The role of gut microbiota in immune homeostasis and autoimmunity

Gut virome: New key players in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

Microbiome-mediated modulation of immune memory to P. yoelii affects the resistance to secondary cerebral malaria challenge

Malaria is caused by protozoan parasites in the genus Plasmodium. Over time individuals slowly develop clinical immunity to malaria, but this process occurs at variable rates, and the mechanism of protection is not fully understood. We have recently demonstrated that in genetically identical C57BL/6N mice, gut microbiota composition dramatically impacts the quality of the humoral immune response to Plasmodium yoelii and subsequent protection against a lethal secondary challenge with Plasmodium berghei ANKA in C57BL/6N mice. Here, we utilize this genetically identical, gut microbiome-dependent model to investigate how the gut microbiota modulate immunological memory, hypothesizing that the gut microbiome impacts the formation and functionality of immune memory. In support of this hypothesis, P. yoelii hyperparasitemia-resistant C57BL/6N mice exhibit increased protection against P. berghei ANKA-induced experimental cerebral malaria (ECM) compared to P. yoelii hyperparasitemia-susceptible C57BL/6N mice. Despite differences in protection against ECM, P. yoelii-resistant and -susceptible mice accumulate similar numbers of memory B cells (MBCs) and memory T cells. Following challenge with P. berghei ANKA, P. yoelii-resistant mice generated more rapid germinal center reactions; however, P. yoelii-resistant and -susceptible mice had similar titers of P. yoelii- and P. berghei-specific antibodies. In contrast, P. yoelii-resistant mice had an increased number of regulatory T cells in response to secondary challenge with P. berghei ANKA, which may dampen the immune-mediated breakdown of the blood-brain barrier and susceptibility to P. berghei-induced ECM. These findings demonstrate the ability of the gut microbiome to shape immune memory and the potential to enhance resistance to severe malaria outcomes.

Gut microbiome diversity is associated with muscle mass, strength and quality in post-stroke patients

BACKGROUND

The gut microbiome has emerged as a potential influencer of muscle health; however, its role in hospitalized patients remains unclear. This study aimed to investigate the association between gut microbiome diversity and skeletal muscle mass, strength, and quality in hospitalized post-stroke patients.

METHODS

We conducted a cross-sectional study of post-stroke patients admitted to a rehabilitation facility. Gut microbiome diversity was assessed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, calculating Operational Taxonomic Unit (OTU) Richness, Faith's Phylogenetic Diversity (PD), and Shannon index. Muscle health was evaluated using skeletal muscle index (SMI) for muscle mass, handgrip strength (HGS) for muscle strength, and bioimpedance analysis-derived phase angle (PhA) for muscle quality. Multiple linear regression analyses were performed, adjusting for potential confounders.

RESULTS

A total of 156 patients (mean age 78.4 years; 55.7 % male) were analyzed. OTU Richness showed significant positive associations with SMI (β = 0.197, p = 0.025), HGS (β = 0.180, p = 0.005), and PhA (β = 0.178, p = 0.022). The Shannon index was also positively associated with SMI (β = 0.120, p = 0.041), HGS (β = 0.140, p = 0.028), and PhA (β = 0.164, p = 0.032). Faith's PD did not demonstrate significant associations with muscle health parameters.

CONCLUSIONS

Higher gut microbiome diversity, assessed by OTU Richness and Shannon index, is associated with better muscle mass, strength, and quality in post-stroke patients. These findings suggest a potential role for gut microbiota in muscle health during stroke rehabilitation.

Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV

This work aims to (1) identify microbial and metabolic alterations and (2) reveal a shift in phenylalanine production-consumption equilibrium in individuals with HIV. We conducted extensive searches in multiple databases [MEDLINE, Web of Science (including Cell Press, Oxford, HighWire, Science Direct, IOS Press, Springer Nature, PNAS, and Wiley), Google Scholar, and Embase] and selected two case-control 16S data sets (GenBank IDs: SRP039076 and EBI ID: ERP003611) for analysis. We assessed alpha and beta diversity, performed univariate tests on genus-level relative abundances, and identified significant microbiome features using random forest. We also utilized the MICOM model to simulate growth and metabolic exchanges within the microbiome, focusing on the Metabolite Exchange Score (MES) to determine key metabolic interactions. We found that L-phenylalanine had a higher MES in HIV-uninfected individuals compared with their infected counterparts. The flux of L-phenylalanine consumption was significantly lower in HIV-infected individuals compared with healthy controls, correlating with a decreased number of consuming species in the chronic HIV stage. Prevotella, Roseburia, and Catenibacterium were demonstrated as the most important microbial species involving an increase in L-phenylalanine production in HIV patients, whereas Bacteroides, Faecalibacterium, and Blautia contributed to a decrease in L-phenylalanine consumption. We also found significant alterations in both microbial diversity and metabolic exchanges in people living with HIV. Our findings shed light on why HIV-1 patients have elevated levels of phenylalanine. The impact on essential amino acids like L-phenylalanine underscores the effect of HIV on gut microbiome dynamics. Targeting the restoration of these interactions presents a potential therapeutic avenue for managing HIV-related dysbiosis.

Microbiome-based therapeutics for ocular diseases

The relationship between the gut microbiome and ocular health has garnered increasing attention within the scientific community. Recent research has focused on the gut-eye axis, examining whether imbalances within the gut microbiome can influence the development, progression and severity of ocular diseases, including dry eye disease, uveitis, and glaucoma. Dysbiosis within the gut microbiome is linked to immune dysregulation, chronic inflammation, and epithelial barrier dysfunction, all of which contribute to ocular pathology. This review synthesises current evidence on these associations, exploring how gut microbiome alterations drive disease mechanisms. Furthermore, it examines the therapeutic potential of microbiome-targeted interventions, including antibiotics, prebiotics, probiotics, and faecal microbiota transplantation, all of which aim to restore microbial balance and modulate immune responses. As the prevalence of these conditions continues to rise, a deeper understanding of the gut-eye axis may facilitate the development of novel, targeted therapies to address unmet needs in the management of ocular diseases.

The Gut Feeling: The Role of Gut Microbiome in Orthopedics

Introduction: Advancements in microbiome-targeted therapies, including probiotics, prebiotics, and fecal microbial transplantation, offer exciting possibilities for orthopedic care. Probiotics, live beneficial microorganisms found in fermented foods, such as yogurt, kefir, sauerkraut, kimchi, and cheese, help maintain a healthy gut microbiome. Prebiotics and fiber-rich foods such as onions, garlic, and whole grains, nourish these bacteria, supporting their growth and activity. Together, these therapies regulate gut health, promote immune resilience, reduce infection risks, and accelerate healing – key factors in orthopedic outcomes [1, 2]. The gut microbiome, a diverse ecosystem of microorganisms, plays a pivotal role in maintaining overall health [3]. Beyond digestion, it influences immune regulation, inflammation control, and musculoskeletal well-being [4]. Gut health significantly impacts orthopedic outcomes, including infection control, bone healing, and maintaining bone density. An imbalance in this ecosystem, known as dysbiosis, can compromise recovery and increase infection risks [5]. Supporting gut health through dietary modifications, probiotics, or prebiotics holds the potential to enhance patient outcomes [6]. Orthopedic Infections and Gut Health: Periprosthetic joint infections and fracture-related infections remain formidable challenges in orthopedic care. Biofilm formation on implants can protect bacteria from antibiotics and immune responses, complicating treatment [7]. Dysbiosis can further exacerbate these risks by allowing bacteria to enter the bloodstream and colonize surgical sites [8]. Maintaining a balanced gut microbiome can enhance the body’s immune defenses, limit bacterial migration, and promote implant longevity. Fracture Healing and Microbial Influence: Bone repair is a finely regulated process involving inflammation, new bone formation, and remodeling [9]. A healthy gut microbiome plays an essential role in managing this process by moderating inflammation and promoting bone cell activity. Disruptions to the microbial ecosystem can lead to excessive inflammation and hinder the body’s ability to heal effectively [10]. Supporting microbial health may improve healing outcomes for patients prone to delayed recovery or complications. Autoimmune Conditions and Increased Susceptibility to Infection: Autoimmune diseases, such as rheumatoid arthritis, heighten susceptibility to infections due to weakened immune function [11]. Dysbiosis can further worsen immune imbalance, increasing the risk of bacterial migration to surgical sites. Ensuring gut health may help fortify immune resilience and reduce post-surgical complications for patients with these conditions [12]. Pain Management and Microbiome Modulation: The gut microbiome affects pain perception by influencing the production of neurotransmitters that regulate pain pathways. An imbalance in gut bacteria can lead to heightened pain sensitivity, posing challenges for managing chronic conditions such as osteoarthritis [13]. Optimizing gut health may offer an additional approach to complement traditional pain management strategies and reduce dependency on medications. Bone Density and Mineral Absorption The gut microbiome plays a critical role in absorbing minerals vital for maintaining bone strength and density. Disruptions in microbial balance can impair this absorption process, contributing to conditions such as osteoporosis [14]. Emerging research suggests that specific probiotics may help enhance mineral absorption, providing a supportive therapy for improving bone health and reducing fracture risk [15]. Post-Surgical Recovery and Systemic Health: The influence of the gut microbiome extends beyond local sites, playing a key role in systemic recovery following surgery. A balanced microbiome supports faster healing, reduced inflammation, and fewer post-operative complications. Conversely, microbial imbalances can delay recovery and increase the risk of infections [16]. Strategies to maintain microbial health in the perioperative period may improve surgical outcomes and accelerate rehabilitation. Innovative Approaches in Orthopedic Care: Screening for microbial imbalances before surgery could allow for timely interventions, minimizing complications and improving outcomes. While some therapies remain experimental, they represent promising avenues for future developments in personalized orthopedic treatment strategies [17]. Recent research has revealed that gut microbial alterations, particularly those affecting arginine metabolism, play a significant role in influencing bone structural remodeling [18]. Mechanical loading is crucial for maintaining bone health, but its effectiveness is often hampered by high variability in bone mechanoreceptor activity influenced by gut microbes. Studies have shown that microbial depletion can profoundly influence this responsiveness, indicating a possible pathway for future therapeutic strategies. The gut-bone axis, a concept gaining increasing attention, connects the state of the microbiome with bone health [19]. This relationship opens up the potential for microbiome-targeted interventions, such as dietary changes or probiotics, to enhance bone strength and treat conditions such as osteoporosis and inflammatory arthritis. By understanding the microbial factors that influence bone metabolism, researchers are uncovering new mechanisms for improving bone health, offering hope for more effective treatments in the future. To summarize the diverse and critical roles of the gut microbiome in orthopedic practice, the following table highlights key conditions and their implications for patient care (Table 1). Conclusion: The gut microbiome’s influence on infection, healing, and overall orthopedic outcomes presents an exciting area of exploration. For orthopedic surgeons and clinicians, understanding the gut microbiome’s role offers new preventive and therapeutic pathways, particularly in managing infection risks associated with implants and fractures. Future research may bring even more microbiome-targeted therapies, transforming orthopedic practices and improving patient care in ways that extend beyond traditional approaches. By integrating gut health into orthopedic treatment strategies, health-care providers can foster stronger, more resilient recovery for their patients, advancing the field toward more holistic and effective care.

A guide to germ-free and gnotobiotic mouse technology to study health and disease

The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.

From Microbes to Metabolites: Advances in Gut Microbiome Research in Type 1 Diabetes

Background: Type 1 diabetes (T1D) is a severe chronic T-cell mediated autoimmune disease that attacks the insulin-producing beta cells of the pancreas. The multifactorial nature of T1D involves both genetic and environmental components, with recent research focusing on the gut microbiome as a crucial environmental factor in T1D pathogenesis. The gut microbiome and its metabolites play an important role in modulating immunity and autoimmunity. In recent years, studies have revealed significant alterations in the taxonomic and functional composition of the gut microbiome associated with the development of islet autoimmunity and T1D. These changes include reduced production of short-chain fatty acids, altered bile acid and tryptophan metabolism, and increased intestinal permeability with consequent perturbations of host (auto)immune responses. Methods/Results: In this review, we summarize and discuss recent observational, mechanistic and etiological studies investigating the gut microbiome in T1D and elucidating the intricate role of gut microbes in T1D pathogenesis. Moreover, we highlight the recent advances in intervention studies targeting the microbiota for the prevention or treatment of human T1D. Conclusions: A deeper understanding of the evolution of the gut microbiome before and after T1D onset and of the microbial signals conditioning host immunity may provide us with essential insights for exploiting the microbiome as a prognostic and therapeutic tool.

Human milk oligosaccharides 2'-fucosyllactose and 3-fucosyllactose attenuate ovalbumin-induced food allergy through immunoregulation and gut microbiota modulation

The prebiotic properties of human milk oligosaccharides (HMOs) and emerging evidence of immunomodulatory effects suggest their potential therapeutic value in allergy management. 2'-Fucosyllactose (2'-FL) has been reported to alleviate food allergies, while the effect of other fucosylated HMOs on food allergy remains unclear. In this study, we assess the effect of two HMOs, 2'-FL and 3-fucosyllactose (3-FL), on symptomatology and immunological responses in an ovalbumin (OVA)-sensitized mouse model of food allergy as well as their influence on gut microbiota. The assessment of allergic symptoms, specific immunoglobulin E (IgE), and related gene expression levels in sensitized mice indicated that 3-FL was as effective as 2'-FL in alleviating food allergy. 2'-FL and 3-FL significantly decreased serum levels of OVA-specific IgE, mouse mast cell protease (mMCP-1) and IL-4 while increasing the levels of IFN-γ. Additionally, 2'-FL and 3-FL down-regulated gene expression of allergy-related cytokines in the small intestine and improved intestinal barrier damage. Furthermore, both 2'-FL and 3-FL treatment positively influenced the gut microbial profiles, in particular by enhancing the proportion of beneficial bacteria such as Lactobacillus and Bifidobacterium and decreasing the percentage of Turicibacter and Lachnospiraceae NK4A136 group, thereby modulating the immune system. Therefore, this study can provide insights into 2'-FL and 3-FL to alleviate OVA-induced allergy.

Systemic inflammation is associated with gut microbiota diversity in post-stroke patients

BACKGROUND

There is growing interest in gut microbiota and health outcomes. However, the relationship between systemic inflammation and gut microbiota diversity in hospitalized patients remains unclear. This study aimed to investigate the association in post-stroke rehabilitation patients.

METHODS

A cross-sectional study was conducted on post-stroke patients admitted to a rehabilitation hospital. Systemic inflammation was assessed using the modified Glasgow Prognostic Score (mGPS). Gut microbiota diversity was evaluated using three indices: Shannon index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analyses were performed to examine the relationship between mGPS and gut microbiota diversity indices, adjusting for potential confounders.

RESULTS

A total of 156 patients (mean age 78.4 years; 55.7% men) were analyzed. The median mGPS was 0 (interquartile range: 0-1), with GPS distribution: 61.8% scored 0, 25.7% scored 1, and 12.5% scored 2. After adjusting for confounders, mGPS was significantly and negatively associated with the Shannon index (B = -0.143, 95% CI -0.288 to -0.002, β = -0.177) and OTU richness (B = -17.832, 95% CI -24.349 to -3.951, β = -0.208). However, no significant association was observed between mGPS and Faith's PD (B = -1.155, 95% CI -2.464 to 0.189, β = -0.155).

CONCLUSION

This study demonstrates a significant negative association between systemic inflammation and both quantitative and qualitative gut microbiota diversity in post-stroke patients.

CD8 + T cells may mediate the effect of gut microbiota on psoriasis: evidence from two-step mendelian randomization and bayesian weighting

Emerging research indicates that gut microbiota and the associated immune responses are crucial in the development of chronic inflammatory skin diseases. This investigation employs Mendelian Randomization (MR) and Bayesian weighting to elucidate the causal links between gut microbiota, immune cells, and psoriasis, with a specific emphasis on CD8 + T cells. We leveraged summary statistics from genome-wide association studies (GWAS) related to gut microbiota, immune cells, and psoriasis. Single nucleotide polymorphisms (SNPs) were chosen as instrumental variables (IVs) to evaluate causal relationships through various MR methods, such as inverse variance weighted (IVW), MR Egger, weighted median, and simple mode. Additionally, Bayesian weighting was used to validate results and account for potential pleiotropy. The IVW analysis revealed significant associations between certain gut microbiota and psoriasis, notably identifying a protective link between Escherichia coli and psoriasis. Further MR analysis demonstrated that Escherichia coli had a causal relationship with CD8 + T cells. Increased levels of CD8 + T cells were associated with a higher risk of psoriasis. BWMR analysis confirmed these findings, showing that CD8 + T cells mediated 10.09% of the protective effect of Escherichia coli on psoriasis. This study underscores the significant role of Escherichia coli and CD8 + T cells in psoriasis, suggesting both protective and exacerbating effects. Understanding these microbiota-immune interactions can lead to the development of more effective, personalized treatments and preventative strategies, ultimately improving patient outcomes and quality of life.

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.

The gut microbiome and osteoarthritis

Osteoarthritis (OA) is one of the most common degenerative diseases, and the number of patients has been constantly increasing. Non-steroidal anti-inflammatory drugs, glucocorticosteroids, opioids, etc., and surgical procedures, e.g. arthroplasty, are among the most common methods of treatment. There are reasons to believe that the gut microbiome (GMB) may influence inflammatory processes occurring in the pathomechanism of OA. The inflammatory processes occurring in the intestines may lead to disruption of tight junctions and increased concentrations of pro-inflammatory cytokines, resulting in increased permeability of intestines, causing low-grade inflammation, including in the joints. Methods of altering the GMB composition to reduce the inflammatory and joint degenerative processes are known only to some extent, and long-term research is required. Osteoarthritis, a particularly well-known and very widespread disease due to the aging population, is characterized by moderate and local inflammation. It occurs due to the effects of biomechanical cartilage wear with damage of joint structures, primarily through degenerative processes. OA represents a therapeutic challenge, and any element that can influence its inhibition is highly sought after. Therefore, these methods seem to offer a promising additional approach to treatment.

Modulation of inflammatory markers in type 2 diabetes mellitus through gut microbiome-targeted interventions: An umbrella review on meta-analyses

BACKGROUND & AIMS

Type 2 diabetes mellitus (T2DM) poses a significant global health challenge due to various lifestyle factors contributing to its prevalence and associated complications. Chronic low-grade inflammation, characterized by elevated levels of inflammatory markers such as C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), plays a pivotal role in the pathogenesis of T2DM. Modulation of the gut microbiota through microbiome-targeted therapy (MTT), including probiotics, prebiotics, and synbiotics, has emerged as a potential strategy to mitigate inflammation and improve metabolic outcomes in T2DM.

METHODS

A systematic review and meta-analysis were conducted following PRISMA guidelines to evaluate the impact of MTT on inflammatory markers in patients with T2DM. Searches were performed in PubMed, Scopus, and Web of Science databases up to June 2024, with inclusion criteria limited to English-language meta-analyses of randomized controlled trials (RCTs) assessing the effects of probiotics, prebiotics, or synbiotics on inflammatory markers in T2DM patients.

RESULTS

Ten meta-analyses met the inclusion criteria, comprising studies investigating the effects of various MTT interventions on CRP, IL-6, and TNF-α levels in T2DM patients. Meta-analysis results indicated significant reductions in CRP (SMD: -0.070; 95 % CI: -0.119 to -0.020) and TNF-α (SMD: -0.370; 95 % CI: -0.554 to -0.186) levels following MTT, while IL-6 reductions (SMD: -0.070; 95 % CI: -0.269 to 0.129) did not reach statistical significance. However, heterogeneity in study quality, intervention protocols, and participant demographics posed challenges in interpretation.

CONCLUSIONS

While improvements in inflammatory markers with MTT have been observed, significant limitations-such as heterogeneity in study quality and variation in intervention protocols-highlight the need for further research to confirm its efficacy and clarify underlying mechanisms. Future studies should aim to address these limitations by exploring variations in dosage, supplement formulations, and bacterial strains, which are crucial for improving the reliability and broader applicability of MTT in the management of T2DM.

Role of Microbiota-Derived Metabolites in Prostate Cancer Inflammation and Progression

Prostate cancer (PCa) is the most commonly detected malignancy in men worldwide. PCa is a slow-growing cancer with the absence of symptoms at early stages. The pathogenesis has not been entirely understood including the key risk factors related to PCa development like diet and microbiota derived metabolites. Microbiota may influence the host's immunological responses, inflammatory responses, and metabolic pathways, which may be crucial for the development and metastasis. Similarly, short-chain fatty acids, methylamines, hippurate, bile acids, and other metabolites generated by microbiota may have potential roles in cancer inflammation and progression of cancer. Most studies have focused on the role of metabolites and their pathways involved in chronic inflammation, tumor initiation, proliferation, and progression. In summary, the review discusses the role of microbiota and microbial-derived metabolite-built strategies in inflammation and progression of the PCa.

Beyond digestion: Exploring how the gut microbiota modulates human social behaviors

For a long time, traditional medicine has acknowledged the gut's impact on general health. Contemporary science substantiates this association through investigations of the gut microbiota, the extensive community of microorganisms inhabiting our gastrointestinal system. These microscopic residents considerably improve digestive processes, nutritional absorption, immunological function, and pathogen defense. Nevertheless, a variety of gastrointestinal and extra-intestinal disorders can result from dysbiosis, an imbalance of the microbial composition of the gut microbiota. A groundbreaking discovery is the gut-brain axis, a complex communication network that links the enteric and central nervous system (CNS). This bidirectional communication allows the brain to influence gut activities and vice versa, impacting mental health and mood disorders like anxiety and depression. The gut microbiota can influence this communication by creating neurotransmitters and short-chain fatty acids, among other biochemical processes. These factors may affect our mental state, our ability to regulate our emotions, and the hypothalamic-pituitary-adrenal (HPA) axis. This study aimed to explore the complex interrelationships between the brain and the gut microbiota. We also conducted a thorough examination of the existing understanding in the area of how microbiota affects social behaviors, including emotions, stress responses, and cognitive functions. We also explored the potential of interventions that focus on the connection between the gut and the brain, such as using probiotics to treat diseases of the CNS. This research opens up new possibilities for addressing mental health and neurological conditions in an innovative manner.

Sleep deprivation-induced shifts in gut microbiota: Implications for neurological disorders

Sleep deprivation is a prevalent issue in contemporary society, with significant ramifications for both physical and mental well-being. Emerging scientific evidence illuminates its intricate interplay with the gut-brain axis, a vital determinant of neurological function. Disruptions in sleep patterns disturb the delicate equilibrium of the gut microbiota, resulting in dysbiosis characterized by alterations in microbial composition and function. This dysbiosis contributes to the exacerbation of neurological disorders such as depression, anxiety, and cognitive decline through multifaceted mechanisms, including heightened neuroinflammation, disturbances in neurotransmitter signalling, and compromised integrity of the gut barrier. In response to these challenges, there is a burgeoning interest in therapeutic interventions aimed at restoring gut microbial balance and alleviating neurological symptoms precipitated by sleep deprivation. Probiotics, dietary modifications, and behavioural strategies represent promising avenues for modulating the gut microbiota and mitigating the adverse effects of sleep disturbances on neurological health. Moreover, the advent of personalized interventions guided by advanced omics technologies holds considerable potential for tailoring treatments to individualized needs and optimizing therapeutic outcomes. Interdisciplinary collaboration and concerted research efforts are imperative for elucidating the underlying mechanisms linking sleep, gut microbiota, and neurological function. Longitudinal studies, translational research endeavours, and advancements in technology are pivotal for unravelling the complex interplay between these intricate systems.

The interplay between gut microbiota composition and dementia

Recently, researchers have been interested in the potential connection between gut microbiota composition and various neuropsychological disorders. Dementia significantly affects the socioeconomics of families. Gut microbiota is considered as a probable factor in its pathogenesis. Multiple bacterial metabolites such as short-chain fatty acids, lipopolysaccharides, and various neurotransmitters that are responsible for the incidence and progression of dementia can be produced by gut microbiota. Various bacterial species such as Bifidobacterium breve, Akkermansia muciniphila, Streptococcus thermophilus, Escherichia coli, Blautia hydrogenotrophica, etc. are implicated in the pathogenesis of dementia. Gut microbiota can be a great target for imitating or inhibiting their metabolites as an adjunctive therapy based on their role in its pathogenesis. Therefore, some diets can prevent or decelerate dementia by altering the gut microbiota composition. Moreover, probiotics can modulate gut microbiota composition by increasing beneficial bacteria and reducing detrimental species. These therapeutic modalities are considered novel methods that are probably safe and effective. They can enhance the efficacy of traditional medications and improve cognitive function.

A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden

Engineered probiotics are an emerging platform for in situ delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered Saccharomyces cerevisiae var. boulardii (Sb), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete "miniature" antibody variants that target programmed death ligand 1 (Sb_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, Sb_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.

Impact of calcineurin inhibitors on gut microbiota: Focus on tacrolimus with evidence from in vivo and clinical studies

Calcineurin Inhibitors (CNIs), including tacrolimus and cyclosporine A, are the most widely used immunosuppressive drugs in solid organ transplantation. Those drugs play a pivotal role in preventing graft rejection and reducing autoimmunity. However, recent studies indicate that CNIs can disrupt the composition of gut microbiota or result in "gut dysbiosis". This dysbiosis has been shown to be a significant factor in reducing host immunity by decreasing innate immune cells and impairing metabolic regulation, leading to lipid and glucose accumulation. Several in vivo and clinical studies have demonstrated a mechanistic link between gut dysbiosis and the side effects of CNI. Those studies have unveiled that gut dysbiosis induced by CNIs contributes to adverse effects such as hyperglycemia, nephrotoxicity, and diarrhea. These adverse effects of the induced gut dysbiosis require interventions to restore microbial balance. Probiotics and dietary supplements have emerged as potential interventions to mitigate the side effects of gut dysbiosis caused by CNIs. In this complex relationship between CNI treatment, gut dysbiosis, and interventions, several types of gut microbiota and host immunity are involved. However, the mechanisms underlying these relationships remain elusive. Therefore, the aim of this review is to comprehensively summarize and discuss the major findings from in vivo and clinical data regarding the impact of treatment with CNIs on gut microbiota. This review also explores interventions to mitigate dysbiosis for therapeutic approaches of the side effects of CNIs. The possible underlying mechanisms of CNIs-induced gut dysbiosis with or without interventions are also presented and discussed.

Chronic Gastrointestinal Disorders and miRNA-Associated Disease: An Up-to-Date

Chronic gastrointestinal disorders such as inflammatory bowel diseases (IBDs) and irritable bowel syndrome (IBS) impose significant health burdens globally. IBDs, encompassing Crohn's disease and ulcerative colitis, are multifactorial disorders characterized by chronic inflammation of the gastrointestinal tract. On the other hand, IBS is one of the principal gastrointestinal tract functional disorders and is characterized by abdominal pain and altered bowel habits. Although the precise etiopathogenesis of these disorders remains unclear, mounting evidence suggests that non-coding RNA molecules play crucial roles in regulating gene expression associated with inflammation, apoptosis, oxidative stress, and tissue permeability, thus influencing disease progression. miRNAs have emerged as possible reliable biomarkers, as they can be analyzed in the biological fluids of patients at a low cost. This review explores the roles of miRNAs in IBDs and IBS, focusing on their involvement in the control of disease hallmarks. By an extensive literature review and employing bioinformatics tools, we identified the miRNAs frequently studied concerning these diseases. Ultimately, specific miRNAs could be proposed as diagnostic biomarkers for IBDs and IBS. Their ability to be secreted into biofluids makes them promising candidates for non-invasive diagnostic tools. Therefore, understanding molecular mechanisms through the ways in which they regulate gastrointestinal inflammation and immune responses could provide new insights into the pathogenesis of IBDs and IBS and open avenues for miRNA-based therapeutic interventions.

A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population

BACKGROUND

The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness. Here, we conducted the first large-scale investigation into the influence of a novel elite athlete-derived probiotic, consisting of a multi-strain Lactobacillus consortium, on sleep quality, exercise recovery, and gut microbiome composition in both elite athletes (n = 11) and the general population (n = 257).

RESULTS

Our two-phase study design, which included an open-label study followed by a controlled longitudinal study in a professional soccer team, allowed us to identify key interactions between probiotics, the gut microbiome, and the host. In the placebo-controlled study, we observed significant improvements in self-reported sleep quality by 69%, energy levels by 31%, and bowel movements by 37% after probiotic intervention relative to after placebo. These improvements were associated with a significant decrease in D-ROMS (a marker of oxidative stress) and a significantly higher free-testosterone/cortisol ratio. Multi-omics analyses revealed specific changes in microbiome composition and function, potentially providing mechanistic insights into these observed effects.

CONCLUSION

This study provides novel insights into how a multi-strain Lactobacillus probiotic modulates sleep quality, exercise recovery, and gut microbiome composition in both the general population and elite athletes, and introduces potential mechanisms through which this probiotic could be influencing overall health. Our results emphasize the untapped potential of tailored probiotic interventions derived from extremely fit and healthy individuals in improving several aspects of health and performance directly in humans. Video Abstract.

Gut microbiome-gut brain axis-depression: interconnection

OBJECTIVES

The relationship between the gut microbiome and mental health, particularly depression, has gained significant attention. This review explores the connection between microbial metabolites, dysbiosis, and depression. The gut microbiome, comprising diverse microorganisms, maintains physiological balance and influences health through the gut-brain axis, a communication pathway between the gut and the central nervous system.

METHODS

Dysbiosis, an imbalance in the gut microbiome, disrupts this axis and worsens depressive symptoms. Factors like diet, antibiotics, and lifestyle can cause this imbalance, leading to changes in microbial composition, metabolism, and immune responses. This imbalance can induce inflammation, disrupt neurotransmitter regulation, and affect hormonal and epigenetic processes, all linked to depression.

RESULTS

Microbial metabolites, such as short-chain fatty acids and neurotransmitters, are key to gut-brain communication, influencing immune regulation and mood. The altered production of these metabolites is associated with depression. While progress has been made in understanding the gut-brain axis, more research is needed to clarify causative relationships and develop new treatments. The emerging field of psychobiotics and microbiome-targeted therapies shows promise for innovative depression treatments by harnessing the gut microbiome's potential.

CONCLUSIONS

Epigenetic mechanisms, including DNA methylation and histone modifications, are crucial in how the gut microbiota impacts mental health. Understanding these mechanisms offers new prospects for preventing and treating depression through the gut-brain axis.

Targeted Drug Nanodelivery and Immunotherapy for Combating Tumor Resistance

Chemotherapy resistance is a common cause of tumor treatment failure. Various molecular responses, such as increased expression of efflux transporter proteins, including Pglycoprotein (P-gp), changes in the tumor microenvironment (TME), the role of platelets, and the effects of cancer stem cells (CSCs), can lead to drug resistance. Through extensive research on the mechanisms of drug resistance, more effective anti-resistance drugs and therapeutic approaches are being developed. This review explores drug resistance mechanisms and summarizes relevant anti-resistance drugs. In addition, due to the therapeutic limitations of the aforementioned treatments, new advances in nanocarrier-based combination immunotherapy to address the challenge of drug resistance have been described. Nanocarriers combined with immunotherapy can not only target tumor sites for targeted drug release but also modulate the autoimmune system and enhance immune efficacy, thereby overcoming tumor drug resistance. This review suggests new strategies for overcoming tumor drug resistance and is expected to inform tumor treatment and prognosis.

Probiotic Bacterium-Derived p40, p75, and HM0539 Proteins as Novel Postbiotics and Gut-Associated Immune System (GAIS) Modulation: Postbiotic-Gut-Health Axis

It is known that probiotics have direct and indirect effects on many systems in the body, especially the gastrointestinal system. Interest in using probiotic strain-derived cell components and metabolites has also increased as a result of the significant benefits of probiotics. Although many terminologies and definitions are used for these components and metabolites, the International Scientific Association of Probiotics and Prebiotics (ISAPP) recommended the use of the term postbiotic in 2021, which is defined as "a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotics are bioactive metabolites such as organic acids, peptides/proteins, cell wall components, functional enzymes, short-chain fatty acids, vitamins, and phenols. These molecules mediate many positive effects such as immunomodulatory, antimicrobial, and antioxidant effects. These positive effects on maintaining health have enabled the identification of many new postbiotic proteins such as p40, p75, and HM0539. In this review, the postbiotic proteins p40, p75, and HM0539 derived from lactobacilli and their functional effects are systematically summarized. The p40 protein, in particular, has been shown to support gut barrier activity and reduce inflammation, potentially through mechanisms involving epidermal growth factor receptor-dependent signaling. Additionally, p40 and p75 proteins exhibit protective effects on intestinal epithelial tight junctions, suggesting their therapeutic potential in preventing intestinal damage and diseases such as colitis. HM0539 enhances intestinal barrier integrity, exhibits antiinflammatory properties, and protects against bacterial infection, suggesting its possible as a therapeutic for inflammatory bowel disease. This review may contribute to future studies on the therapeutic use of p40, p75, and HM0539 postbiotic proteins in inflammatory gastrointestinal system diseases.

Benzo(a)pyrene and Gut Microbiome Crosstalk: Health Risk Implications

This review delves into the impact of benzo(a)pyrene (B(a)P), which is a toxic and pervasive polycyclic aromatic hydrocarbon (PAH) and known carcinogen, on the human health risk from a gut microbiome perspective. We retrieved the relevant articles on each PAH and summarized the reporting to date, with a particular focus on benzo(a)pyrene, which has been reported to have a high risk of gut microbiome-related harm. B(a)P exposure can compromise the homeostasis of the gut microbiota, leading to dysbiosis, a state of microbial imbalance. The consequences of B(a)P-induced gut dysbiosis can be far-reaching, potentially contributing to inflammation, metabolic disorders, and an increased risk of various diseases. Additionally, due to the strong coupling between B(a)P and microparticles, the toxicity of B(a)P may be further compounded by its reaction with strong gut disruptors such as micro-/nanoplastics, which have recently become a serious environmental concern. This review summarizes current research on the impact of B(a)P on the gut microbiome, highlighting the intricate relationship between environmental exposure, gut health, and human disease. Further research is necessary to elucidate the underlying mechanisms and develop effective strategies to mitigate the adverse health effects of B(a)P exposure.

The Gut Microbiota's Role in Neurological, Psychiatric, and Neurodevelopmental Disorders

AIM

This article aims to explore the role of the human gut microbiota (GM) in the pathogenesis of neurological, psychiatric, and neurodevelopmental disorders, highlighting its influence on health and disease, and investigating potential therapeutic strategies targeting GM modulation.

MATERIALS AND METHODS

A comprehensive analysis of the gut microbiota's composition and its interaction with the human body, particularly, its role in neurological and psychiatric conditions, is provided. The review discusses factors influencing GM composition, including birth mode, breastfeeding, diet, medications, and geography. Additionally, it examines the GM's functions, such as nutrient absorption, immune regulation, and pathogen defense, alongside its interactions with the nervous system through the gut-brain axis, neurotransmitters, and short-chain fatty acids (SCFAs).

RESULTS

Alterations in the GM are linked to various disorders, including Parkinson's disease, multiple sclerosis, depression, schizophrenia, ADHD, and autism. The GM influences cognitive functions, stress responses, and mood regulation. Antibiotic use disrupts GM diversity, increasing the risk of metabolic disorders, obesity, and allergic diseases. Emerging therapies such as probiotics, prebiotics, and microbiota transplantation show promise in modulating the GM and alleviating symptoms of neurological and psychiatric conditions.

CONCLUSIONS

The modulation of the GM represents a promising approach for personalized treatment strategies. Further research is needed to better understand the underlying mechanisms and to develop targeted therapies aimed at restoring GM balance for improved clinical outcomes.

Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study

Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.

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.

Molecular Mimicry Between Gut Microbiome and Rheumatoid Arthritis: Current Concepts

Rheumatoid arthritis (RA) represents an autoimmune condition impacted by a combination of genetic and environmental factors, with the gut microbiome (GMB) being one of the influential environmental factors. Patients with RA display notable modifications in the composition of their GMB, characterised by decreased diversity and distinct bacterial alterations. The GMB, comprising an extensive array of approximately 35,000 bacterial species residing within the gastrointestinal tract, has garnered considerable attention as a pivotal contributor to both human health and the pathogenesis of diseases. This article provides an in-depth exploration of the intricate involvement of the GMB in the context of RA. The oral-GMB axis highlights the complex role of bacteria in RA pathogenesis by producing antibodies to citrullinated proteins (ACPAs) through molecular mimicry. Dysbiosis affects Tregs, cytokine levels, and RA disease activity, suggesting that regulating cytokines could be a strategy for managing inflammation in RA. The GMB also has significant implications for drug responses and toxicity, giving rise to the field of pharmacomicrobiomics. The composition of the microbiota can impact the efficacy and toxicity of drugs, while the microbiota's metabolites can influence drug response. Recent research has identified specific bacteria, metabolites, and immune responses associated with RA, offering potential targets for personalised management. However, several challenges, including the variation in microbial composition, establishing causality, accounting for confounding factors, and translating findings into clinical practice, need to be addressed. Microbiome-targeted therapy is still in its early stages and requires further research and standardisation for effective implementation.

Nutritional management and autism spectrum disorder: A systematic review

BACKGROUND

Autism spectrum disorder (ASD) presents unique challenges related to feeding and nutritional management. Children with ASD often experience feeding difficulties, including food selectivity, refusal, and gastrointestinal issues. Various interventions have been explored to address these challenges, including dietary modifications, vitamin supplementation, feeding therapy, and behavioral interventions.

AIM

To provide a comprehensive overview of the current evidence on nutritional management in ASD. We examine the effectiveness of dietary interventions, vitamin supplements, feeding therapy, behavioral interventions, and mealtime practices in addressing the feeding challenges and nutritional needs of children with ASD.

METHODS

We systematically searched relevant literature up to June 2024, using databases such as PubMed, PsycINFO, and Scopus. Studies were included if they investigated dietary interventions, nutritional supplements, or behavioral strategies to improve feeding behaviors in children with ASD. We assessed the quality of the studies and synthesized findings on the impact of various interventions on feeding difficulties and nutritional outcomes. Data extraction focused on intervention types, study designs, participant characteristics, outcomes measured, and intervention effectiveness.

RESULTS

The review identified 316 studies that met the inclusion criteria. The evidence indicates that while dietary interventions and nutritional supplements may offer benefits in managing specific symptoms or deficiencies, the effectiveness of these approaches varies. Feeding therapy and behavioral interventions, including gradual exposure and positive reinforcement, promise to improve food acceptance and mealtime behaviors. The findings also highlight the importance of creating supportive mealtime environments tailored to the sensory and behavioral needs of children with ASD.

CONCLUSION

Nutritional management for children with ASD requires a multifaceted approach that includes dietary modifications, supplementation, feeding therapy, and behavioral strategies. The review underscores the need for personalized interventions and further research to refine treatment protocols and improve outcomes. Collaborative efforts among healthcare providers, educators, and families are essential to optimize this population's nutritional health and feeding practices. Enhancing our understanding of intervention sustainability and long-term outcomes is essential for optimizing care and improving the quality of life for children with ASD and their families.

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.

Managing Cardiovascular Risk in Patients with Autoimmune Diseases: Insights from a Nutritional Perspective

PURPOSE OF REVIEW

Autoimmune diseases manifest as an immune system response directed against endogenous antigens, exerting a significant influence on a substantial portion of the population. Notably, a leading contributor to morbidity and mortality in this context is cardiovascular disease (CVD). Intriguingly, individuals with autoimmune disorders exhibit a heightened prevalence of CVD compared to the general population. The meticulous management of CV risk factors assumes paramount importance, given the current absence of a standardized solution to this perplexity. This review endeavors to address this challenge from a nutritional perspective.

RECENT FINDINGS

Emerging evidence suggests that inflammation, a common thread in autoimmune diseases, also plays a pivotal role in the pathogenesis of CVD. Nutritional interventions aimed at reducing inflammation have shown promise in mitigating cardiovascular risk. The integration of nutritional strategies into the management plans for patients with autoimmune diseases offers a holistic approach to reducing cardiovascular risk. While conventional pharmacological treatments remain foundational, the addition of targeted dietary interventions can provide a complementary pathway to improve cardiovascular outcomes.

A potential role of gut microbiota in stroke: mechanisms, therapeutic strategies and future prospective

RATIONALE

Neurological conditions like Stroke and Alzheimer's disease (AD) often include inflammatory responses in the nervous system. Stroke, linked to high disability and mortality rates, poses challenges related to organ-related complications. Recent focus on understanding the pathophysiology of ischemic stroke includes aspects like cellular excitotoxicity, oxidative stress, cell death mechanisms, and neuroinflammation.

OBJECTIVE

The objective of this paper is to summarize and explore the pathophysiology of ischemic stroke, elucidates the gut-brain axis mechanism, and discusses recent clinical trials, shedding light on novel treatments and future possibilities.

RESULTS

Changes in gut architecture and microbiota contribute to dementia by enhancing intestinal permeability, activating the immune system, elevating proinflammatory mediators, altering blood-brain barrier (BBB) permeability, and ultimately leading to neurodegenerative diseases (NDDs). The gut-brain axis's potential role in disease pathophysiology offers new avenues for cell-based regenerative medicine in treating neurological conditions.

CONCLUSION

In conclusion, the gut microbiome significantly impacts stroke prognosis by highlighting the role of the gut-brain axis in ischemic stroke mechanisms. This insight suggests potential therapeutic strategies for improving outcomes.

Epithelial barrier dysfunction, type 2 immune response, and the development of chronic inflammatory diseases

The prevalence of many chronic noncommunicable diseases has been steadily rising over the past six decades. During this time, humans have been increasingly exposed to substances toxic for epithelial cells, including air pollutants, laundry and dishwashers, household chemicals, toothpaste, food additives, microplastics, and nanoparticles, introduced into our daily lives as part of industrialization, urbanization, and modernization. These substances disrupt the epithelial barriers and lead to microbial dysbiosis and cause immune response to allergens, opportunistic pathogens, bacterial toxins, and autoantigens followed by chronic inflammation due to epigenetic mechanisms. Recent evidence from studies on the mechanisms of epithelial barrier damage has demonstrated that even trace amounts of toxic substances can damage epithelial barriers and induce tissue inflammation. Further research in this field is essential for our understanding of the causal substances and molecular mechanisms involved in the initiation of leaky epithelial barriers that cascade into chronic inflammatory diseases.

The Intestine in Acute and Long COVID: Pathophysiological Insights and Key Lessons

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, represents a significant and complex health challenge with a wide range of symptoms affecting multiple organ systems. This review examines the emerging evidence suggesting a critical role of the gut and gut-brain axis in the pathophysiology of Long COVID. It explores how changes in the gut microbiome, disruption of gut barrier integrity, and the persistence of SARS-CoV-2 antigens within the gastrointestinal tract may contribute to the prolonged and varied symptoms seen in Long COVID, including chronic inflammation and neuropsychiatric disturbances. The review also summarizes key insights gained about Long COVID, highlighting its multifactorial nature, which involves immune dysregulation, microvascular damage, and autonomic nervous system dysfunction, with the gut playing a central role in these processes. While progress has been made in understanding these mechanisms, current evidence remains inconclusive. The challenges of establishing causality, standardizing research methodologies, and addressing individual variations in the microbiome are discussed, emphasizing the need for further longitudinal studies and more comprehensive approaches to enhance our understanding of these complex interactions. This review underscores the importance of personalized approaches in developing effective diagnostic and therapeutic strategies for Long COVID, while also acknowledging the significant gaps in our current understanding. Future research should aim to further unravel the complex interplay between the gut and Long COVID, ultimately improving outcomes for those affected by this condition.

Exploring the hypothetical links between environmental pollutants, diet, and the gut-testis axis: The potential role of microbes in male reproductive health

The gut system, commonly referred to as one of the principal organs of the human "superorganism," is a home to trillions of bacteria and serves an essential physiological function in male reproductive failures or infertility. The interaction of the endocrine-immune system and the microbiome facilitates reproduction as a multi-network system. Some recent studies that link gut microbiota to male infertility are questionable. Is the gut-testis axis (GTA) real, and does it affect male infertility? As a result, this review emphasizes the interconnected links between gut health and male reproductive function via changes in gut microbiota. However, a variety of harmful (endocrine disruptors, heavy metals, pollutants, and antibiotics) and favorable (a healthy diet, supplements, and phytoconstituents) elements promote microbiota by causing dysbiosis and symbiosis, respectively, which eventually modify the activities of male reproductive organs and their hormones. The findings of preclinical and clinical studies on the direct and indirect effects of microbiota changes on testicular functions have revealed a viable strategy for exploring the GTA-axis. Although the GTA axis is poorly understood, it may have potential ties to reproductive issues that can be used for therapeutic purposes in the future.

Maternal gut-microbiota impacts the influence of intrauterine environmental stressors on the modulation of human cognitive development and behavior

This review examines the longstanding debate of nature and intrauterine environmental challenges that shapes human development and behavior, with a special focus on the influence of maternal prenatal gut microbes. Recent research has revealed the critical role of the gut microbiome in human neurodevelopment, and evidence suggest that maternal microbiota can impact fetal gene and microenvironment composition, as well as immunophysiology and neurochemical responses. Furthermore, intrauterine neuroepigenetic regulation may be influenced by maternal microbiota, capable of having long-lasting effects on offspring behavior and cognition. By examining the complex relationship between maternal prenatal gut microbes and human development, this review highlights the importance of early-life environmental factors in shaping neurodevelopment and cognition.

Inclusion of Tenebrio molitor larvae meal in the diet of barbary partridge (Alectoris barbara) improves caecal bacterial diversity and composition

In this study, we investigated the influence of the inclusion of Tenebrio molitor (TM) larvae meal in the diet on the diversity and structure of the bacterial community in the caecal content of Barbary partridges. A total of 36 partridges, selected randomly for slaughter from 54 animals, were divided equally into three treatment groups, including the control group (C) with a diet containing corn-soybean meal and two experimental groups, in which 25% (TM25) and 50% (TM50) of the soybean meal protein was replaced by the meal from TM larvae. After slaughtering, the bacterial community of the 30 caecal samples (10 samples per each experimental group) was analysed by high-throughput sequencing using the V4-V5 region of the 16 S rRNA gene. Alpha diversity showed a higher diversity richness in the TM50 group. Beta diversity showed statistical dissimilarities among the three groups. Firmicutes was the dominant phylum regardless of the diet, with the predominant families Ruminococcaceae and Lachnospiraceae. Clostridia and Faecalibacterium were decreased in both TM groups, Lachnospiraceae was suppressed in the TM50 group, but still this class, genus and family were abundantly present in all samples. Several potentially beneficial genera, such as Bacillus, Ruminococcaceae UCG-009, Oscillibacter and UC1-2E3 (Lachnospiraceae) were increased in the TM50 group. The results showed a beneficial effect of the T. molitor larvae meal on the caecal microbiota of Barbary partridges, particularly in the TM50 group, which showed an increase in bacterial diversity.

Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions

MOTIVATION

Extensive research has uncovered the critical role of the human gut microbiome in various aspects of health, including metabolism, nutrition, physiology, and immune function. Fecal microbiota is often used as a proxy for understanding the gut microbiome, but it represents an aggregate view, overlooking spatial variations across different gastrointestinal (GI) locations. Emerging studies with spatial microbiome data collected from specific GI regions offer a unique opportunity to better understand the spatial composition of the stool microbiome.

RESULTS

We introduce Micro-DeMix, a mixture beta-multinomial model that deconvolutes the fecal microbiome at the compositional level by integrating stool samples with spatial microbiome data. Micro-DeMix facilitates the comparison of microbial compositions across different GI regions within the stool microbiome through a hypothesis-testing framework. We demonstrate the effectiveness and efficiency of Micro-DeMix using multiple simulated datasets and the inflammatory bowel disease data from the NIH Integrative Human Microbiome Project.

AVAILABILITY AND IMPLEMENTATION

The R package is available at https://github.com/liuruoqian/MicroDemix.

Present and future of fecal microbiome transplantation in cirrhosis

Over the last few decades, there have been tremendous advances in our understanding of the role of the gut microbiome in cirrhosis and the clinical sequelae that follow. Progressive dysbiosis and immune dysregulation occur in patients with cirrhosis. In fact, alterations in the gut microbiome occur long before a diagnosis of cirrhosis is made. Understandably, our attention has recently been diverted toward potential modulators of the gut microbiome and the gut-liver axis as targets for treatment. The goal of this review is to highlight the utility of manipulating the gut microbiome with a focus on fecal microbiome transplantation (FMT) in patients with cirrhosis. In addition, we will provide an overview of disease-specific microbial alterations and the resultant impact this has on cirrhosis-related complications.

The gut-brain-metabolic axis: exploring the role of microbiota in insulin resistance and cognitive function

The gut-brain-metabolic axis has emerged as a critical area of research, highlighting the intricate connections between the gut microbiome, metabolic processes, and cognitive function. This review article delves into the complex interplay between these interconnected systems, exploring their role in the development of insulin resistance and cognitive decline. The article emphasizes the pivotal influence of the gut microbiota on central nervous system (CNS) function, demonstrating how microbial colonization can program the hypothalamic-pituitary-adrenal (HPA) axis for stress response in mice. It further elucidates the mechanisms by which gut microbial carbohydrate metabolism contributes to insulin resistance, a key factor in the pathogenesis of metabolic disorders and cognitive impairment. Notably, the review highlights the therapeutic potential of targeting the gut-brain-metabolic axis through various interventions, such as dietary modifications, probiotics, prebiotics, and fecal microbiota transplantation (FMT). These approaches have shown promising results in improving insulin sensitivity and cognitive function in both animal models and human studies. The article also emphasizes the need for further research to elucidate the specific microbial species and metabolites involved in modulating the gut-brain axis, as well as the long-term effects and safety of these therapeutic interventions. Advances in metagenomics, metabolomics, and bioinformatics are expected to provide deeper insights into the complex interactions within the gut microbiota and their impact on host health. Overall, this comprehensive review underscores the significance of the gut-brain-metabolic axis in the pathogenesis and treatment of metabolic and cognitive disorders, offering a promising avenue for the development of novel therapeutic strategies targeting this intricate system.

Layer segmented filamentous bacteria colonize and impact gut health of broiler chickens

In commercial poultry farms, chicks hatch away from their progenitors from which they acquire key host-specific microbiota, like segmented filamentous bacteria (SFB) involved in gut maturation in early life. This study investigated whether providing chicken SFB to newly hatched broilers would increase their gut maturation and resistance to bacteria relevant to broiler and human health. One-day-old Ross308 broilers were orally treated with either phosphate-buffered saline (CON) or layer-derived SFB (D-SFB). On days 5, 10, 17, and 24, feces were collected to detect and enumerate SFB and Enterobacteriaceae. On days 8, 15, 22, and 29, birds were euthanized, intestinal samples were collected to detect and enumerate SFB through quantitative PCR (qPCR) and microscopy and expression of genes associated with gut immune function through reverse transcription-qPCR. This study showed that, despite their host specificity, layer SFB can colonize their genetically distinct relative broilers. Ileal SFB colonization was accelerated by a week with the SFB treatment and covered the proximal, medial, and distal sections of the ileum. Colonization of the ileum by SFB in early life highly activated gene expression of intestinal barrier proteins and cytokines, e.g., IL-10 and IFNγ but not IL-17. SFB treatment reduced the level of Enterobacteriaceae in the gut and provided superior resistance to intestinal and extraintestinal pathogens as tested in vitro. Overall, early gut colonization of SFB is imperative for the maturation of the gut immune system and the establishment of a homeostatic gut environment. Improving our understanding of gut immune maturation in food-producing animals is crucial for both human and animal health.IMPORTANCEIn commercial farms, newly hatched chicks may lack host-specific microbiota that help mature their gut immune system for lifelong health benefits. Here, introducing an avian segmented filamentous bacteria (SFB) to commercially sourced chickens orally at hatch accelerated SFB colonization of the ileum. Remarkably, SFB from layers were able to colonize broilers and enhance gut immune maturation, and this immunomodulation impacted the ability to increase intestinal and extraintestinal resistance to bacteria relevant to poultry and human health. With the antibiotic restrictions in animal production, strategies that will help mitigate infections are urgently needed. In summary, we developed a live prophylactic for newly hatched chicks to improve animal health and food safety. Due to the host specificity of SFB, our data highlight the importance of investigating the molecular mechanism of SFB interaction in their own host.

Distinct fecal microbiome between wild and habitat-housed captive polar bears (Ursus maritimus): Impacts of captivity and dietary shifts

Understanding the gut microbiome of polar bears can shed light on the effects of climate change-induced prolonged ice-free seasons on their health and nutritional status as a sentinel species. The fecal microbiome of habitat-housed captive polar bears who had consumed a high protein diet long-term was compared with that of the wild population. Individual differences, season, year and dietary inclusion of a brown seaweed (Fucus spiralis; part of the natural diet of wild polar bears), as a representation for nutritional change, were investigated for their effects on the fecal microbiome of captive polar bears. Microbial variations among fecal samples from wild and captive polar bears were investigated using 16s rRNA gene based metataxonomic profiling. The captive bears exhibited more diverse fecal microbiota than wild bears (p<0.05). The difference was due to significantly increased Firmicutes, Campilobacterota and Fusobacteriota, decreased Actinobacteriota (p<0.05), and absent Bdellovibrionota and Verrucomicrobiota in the captive bears. Compared with other factors, individual variation was the main driver of differences in fecal microbial composition in the captive bears. Seaweed consumption did not alter microbial diversity or composition, but this did not rule out dietary influences on the hosts. This is the first study, to the best of our knowledge, comparing the fecal microbiota of captive and wild polar bears and it reveals distinct differences between the two groups, which could result from many factors, including available food sources and the ratio of dietary macronutrients. Our findings provide preliminary insights into climate-change induced dietary shifts in polar bears related to climate-associated habitat change.

Gut microbiota in very early systemic sclerosis: the first case-control taxonomic and functional characterisation highlighting an altered butyric acid profile

OBJECTIVES

In systemic sclerosis (SSc), gastrointestinal involvement is one of the earliest events. We compared the gut microbiota (GM), its short-chain fatty acids (SCFAs) and host-derived free fatty acids (FFAs) in patients with very early diagnosis of SSc (VEDOSS) and definite SSc.

METHODS

Stool samples of 26 patients with SSc, 18 patients with VEDOSS and 20 healthy controls (HC) were collected. The GM was assessed through 16S rRNA sequencing, while SCFAs and FFAs were assessed by gas chromatography-mass spectrometry.

RESULTS

In patients with VEDOSS, an increase in Bacteroidales and Oscillospirales orders and a decrease in Bacilli class, Blautia, Romboutsia, Streptococcus and Turicibacter genera was detected in comparison with HC. In patients with SSc, an elevated number of Acidaminococcaceae and Sutterellaceae families, along with a decrease of the Peptostreptococcaceae family and Anaerostipes, Blautia, Romboutsia and Turicibacter genera was found in comparison with HC. Patients with SSc and VEDOSS had a significantly lower butyrate and higher acetate with respect to HC. In VEDOSS, an increase in Oscillospiraceae family and Anaerostipes genus, and a decrease in Alphaproteobacteria class, and Lactobacillales order was identified with respect to SSc. Moreover, patients with VEDOSS exhibited higher acetate and lower valerate compared with definite SSc.

CONCLUSION

A GM dysbiosis with depletion of beneficial anti-inflammatory bacteria (especially butyrate-producing) and a significant decrease in faecal butyrate was identified in patients with VEDOSS. This early GM imbalance may foster the growth of inflammatory microbes, worsening intestinal dysbiosis and inflammation in early SSc stages. The potential butyrate administration in early disease phases might be considered as a novel therapeutic approach to mitigate gastrointestinal discomfort and progression preserving patient's quality of life.

Unraveling the Role of the Human Gut Microbiome in Health and Diseases

The human gut is a complex ecosystem that supports billions of living species, including bacteria, viruses, archaea, phages, fungi, and unicellular eukaryotes. Bacteria give genes and enzymes for microbial and host-produced compounds, establishing a symbiotic link between the external environment and the host at both the gut and systemic levels. The gut microbiome, which is primarily made up of commensal bacteria, is critical for maintaining the healthy host's immune system, aiding digestion, synthesizing essential nutrients, and protecting against pathogenic bacteria, as well as influencing endocrine, neural, humoral, and immunological functions and metabolic pathways. Qualitative, quantitative, and/or topographic shifts can alter the gut microbiome, resulting in dysbiosis and microbial dysfunction, which can contribute to a variety of noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer, and irritable bowel syndrome. While most evidence to date is observational and does not establish direct causation, ongoing clinical trials and advanced genomic techniques are steadily enhancing our understanding of these intricate interactions. This review will explore key aspects of the relationship between gut microbiota, eubiosis, and dysbiosis in human health and disease, highlighting emerging strategies for microbiome engineering as potential therapeutic approaches for various conditions.

Gut microbiota and renal fibrosis

Renal fibrosis represents a critical pathological condition in the progression of renal dysfunction, characterized by aberrant accumulation of extracellular matrix (ECM) and structural alterations in renal tissue. Recent research has highlighted the potential significance of gut microbiota and demonstrated their influence on host health and disease mechanisms through the production of bioactive metabolites. This review examines the role of alterations in gut microbial composition and their metabolites in the pathophysiological processes underlying renal fibrosis. It delineates current therapeutic interventions aimed at modulating gut microbiota composition, encompassing dietary modifications, pharmacological approaches, and probiotic supplementation, while evaluating their efficacy in mitigating renal fibrosis. Through a comprehensive analysis of current research findings, this review enhances our understanding of the bidirectional interaction between gut microbiota and renal fibrosis, establishing a theoretical foundation for future research directions and potential clinical applications in this domain.

Western diet promotes endometriotic lesion growth in mice and induces depletion of Akkermansia muciniphila in intestinal microbiota

BACKGROUND

Endometriosis, affecting 10% of women in their reproductive years, remains poorly understood. Both individual and environmental unexplained factors are implicated in this heterogenous condition. This study aims to examine the influence of a Western diet on endometriosis lesion development in mice and to uncover the mechanisms involved.

METHODS

Mice were fed either a control diet or a Western diet (high in fatty acids and low in fiber) for 4 weeks. Endometriosis was then surgically induced, and lesion development was monitored by ultrasound. After 7 weeks, the mice were sacrificed for analysis of lesion characteristics through RT-qPCR, immunohistochemistry, and flow cytometry. Additionally, the intestinal microbiota was assessed using 16S rRNA gene sequencing.

RESULTS

Mice on the Western diet developed lesions that were significantly twice as large compared to those on the control diet. These lesions exhibited greater fibrosis and proliferation, alongside enhanced macrophage activity and leptin pathway expression. Changes in the intestinal microbiota were significantly noted after endometriosis induction, regardless of diet. Notably, mice on the Western diet with the most substantial lesions showed a loss of Akkermansia Muciniphila in their intestinal microbiota.

CONCLUSIONS

A Western diet significantly exacerbates lesion size in a mouse model of endometriosis, accompanied by metabolic and immune alterations. The onset of endometriosis also leads to substantial shifts in intestinal microbiota, suggesting a potential link between diet, intestinal health, and endometriosis development.

Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine

Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota-host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to highlight how gut microbiota modulate metabolic and immune functions, contributing to disease susceptibility and wellbeing. The review synthesizes recent research findings, analyzing key studies on the influence of gut microbiota on lipid and carbohydrate metabolism, intestinal health, neurobehavioral regulation, and endocrine signaling. Data were drawn from both experimental and clinical trials examining microbiota-host interactions relevant to precision nutrition. Our findings highlight the essential role of gut microbiota-derived metabolites in regulating host metabolism, including lipid and glucose pathways. These metabolites have been found to influence immune responses and gut barrier integrity. Additionally, the microbiota impacts broader physiological processes, including neuroendocrine regulation, which could be crucial for dietary interventions. Therefore, understanding the molecular mechanisms of dietary-microbiota-host interactions is pivotal for advancing personalized nutrition strategies. Tailored dietary recommendations based on individual gut microbiota compositions hold promise for improving health outcomes, potentially revolutionizing future healthcare approaches across diverse populations.

Mapping Lipid C═C Isomer Profiles of Human Gut Bacteria through a Novel Structural Lipidomics Workflow Assisted by Chemical Epoxidation

The unsaturated lipids produced by human gut bacteria have an extraordinary range of structural diversity, largely because of the isomerism of the carbon-carbon double bond (C═C) in terms of its position and stereochemistry. Characterizing distinct C═C configurations poses a considerable challenge in research, primarily owing to limitations in current bioanalytical methodologies. This study developed a novel structural lipidomics workflow by combining MELDI (meta-chloroperoxybenzoic acid epoxidation for lipid double-bond identification) with liquid chromatography-tandem mass spectrometry for C═C characterization. We utilized this workflow to quantitatively assess more than 50 C═C positional and cis/trans isomers of fatty acids and phospholipids from selected human gut bacteria. Strain-specific isomer profiles revealed unexpectedly high productivity of trans-10-octadecenoic acid by Enterococcus faecalis, Bifidobacterium longum, and Lactobacillus acidophilus among numerous trans-fatty acid isomers produced by gut bacteria. Isotope-tracking experiments suggested that gut bacteria produce trans-10-octadecenoic acid through the isomeric biotransformation of oleic acid in vitro and that such isomeric biotransformation of dietary oleic acid is dependent on the presence of gut bacteria in vivo.