Microbiome-based interventions to modulate gut ecology and the immune system

Maternal probiotic exposure enhances CD8 T cell protective neonatal immunity and modulates offspring metabolome to control influenza virus infection

Maternal gut microbiota composition contributes to the status of the neonatal immune system and could influence the early life higher susceptibility to viral respiratory infections. Using a novel protocol of murine maternal probiotic supplementation, we report that perinatal exposure to Lacticaseibacillus rhamnosus (L.rh) or Bifidobacterium animalis subsp. lactis (B.lac) increases the influenza A/PR8 virus (IAV) clearance in neonates. Following either supplementation, type 1 conventional dendritic cells (cDC1) were amplified in the lymph nodes leading to an enhanced IAV antigen-experienced IFN-γ producing effector CD8 T cells in neonates and IAV-specific resident memory CD8 T cells in adulthood. This was compatible with a higher protection of the offspring upon a secondary infection. Interestingly, only mice born to L.rh supplemented mothers further displayed an increased activation of IFN-γ producing virtual memory CD8 T cells and a production of IL-10 by CD4 and CD8 T cells that could explain a better control of the lung damages upon infection. In the offspring and the mothers, no disturbance of the gut microbiota was observed but, as analyzed through an untargeted metabolomic approach, both exposures modified neonatal plasma metabolites. Among them, we further demonstrated that genistein and 3-(3-hydroxyphenyl)propionic acid recapitulate viral clearance or cDC1 activation in neonates exposed to IAV. We conclude that maternal L.rh or B.lac supplementation confers the neonates specific metabolomic modulations with a better CD8 T cell-mediated immune protection against IAV infection.

Impact of prophages on gut microbiota and disease associations

The gut microbiota plays an important role in maintaining host health by affecting various physiological functions. Among the diverse microbial communities in the gut, prophages are integral components of bacterial genomes, contributing significantly to bacterial evolution, ecology and pathogenicity. Prophages are capable of switching to lytic cycles in response to various internal and external factors. Factors that induce prophage induction include DNA damage, oxidative stress, nutrient availability, host immune response, quorum sensing, diet, secondary metabolites, antibiotics, and lifestyle changes. Prophage induction could contribute to both gut homeostasis and dysbiosis. Importantly, the connections between prophage induction and disorders such as inflammatory bowel disease, ulcerative colitis, and bacterial vaginosis highlight the dual roles of prophages in both health and disease. Although therapeutic approaches such as phage therapy (PT), fecal microbiota transplants (FMT), and fecal virome transplants (FVT) have gained attention, the concept of dietary prophage induction therapy offers a novel, targeted method to modulate gut microbiota. In spite of recent advances in understanding the role of prophages in gut health, the exact mechanisms by which they influence gut health remain only partially understood. Therefore, further research is needed to elucidate additional molecular mechanisms of prophage induction pathways and to explore their implications for gut microbiota dynamics and disease associations. This review discusses the molecular mechanisms and key factors that trigger prophage induction in the gut. Insights into these processes could lead to innovative therapeutic strategies that utilize prophages to support gut health.

Environmental contaminants and insects: Genetic strategies for ecosystem and agricultural sustainability

Insects, with their vast biodiversity and essential ecological roles, are crucial to agriculture, textile production, and environmental stability. As pollinators, decomposers, and bioindicators, they support ecosystem functions and human industries. Their short generation time, high reproductive rates, and genetic adaptability make them valuable models for studying human diseases like cancer. However, contaminants pose significant threats to industrially important insects, impacting ecosystems and industries alike. Excessive pesticide use disrupts ecological balance, contributing to the global decline of insect populations. Understanding how contaminants affect insect physiology is critical for assessing their broader implications on agriculture, food security, and biodiversity. This interdisciplinary review integrates entomology, genetics, and environmental science to explore these impacts. Additionally, it examines the potential of genetic interventions to mitigate contaminant-induced harm, ensuring the sustainability of insect-mediated services. To safeguard these vital species, a comprehensive approach that integrates conservation and sustainable utilization strategies is essential.

Fecal microbiome of pigs fed diets differing in protein and amino acid content raised in thermoneutral or cyclical heat stress conditions

The pig microbiome composition is affected by factors such as dietary changes, genetics, and diseases. Recent evidence suggests that housing temperature may also contribute to the variability in community structure and composition. Therefore, we investigated the interactive effects of different nutritional strategies and heat stress (HS) on the fecal microbiota composition, community structure, taxon distribution, and taxa correlation structure of pigs. Forty-eight (Landrace × Large White) finishing gilts with an average of 67.7 ± 6.2 kg of body weight (BW) were distributed in a 2 × 3 factorial arrangement: two temperatures [thermoneutral (TN, 22°C for 24 h) and cyclic heat stress (CHS, 12 h to 35°C and 12 h to 22°C)] and three diets varying in the dietary crude protein (CP) contents and amino acid (AA) levels [high CP (HP); low CP-free AA-supplemented diet (LPAA); low CP-free AA-supplemented diet and digestible Lys level (+20%), and Lys:AA ratios above recommendations (LPAA+)] originating six treatments (eight replicates of one pig). Pigs were fed ad libitum throughout the study. The 16S ribosomal RNA (rRNA)-based microbiome analysis was conducted in fecal samples collected on days 0 and 27 (endpoint). Overall, microbiome analysis suggested an increased richness in the fecal microbiome of pigs raised in TN conditions fed a diet supplemented with higher levels of AA (LPAA+). In addition, changes in the fecal microbiome composition indicated that Mogibacterium was significantly diminished in the feces of pigs fed the LPAA diet when compared to pigs fed the LPAA+, both in CHS conditions. Oscillospira was reduced in the feces of pigs fed a diet containing exclusively protein-bound as the source of AA, while the more the feed-grade AA was included in the remaining diets, the more the abundance of this taxon in fecal samples. Despite dietary alterations, Corynebacterium was enriched under CHS compared to TN, whereas the enrichment of Prevotella and Eubacterium hallii group was higher in the TN group. Outcomes of this study suggest that changes in fecal microbiota composition were mainly associated with temperature, pointing toward potential taxa that may contribute to physiological adaptation to heat stress.

Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture

The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.

The Effect of Microbiome-Derived Metabolites in Inflammation-Related Cancer Prevention and Treatment

Chronic inflammation plays a crucial role in cancer development, yet the mechanisms linking the microbiome to inflammation-related carcinogenesis remain unclear. Emerging evidence suggests that microbiome-derived metabolites influence inflammatory pathways, presenting both challenges and opportunities for therapy. However, a deeper understanding of how these metabolites regulate inflammation and contribute to cancer prevention is still needed. This review explores recent advances in microbiome-derived metabolites and their roles in inflammation-related carcinogenesis. It highlights key molecular mechanisms, emerging therapies, and unresolved challenges. Synthesizing current research, including clinical trials and experimental models, bridges the gap between microbiome science and cancer therapy. Microbial metabolites such as short-chain fatty acids (SCFAs), polyamines, indoles, and bile acids play vital roles in regulating inflammation and suppressing cancer. Many metabolites exhibit potent anti-inflammatory and immunomodulatory effects, demonstrating therapeutic potential. Case studies show promising results, but challenges such as metabolite stability, bioavailability, and individual variability remain. Understanding microbiome-metabolite interactions offers novel strategies for cancer prevention and treatment. This review identifies knowledge gaps and proposes future research directions to harness microbiome-derived metabolites for innovative cancer therapies. Addressing these issues may pave the way for microbiome-targeted cancer interventions.

The heart of the matter: How gut microbiota-targeted interventions influence cardiovascular diseases

The human body is habitat to a wide spectrum of microbial populations known as microbiota, which play an important role in overall health. The considerable research has mostly focused on the gut microbiota due to its potential to impact numerous physiological functions and its correlation with a variety of disorders, such as cardiovascular diseases (CVDs). Imbalances in the gut microbiota, known as dysbiosis, have been linked to the development and progression of CVDs through various processes, including the generation of metabolites like trimethylamine-N-oxide and short-chain fatty acids. Studies have also looked at the idea of using therapeutic interventions, like changing your diet, taking probiotics or prebiotics, or even fecal microbiota transplantation (FMT), to change the gut microbiota's make-up and how it works in order to prevent or treat CVDs. Exploring the cause-and-effect connection between the gut microbiota and CVDs offers a hopeful path for creating innovative microbiome-centered strategies to prevent and cure CVDs. This review presents an in-depth review of the correlation between the gut microbiota and CVDs, as well as potential therapeutic approaches for manipulating the gut microbiota to enhance cardiovascular health.

Unveiling the microbial orchestra: exploring the role of microbiota in cancer development and treatment

The human microbiota comprises a diverse microbial ecosystem that significantly impacts health and disease. Among its components, the gut microbiota plays a crucial role in regulating metabolic, immunologic, and inflammatory responses. Dysbiosis, an imbalance in microbial composition, has been linked to carcinogenesis through mechanisms such as chronic inflammation, metabolic disturbances, epigenetic modifications, and immune system dysregulation. Additionally, dysbiosis influences the efficacy and toxicity of cancer therapies. Given these associations, there is growing interest in leveraging the microbiota as a biomarker for cancer detection and outcome prediction. Notably, distinct microbial signatures have been identified across various cancer types, suggesting their potential as diagnostic markers. Furthermore, modulation of the microbiota presents a promising avenue for improving cancer treatment outcomes through strategies such as antibiotics, prebiotics, probiotics, fecal microbiota transplantation, dietary interventions, small-molecule inhibitors, and phage therapy. To explore these relationships, we conducted a comprehensive literature review using Web of Science, Scopus, PubMed, MEDLINE, Embase, and Google Scholar as our primary online databases, focusing on indexed peer-reviewed articles up to the present year. This review aims to elucidate the role of dysbiosis in cancer development, examine the molecular mechanisms involved, and assess the impact of microbiota on cancer therapies. Additionally, we highlight microbiota-based therapeutic strategies and discuss their potential applications in cancer management. A deeper understanding of the intricate interplay between the microbiota and cancer may pave the way for novel approaches to cancer prevention, early detection, and treatment optimization.

Therapeutic targeting of the host-microbiota-immune axis: implications for precision health

The human body functions as a complex ecosystem, hosting trillions of microbes that collectively form the microbiome, pivotal in immune system regulation. The host-microbe immunological axis maintains homeostasis and influences key physiological processes, including metabolism, epithelial integrity, and neural function. Recent advancements in microbiome-based therapeutics, including probiotics, prebiotics and fecal microbiota transplantation, offer promising strategies for immune modulation. Microbial therapies leveraging microbial metabolites and engineered bacterial consortia are emerging as novel therapeutic strategies. However, significant challenges remain, including individual microbiome variability, the complexity of host-microbe interactions, and the need for precise mechanistic insights. This review comprehensively examines the host microbiota immunological interactions, elucidating its mechanisms, therapeutic potential, and the future directions of microbiome-based immunomodulation in human health. It will also critically evaluate challenges, limitations, and future directions for microbiome-based precision medicine.

The aryl hydrocarbon receptor: a rehabilitated target for therapeutic immune modulation

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor originally identified as the target mediating the toxic effects of environmental pollutants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and dioxins. For years, AHR activation was actively avoided during drug development. However, the AHR was later identified as an important physiological regulator of the immune response. These findings triggered a paradigm shift that resulted in identification of the AHR as a regulator of both innate and adaptive immunity and outlined a pathway for its modulation by the diet, commensal flora and metabolism in the context of autoimmunity, cancer and infection. Moreover, the AHR was revealed as a candidate target for the therapeutic modulation of the immune response. Indeed, the first AHR-activating drug (tapinarof) was recently approved for the treatment of psoriasis. Clinical trials are underway to evaluate the effects of tapinarof and other AHR-targeting therapeutics in inflammatory diseases, cancer and infections. This Review outlines the molecular mechanism of AHR action, and describes how it regulates the immune response. We also discuss links to disease and AHR-targeting therapeutics that have been tested in past and ongoing clinical trials.

Probiotics and nanoparticle-mediated nutrient delivery in the management of transfusion-supported diseases

Bone marrow is vital for hematopoiesis, producing blood cells essential for oxygen transport, immune defense, and clotting. However, disorders like leukemia, lymphoma, aplastic anemia, and myelodysplastic syndromes can severely disrupt its function, leading to life-threatening complications. Traditional treatments, including chemotherapy and stem cell transplants, have significantly improved patient outcomes but are often associated with severe side effects and limitations, necessitating the exploration of safer, more targeted therapeutic strategies. Nanotechnology has emerged as a promising approach for addressing these challenges, particularly in the delivery of nutraceuticals-bioactive compounds derived from food sources with potential therapeutic benefits. Despite their promise, nutraceuticals often face clinical limitations due to poor bioavailability, instability, and inefficient delivery to target sites. Nanoparticles offer a viable solution by enhancing the stability, absorption, and targeted transport of nutraceuticals to bone marrow while minimizing systemic side effects. This study explores a range of bone marrow disorders, conventional treatment modalities, and the potential of nanoparticles to enhance nutraceutical-based therapies. By improving targeted delivery and therapeutic efficacy, nanoparticles could revolutionize bone marrow disease management, providing patients with more effective and less invasive treatment options. These advancements represent a significant step toward safer and more efficient therapeutic approaches, ultimately improving patient prognosis and overall health.

The Impact of Antibiotic Therapy on Intestinal Microbiota: Dysbiosis, Antibiotic Resistance, and Restoration Strategies

The human gut microbiota-an intricate and dynamic ecosystem-plays a pivotal role in metabolic regulation, immune modulation, and the maintenance of intestinal barrier integrity. Although antibiotic therapy is indispensable for managing bacterial infections, it profoundly disrupts gut microbial communities. Such dysbiosis is typified by diminished diversity and shifts in community structure, especially among beneficial bacterial genera (e.g., Bifidobacterium and Eubacterium), and fosters antibiotic-resistant strains and the horizontal transfer of resistance genes. These alterations compromise colonization resistance, increase intestinal permeability, and amplify susceptibility to opportunistic pathogens like Clostridioides difficile. Beyond gastrointestinal disorders, emerging evidence associates dysbiosis with systemic conditions, including chronic inflammation, metabolic syndrome, and neurodegenerative diseases, underscoring the relevance of the microbiota-gut-brain axis. The recovery of pre-existing gut communities post-antibiotic therapy is highly variable, influenced by drug spectrum, dosage, and treatment duration. Innovative interventions-such as fecal microbiota transplantation (FMT), probiotics, synbiotics, and precision microbiome therapeutics-have shown promise in counteracting dysbiosis and mitigating its adverse effects. These therapies align closely with antibiotic stewardship programs aimed at minimizing unnecessary antibiotic use to preserve microbial diversity and curtail the spread of multidrug-resistant organisms. This review emphasizes the pressing need for microbiota-centered strategies to optimize antibiotic administration, promote long-term health resilience, and alleviate the disease burden associated with antibiotic-induced dysbiosis.

The human gut microbiome and sleep across adulthood: associations and therapeutic potential

Sleep is an essential homeostatic process that undergoes dynamic changes throughout the lifespan, with distinct life stages predisposed to specific sleep pathologies. Similarly, the gut microbiome also varies with age, with different signatures associated with health and disease in the latest decades of life. Emerging research has shown significant cross-talk between the gut microbiota and the brain through several pathways, suggesting the microbiota may influence sleep, though the specific mechanisms remain to be elucidated. Here, we critically examine the existing literature on the potential impacts of the gut microbiome on sleep and how this relationship varies across adulthood. We suggest that age-related shifts in gut microbiome composition and immune function may, in part, drive age-related changes in sleep. We conclude with an outlook on the therapeutic potential of microbiome-targeted interventions aimed at improving sleep across adulthood, particularly for individuals experiencing high stress or with sleep complaints.

Updating the Discontinuity Theory to the Extended Immunity: The Symmunobiome Concept

The immune system (IS) is commonly understood as a system composed of specific cells and tissues that have evolved to contrast pathogens and defend the host. By virtue of this capacity, it has come to be considered capable of making an essential distinction, that between self versus non-self, which would contribute to a clear identity of the organism. However, in the wake of evolution and ecology, growing evidence suggests that the so-called immune system, which also evolved from symbiotic interactions with external agents, is not just a defensive system that merely protects the organism but, on the contrary, is involved in many global regulatory and homeostatic functions. Moreover, in performing these many functions, IS is not only an ensemble of host cells and tissues but functionally is constitutively determined by the interaction with a set of associated microorganisms, that is, the human microbiome. In this scenario, it is open-and-shut that the microbiome itself is a functional part of this extended immune system. Organisms and microbiomes together, therefore, form a functional whole, which constitutes a privileged form of biological organization. In light of this evidence showing the inadequacy of traditional accounts, we propose to extend and supplement the current IS conceptualization by introducing the notion of the symmunobiome. With this term, we intend to characterize the microbiome's own and unavoidable component to overall immune functionality. Therefore, we suggest a new immune system determination, articulated in three linked pillars-adaptive immunity, innate immunity, and symmunobiome-to better grasp the diverse functionality of extended immunity.

Role of the microbiome in regulation of the immune system

Immune health and metabolic functions are intimately connected via diet and the microbiota. Immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important mucosal and systemic ramifications. Microbial fermentation of dietary components in vivo generates thousands of molecules, some of which are integral components of the molecular circuitry that regulates immune and metabolic functions. These in turn protect against aberrant inflammatory or hyper-reactive processes and promote effector immune responses that quickly eliminate pathogens, such as SARS-CoV-2. Potent tolerance mechanisms should ensure that these immune cells do not over-react to non-pathogenic factors (e.g. food proteins), while maintaining the ability to respond to infectious challenges in a robust, effective and well controlled manner. In this review we examine the factors and mechanisms that shape microbiota composition and interactions with the host immune system, their associations with immune mediated disorders and strategies for intervention.

Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

Oncologists increasingly recognize the microbiome as an important facilitator of health as well as a contributor to disease, including, specifically, cancer. Our knowledge of the etiologies, mechanisms, and modulation of microbiome states that ameliorate or promote cancer continues to evolve. The progressive refinement and adoption of "omic" technologies (genomics, transcriptomics, proteomics, and metabolomics) and utilization of advanced computational methods accelerate this evolution. The academic cancer center network, with its immediate access to extensive, multidisciplinary expertise and scientific resources, has the potential to catalyze microbiome research. Here, we review our current understanding of the role of the gut microbiome in cancer prevention, predisposition, and response to therapy. We underscore the promise of operationalizing the academic cancer center network to uncover the structure and function of the gut microbiome; we highlight the unique microbiome-related expert resources available at the City of Hope of Comprehensive Cancer Center as an example of the potential of team science to achieve novel scientific and clinical discovery.

Balancing act: counteracting adverse drug effects on the microbiome

The human gut microbiome, a community of microbes that plays a crucial role in our wellbeing, is highly adaptable but also vulnerable to drug treatments. This vulnerability can have serious consequences for the host, for example, increasing susceptibility to infections, immune, metabolic, and cognitive disorders. However, the microbiome's adaptability also provides opportunities to prevent, protect, or even reverse drug-induced damage. Recently, several innovative approaches have emerged aimed at minimizing the collateral damage of drugs on the microbiome. Here, we outline these approaches, discuss their applicability in different treatment scenarios, highlight current challenges, and suggest avenues that may lead to an effective protection of the microbiome.

Genetically Engineered Bacteria as a Promising Therapeutic Strategy Against Cancer: A Comprehensive Review

As a significant cause of global mortality, the cancer has also economic impacts. In the era of cancer therapy, mitigating side effects and costs and overcoming drug resistance is crucial. Microbial species can grow inside the tumor microenvironment and inhibit cancer growth through direct killing of tumor cells and immunoregulatory effects. Although microbiota or their products have demonstrated anticancer effects, the possibility of acting as pathogens and exerting side effects in certain individuals is a risk. Hence, several genetically modified/engineered bacteria (GEB) have been developed to this aim with ability of diagnosing and selective targeting and destruction of cancers. Additionally, GEB are expected to be considerably more efficient, safer, more permeable, less costly, and less invasive theranostic approaches compared to wild types. Potential GEB strains such as Escherichia coli (Nissle 1917, and MG1655), Salmonella typhimurium YB1 SL7207 (aroA gene deletion), VNP20009 (∆msbB/∆purI) and ΔppGpp (PTet and PBAD), and Listeria monocytogenes Lmat-LLO have been developed to combat cancer cells. When used in tandem with conventional treatments, GEB substantially improve the efficacy of anticancer therapy outcomes. In addition, public acceptance, optimal timing (s), duration (s), dose (s), and strains identification, interactions with other strains and the host cells, efficacy, safety and quality, and potential risks and ethical dilemmas include major challenges.

Rapid shift of gut microbiome and enrichment of beneficial microbes during arhatic yoga meditation retreat in a single-arm pilot study

BACKGROUND

The human microbiome plays a vital role in human health, mediated by the gut-brain axis, with a large diversity of functions and physiological benefits. The dynamics and mechanisms of meditations on oral and gut microbiome modulations are not well understood. This study investigates the short-term modulations of the gut and oral microbiome during an Arhatic Yoga meditation retreat as well as on the role of microbiome in improving well-being through a possible gut-brain axis.

METHODS

A single-arm pilot clinical trial was conducted in a controlled environment during a 9-day intensive retreat of Arhatic Yoga meditation practices with vegetarian diet. Oral and fecal samples of 24 practitioners were collected at the start (Day0: T1), middle (Day3: T2), and end (Day9:T3) of the retreat. Targeted 16S rRNA gene amplicon sequencing was performed for both oral and gut samples. Functional pathway predictions was identified using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2). DESeq2 was used to identify the differential abundant taxa. Various statistical analyses were performed to assess the significant changes in the data.

RESULTS

Our findings revealed that Arhatic Yoga meditation together with a vegetarian diet led to changes in the oral and gut microbiome profiles within the 9-day retreat. Oral microbiome profile showed a significant (p < 0.05) difference in the species richness and evenness at the end of study, while non-metric multidimensional scaling (NMDS) confirmed the shift in the gut microbiome profile of the practitioners by T2 timepoint, which was further supported by PERMANOVA analysis (p < 0.05). Health-benefiting microbes known to improve the gastrointestinal and gut-barrier functions, immune modulation, and gut-brain axis were enriched. Gut microbiome of both beginner and advanced Arhatic Yoga practitioners showed similar trends of convergence by the end of study. This implies a strong selection pressure by Arhatic Yoga meditation together with a vegetarian diet on the beneficial gut microbiome.

CONCLUSION

This pilot study demonstrates that Arhatic Yoga meditation practices combined with a vegetarian diet during a short intensive retreat resulted in enrichment of known health-promoting microbes. Such microbial consortia may be developed for potential health benefits and used as probiotics to improve the gastrointestinal and immune systems, as well as functions mediated by the gut-brain axis.

TRIAL REGISTRATION

Study was submitted in https://clinicaltrials.gov/on28-02-2024 . Retrospective registered.

Microbiome Integrity Enhances the Efficacy and Safety of Anticancer Drug

The intricate relationship between anticancer drugs and the gut microbiome influences cancer treatment outcomes. This review paper focuses on the role of microbiome integrity in enhancing the efficacy and safety of anticancer drug therapy, emphasizing the pharmacokinetic interactions between anticancer drugs and the gut microbiota. It explores how disruptions to microbiome composition, or dysbiosis, can alter drug metabolism, immune responses, and treatment side effects. By examining the mechanisms of microbiome disruption caused by anticancer drugs, this paper highlights specific case studies of drugs like cyclophosphamide, 5-fluorouracil, and irinotecan, and their impact on microbial diversity and clinical outcomes. The review also discusses microbiome-targeted strategies, including prebiotics, probiotics, postbiotics, and fecal microbiota transplantation (FMT), as promising interventions to enhance cancer treatment. Furthermore, the potential of microbiome profiling in personalizing therapy and integrating these interventions into clinical practice is explored. Finally, this paper proposes future research directions, including developing novel biomarkers and a deeper comprehension of drug-microbiome interactions, to respond to current gaps in knowledge and improve patient outcomes in cancer care.

Unlocking the secrets of the human gut microbiota: Comprehensive review on its role in different diseases

The human gut microbiota, a complex and diverse community of microorganisms, plays a crucial role in maintaining overall health by influencing various physiological processes, including digestion, immune function, and disease susceptibility. The balance between beneficial and harmful bacteria is essential for health, with dysbiosis - disruption of this balance - linked to numerous conditions such as metabolic disorders, autoimmune diseases, and cancers. This review highlights key genera such as Enterococcus, Ruminococcus, Bacteroides, Bifidobacterium, Escherichia coli, Akkermansia muciniphila, Firmicutes (including Clostridium and Lactobacillus), and Roseburia due to their well-established roles in immune regulation and metabolic processes, but other bacteria, including Clostridioides difficile, Salmonella, Helicobacter pylori, and Fusobacterium nucleatum, are also implicated in dysbiosis and various diseases. Pathogenic bacteria, including Escherichia coli and Bacteroides fragilis, contribute to inflammation and cancer progression by disrupting immune responses and damaging tissues. The potential for microbiota-based therapies, such as probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions, to improve health outcomes is examined. Future research directions in the integration of multi-omics, the impact of diet and lifestyle on microbiota composition, and advancing microbiota engineering techniques are also discussed. Understanding the gut microbiota's role in health and disease is essential for formulating personalized, efficacious treatments and preventive strategies, thereby enhancing health outcomes and progressing microbiome research.

Oral microbiome alpha diversity and all-cause, cardiovascular, and non-cardiovascular mortality in US adults: Evidence from the NHANES 2009-2019

BACKGROUND AND AIMS

Knowledge about the association between oral microbiome diversity within individuals and cardiovascular disease (CVD) and non-CVD mortality is scarce. Besides, variation by sex and racial and ethnic groups, and the potential mediators of these associations remain unclear. We aimed to investigate the associations of oral microbiome alpha diversity with all-cause, CVD, and non-CVD mortality, and the interaction effects of sex and racial and ethnic groups and potential mediators in the associations.

METHODS

The National Health and Nutrition Examination Survey (NHANES) is a population-based observational study, conducted periodically in Mexican American, Other Hispanic, Non-Hispanic (NH) White, NH Black, and other racial/ethnic participants. We linked 2009-12 survey data of 8199 adults to the mortality data until 2019. By analyzing RNA gene sequences from oral rinse samples, microbiome alpha diversity within individuals was assessed using operational taxonomic unit (OTU) richness. Potential mediators included obesity, diabetes mellitus, dyslipidemia, hypertension, and periodontitis. Multivariable Cox proportional hazards regression and causal mediation analysis were used.

RESULTS

Baseline mean ± standard deviation (SD) age was 42.1 ± 15.1 years. Over a median follow-up of 9.1 years, 405 all-cause mortality occurred (CVD, 105; non-CVD, 300). Each 1-SD increment in OTU richness was inversely associated with all-cause mortality (hazard ratio [HR] 0.92, 95 % confidence interval [CI] 0.90-0.95), CVD mortality (HR, 0.92; 95 % CI, 0.90-0.95), and non-CVD mortality (HR, 0.92; 95 % CI, 0.90-0.95). With evidence of significant racial and ethnic groups-interaction (p <0.05), these associations were evident in Mexican American, NH White, and others racial/ethnic participants. None of the potential mediators significantly mediated the associations of OTU richness with all-cause, CVD, and non-CVD mortality.

CONCLUSIONS

Lower oral microbiome alpha diversity is associated with higher risk for all-cause, CVD, and non-CVD mortality, and the associations are varied by racial and ethnic groups.

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

Exploring How Adipose Tissue, Obesity, and Gender Influence the Immune Response to Vaccines: A Comprehensive Narrative Review

Vaccines represent an essential tool for the prevention of infectious diseases. Upon administration, a complex interaction occurs between the vaccine formulation and the recipient's immune system, ultimately resulting in protection against disease. Significant variability exists in individual and population responses to vaccination, and these differences remain the focus of the ongoing research. Notably, well-documented factors, such as age, gender, and genetic predisposition, influence immune responses. In contrast, the effects of overweight and obesity have not been as thoroughly investigated. The evidence indicates that a high body mass index (BMI) constitutes a significant risk factor for infections in general, with adipose tissue playing a crucial role in modulating the immune response. Furthermore, suboptimal levels of vaccine seroconversion have been observed among individuals with obesity. This review provides a plausible examination of the immunity and protection conferred by various vaccines in individuals with an overweight status, offering a comprehensive analysis of the mechanisms to enhance vaccination efficiency.

Sex differences in gut microbiota, hypertension, and cardiovascular risk

The intricate ecosystem of the gut microbiome exhibits sex-specific differences, influencing the susceptibility to cardiovascular diseases (CVD). Imbalance within the gut microbiome compromises the gut barrier, activates inflammatory pathways, and alters the production of metabolites, all of which initiate chronic diseases including CVD. In particular, the interplay between lifestyle choices, hormonal changes, and metabolic byproducts uniquely affects sex-specific gut microbiomes, potentially shaping the risk profiles for hypertension and CVD differently in men and women. Understanding the gut microbiome's role in CVD risk offers informative reasoning behind the importance of developing tailored preventative strategies based on sex-specific differences in CVD risk. Furthermore, insight into the differential impact of social determinants and biological factors on CVD susceptibility emphasizes the necessity for more nuanced approaches. This review also outlines specific dietary interventions that may enhance gut microbiome health, offering a glimpse into potential therapeutic avenues for reducing CVD risk that require greater awareness. Imbalance in natural gut microbiomes may explain etiologies of chronic diseases; we advocate for future application to alter the gut microbiome as possible treatment of the aforementioned diseases. This review mentions the idea of altering the gut microbiome through interventions such as fecal microbiota transplantation (FMT), a major application of microbiome-based therapy that is first-line for Clostridium difficile infections and patient-specific probiotics highlights more innovative approaches to hypertension and CVD prevention. Through increased analysis of gut microbiota compositions along with patient-centric probiotics and microbiome transfers, this review advocates for future preventative strategies for hypertension.

Probiotics and Food Bioactives: Unraveling Their Impact on Gut Microbiome, Inflammation, and Metabolic Health

This review paper delves into the role of probiotics and food bioactives in influencing gut health and overall well-being, within the context of probiotics and food bioactives, emphasizing their roles in modulating inflammation, gut microbiota, and metabolic health. Probiotics are defined as live microorganisms that confer health benefits to the host, primarily through their impact on the gut microbiome; a complex community of microorganisms crucial for maintaining health. The review aims to elucidate how probiotics, incorporated into both traditional and modern food systems, can enhance gut health and address metabolic disorders. It examines the types of probiotics present in various foods and their mechanisms of action, including their effects on immune function and metabolic health. By exploring the links between probiotics and health outcomes such as digestive health, immune support, and mental health, the review identifies specific conditions where probiotics show significant promise. Hurldes such as inconsistencies in research findings, variability in probiotic strains, and dosages are addressed. The paper also suggests future research directions, including the potential for personalized probiotic interventions. The review concludes by summarizing key findings and emphasizing the critical role of probiotics in food systems for promoting overall health and mitigating metabolic diseases.

Ferroptosis: A New Pathway in the Interaction between Gut Microbiota and Multiple Sclerosis

Multiple sclerosis (MS) is a chronic autoimmune disorder marked by neuroinflammation, demyelination, and neuronal damage. Recent advancements highlight a novel interaction between iron-dependent cell death, known as ferroptosis, and gut microbiota, which may significantly influences the pathophysiology of MS. Ferroptosis, driven by lipid peroxidation and tightly linked to iron metabolism, is a pivotal contributor to the oxidative stress observed in MS. Concurrently, the gut microbiota, known to affect systemic immunity and neurological health, emerges as an important regulator of iron homeostasis and inflammatory responses, thereby influencing ferroptotic pathways. This review investigates how gut microbiota dysbiosis and ferroptosis impact MS, emphasizing their potential as therapeutic targets. Through an integrated examination of mechanistic pathways and clinical evidence, we discuss how targeting these interactions could lead to novel interventions that not only modulate disease progression but also offer personalized treatment strategies based on gut microbiota profiling. This synthesis aims at deepening insights into the microbial contributions to ferroptosis and their implications in MS, setting the stage for future research and therapeutic exploration.

Dysregulation in the microbiota by HBV and HCV infection induces an altered cytokine profile in the pathobiome of infection

Viral hepatitis is a public health problem, about 1 million people die due to complications of this viral disease, the etiological agents responsible for inducing cirrhosis and cellular hepatocarcinoma are HBV and HCV, both hepatotropic viruses that cause asymptomatic infection in most cases. The regulation of the microbiota performs many physiological functions, which can induce normal intestinal function and produce essential nutrients for the human body. Metabolites derived from gut microbiota or direct regulation of host immunity and metabolism have been reported to profoundly affect tumorigenesis in liver disease. If the microbiota is unbalanced, both exogenous and symbiotic microorganisms can affect a pathological process. It is well understood that the microbiota plays a role in viral diseases and infections, specifically the hepatic portal pathway has been linked to the gut-liver axis. In HBV and HCV infections, the altered bacterial representatives undergo a state of dysbiosis, with subsequent establishment of the pathobiome with overexpression of taxons such as Bacteroides, Clostridium, Lactobacillus, Enterobacter, and Enterococcus. This dysregulated microbiome induces a microenvironment conducive to the development of hepatic complications in patients with acute and chronic HBV and HCV infection, with subsequent dysregulation of cytokines IFN-α/β, TNF-α, IL-1β, TGF-β, IL-6 and IL-10, which alter the dysfunction and damage of the hepatic portal system. In view of the above, this review aimed to correlate the pathophysiological mechanisms in HBV and HCV infection, the dysregulation of the microbiome in patients infected with HBV and HCV, the most altered cytokines in the microbiome, and the most altered bacterial representatives in the pathobiome of infection.

The future of clinical trials of gut microbiome therapeutics in cirrhosis

The last two decades have witnessed an explosion of microbiome research, including in hepatology, with studies demonstrating altered microbial composition in liver disease. More recently, efforts have been made to understand the association of microbiome features with clinical outcomes and to develop therapeutics targeting the microbiome. While microbiome therapeutics hold much promise, their unique features pose certain challenges for the design and conduct of clinical trials. Herein, we will briefly review indications for microbiome therapeutics in cirrhosis, currently available microbiome therapeutics, and the biological pathways targeted by these therapies. We will then focus on the best practices and important considerations for clinical trials of gut microbiome therapeutics in cirrhosis.

Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine

Over recent years, studies on microbiota research and synthetic biology have explored novel approaches microbial manipulation for therapeutic purposes. However, fragmented information is available on this aspect with key insights scattered across various disciplines such as molecular biology, genetics, bioengineering, and medicine. This review aims to the transformative potential of synthetic biology in advancing microbiome research and therapies, with significant implications for healthcare, agriculture, and environmental sustainability. By merging computer science, engineering, and biology, synthetic biology allows for precise design and modification of biological systems via cutting edge technologies like CRISPR/Cas9 gene editing, metabolic engineering, and synthetic oligonucleotide synthesis, thus paving the way for targeted treatments such as personalized probiotics and engineered microorganisms. The review will also highlight the vital role of gut microbiota in disorders caused by its dysbiosis and suggesting microbiota-based therapies and innovations such as biosensors for real-time gut health monitoring, non-invasive diagnostic tools, and automated bio foundries for better outcomes. Moreover, challenges including genetic stability, environmental safety, and robust regulatory frameworks will be discussed to understand the importance of ongoing research to ensure safe and effective microbiome interventions.

Impact of perinatal administration of probiotics on immune cell composition in neonatal mice

BACKGROUND

Newborns and especially preterm infants are much more susceptible to infections than adults. The pathogens causing infections in newborns are often detectable in the intestinal flora of affected children even before disease onset. Therefore, it seems reasonable to prevent dysbiosis in newborns and preterm infants. An approach followed in many neonatal intensive care units (NICUs) is to prevent infections in preterm infants with probiotics however their mechanisms of action of probiotics are incompletely understood. Here, we investigated the effect of perinatal probiotic exposure on immune cells in newborn mice.

METHODS

Pregnant mice were orally treated with a combination of Lactobacillus acidophilus and Bifidobacterium bifidum (Infloran®) from mid-pregnancy until the offspring were harvested. Immune cell composition in organs of the offspring were analyzed by flow cytometry.

RESULTS

Perinatal probiotic exposure had profound effects on immune cell composition in the intestine, liver and lungs of newborn mice with reduction of myeloid and B cells and induction of T cells in the probiotic treated animals' organs at weaning. Furthermore, probiotic exposure had an effect on T cell development in the thymus.

CONCLUSION

Our results contribute to a better understanding of the interaction of probiotics with the developing immune system.

IMPACT

probiotics have profound effects on immune cell composition in intestines, livers and lungs of newborn mice. probiotics modulate T cell development in thymus of newborn mice. effects of probiotics on neonatal immune cells are particularly relevant in transition phases of the microbiome. our results contribute to a better understanding of the mechanisms of action of probiotics in newborns.

A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes

BACKGROUND

Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.

METHODS

This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.

RESULTS

When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.

CONCLUSIONS

The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.

Primary Prevention Strategy for Non-Communicable Diseases (NCDs) and Their Risk Factors: The Role of Intestinal Microbiota

Non-communicable diseases (NCDs) are the leading cause of morbidity and mortality worldwide. These conditions have numerous health consequences and significantly impact patients' lifestyles. Effective long-term treatment is essential since NCDs are irreversible. Therefore, primary healthcare must be both exclusive and of the highest quality, ensuring comprehensive care. The primary goal should be to improve quality of life with a focus on patients, families, and communities, as most of these diseases can be prevented and controlled, although not cured. Several factors have been linked to individual health, including social, cultural, and economic aspects, lifestyle, and certain environmental factors, including work, that can have positive or negative effects. More of these variables may contribute to the onset of NCDs, which are defined by their chronic nature, propensity for prolongation, and generally slow rate of progression. Examples of NCDs include hypertension, type 2 diabetes (T2D), dyslipidemia, and fatty liver disease linked to metabolic dysfunction. The onset of these diseases has been associated with an imbalance in certain microbial niches, such as the gut, which hosts billions of microorganisms performing multiple metabolic functions, such as the production of metabolites like bile acids (BAs), short-chain fatty acids (SCFAs), and trimethylamine N-oxide (TMAO). Therefore, lifestyle changes and personal habits can significantly impact the gut microbiota (GM), potentially preventing chronic diseases associated with metabolism. NCDs are highly prevalent worldwide, prompting increased attention to strategies for modifying the intestinal microbiota (IM). Approaches such as probiotics, prebiotics, synbiotics, and fecal transplantation (FMT) have demonstrated improvements in the quality of life for individuals with these conditions. Additionally, lifestyle changes and the adoption of healthy habits can significantly impact IM and may help prevent chronic diseases related to metabolism. Therefore, the main aim of this review is to analyze and understand the importance of microbiota intervention in the prevention of non-communicable diseases. R3:A1.

Diagnosing and engineering gut microbiomes

The microbes, nutrients and toxins that we are exposed to can have a profound effect on the composition and function of the gut microbiome. Thousands of peer-reviewed publications link microbiome composition and function to health from the moment of birth, right through to centenarians, generating a tantalizing glimpse of what might be possible if we could intervene rationally. Nevertheless, there remain relatively few real-world examples where successful microbiome engineering leads to beneficial health effects. Here we aim to provide a framework for the progress needed to turn gut microbiome engineering from a trial-and-error approach to a rational medical intervention. The workflow starts with truly understanding and accurately diagnosing the problems that we are trying to fix, before moving on to developing technologies that can achieve the desired changes.

Changes in Gut Microbial Composition and DNA Methylation in Obese Patients with NAFLD After Bariatric Surgery

This study investigates the effects of bariatric surgery on non-alcoholic fatty liver disease (NAFLD) by examining the interplay between gut microbiota, epigenetics, and metabolic health. A cohort of 22 patients undergoing sleeve gastrectomy (SG) was analyzed for changes in gut microbial composition and DNA methylation profiles before and six months after surgery. Correlations between gut microbial abundance and clinical markers at baseline revealed that certain genera were associated with worse metabolic health and liver markers. Following SG, significant improvements were observed in the clinical, anthropometric, and biochemical parameters of the NAFLD patients. Although alpha-diversity indices (i.e., Chao1, Simpson, Shannon) did not show significant changes, beta-diversity analysis revealed a slight shift in microbial composition (PERMANOVA, p = 0.036). Differential abundance analysis identified significant changes in specific bacterial taxa, including an increase in beneficial Lactobacillus species such as Lactobacillus crispatus and Lactobacillus iners and a decrease in harmful taxa like Erysipelotrichia. Additionally, DNA methylation analysis revealed 609 significant differentially methylated CpG sites between the baseline values and six months post-surgery, with notable enrichment in genes related to the autophagy pathway, such as IRS4 and ATG4B. The results highlight the individualized responses to bariatric surgery and underscore the potential for personalized treatment strategies. In conclusion, integrating gut microbiota and epigenetic factors into NAFLD management could enhance treatment outcomes, suggesting that future research should explore microbiome-targeted therapies and long-term follow-ups on liver health post-surgery.

What We Know About the Actual Role of Traditional Probiotics in Health and Disease

The complex relationship between probiotics and human health goes beyond their traditional function in gut health, generating considerable interest for their broad potential in disease treatment. This review explores the various functions of probiotics, highlighting their impact on the immune system, their benefits for gut and oral health, their effects on metabolic and neurological disorders, and their emerging potential in cancer therapy. We give significant importance to studying the effects of probiotics on the gut-brain axis, revealing new and non-invasive therapeutic approaches for complex neurological disorders. In addition, we expand the discussion to encompass the impact of probiotics on the gut-liver and gut-lung axes, recognizing their systemic effects and potential in treating respiratory and hepatic conditions. The use of probiotic "cocktails" to improve cancer immunotherapy outcomes indicates a revolutionary approach to oncological treatments. The review explores the specific benefits associated with various strains and the genetic mechanisms that underlie them. This study sets the stage for precision medicine, where probiotic treatments can be tailored to meet the unique needs of each patient. Recent developments in delivery technologies, including microencapsulation and nanotechnology, hold great potential for enhancing the effectiveness and accuracy of probiotic applications in therapeutic settings. This study provides a strong basis for future scientific research and clinical use, promoting the incorporation of probiotics into treatment plans for a wide range of diseases. This expands our understanding of the potential benefits of probiotics in modern medicine.

Next-Generation Sequencing to Determine Changes in the Intestinal Microbiome of Juvenile Sturgeon Hybrid (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) Resulting from Sodium Butyrate, Β-Glucan and Vitamin Supplementation

BACKGROUND/OBJECTIVES

The effect of sodium butyrate (NaB), β-glucan (βG) and vitamins in the diet on gut microbiome, cortisol level, lysozyme activity and growth parameters of juvenile hybrid sturgeon (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) was determined.

METHODS

Sturgeon hybrids (n = 144) were divided into three groups with enriched feeding (mg/kg of feed): FQV1 (50 NaB; 20 βG; const. vitamins), FQV2 (150 NaB; 20 βG; const. vitamins), FQV3 (50 NaB; 60 βG; const. vitamins) and control (not supplemented), each group in triplicate, 12 fish in each repetition. Rearing was carried out for 30 days in controlled conditions. Gut microbiome was characterized using Next Generation Sequencing (NGS) of DNA samples isolated from intestinal content. Cortisol level was determined using the ELISA test. Lysozyme activity was measured by turbidimetric test.

RESULTS

Based on data obtained from NGS, it was determined that the FQV1 group is characterized by the highest values of diversity indices (Shannon, Simpson and Chao-1) and the largest number of ASVs (Amplicon Sequence Variants). The highest abundance of probiotic bacteria (Lactobacillus, Lactococcus) was determined in the FQV1 group. The highest cortisol concentration was determined in the control (33.26 ng/mL), while the lowest was in FQV3 (27.75 ng/mL). The highest lysozyme activity was observed in FQV1 (154.64 U/mL), and the lowest in FQV2 (104.39 U/mL) and control (121.37 U/mL) (p < 0.05). FQV2 was characterized by significantly more favorable values of breeding indicators (p < 0.05).

CONCLUSIONS

The obtained results prove that an appropriate composition of NaB, βG and vitamins can be used in the commercial breeding of juvenile hybrid sturgeons.

Biomarkers of lymph node metastasis in esophageal cancer

Esophageal cancer (EC) is among the most aggressive malignancies, ranking as the seventh most prevalent malignant tumor worldwide. Lymph node metastasis (LNM) indicates localized spread of cancer and often correlates with a poorer prognosis, emphasizing the necessity for neoadjuvant systemic therapy before surgery. However, accurate identification of LNM in EC presents challenges due to the lack of satisfactory diagnostic techniques. Imaging techniques, including ultrasound and computerized tomography scans, have low sensitivity and accuracy in assessing LNM. Additionally, the existing serological detection lacks precise biomarkers. The intricate and not fully understood molecular processes involved in LNM of EC contribute to current detective limitations. Recent research has shown potential in using various molecules, circulating tumor cells (CTCs), and changes in the microbiota to identify LNM in individuals with EC. Through summarizing potential biomarkers associated with LNM in EC and organizing the underlying mechanisms involved, this review aims to provide insights that facilitate biomarker development, enhance our understanding of the underlying mechanisms, and ultimately address the diagnostic challenges of LNM in clinical practice.

Investigating the causal link between gut microbiota and dry age-related macular degeneration: a bidirectional Mendelian randomization study

AIM

To assess the causal link between 211 gut microbiota (GM) taxa and dry age-related macular degeneration (dAMD) risk.

METHODS

Mendelian randomization using instrumental factors taken from a genome-wide association study (GWAS) were used. Inverse variance weighted (IVW) analysis and sensitivity analysis were performed on the FinnGen project, which included 5095 cases and 222 590 controls.

RESULTS

The IVW analysis showed substantial genus- and family-level relationships between GM taxa and dAMD risk. Specifically, the family Peptococcaceae (P=0.03), genus Bilophila (P=3.91×10-3), genus Faecalibacterium (P=6.55×10-3), and genus Roseburia (P=0.04) were linked to a higher risk of developing dAMD, while the genus Candidatus Soleaferrea (P=7.75×10-4), genus Desulfovibrio (P=0.04) and genus Eubacterium ventriosum group (P=0.04) exhibited a protective effect against dAMD. No significant causal relationships were observed at higher taxonomic levels. Additionally, in the reverse IVW analysis, no meaningful causal effects of the 7 GM taxa.

CONCLUSION

These findings give support for the gut-retina axis participation in dAMD and shed light on putative underlying processes. Investigations on the connection between GM and dAMD have not yet revealed the underlying mechanism.

Health by design; optimising our urban environmental microbiomes for human health

Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.

Comparative genome analysis of microbial strains marketed for probiotic interventions: an extension of the Integrated Probiotic Database

Background: Members of the Bifidobacterium genus and lactobacilli are the most commonly used probiotics to promote human health. In this context, genome-based in silico analyses have been demonstrated as a fast and reliable tool for identifying and characterizing health-promoting activities imputed to probiotics. Methods: This study is an extension of the Integrated Probiotic Database (IPDB) previously created on probiotics of the genus Bifidobacterium, facilitating a comprehensive understanding of the genetic characteristics that contribute to the diverse spectrum of beneficial effects of probiotics. The strains integrated into this new version of the IPDB, such as various lactobacilli and strains belonging to the species Streptococcus thermophilus (S. thermophilus) and Heyndrickxia coagulans (H. coagulans) (formerly Bacillus coagulans), were selected based on the labels of probiotic formulations currently on the market and using the bacterial strains whose genome had already been sequenced. On these bacterial strains, comparative genome analyses were performed, mainly focusing on genetic factors that confer structural, functional, and chemical characteristics predicted to be involved in microbe-host and microbe-microbe interactions. Results: Our investigations revealed marked inter- and intra-species variations in the genetic makeup associated with the biosynthesis of external structures and bioactive metabolites putatively associated with microbe- and host-microbe interactions. Conclusion: Although genetic differences need to be confirmed as functional or phenotypic differences before any probiotic intervention, we believe that considering these divergences will aid in improving effective and personalized probiotic-based interventions.

Microbiome and infectious disease: diagnostics to therapeutics

Over 300 years of research on the microbial world has revealed their importance in human health and disease. This review explores the impact and potential of microbial-based detection methods and therapeutic interventions, integrating research of early microbiologists, current findings, and future perspectives.

Transgenerational impacts of early life adversity: from health determinants, implications to epigenetic consequences

Exposure to different environmental factors, social and socioeconomic factors promotes development of the early-life adversity (ELA) phenotype. The persistence of this phenotype across generations is an interesting phenomenon that remains unexplored. Of late many studies have focused on disease-associated outcomes of ELA following exposure during childhood but the persistence of epigenetic imprints transmitted by ELA exposed parents to their offspring remains poorly described. It is possible that both parents are able to transmit ELA-associated genetic imprints to their offspring via transgenerational inheritance mechanisms. Here, we highlight the role of the mother and father in the biological process of conception, from epigenetic reprogramming cycles to later environmental exposures. We explain some of the known determinants of ELA (pollution, socioeconomic challenges, infections, etc.) and their disease-associated outcomes. Finally, we highlight the role of epigenetics, mitochondria and ncRNAs as mechanisms mediating transgenerational inheritance. Whether these transgenerational inheritance mechanisms occur in the human context remains unclear but there is a large body of suggestive evidence in non-human models that points out to its existence.

Harnessing the Power of the Gut Microbiome: A Review of Supplementation Therapies for Metabolic Syndrome

Metabolic syndrome (MetS) is a complex condition characterized by abdominal obesity, insulin resistance, dyslipidemia, and hypertension, all of which increase the risk of cardiovascular disease and type 2 diabetes. The gut microbiome plays a significant role in metabolic health, influencing digestion, immune function, and energy metabolism. When the gut microbiota becomes imbalanced due to poor diet and antibiotic use, it can lead to systemic inflammation, insulin resistance, and abnormal lipid metabolism, which are central features of MetS. This review explores the connection between gut microbial imbalances and MetS, focusing on the impact of the gut microbiome on metabolic health. Supplementation therapies targeting the gut microbiome, such as probiotics, prebiotics, synbiotics, and postbiotics, are evaluated for their potential to improve metabolic parameters in MetS patients. These interventions hold promise for enhancing insulin sensitivity, reducing inflammation, and improving lipid profiles. However, further research is needed to optimize these approaches for managing MetS. Understanding how to leverage the gut microbiome could lead to innovative, non-invasive treatments for this growing global health concern.

The causal relationship between gut microbiota and constipation: a two-sample Mendelian randomization study

BACKGROUND

Constipation is one of the most common gastrointestinal disorders afflicting the population, with recent observational studies implicating dysfunction of the gut microbiota in constipation. Despite observational studies indicating a relationship, a clear causality remains unclear. This study aims to use two-sample Mendelian randomization (MR) to establish a clearer causal relationship between the two.

METHODS

A two-sample Mendelian randomization (MR) study was performed using the gut microbiota summary Genome-Wide Association Studies (GWAS) statistics from MiBioGen consortium (n = 13,266) and constipation GWAS summary statistics from the IEU OpenGWAS database. The causality between gut microbiota and constipation is primarily analyzed using the inverse-variance weighted (IVW) method and reinforced by an additional four methods, including MR-Egger, Weighted Median, Simple Mode, and Weighted Mode. Finally, funnel plot, heterogeneity test, horizontal pleiotropy test, and leave-one-out test were used to evaluate the reliability of MR results.

RESULTS

IVW estimates suggested that the bacterial species Anaerotruncus, Butyricimonas, and Hungatella were causally associated with constipation. The odds ratio (OR) values of Anaerotruncus, Butyricimonas, and Hungatella were 1.08 (95% CI = 1.02-1.13; P = 0.007), 1.07 (95% CI = 1.01-1.13; P = 0.015), 1.03 (95% CI = 1.00-1.06; P = 0.037) respectively. Meanwhile, Ruminiclostridium 9 and Intestinibacter have been shown to be associated with a reduced risk of constipation. The OR of Ruminiclostridium 9 = 0.75(95% CI = 0.73-0.78, P < 0.001 and Intestinibacter of OR = 0.89 (95% CI = 0.86-0.93, P < 0.001). Furthermore, validation by funnel plot, heterogeneity test, and horizontal pleiotropy test showed that MR results were reliable.

CONCLUSION

This is the first Mendelian randomization study to explore the causalities between specific gut microbiota taxa and constipation, and as such may be useful in providing insights into the unclear pathology of constipation which can in turn aid in the search for prevention and treatment.

Probiotics and the microbiota-gut-brain axis in neurodegeneration: Beneficial effects and mechanistic insights

Neurodegenerative diseases (NDs) are a group of heterogeneous disorders with a high socioeconomic burden. Although pharmacotherapy is currently the principal therapeutic approach for the management of NDs, mounting evidence supports the notion that the protracted application of available drugs would abate their dopaminergic outcomes in the long run. The therapeutic application of microbiome-based modalities has received escalating attention in biomedical works. In-depth investigations of the bidirectional communication between the microbiome in the gut and the brain offer a multitude of targets for the treatment of NDs or maximizing the patient's quality of life. Probiotic administration is a well-known microbial-oriented approach to modulate the gut microbiota and potentially influence the process of neurodegeneration. Of note, there is a strong need for further investigation to map out the mechanistic prospects for the gut-brain axis and the clinical efficacy of probiotics. In this review, we discuss the importance of microbiome modulation and hemostasis via probiotics, prebiotics, postbiotics and synbiotics in ameliorating pathological neurodegenerative events. Also, we meticulously describe the underlying mechanism of action of probiotics and their metabolites on the gut-brain axis in different NDs. We suppose that the present work will provide a functional direction for the use of probiotic-based modalities in promoting current practical treatments for the management of neurodegenerative-related diseases.

Microbiome in Teenagers – Acquisition and Development

Adolescence is the stage of life between childhood and adulthood, ranging from 10 to 19 years. It is a distinct period in human development and crucial for setting the groundwork for long-term health. Teenagers grow quickly in terms of their physical, cognitive, and emotional development.In the body of teenagers, major changes in microorganisms take place. With the development of these changes in the microbiome of teenagers, diseases are also developed. Teenagers are the future of the world. Microbiota and diseases have an impact on their emotions, thoughts, decisions, and interactions with others and their environment. This chapter is written to acknowledge the readers about the resident microorganisms of the human body during adolescence and the many kinds of changes that occur in the microbiome due to lifestyle changes.

Revolutionizing Gastrointestinal Disorder Management: Cutting-Edge Advances and Future Prospects

In recent years, remarkable strides have been made in the management of gastrointestinal disorders, transforming the landscape of patient care and outcomes. This article explores the latest breakthroughs in the field, encompassing innovative diagnostic techniques, personalized treatment approaches, and novel therapeutic interventions. Additionally, this article emphasizes the use of precision medicine tailored to individual genetic and microbiome profiles, and the application of artificial intelligence in disease prediction and monitoring. This review highlights the dynamic progress in managing conditions such as inflammatory bowel disease, gastroesophageal reflux disease, irritable bowel syndrome, and gastrointestinal cancers. By delving into these advancements, we offer a glimpse into the promising future of gastroenterology, where multidisciplinary collaborations and cutting-edge technologies converge to provide more effective, patient-centric solutions for individuals grappling with gastrointestinal disorders.

Impact of cadmium and diclofenac exposure on biochemical responses, transcriptome, gut microflora, and growth performance in grass carp (Ctenopharyngodonidella)

In recent years, the concentrations of cadmium (Cd) and diclofenac (DCF) in water have frequently exceeded the standard; however, the toxic effects of these two pollutants on grass carp under single and combined exposure are unknown. In this study, the concentrations of pollutants in different tissues were detected, and the toxicities of the two pollutants to grass carp under different exposure conditions were compared based on growth traits, biochemical responses, gut microbiome, and transcriptomes. Based on these findings, the brain showed the lowest levels of Cd and DCF accumulation. Oxidative stress and pathological damage were observed in the brain and intestines. Changes in the structure and abundance of the gut microflora affect the synthesis of neurotransmitters, such as GABA and steroids. Differentially expressed genes in the brain were enriched in circadian rhythm functions. The expression of PER, CLOCK,1L-1β, 1L-17, and other genes are related to the abundance of Akkermansia, which indicates that the disorder of gut microflora will affect the normal circadian rhythm of the brain. All indices in the recovery group showed an increasing trend. Overall, the toxicity of Cd and DCF showed antagonism, and a single exposure had a stronger effect on gut microorganisms and circadian rhythm, which provided a scientific basis for exploring the comprehensive effects of different pollutants.