopenia sepsis, with a significant reduction in gut microbiota diversity and bile acid metabolites. That can affect various inflammatory pathways of gut immune cells, causing immune dysfunction in the body, which may be one of the main causes of death.

Targeting inflammation and gut microbiota with antibacterial therapy: Implications for central nervous system health

The complex symbiotic relationship between inflammation, the gut microbiota, and the central nervous system (CNS) has become a pivotal focus of contemporary biomedical research. Inflammation, as a physiological defense mechanism, plays a dual role as both a protective and pathological factor, and is intricately associated with gut microbiota homeostasis, often termed the "second brain." The gutbrain axis (GBA) exemplifies this multifaceted interaction, where gut health exerts significantly regulatory effects on CNS functions. Antibacterial therapies represent both promising and challenging strategies for modulating inflammation and gut microbiota composition to confer CNS benefits. However, while such therapies may exert positive modulatory effects on the gut microbiota, they also carry the potential to disrupt microbial equilibrium, potentially exacerbating neurological dysfunction. Recent advances have provided critical insights into the therapeutic implications of antibacterial interventions; nevertheless, the application of these therapies in the context of CNS health warrants a judicious and evidence-based approach. As research progresses, deeper investigation into the microbial-neural interface is essential to fully realize the potential of therapies targeting inflammation and the gut microbiota for CNS health. Future efforts should focus on refining antibacterial interventions to modulate the gut microbiota while minimizing disruption to microbial balance, thereby reducing risks and enhancing efficacy in CNS-related conditions. In conclusion, despite challenges, a more comprehensive understanding of the GBA, along with precise modulation through targeted antibacterial therapies, offers significant promise for advancing CNS disorder treatment. Continued research in this area will lead to innovative interventions and improved patient outcomes.

The progress on the relationship between gut microbiota and immune checkpoint blockade in tumors

Immune checkpoint blockade (ICB) has emerged as a promising immunotherapeutic approach for the treatment of various tumors. However, the efficacy of this therapy is limited in a subset of patients, and it is important to develop strategies to enhance immune responses. Studies have demonstrated a critical role of gut microbiota in regulating the therapeutic response to ICB. Gut microbiota composition, diversity, and function are mediated by metabolites, such as short-chain fatty acids and secondary bile acids, that interact with host immune cells through specific receptors. In addition, gut bacteria may translocate to the tumor site and stimulate antitumor immune responses. Therefore, maintaining a healthy gut microbiota composition, for instance through avoiding the use of antibiotics or probiotic interventions, can be an effective approach to optimize ICB therapy. This review summarizes the current understanding of the microbiota-immunity interactions in the context of ICB therapy, and discusses potential clinical implications of these findings.

Intestinal microbiome and myelodysplastic syndromes: Current state of knowledge and perspectives for future

The intestinal microbiome has been mechanistically linked with health and many disease processes. Cancer is no exception. Both in solid tumors and hematologic malignancies, there is increasing evidence supporting the involvement of the intestinal microbiome in tumor development, disease progression, response to treatment, and treatment toxicity. Consistent with microbiome mediation of the immune system and the potent effect of the immune system on cancer, the most compelling evidence has been obtained in the setting of cancer immunotherapy. Here, we review the current state of knowledge about microbiome effects in myelodysplastic syndromes, identify gaps and challenges in related research, and provide insights for future work.

Dysregulation of T cell response in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are gut inflammatory diseases that were earlier prevalent in the Western Hemisphere but now are on the rise in the East, with India standing second highest in the incidence rate in the world. Inflammation in IBD is a cause of dysregulated immune response, wherein helper T (Th) cell subsets and their cytokines play a major role in the pathogenesis of IBD. In addition, gut microbiota, environmental factors such as dietary factors and host genetics influence the outcome and severity of IBD. Dysregulation between effector and regulatory T cells drives gut inflammation, as effector T cells like Th1, Th17 and Th9 subsets Th cell lineages were found to be increased in IBD patients. In this review, we attempted to discuss the role of different Th cell subsets together with other T cells like CD8+ T cells, NKT and γδT cells in the outcome of gut inflammation in IBD. We also highlighted the potential therapeutic candidates for IBD.

Therapeutic success in primary biliary cholangitis and gut microbiota: a safe highway?

Primary biliary cholangitis (PBC) is a chronic, cholestatic, autoimmune disease, characterized by destruction of bile ducts. PBC predominantly affects women between 40 and 60 years of age. The presence of antimitochondrial antibodies (AMA) is a serological feature of PBC. These highly specific antibodies are found in about 95% of patients with the disease. The family of enzymes located in the inner membrane of the mitochondria, called the 2-oxo-acid dehydrogenase complex represents the target of the AMA. Ursodeoxycholic acid (UDCA) is a synthetic bile acid capable of protecting cholangiocytes from cholestatic damage caused by the accumulation of bile acids with a mechanism of action not yet well clarified. UDCA represents the gold standard therapy for PBC patients with recommended dose of 13-15 mg/kg/day. However, not every patient responds to therapy. On the other hand, the gut microbiota plays a key role in the onset of PBC through still unclear biochemical pathways. Less is known about its role as a potential biomarker after drug treatment. Actually, few studies analyzed the changes in gut microbiota composition before and after UDCA treatment. For this reason, this review represents an examination of the studies carried out on changes in gut microbiota composition in patients affected by PBC before and after treatment.

Fecal Microbiota Transplantation: Indications, Methods, and Challenges

Over the past two decades, as the importance of gut microbiota to human health has become widely known, attempts have been made to treat diseases by correcting dysbiosis of gut microbiota through fecal microbiota transplantation (FMT). Apart from current knowledge of gut microbiota, FMT to treat disease has a long history, from the treatment of food poisoning in the fourth century to the treatment of Clostridioides difficile infections in the twentieth century. In 2013, FMT was recognized as a standard treatment for recurrent C. difficile because it consistently showed high efficacy. Though recurrent C. difficile is the only disease internationally recognized for FMT efficacy, FMT has been tested for other diseases and shown some promising preliminary results. Different FMT methods have been developed using various formulations and administration routes. Despite advances in FMT, some issues remain to be resolved, such as donor screening, manufacturing protocols, and unknown components in the fecal microbiota. In this review, we discuss the mechanisms, clinical indications, methods, and challenges of current FMT. We also discuss the development of alternative therapies to overcome the challenges of FMT.

The Oral-Gut-Brain Axis: The Influence of Microbes as a Link of Periodontitis With Ischemic Stroke

Periodontitis, a non-communicable chronic inflammation disease resulting from dysbiosis of the oral microbiota, has been demonstrated to have a positive association with the risk of ischemic stroke (IS). The major periodontal pathogens contribute to the progression of stroke-related risk factors such as obesity, diabetes, atherosclerosis, and hypertension. Transcriptional changes in periodontitis pathogens have been detected in oral samples from stroke patients, suggesting a new conceptual framework involving microorganisms. The bidirectional regulation between the gut and the central nervous system (CNS) is mediated by interactions between intestinal microflora and brain cells. The connection between the oral cavity and gut through microbiota indicates that the oral microbial community may play a role in mediating complex communication between the oral cavity and the CNS; however, underlying mechanisms have yet to be fully understood. In this review, we present an overview of key concepts and potential mechanisms of interaction between the oral-gut-brain axis based on previous research, focusing on how the oral microbiome (especially the periodontal pathogens) impacts IS and its risk factors, as well as the mediating role of immune system homeostasis, and providing potential preventive and therapeutic approaches.

A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach

Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.