Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

Gut dysbiosis-induced vitamin B6 metabolic disorder contributes to chronic stress-related abnormal behaviors in a cortisol-independent manner

Chronic stress can result in various conditions, including psychological disorders, neurodegenerative diseases, and accelerated brain aging. Gut dysbiosis potentially contributes to stress-related brain disorders in individuals with chronic stress. However, the causal relationship and key factors between gut dysbiosis and brain disorders in chronic stress remain elusive, particularly under non-sterile conditions. Here, using a repeated restraint stress (RRS) rat model, we show that sequential transplantation of the cecal contents of different RRS stages to normal rats reproduced RRS-induced core phenotypes, including abnormal behaviors, increased peripheral blood corticosterone and inflammatory cytokines, and a unique gut microbial phenotype. This core phenotypic development was effectively inhibited with probiotic supplement. The RRS-induced unique gut microbial phenotypes at the genus level were positively or negatively associated with the levels of 20 plasma metabolites, including vitamin B6 metabolites 4-pyridoxic acid and 4-pyridoxate. Vitamin B6 supplement during RRS alleviated weight loss, abnormal behaviors, peripheral inflammation, and neuroinflammation, but did not affect the peripheral corticosterone levels in chronic stressed rats. Dampening inflammatory signaling via knocking out caspase 11 or caspase 1 inhibitor abolished RRS-induced abnormal behaviors and peripheral and neuroinflammation but did not decrease peripheral corticosterone in mice. These findings show that gut dysbiosis-induced vitamin B6 metabolism disorder is a new non-hypothalamic-pituitary-adrenal axis mechanism of chronic stress-related brain disorders. Both probiotics and vitamin B6 supplement have potential to be developed as therapeutic strategies for preventing and/or treating chronic stress-related illness.

Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice

The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.

Interactions between the intestinal microbiota and drug metabolism - Clinical implications and future opportunities

The importance of the intestinal microbita in a multitude of physiological processes is well-evidenced. These include metabolism of nutrients and xenobiotics, biosynthesis of vitamin K and vitamin B12, immunomodulation, maintenance of the gut mucosal barrier integrity and protection against some pathogens. Interindividual differences in the intestinal microbiota composition have impacts on health. The bioavailability and activity of some pharmaceuticals are heavily influenced by interindividual variability in metabolism, which has a genetic basis. This variability, primarily occurring in the liver but also in the intestine, has been studied extensively. Despite the advancement of this field - pharmacogenetics - its integration into clinical practice remains limited for reasons discussed herein. This highlights the even greater challenge of applying emerging knowledge on variability in the gut microbiota to drug therapy. However, ignoring these opportunities would be a mistake. While clinical applications of microbiota-guided drug therapy are currently absent and the ideas in this article are largely theoretical, research is uncovering that in cases where a substantial portion of a drug or its metabolites reaches the colon, or where drugs are formulated for colonic delivery, the gut microbiota can significantly affect drug metabolism and activity. Greater focus should be placed on research into how interindividual variability in the intestinal microbiome can modify pharmaceutical bioavailability and activity. This article is deliberately speculative and exploratory but proposes that, though there are still no clinical examples of microbiome-guided drug therapy, these interactions could afford opportunities for improvements in personalised medicine and also for drug design.

Recent advances in therapeutic probiotics: insights from human trials

SUMMARYRecent advances in therapeutic probiotics have shown promising results across various health conditions, reflecting a growing understanding of the human microbiome's role in health and disease. However, comprehensive reviews integrating the diverse therapeutic effects of probiotics in human subjects have been limited. By analyzing randomized controlled trials (RCTs) and meta-analyses, this review provides a comprehensive overview of key developments in probiotic interventions targeting gut, liver, skin, vaginal, mental, and oral health. Emerging evidence supports the efficacy of specific probiotic strains and combinations in treating a wide range of disorders, from gastrointestinal (GI) and liver diseases to dermatological conditions, bacterial vaginosis, mental disorders, and oral diseases. We discuss the expanding understanding of microbiome-organ connections underlying probiotic mechanisms of action. While many clinical trials demonstrate significant benefits, we acknowledge areas requiring further large-scale studies to establish definitive efficacy and optimal treatment protocols. The review addresses challenges in standardizing probiotic research methodologies and emphasizes the importance of considering individual variations in microbiome composition and host genetics. Additionally, we explore emerging concepts such as the oral-gut-brain axis and future directions, including high-resolution microbiome profiling, host-microbe interaction studies, organoid models, and artificial intelligence applications in probiotic research. Overall, this review offers a comprehensive update on the current state of therapeutic probiotics across multiple domains of human health, providing insights into future directions and the potential for probiotics to revolutionize preventive and therapeutic medicine.

Gut microbiome research: Revealing the pathological mechanisms and treatment strategies of type 2 diabetes

The high prevalence and disability rate of type 2 diabetes (T2D) caused a huge social burden to the world. Currently, new mechanisms and therapeutic approaches that may affect this disease are being sought. With in-depth research on the pathogenesis of T2D and growing advances in microbiome sequencing technology, the association between T2D and gut microbiota has been confirmed. The gut microbiota participates in the regulation of inflammation, intestinal permeability, short-chain fatty acid metabolism, branched-chain amino acid metabolism and bile acid metabolism, thereby affecting host glucose and lipid metabolism. Interventions focusing on the gut microbiota are gaining traction as a promising approach to T2D management. For example, dietary intervention, prebiotics and probiotics, faecal microbiota transplant and phage therapy. Meticulous experimental design and choice of analytical methods are crucial for obtaining accurate and meaningful results from microbiome studies. How to design gut microbiome research in T2D and choose different machine learning methods for data analysis are extremely critical to achieve personalized precision medicine.

Diet-microbiome interactions in cancer

Diet impacts cancer in diverse manners. Multiple nutritional effects on tumors are mediated by dietary modulation of commensals, residing in mucosal surfaces and possibly also within the tumor microenvironment. Mechanistically understanding such diet-microbiome-host interactions may enable to develop precision nutritional interventions impacting cancer development, dissemination, and treatment responses. However, data-driven nutritional strategies integrating diet-microbiome interactions are infrequently incorporated into cancer prevention and treatment schemes. Herein, we discuss how dietary composition affects cancer-related processes through alterations exerted by specific nutrients and complex foods on the microbiome. We highlight how dietary timing, including time-restricted feeding, impacts microbial function in modulating cancer and its therapy. We review existing and experimental nutritional approaches aimed at enhancing microbiome-mediated cancer treatment responsiveness while minimizing adverse effects, and address challenges and prospects in integrating diet-microbiome interactions into precision oncology. Collectively, mechanistically understanding diet-microbiome-host interactomes may enable to achieve a personalized and microbiome-informed optimization of nutritional cancer interventions.

Living on the edge: Mucus-associated microbes in the colon

The colonic mucus layer acts as a physicochemical barrier to pathogen invasion and as a habitat for mucus-associated microbes. This mucosal microbiome plays a crucial role in moderating mucus production, maintaining barrier integrity, and shaping the host immune response. However, unchecked mucin foraging may render the host vulnerable to disease. To better understand these dynamics in the mucus layer, it is essential to advance fundamental knowledge on how commensals bind to and utilize mucin as well as their interactions with both the host and their microbial neighbors. We present an overview of approaches for surveying mucus-associated bacteria and assessing their mucin-utilizing capacity, alongside a discussion of the limitations of existing methods. Additionally, we highlight how diet and host secretory immunoglobulin A interact with the mucosal bacterial community in the colon. Insights into this subset of the microbial community can guide therapeutic strategies to optimally support and modulate mucosal barrier integrity.

Designing live bacterial therapeutics for cancer

Humans are home to a diverse community of bacteria, many of which form symbiotic relationships with their host. Notably, tumors can also harbor their own unique bacterial populations that can influence tumor growth and progression. These bacteria, which selectively colonize hypoxic and acidic tumor microenvironments, present a novel therapeutic strategy to combat cancer. Advancements in synthetic biology enable us to safely and efficiently program therapeutic drug production in bacteria, further enhancing their potential. This review provides a comprehensive guide to utilizing bacteria for cancer treatment. We discuss key considerations for selecting bacterial strains, emphasizing their colonization efficiency, the delicate balance between safety and anti-tumor efficacy, and the availability of tools for genetic engineering. We also delve into strategies for precise spatiotemporal control of drug delivery to minimize adverse effects and maximize therapeutic impact, exploring recent examples of engineered bacteria designed to combat tumors. Finally, we address the underlying challenges and future prospects of bacterial cancer therapy. This review underscores the versatility of bacterial therapies and outlines strategies to fully harness their potential in the fight against cancer.

Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut

Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107 viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.

Gut microbiota reshapes the TNBC immune microenvironment: Emerging immunotherapeutic strategies

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options and poor prognosis. The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, plays a crucial role in regulating immune responses through the gut-immune axis. Recent studies have highlighted its significant impact on TNBC progression and the efficacy of immunotherapies. This review examines the interactions between gut microbiota and the immune system in TNBC, focusing on key immune cells and pathways involved in tumor immunity. It also explores microbiota modulation strategies, including probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation, as potential methods to enhance immunotherapeutic outcomes. Understanding these mechanisms offers promising avenues for improving treatment efficacy and patient prognosis in TNBC.

Clinical translation of microbiome research

The landscape of clinical microbiome research has dramatically evolved over the past decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the past 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.

Gut microbiota regulates gut homeostasis, mucosal immunity and influences immune-related diseases

The intestinal microbiome constitutes a sophisticated and massive ecosystem pivotal for maintaining gastrointestinal equilibrium and mucosal immunity via diverse pathways. The gut microbiota is continuously reshaped by multiple environmental factors, thereby influencing overall wellbeing or predisposing individuals to disease state. Many observations reveal an altered microbiome composition in individuals with autoimmune conditions, coupled with shifts in metabolic profiles, which has spurred ongoing development of therapeutic interventions targeting the microbiome. This review delineates the microbial consortia of the intestine, their role in sustaining gastrointestinal stability, the association between the microbiome and immune-mediated pathologies, and therapeutic modalities focused on microbiome modulation. We emphasize the entire role of the intestinal microbiome in human health and recommend microbiome modulation as a viable strategy for disease prophylaxis and management. However, the application of gut microbiota modification for the treatment of immune-related diseases, such as fecal microbiota transplantation and probiotics, remain quite challenging. Therefore, more research is needed into the role and mechanisms of these therapeutics.

Strain diversity and host specificity of the gut symbiont Gilliamella in Apis mellifera, Apis cerana and Bombus terrestris

Social bees, with their specialized gut microbiota and societal transmission between individuals, provide an ideal model for studying host-gut microbiota interactions. While the functional disparities arising from strain-level diversity of gut symbionts and their effects on host health have been studied in Apis mellifera and bumblebees, studies focusing on host-specific investigations of individual strains across different honeybee hosts remain relatively unexplored. In this study, the complete genomic sequences of 17 strains of Gilliamella from A. mellifera, Apis cerana and Bombus terrestris were analyzed. The analysis revealed that the strains of A. mellifera display a more expansive genomic and functional content compared to the strains of A. cerana and B. terrestris. Phylogenetic analysis showed a deep divergence among the Gilliamella strains from different hosts. Additionally, biochemistry tests and antibiotic susceptibility tests revealed that gut strains from A. mellifera exhibited a more extensive pathway for carbohydrate metabolism and a greater resistance to antibiotics than gut strains from A. cerana and B. terrestris. Strains from A. mellifera and A. cerana showed higher colonization efficiency and competitive ability whithin their respective host species, indicating a higher degree of host-specific adaptation of local gut microbiota. In addition, colonization by A. mellifera-derived strain triggers a stronger transcriptional response in the host than A. cerana-derived strain. The variation in the number of differentially expressed genes and the involvement of distinct signaling pathways across these two host species suggest species-specific adaptations to Gilliamella strains. These findings suggest that despite occupying similar niches in the bee gut, strain-level variations can influence microbial functions, and their impact on host physiological functions may vary across different strains.

The gut microbiome and dietary metabolites in the treatment of renal cell carcinoma

The gut microbiome is interlinked with renal cell carcinoma (RCC) and its response to systemic treatment. Mounting data suggests that certain elements of the gut microbiome may correlate with improved outcomes. New generation sequencing techniques and advanced bioinformatic data curation are accelerating the investigation of specific markers and metabolites that could predict treatment response. A variety of new therapeutic strategies, such as fecal microbiota transplantation, probiotic supplements, and dietary interventions, are currently being developed to modify the gut microbiome and improve anticancer therapies in patients with RCC. This review discusses the preliminary evidence indicating the role of the microbiome in cancer treatment, the techniques and tools necessary for its proper study and some of the current forms with which the microbiome can be modulated to improve patient outcomes.

Diet shapes and maintains the personalized native gut microbiomes in mice

BACKGROUND

The gut microbiome plays a critical role in human health and disease. Different dietary backgrounds play an important role in the uniqueness and diversity of the gut microbiota in different individuals, which promotes heterogeneity in disease phenotypes and treatment responses. Here, we explored how diet affects the composition and function of the native gut microbiome of model mice, based on the shotgun metagenomic and metabolomic, by analyzing the gut microbiome of C57B/6J mice in different dietary backgrounds.

RESULTS

The gut microbiomes of mice receiving different diets consistently exhibit distinct compositions across bacterial species, strains, fungi and phages. This implies that native microbial communities cannot 'homogenize' rapidly becaise of priority effects and unchanging diets. Notably, hotspot bacteria such as Limosilactobacillus reuteri, Parabacteroides distasonis and Akkermansia muciniphila were significantly different among the groups. These species harbor diverse adaptive mutations, reflecting genomic evolutionary diversity. The functional profiles of the gut microbiota also exhibit selective differences, involving the capacity for carbohydrate, branched-chain amino acid and fatty acid synthesis, as well as virulence factors, carbohydrate-active enzymes and antibiotic resistance. Furthermore, the differences in the gut microbiota also propagate to the host's serum, where structural and specific metabolite differences were observed. Metabolites that directly impact host health, such as d-glucosamine 6-phosphate and testolic acid, also show significant differences between the different dietary groups.

CONCLUSION

Our findings underscore the profound influence of different dietary the composition and functionality of the gut microbiome, offering valuable insights into optimizing health outcomes through personalized nutritional interventions. © 2024 Society of Chemical Industry.

Neonatal administration of Lactiplantibacillus plantarum ATCC 202195 with or without fructooligosaccharide in Bangladesh: a placebo-controlled randomized trial

Lactiplantibacillus plantarum ATCC 202195 (LP202195) plus fructooligosaccharide (FOS) for 7 days was previously shown to colonize the infant intestine up to 6 months of age and reduced sepsis rates among young infants in rural India. In a phase 2 randomized controlled trial in Dhaka, Bangladesh (N = 519), neonatal administration of LP202195 for 1 or 7 days, with or without FOS, increased LP202195 stool abundance from 14 to 60 days of age, versus placebo. Abundance progressively declined in the post-administration period and did not persist beyond 2 months of age. FOS did not affect LP202195 abundance or its duration of persistence. All regimens were well-tolerated and safe. The absence of LP202195 colonization was inconsistent with results from a prior trial. Additional large-scale trials of LP202195 ± FOS are needed to establish its efficacy in infants who do not become LP202195-colonized.

IMPORTANCE

Among infants born in Dhaka, Bangladesh, a 7-day regimen of Lactiplantibacillus plantarum ATCC 202195 (LP202195) plus fructooligosaccharide (FOS) did not colonize the infant gastrointestinal (GI) tract. The absence of colonization is inconsistent with a prior study of the same synbiotic regimen in India, in which LP202195 was shown to persist in the infant GI tract for up to 6 months. Sustained LP202195 colonization was thought to be required for the probiotic to impart its beneficial impact on newborn sepsis. Therefore, additional trials are warranted to confirm the previously observed effects of LP202195 on infant clinical outcomes in the absence of LP202195 colonization. Moreover, since regimens of LP202195 that did not include FOS were indistinguishable from the synbiotic in terms of colonization, safety, and tolerability, future trials should assess the role of FOS for clinical efficacy; removing FOS would reduce costs, an important consideration for scale-up.

CLINICAL TRIALS

This study has been registered at ClinicalTrials.gov as NCT05180201.

Self-Nourishing and Armored Probiotics via Egg-Inspired Encapsulation

The gut microbiota plays an essential role in regulating overall physiology, including metabolism and neurological and immune functions. Therefore, their dysregulation is closely associated with metabolic disorders, such as obesity and diabetes, as well as other pathological conditions, including inflammatory bowel diseases, cancer, and neurological disorders. Probiotics are commonly used to maintain a healthy gut microbiome, but their oral delivery is inefficient mainly due to their poor stability in the harsh gastrointestinal (GI) environment. This work presents an innovative encapsulation strategy, inspired by the natural structure of an egg, for the effective oral delivery of probiotics, termed PIE (Probiotics-In-Egg). The PIE technology is based upon encapsulating probiotics with phosvitin and ovalbumin derived from egg yolk and egg white, respectively. PIE exhibits significantly enhanced survival and proliferation in a simulated GI tract, as well as the ability to neutralize harmful reactive oxygen species (ROS) and sustain in nutrient-depleted conditions. Moreover, when administered orally in mouse models, PIE demonstrates excellent bioavailability and enhanced colonization in the GI tract. This egg-inspired encapsulation technology has great potential as a practical and effective platform for oral delivery of probiotics, which can significantly help maintain a healthy gut microbiome.

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

The long-term success of introduced populations depends on both their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization dynamics. Here, we investigate how initial population (propagule) size shapes the outcome of community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to neutral ecological theory. Although the composition of the resulting cocultures deviated substantially from neutral expectations, each coculture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. Strain isolates displayed longer-lasting dose dependence when introduced into diverse communities than in pairwise cocultures, consistent with our model's prediction that propagule size should have larger, more persistent effects in diverse communities. Our model also successfully predicted that species with similar resource-utilization profiles, as inferred from growth in spent media and untargeted metabolomics, would show stronger dose dependence in pairwise coculture. This work demonstrates that transient, dose-dependent colonization dynamics can emerge from resource competition and exert long-term effects on the outcomes of community coalescence.

Changes in the gut microbiome due to diarrhea in neonatal Korean indigenous calves

Studies on gut microbiome changes in neonatal Korean indigenous calves with diarrhea are rare. In this study, 14 normal calves and 11 calves with diarrhea were selected from Korean indigenous calves up to 30 days of age and classified into three groups at 10-day intervals (1-10, 11-20, and 21-30 days). Feces from 25 calves were collected, and the diversity, similarity, structure, and correlation of the gut microbiome were analyzed. Firmicutes, Bacteroidetes, and Proteobacteria were predominant in the taxonomic composition of the gut microbiome of the calves regardless of the presence of diarrhea. However, Proteobacteria increased and Bacteroidetes and Actinobacteria decreased in calves with diarrhea. In addition, calves with diarrhea showed a significant decrease in the diversity of the gut microbiome, especially for anaerobic microorganisms Faecalibacterium prausnitzii, Gemmiger formicilis, and Collinsella aerofaciens. The microbial communities in calves with diarrhea and normal calves were distinct. By analyzing the microorganisms that showed correlation with diarrhea and age using linear discriminant analysis effect size, at the genus level, Prevotella and Lachnospiraceae_uc were significantly related in the normal (11-20 days) group whereas Enterobacterales, Gammaproteobacteria, Enterobacteriaceae, Escherichia, and Proteobacteria were significantly associated with diarrhea in the 11-20 days group. Futhermore, the normal (21-30 days) group showed significant correlation with Blautia, Provotellaceae, Muribaculaceae, Christensenellaceae, and Catenella, whereas the diarrhea (21-30 days) group showed significant correlation with Dorea. The microorganisms associated with diarrhea in calves were mainly known as harmful microorganisms, we confirmed that there is a relationship between the increase in harmful bacteria and diarrhea. These results show that diarrhea significantly affects the gut microbiome of Korean indigenous calves. The changes in the gut microbiome of Korean indigenous calves observed in this study could be helpful in predicting and managing diarrhea calves, and furthermore, in establishing preventive measures for calf diarrhea through management of gut microbiome.

A WYL domain transcription factor regulates Lactiplantibacillus plantarum intestinal colonization via perceiving c-di-GMP

Cyclic diguanosine monophosphate (c-di-GMP) functions as a crucial bacterial second messenger to control diverse biological functions. Although numerous studies have reported the health effects of Lactiplantibacillus plantarum, the regulatory role of c-di-GMP in L. plantarum remains elusive. Here we show that c-di-GMP functions as an important signal molecule for intestinal colonization of L. plantarum. The intracellular c-di-GMP pool in this probiotic is governed principally by the diguanylate cyclases DgcB, DgcC, and DgcD and the phosphodiesterases PdeA and PdeD. Moreover, we reveal that the WYL domain transcription factor MbpR is a c-di-GMP effector in L. plantarum WCFS1. MbpR reduces the transcription level of mucin-binding proteins (MucBPs) via binding to a special motif within the coding sequences. Perception of c-di-GMP by the WYL domain reversed the inhibitory effect of MbpR on the expression of MucBPs, resulting in increased adherence to intestinal epithelial cells by L. plantarum. Overall, our study provides evidence that a WYL domain transcription factor participates in probiotic colonization by sensing c-di-GMP.

Orally-administrable supramolecular probiotic capsules enable cooperative colon-targeted inflammation inhibition for ameliorating ulcerative colitis

Ulcerative colitis (UC) is a prevalent gastrointestinal disease characterized by the chronical and refractory inflammation of colorectal mucosa and walls, which severely impairs overall well-being of individuals. Probiotics has shown tremendous promise for UC therapy due to its multifaceted mucosal barrier restoration and immunomodulation capabilities. Nevertheless, the successful administration of probiotics remains a clinical obstacle. Herein, we report a multifunctional supramolecular probiotic capsule based on clinically-tested biopolymers for UC therapy, which not only allow colon-targeted probiotic delivery via oral route but also enable concurrent delivery of hemostatic and anti-inflammatory drugs. Specifically, Clostridium butyricum (CB) was first engineered with protective norepinephrine (NE) coating and then encapsulated by self-assembled gelatin-based nanocomplexes modified with balsalazide and matrix metalloproteinase 2/9 (MMP2-/9)-responsive fibronectin peptides. The released balsalazide and fibronectin could induce rapid hemostasis and anti-inflammation actions to alleviate inflammation damage of the UC-affected colons in the short term, while CB could restore gut microbiota homeostasis to remodel intestinal immunocomposition and repair mucosal barrier for reducing UC risk in the long term. Overall, this study provides a promising option for UC treatment with good efficacy and minimal invasiveness. STATEMENT OF SIGNIFICANCE: This study reports a supramolecular probiotic capsule with nanointegrative hemostatic and anti-inflammatory capacities for ulcerative colitis (UC) therapy, which could be orally administrated and activated in the inflamed colorectal sites. The probiotic capsules enable immediate UC symptom relief while also accelerating mucosal repair and preventing UC relapse in the long-term, offering an approach for UC treatment in the clinic.

Antibiotic-perturbed microbiota and the role of probiotics

The disruptive effect of antibiotics on the composition and function of the human microbiota is well established. However, the hypothesis that probiotics can help restore the antibiotic-disrupted microbiota has been advanced, with little consideration of the strength of evidence supporting it. Some clinical data suggest that probiotics can reduce antibiotic-related side effects, including Clostridioides difficile-associated diarrhoea, but there are no data that causally link these clinical effects to microbiota protection or recovery. Substantial challenges hinder attempts to address this hypothesis, including the absence of consensus on the composition of a 'normal' microbiota, non-standardized and evolving microbiome measurement methods, and substantial inter-individual microbiota variation. In this Review, we explore these complexities. First, we review the known benefits and risks of antibiotics, the effect of antibiotics on the human microbiota, the resilience and adaptability of the microbiota, and how microbiota restoration might be defined and measured. Subsequently, we explore the evidence for the efficacy of probiotics in preventing disruption or aiding microbiota recovery post-antibiotic treatment. Finally, we offer insights into the current state of research and suggest directions for future research.

Clinical significance of perioperative probiotic intervention on recovery following intestinal surgery

Restoring the balance of gut microbiota has emerged as a critical strategy in treating intestinal disorders, with probiotics playing a pivotal role in maintaining bacterial equilibrium. Surgical preparations, trauma, and digestive tract reconstruction associated with intestinal surgeries often disrupt the intestinal flora, prompting interest in the potential role of probiotics in postoperative recovery. Lan et al conducted a prospective randomized study on 60 patients with acute appendicitis, revealing that postoperative administration of Bacillus licheniformis capsules facilitated early resolution of inflammation and restoration of gastrointestinal motility, offering a novel therapeutic avenue for accelerated postoperative recovery. This editorial delves into the effects of perioperative probiotic supplementation on physical and intestinal recovery following surgery. Within the framework of enhanced recovery after surgery, the exploration of new probiotic supplementation strategies to mitigate surgical complications and reshape gut microbiota is particularly intriguing.

Bifidobacterium animalis subsp. lactis A6 ameliorates bone and muscle loss via modulating gut microbiota composition and enhancing butyrate production

Systematic bone and muscle loss is a complex metabolic disease, which is frequently linked to gut dysfunction, yet its etiology and treatment remain elusive. While probiotics show promise in managing diseases through microbiome modulation, their therapeutic impact on gut dysfunction-induced bone and muscle loss remains to be elucidated. Employing dextran sulfate sodium (DSS)-induced gut dysfunction model and wide-spectrum antibiotics (ABX)-treated mice model, our study revealed that gut dysfunction instigates muscle and bone loss, accompanied by microbial imbalances. Importantly, Bifidobacterium animalis subsp. lactis A6 (B. lactis A6) administration significantly ameliorated muscle and bone loss by modulating gut microbiota composition and enhancing butyrate-producing bacteria. This intervention effectively restored depleted butyrate levels in serum, muscle, and bone tissues caused by gut dysfunction. Furthermore, butyrate supplementation mitigated musculoskeletal loss by repairing the damaged intestinal barrier and enriching beneficial butyrate-producing bacteria. Importantly, butyrate inhibited the NF-κB pathway activation, and reduced the secretion of corresponding inflammatory factors in T cells. Our study highlights the critical role of dysbiosis in gut dysfunction-induced musculoskeletal loss and underscores the therapeutic potential of B. lactis A6. These discoveries offer new microbiome directions for translational and clinical research, providing promising strategies for preventing and managing musculoskeletal diseases.

Effects of oral supplementation of probiotics on body weight and visceral fat in obese patients: a meta-analysis and systematic review

Obesity can mediate the occurrence of many cardiovascular metabolic diseases, such as coronary heart disease and diabetes, which will lead to a significant increase in all-cause mortality in obese people. Visceral fat refers to the excessive accumulation of adipose tissue in abdominal organs, which can lead to impaired normal function of organs. In recent years, it has been reported that probiotics can reduce obesity and visceral fat content, and some studies have put forward the opposite conclusion. In order to guide the practice of nutrition, we use Meta-analysis method to analyze these conclusions. The authors searched randomized controlled trials on the effects of oral probiotics on body weight and visceral fat content in obese people published before January 2024 in several public databases, such as PubMed, Web of Science, EMBASE, Cochrane Library and CNKI. The primary outcome was body weight, and the secondary outcomes included BMI, waist circumference, visceral fat content, and low-density lipoprotein levels. This trial has been registered in PROSPERO (CRD42024521353). A total of 8 randomized controlled trials involving 412 patients were included in this meta-analysis. Meta-analysis showed that the weight loss of the experimental group taking probiotics was significantly higher than that of the control group (P < 0.00001). The reduction of waist circumference in the experimental group taking probiotics was significantly different from that in the control group (P = 0.01). The decrease of visceral fat content in the experimental group taking probiotics was significantly different from that in the control group (P < 0.00001). There was no significant difference in BMI and LDL-C levels between the experimental group and the control group. Oral probiotics can reduce weight loss, waist circumference and visceral fat content in obese patients, which may be a potential nutritional treatment for obese patients in the future. However, whether oral probiotics can reduce BMI and LDL-C levels in obese patients needs to be included in more RCTs and further discussed in the future.

Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease

Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.

Effects of Lactiplantibacillus plantarum HNU082 intervention on fungi and bacteriophages in different intestinal segments of mice

BACKGROUND

Gut fungi and bacteriophages, as members of the gut microbiota, can affect the interactions between gut bacteria and the host, participate in host metabolism, and are associated with various diseases. Probiotics substantially influence gut fungi and bacteriophages, modulating their composition through both direct and indirect mechanisms, thereby influencing host health. Current research primarily focuses on the effects of probiotics on the intestinal bacterial community. However, the alterations in the compositions of gut fungi and bacteriophages following probiotic intervention are not yet fully understood. Therefore, this study used Lactiplantibacillus plantarum HNU082 (Lp082) as the research subject and aimed to investigate the changes of the gut fungi and bacteriophages in the small intestine and the large intestine after the gavage of Lp082.

RESULTS

After probiotics entered the gut, the changes of the gut fungi and bacteriophages caused by the probiotics were more pronounced in the small intestine compared to the large intestine. The relative abundance of pathogenic fungi, such as Candida albicans, decreased in the small intestine. Furthermore, a strong positive correlation between the relative abundance of bacteriophages and their host bacteria in the gut was observed. The relative abundance of both Clostridia class bacteria and their bacteriophages increased.

CONCLUSIONS

In summary, the effects of probiotics on gut fungi and bacteriophages differed between the small intestine and the large intestine. This study contributed to a better understanding of the impact of probiotics on gut fungi and bacteriophages and provided data support for the association and dynamic changes between gut bacteria and their bacteriophages.

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health

BACKGROUND

Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of penicillin in the early 1940s, has been proposed as a primary contributor to the cumulative alteration of microbiota over generations. However, the mechanistic link between the antibiotics-altered microbiota and chronic conditions remains unclear.

RESULTS

In this study, we discovered that variants of the key beneficial gut microbe, Akkermansia muciniphila, were selected upon exposure to penicillin. These variants had mutations in the promoter of a TEM-type β-lactamase gene or pur genes encoding the de novo purine biosynthesis pathway, and they exhibited compromised abilities to mitigate host obesity in a murine model. Notably, variants of A. muciniphila are prevalent in the human microbiome worldwide.

CONCLUSIONS

These findings highlight a previously unknown mechanism through which antibiotics influence host health by affecting the beneficial capacities of the key gut microbes. Furthermore, the global prevalence of A. muciniphila variants raises the possibility that these variants contribute to global epidemics of chronic conditions, warranting further investigations in human populations. Video Abstract.

Gut Microecological Prescription: A Novel Approach to Regulating Intestinal Micro-Ecological Balance

The intestinal microecology is comprises intestinal microorganisms and other components constituting the entire ecosystem, presenting characteristics of stability and dynamic balance. Current research reveals intestinal microecological imbalances are related to various diseases. However, fundamental research and clinical applications have not been effectively integrated. Considering the importance and complexity of regulating the intestinal microecological balance, this study provides an overview of the high-risk factors affecting intestinal microecology and detection methods. Moreover, it proposes the definition of intestinal microecological imbalance and the definition, formulation, and outcomes of gut microecological prescription to facilitate its application in clinical practice, thus promoting clinical research on intestinal microecology and improving the quality of life of the population.

The Role of the Gut Microbiota in Health, Diet, and Disease with a Focus on Obesity

The gut microbiota has been increasingly recognised as a critical determinant of human health, influencing a wide range of physiological processes. A healthy gut microbiota is essential for maintaining metabolic, immune, and gastrointestinal homeostasis, contributing to overall well-being. Alterations in its composition and functionality, often referred to as microbial dysbiosis, are strongly associated with the development of gut-related and systemic diseases. The gut microbiota synthesises several components and interacts with epithelial cell receptors, influencing processes that extend beyond nutritional status to the pathogenesis of diseases such as obesity, which extend beyond their known contribution to nutritional status. Therefore, this state-of-the-art review synthesises findings from recent studies on the composition, functions, and influencing factors of the gut microbiota, with a focus on its role in obesity. A systematic search of peer-reviewed literature was conducted to ensure comprehensive coverage, while expert insights are incorporated to discuss emerging research directions and future perspectives in the field.

Gut colonization of Bacteroides plebeius suppresses colitis-associated colon cancer development

Colon cancer development may be initiated by multiple factors, including chronic inflammation, genetic disposition, and gut dysbiosis. The loss of beneficial bacteria and increased abundance of detrimental microbes exacerbates disease progression. Bacteroides plebeius (B. plebeius) is a human gut microbe, and its colon colonization is enhanced by a seaweed-supplemented diet. We found that mice orally administered with B. plebeius and fed a diet containing 1% seaweed developed a unique gut microbial composition. By linear discriminant analysis effect size analysis, we found that B. plebeius colonization increased the abundance of Blautia coccoides and reduced the abundance of Akkermansia sp. and Dubosiella sp. We also showed that colonization of B. plebeius suppressed the colon tumor development induced by azoxymethane/dextran sulfate sodium in specific-pathogen-free mice, coinciding with a reduced abundance of Muribaculaceae sp., Closteridale sp., and Bilophila sp. Moreover, B. plebeius colonization in gnotobiotic mice resulted in enhanced production of selected metabolites, including propionic, taurocholic, cholic, alpha-, and beta-muricholic, as well as ursodeoxycholic acids. Importantly, some of these metabolites show anti-inflammatory and tumor-suppressive effects. We conclude that B. plebeius is able to restructure the gut microbial community and produce beneficial metabolites, leading to inhibition of colitis-associated colon cancer development.IMPORTANCEThis work delves into the pivotal role of gut microbiota in suppressing the progression of colitis-associated colon cancer. By investigating the impact of Bacteroides plebeius that can be colonized in mouse gut by feeding the animal with seaweed diet, we unveil a novel mechanism through which this beneficial bacterium reshapes the gut microbial community and produces metabolites with anti-inflammatory and tumor-suppressive properties. Such findings underscore the potential of harnessing specific microbes, like B. plebeius shown in this study, to modulate the gut ecosystem and mitigate the risk of colitis-associated colon cancer.

Effect of caloric restriction with probiotic supplementation on body composition, quality of life, and psychobiological factors of obese men: A randomized, double-blinded placebo-controlled clinical trial

BACKGROUND & AIMS

Obesity is a chronic disease characterized by an excess of fat mass. It is accompanied by a low-grade chronic systemic inflammation state that leads to numerous health disorders. To counteract this scenario, dietary-derived caloric restriction (CR) is the principal intervention for weight loss. Furthermore, probiotic supplementation has gained attention as a co-intervention to optimize weight loss and other health-related factors. As such, we aimed to verify the effect of CR with probiotic supplementation on the body composition, quality of life, sleep quality, anxiety, stress, and depression symptoms of adult men living with obesity.

METHODS

The study is called the Clinical Study of Obesity and Intestinal Microbiota (ECOMI). It is a randomized, double-blind, placebo-controlled clinical trial involving two parallel groups of stable-weight adult men living with obesity. The inclusion criteria were male individuals aged 25-44 years, with body mass index (BMI) ranging from 30.0 to 39.99 kg/m2, and stable body mass over the preceding three months. Participants were randomly assigned to two groups: Caloric Restriction with Probiotic (CRPRO) and Caloric Restriction with Placebo (CRPLA). The achieved CR was 30 % of the total daily energy expenditure. Macronutrients were distributed as 50 % carbohydrates, 30 % lipids, and 20 % proteins. Probiotic supplementation was carried out using two sachets/day of 1 g, containing 1 × 109 Colony Forming Units (CFU) of each strain: Lactobacillus acidophilus NCFM, Lactobacillus rhamnosus HN001, Lactobacillus paracasei Lpc-37 and Bifidobacterium lactis HN019, totaling 8 billion CFU/day. CR and probiotic (or placebo) supplementation intervention lasted 12 weeks. Body composition and psychobiological-related parameters (e.g., sleep, anxiety, stress, and depression) were assessed at baseline and following 12 weeks of intervention. Data are presented as mean and 95 % confidence interval (CI) and mean difference (MD).

RESULTS

The present study applied the per protocol analysis. Thirty-three subjects were evaluated and randomized, but only data from 25 (CRPLA n = 12 vs CRPRO n = 13) participants were included in the final analysis. We verified that CR resulted in weight loss (p < 0.001; η2ρ = 0.754) in both CRPLA (MD: -6.30 kg; p < 0.001) and CRPRO (MD: -5.97 kg; p < 0.001), without differences between groups (p = 0.823; η2ρ = 0.002). Moreover, both CRPLA (MD: -4.83 kg; p < 0.001) and CRPRO (MD: -5.20 kg; p < 0.001) decreased body fat without difference between groups (p = 0.712; η2ρ = 0.006). Regarding obesity-related problems, only the corporeality dimension (p < 0.001; η2ρ = 0.474) in both CRPLA (p = 0.028) and CRPRO (p = 0.039) improved. World Health Organization Quality of Life (WHOQoL)-related dimensions were improved for perception (p < 0.001; η2ρ = 0.630), satisfaction (p < 0.001; η2ρ = 0.778), and psychological domain (p < 0.001; η2ρ = 0.567), without differences between groups. Moreover, sleep quality (p < 0.001; η2ρ = 0.522) improved in both groups, without differences between groups. Finally, anxiety (p = 0.013; η2ρ = 0.250) and depression (p = 0.003; η2ρ = 0.345) scores assessed via the Depression, Anxiety and Stress Scale-21 (DASS-21) and the Beck Depression Inventory (BDI-II) (p < 0.001; η2ρ = 0.448) improved only in the CRPRO group.

CONCLUSIONS

Probiotic supplementation did not enhance the effects of caloric restriction on body composition, QoL-, or sleep-related parameters. However, anxiety and depressive symptoms improved only in the CRPRO group, despite no differences between groups after 12 weeks. Further studies are needed to confirm these findings.

Navigating a challenging path: precision disease treatment with tailored oral nano-armor-probiotics

Oral probiotics have significant potential for preventing and treating many diseases. Yet, their efficacy is often hindered by challenges related to survival and colonization within the gastrointestinal tract. Nanoparticles emerge as a transformative solution, offering robust protection and enhancing the stability and bioavailability of these probiotics. This review explores the innovative application of nanoparticle-armored engineered probiotics for precise disease treatment, specifically addressing the physiological barriers associated with oral administration. A comprehensive evaluation of various nano-armor probiotics and encapsulation methods is provided, carefully analyzing their respective merits and limitations, alongside strategies to enhance probiotic survival and achieve targeted delivery and colonization within the gastrointestinal tract. Furthermore, the review explores the potential clinical applications of nano-armored probiotics in precision therapeutics, critically addressing safety and regulatory considerations, and proposing the innovative concept of 'probiotic intestinal colonization with nano armor' for brain-targeted therapies. Ultimately, this review aspires to guide the advancement of nano-armored probiotic therapies, driving progress in precision medicine and paving the way for groundbreaking treatment modalities.

Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.

Leaky Gut Syndrome: An Interplay Between Nutrients and Dysbiosis

PURPOSE OF REVIEW

The gut microbiota (GM) is directly related to health and disease. In this context, disturbances resulting from excessive stress, unbalanced diet, alcohol abuse, and antibiotic use, among other factors, can contribute to microbiota imbalance, with significant impacts on host health. This review provides a comprehensive examination of the literature on the influence of diet on dysbiosis and increased intestinal permeability over the past five years.

RECENT FINDINGS

Diet can be considered one of the main modulating factors of GM, impacting its composition and functionality. Excessive consumption of simple carbohydrates, saturated fats, and processed foods appears to be directly linked to dysbiosis, which can lead to intestinal hyperpermeability and leaky gut syndrome. On the other hand, diets primarily composed of food groups such as nuts, vegetables, fruits, fish, and poultry in moderate quantities, along with limited consumption of red and processed meats, are associated with a more diverse, healthier, and beneficial GM for the host. It is worth noticing that the use of prebiotics and probiotics, omega-3 supplementation, polyunsaturated fatty acids, and vitamins A, B, C, D, and E can positively modulate the intestinal microbiota by altering its metabolic activity, microbial composition, and improve intestinal barrier function. This review points to a new perspective regarding individualized dietary intervention and the need to integrate it into several aspects of cellular biology, biochemistry, and microbiology to prescribe more effective diets and thus contribute to patients' comprehensive health.

Synbiotics effects of d-tagatose and Lactobacillus rhamnosus GG on the inflammation and oxidative stress reaction of Gallus gallus based on the genus of cecal bacteria and their metabolites

BACKGROUNDS

Abuse of feed supplement can cause oxidative stress and inflammatory responses in Gallus gallus. Synbiotics are composed of prebiotics and probiotics and it possess huge application potentials in the treatment of animal diseases.

METHODS

This study examined the effect of d-tagatose on the probiotic properties of L. rhamnosus GG, L. paracasei, and S. lactis so as to screen the best synbiotic combinations. Treat Gallus gallus exhibiting oxidative stress and immune response caused by aflatoxin b1 with optimal synbiotics for 14 days, detect the changes of inflammatory markers and oxidative stress markers of Gallus gallus using qRT-PCR, and identified the intestinal bacteria genera and their metabolites in the cecum of Gallus gallus using gut microbiota and metabolomics analysis.

RESULTS AND CONCLUSION

The results indicated that oxidative stress and immune response factor expressions quantity in Gallus gallus decreased significantly after 14 days of treatment, compared with model group, the low-dose treatment group's SOD1, SOD3, GPX1, GPX2, GSR, H6DP, and HO-1 genes in liver were downregulated by 36.03%, 40.01%, 45.86%, 40.79%, 37.68%, 25.04%, and 29.89%, the IL-1, IL-2, IL-4, IL-6, IgA, IgM, and IgG genes in blood and spleen were downregulated by 26.59%, 34.19%, 21.19%, 28.18%, 35.93%, 12.67%, 21.81 and 35.93%, 22.85%, 21.19%, 28.78%, 35.93%, 15.36%, 29.73%. The intestinal bacteria genera and metabolomics analysis results indicated that the abundance of beneficial bacteria genus was up-regulated, and the proportion of pathogenic bacteria genera decreased. The amount of beneficial metabolites associated with antioxidant and anti-inflammatory effects was upregulated. The synbiotic composed of d-tagatose and L. rhamnosus GG can treat oxidative stress and immune response by altering the structure of intestinal bacteria genera and the production of metabolites.

Mechanisms by which microbiome-derived metabolites exert their impacts on neurodegeneration

Recent developments in microbiome research suggest that the gut microbiome may remotely modulate central and peripheral neuronal processes, ranging from early brain development to age-related changes. Dysbiotic microbiome configurations have been increasingly associated with neurological disorders, such as neurodegeneration, but causal understanding of these associations remains limited. Most mechanisms explaining how the microbiome may induce such remote neuronal effects involve microbially modulated metabolites that influx into the 'sterile' host. Some metabolites are able to cross the blood-brain barrier (BBB) to reach the central nervous system, where they can impact a variety of cells and processes. Alternatively, metabolites may directly signal to peripheral nerves to act as neurotransmitters or exert modulatory functions, or impact immune responses, which, in turn, modulate neuronal function and associated disease propensity. Herein, we review the current knowledge highlighting microbiome-modulated metabolite impacts on neuronal disease, while discussing unknowns, controversies and prospects impacting this rapidly evolving research field.

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface

AIMS

The gastrointestinal (GI) tract is composed of distinct sub-regions, which exhibit segment-specific differences in microbial colonization and (patho)physiological characteristics. Gut microbes can be collectively considered as an active endocrine organ. Microbes produce metabolites, which can be taken up by the host and can actively communicate with the immune cells in the gut lamina propria with consequences for cardiovascular health. Variation in bacterial load and composition along the GI tract may influence the mucosal microenvironment and thus be reflected its interstitial fluid (IF). Characterization of the segment-specific microenvironment is challenging and largely unexplored because of lack of available tools.

METHODS AND RESULTS

Here, we developed methods, namely tissue centrifugation and elution, to collect IF from the mucosa of different intestinal segments. These methods were first validated in rats and mice, and the tissue elution method was subsequently translated for use in humans. These new methods allowed us to quantify microbiota-derived metabolites, mucosa-derived cytokines, and proteins at their site-of-action. Quantification of short-chain fatty acids showed enrichment in the colonic IF. Metabolite and cytokine analyses revealed differential abundances within segments, often significantly increased compared to plasma, and proteomics revealed that proteins annotated to the extracellular phase were site-specifically identifiable in IF. Lipopolysaccharide injections in rats showed significantly higher ileal IL-1β levels in IF compared to the systemic circulation, suggesting the potential of local as well as systemic effect.

CONCLUSION

Collection of IF from defined segments and the direct measurement of mediators at the site-of-action in rodents and humans bypasses the limitations of indirect analysis of faecal samples or serum, providing direct insight into this understudied compartment.

The impact of fibre and prebiotic interventions on outcomes in cancer and haematopoietic stem cell transplantation: A systematic review

BACKGROUND & AIMS

Cancer therapy is associated with a range of toxicities that severely impact patient well-being and a range of clinical outcomes. Dietary fibre/prebiotics characteristically improve the gastrointestinal microenvironment, which consequently elicits beneficial downstream effects that could be relevant to the prevention and management of treatment-related toxicities. Despite the compelling theoretical scientific rationale there has been limited effort to synthesise the available evidence to conclude such scientific underpinning to the clinical use of fibre/prebiotics in cancer patients. Therefore, this systematic review aimed to evaluate the clinical impact of fibre/prebiotic-based interventions on gastrointestinal-side effects; gastrointestinal-microbiome; clinical outcomes; nutrition status and body composition; and quality-of-life in children and adults being treated for cancer or undergoing a haematopoietic stem cell transplant (HSCT).

METHODS

This study was conducted in adherence to PRISMA guidelines, and the protocol was published prospectively with PROSPERO (CRD42022299428). Three databases (MEDLINE (Ovid), CINHAL, EMBASE) were searched from inception to December 2023. All articles were assessed for bias using the Cochrane risk-of-bias tool RoB 2.0 (for RCTs) and ROBINS-I (for non-RCTs).

RESULTS

A total of 9989 de-duplicated records were identified, of these, 14 (paediatrics [n = 1], adults [n = 13]) met the inclusion criteria (randomised controlled trials (RCT) [n = 11], observational or non-RCTs [n = 3]). The risk-of-bias was graded to be serious/high (n = 6); moderate/some concerns (n = 7); low (n = 1). Interventions included prebiotic supplement (n = 8), nutrition supplement/formula with added fibre/prebiotic (n = 3) and dietary modification (n = 3). The dose of fibre intervention ranged from 2.4g to 30g per day. Substantial heterogeneity of target parameters was identified across a range all outcome categories, precluding definitive conclusions.

CONCLUSION

The scientific rationale for fibre/prebiotics-based interventions for the prevention or management of cancer treatment-related toxicities is compelling. However, it is clear that the scientific and clinical field remains disconnected in how to effectively translate this approach to improve cancer outcomes. High-quality intervention studies translatable to clinical practice are now evidently crucial to determine if and how fibre/prebiotics should be used to support people undergoing cancer or HSCT therapy.

Roles of Probiotics, Prebiotics, and Postbiotics in B-Cell-Mediated Immune Regulation

Probiotics, prebiotics, and postbiotics can significantly influence B-cell-related diseases through their immunomodulatory effects. They enhance the immune system's function, particularly affecting B cells, which originate in the bone marrow and are crucial for antibody production and immune memory. These substances have therapeutic potential in managing allergies, autoimmune diseases, and inflammatory conditions by regulating the gut microbiota, strengthening epithelial barriers, and directly interacting with various components of the innate and adaptive immune systems. The review highlights the critical need for further research into the precise mechanisms through which probiotics, prebiotics, and postbiotics modulate B cells. Gaining this understanding could facilitate the development of more effective treatments for B-cell-related diseases by harnessing the immunomodulatory properties of these dietary components.

Rebalancing immune homeostasis in combating disease: The impact of medicine food homology plants and gut microbiome

BACKGROUND

Gut microbiota plays an important role in multiple human physiological processes and an imbalance in it, including the species, abundance, and metabolites can lead to diseases. These enteric microorganisms modulate immune homeostasis by presenting a myriad of antigenic determinants and microbial metabolites. Medicinal and food homologous (MFH) plants, edible herbal materials for both medicine and food, are important parts of Traditional Chinese Medicine (TCM). MFH plants have drawn much attention due to their strong biological activity and low toxicity. However, the interplay of MFH and gut microbiota in rebalancing the immune homeostasis in combating diseases needs systematic illumination.

PURPOSE

The review discusses the interaction between MFH and gut microbiota, including the effect of MFH on the major group of gut microbiota and the metabolic effect of gut microbiota on MFH. Moreover, how gut microbiota influences the immune system in terms of innate and adaptive immunity is addressed. Finally, the immunoregulatory mechanisms of MFH in regulation of host pathophysiology via gut microbiota are summarized.

METHODS

Literature was searched, analyzed, and collected using databases, including PubMed, Web of Science, and Google Scholar using relevant keywords. The obtained articles were screened and summarized by the research content of MFH and gut microbiota in immune regulation.

RESULTS

The review demonstrates the interaction between MFH and gut microbiota in disease prevention and treatment. Not only do the intestinal microorganisms and intestinal mucosa constitute an important immune barrier of the human body, but also lymphoid tissue and diffused immune cells within the mucosa participate in the response of innate immunity and adaptive immunity. MFH modulates immune regulation by affecting intestinal flora, helps maintain the balance of the immune system and interfere with the occurrence and development of a broad category of diseases.

CONCLUSION

Being absorbed from the gastrointestinal tract, MFH can have profound effects on gut microbiota. In turn, the gut microbiota also actively participate in the bioconversion of complex constituents from MFH, which could further influence their physiological and pharmacological properties. The review deepens the understanding of the relationship among MFH, gut microbiota, immune system, and human diseases and further promotes the progression of additional relevant research.

Delving the depths of 'terra incognita' in the human intestine - the small intestinal microbiota

The small intestinal microbiota has a crucial role in gastrointestinal health, affecting digestion, immune function, bile acid homeostasis and nutrient metabolism. The challenges of accessibility at this site mean that our knowledge of the small intestinal microbiota is less developed than of the colonic or faecal microbiota. Here, we summarize the features and fluctuations of the microbiota along the small intestinal tract, focusing on humans, and discuss physicochemical factors and assessment methods, including the technical challenges of investigating the low microbial biomass of the proximal small bowel. We highlight the essential protective mechanisms of the small intestine, including motility, the paracellular barrier and mucus, and secretory immunity, to show their roles in limiting excessive exposure of host tissues to microbial metabolites. We address current knowledge gaps, particularly the variability among individuals, the effects of dysbiosis of the small intestinal microbiota on health and how different taxa in small intestinal microbiota could compensate for each other functionally.

Metabolic modelling uncovers the complex interplay between fungal probiotics, poultry microbiomes, and diet

BACKGROUND

The search for alternatives to antibiotic growth promoters in poultry production has increased interest in probiotics. However, the complexity of the interactions between probiotics, gut microbiome, and the host hinders the development of effective probiotic interventions. This study explores metabolic modelling to examine the possibility of designing informed probiotic interventions within poultry production.

RESULTS

Genomic metabolic models of fungi were generated and simulated in the context of poultry gut microbial communities. The modelling approach correlated with short-chain fatty acid production, particularly in the caecum. Introducing fungi to poultry microbiomes resulted in strain-specific and diet-dependent effects on the gut microbiome. The impact of fungal probiotics on microbiome diversity and pathogen inhibition varied depending on the specific strain, resident microbiome composition, and host diet. This context-dependency highlights the need for tailored probiotic interventions that consider the unique characteristics of each poultry production environment.

CONCLUSIONS

This study demonstrates the potential of metabolic modelling to elucidate the complex interactions between probiotics, the gut microbiome, and diet in poultry. While the effects of specific fungal strains were found to be context-dependent, the approach itself provides a valuable tool for designing targeted probiotic interventions. By considering the specific characteristics of the host microbiome and dietary factors, this methodology could guide the deployment of effective probiotics in poultry production. However, the current work relies on computational predictions, and further in vivo validation studies are needed to confirm the efficacy of the identified probiotic candidates. Nonetheless, this study represents a significant step in using metabolic models to inform probiotic interventions in the poultry industry. Video Abstract.

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

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

The oral-gut microbiome axis in health and disease

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

Attenuation of Hyperglycemia in Diabetic Rats Assisted by Immobilized Probiotic in Sodium Alginate

Diabetes mellitus type 2 (DM2) is the most common chronic disease worldwide, characterized mainly by increased glucose concentration in the blood and affecting several organs' functionality. The daily consumption of probiotic bacteria can help control diabetes and reduce the damage caused. Cell immobilization techniques are a powerful tool that provides physical cell protection to such probiotic bacteria against gastrointestinal conditions. We suggest that cell immobilization could be a significant vector for delivering a high quantity of viable probiotics to the gut, helping attenuate hyperglycemia in diabetic rats. Seventy male Wistar rats were used in this work. Nicotinamide was administrated via intraperitoneal injection 15 minutes before inducing type 2 diabetes (DM2), followed by a second intraperitoneal injection of streptozotocin to induce DM2. Rats were divided into seven groups. For 45 days, a specific treatment was applied to each group. The group of rats, supplied with immobilized Lactobacillus casei, showed a serum glucose concentration of 137 mg/dL, which was close to the one observed in the groups of healthy rats (117 mg/dL) and rats treated with metformin (155 mg/dL). The diabetic rats without treatment presented a higher serum glucose concentration (461 mg/dL). In the rats treated with immobilized L. casei, there was no biochemical parameter alteration, and the cell morphology of the analyzed tissues was similar to those of the healthy group. The consumption of immobilized L. casei could allow a high quantity of viable probiotics to be delivered to the gut, reducing serum glucose concentration by up to 70% compared to diabetic rats and reducing organ damage caused by diabetes.

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut

While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.

Microbiome Shifts and Their Impact on Gut Physiology in Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is one of the most prevalent functional gastrointestinal disorders characterized by recurrent abdominal pain and altered bowel habits. The exact pathophysiological mechanisms for IBS development are not completely understood. Several factors, including genetic predisposition, environmental and psychological influences, low-grade inflammation, alterations in gastrointestinal motility, and dietary habits, have been implicated in the pathophysiology of the disorder. Additionally, emerging evidence highlights the role of gut microbiota in the pathophysiology of IBS. This review aims to thoroughly investigate how alterations in the gut microbiota impact physiological functions such as the brain-gut axis, immune system activation, mucosal inflammation, gut permeability, and intestinal motility. Our research focuses on the dynamic "microbiome shifts", emphasizing the enrichment or depletion of specific bacterial taxa in IBS and their profound impact on disease progression and pathology. The data indicated that specific bacterial populations are implicated in IBS, including reductions in beneficial species such as Lactobacillus and Bifidobacterium, along with increases in potentially harmful bacteria like Firmicutes and Proteobacteria. Emphasis is placed on the imperative need for further research to delineate the role of specific microbiome alterations and their potential as therapeutic targets, providing new insights into personalized treatments for IBS.

Utilization of diverse probiotics to create human health promoting fatty acids: A review

Many probiotics produce functional lipids with health-promoting properties, such as short-chain fatty acids, linoleic acid and omega-3 fatty acids. They have been shown to maintain gut health, strengthen the intestinal barrier, and have anti-inflammatory and antioxidant effects. In this article, we provide an up-to-date review of the various functional lipids produced by probiotics. These probiotics can be incorporated into foods, supplements, or pharmaceuticals to produce these functional lipids in the human colon, or they can be used in industrial biotechnology processes to generate functional lipids, which are then isolated and used as ingredients. We then highlight the different physiological functions for which they may be beneficial to human health, in addition to discussing some of the challenges of incorporating probiotics into commercial products and some potential solutions to address these challenges. Finally, we highlight the importance of testing the efficacy and safety of the new generation of probiotic-enhanced products, as well as the great potential for the marketization of related products.