Lactobacillus plantarum-derived indole-3-lactic acid ameliorates colorectal tumorigenesis via epigenetic regulation of CD8+ T cell immunity

Role of gut microbiome in suppression of cancers

The pathogenesis of cancer is closely related to the disruption of homeostasis in the human body. The gut microbiome plays crucial roles in maintaining the homeostasis of its host throughout lifespan. In recent years, a large number of studies have shown that dysbiosis of the gut microbiome is involved in the entire process of cancer initiation, development, and prognosis by influencing the host immune system and metabolism. Some specific intestinal bacteria promote the occurrence and development of cancers under certain conditions. Conversely, some other specific intestinal bacteria suppress the oncogenesis and progression of cancers, including inhibiting the occurrence of cancers, delaying the progression of cancers and boosting the therapeutic effect on cancers. The promoting effects of the gut microbiome on cancers have been comprehensively discussed in the previous review. This article will review the latest advances in the roles and mechanisms of gut microbiome in cancer suppression, providing a new perspective for developing strategies of cancer prevention and treatment.

Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming

Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.

Bacillus paralicheniformis-mediated gut microbiota promotes M2 macrophage polarization by inhibiting P38 MAPK signaling to alleviate necrotizing enterocolitis and apoptosis in mice

Clostridial necrotizing enterocolitis is a severe gastrointestinal disease induced by Clostridium, strongly associated with intestinal dysbiosis. Fecal microbiota transplantation (FMT) has proven effective in treating gastrointestinal diseases by remodeling intestinal microbial homeostasis. However, it remains unclear whether FMT from donors with beneficial microbiota can improve the recipient's intestinal function more efficiently. This study found that probiotic Bacillus paralicheniformis SN-6-mediated gut microbiota effectively prevent Clostridial necrotizing enteritis and explored the underlying molecular mechanisms. Data demonstrated that SN-6 altered gut microbiota composition, ameliorated Clostridium perfringens-induced intestinal microbiota dysbiosis and metabolic reprogramming, particularly enhancing tryptophan metabolism. This led to a marked reduction in intestinal barrier damage and inflammation. FMT from SN-6-treated mice reduced jejunal inflammation in Clostridium perfringens-infected mice, strengthened jejunal barrier and enriched beneficial bacteria, such as Lactobacillus, Blautia, Akkermansia. Furthermore, 3-indoleacetic acid (IAA), a metabolite enriched by SN-6, activated aryl hydrocarbon receptor (AhR), suppressed the P38 mitogen-activated protein kinase (P38 MAPK) signaling, and drove macrophage polarization from M0 to M2-type, thereby reducing apoptosis and excessive inflammation. This study highlights Bacillus paralicheniformis SN-6 as a key modulator of intestinal immunomodulation via the gut microbiota-IAA-AhR-P38 MAPK axis, offering a potential therapeutic target for preventing and controlling clostridial necrotizing enteritis.

Comparative study on the alleviating effect of neohesperidin dihydrochalcones and its synthetic precursor neohesperidin on ovalbumin-induced food allergy

The biological activities of natural flavonoids are structure-dependent. To investigate the structure-dependent activities of neohesperidin dihydrochalcone (NHDC) and neohesperidin (NH), which have the same basic skeletal structure, we systematically compared their roles in alleviating ovalbumin-induced food allergies in mice. Our results indicate that NHDC is superior to NH in ameliorating allergic symptoms, especially in restoring T helper 1 and T helper 2 cells (Th1 and Th2, respectively)balance and inhibiting splenic NOTCH/nuclear factor kappa-B (NF-κB) activation by enhancing binding to Hes1, which was validated by molecular docking. Both compounds increased the abundance of beneficial gut microbiota (e.g., Lactobacillus). Still, the dihydrochalcone portion of NHDC possessed superior intestinal barrier repair and immunomodulatory effects, synergizing anti-inflammatory and microbiota modulatory effects. These results provide new insights into the structure-dependent activity of natural flavonoids in treating food allergies.

Indole lactic acid derived from Akkermansia muciniphila activates the aryl hydrocarbon receptor to inhibit ferroptosis in ischemic stroke

Ischemic stroke concurrent with gut microbiome dysbiosis induces intestinal damage, which exacerbates cerebral infarction. Probiotic or prebiotic interventions that reverse gut microbiome dysbiosis can promote recovery after ischemic stroke. Akkermansia muciniphila (AKK) safeguards intestinal health and is a promising probiotic; however, its role in ischemic stroke remains unclear. In this study, we found that live AKK, but not pasteurized AKK, mitigated ischemic-stroke-induced neurological injury, reduced cerebral infarction, and enhanced both blood-brain and intestinal barrier integrity. Moreover, the AKK supernatant reduced intestinal and cerebral injury, demonstrating efficacy comparable to that of live AKK. Metabolomic analysis revealed that the AKK supernatant was significantly enriched in indole lactic acid (ILA), a tryptophan metabolite. ILA levels were elevated in the serum and brains of pseudo-germ-free stroke rats administered AKK. Exogenous gavage with ILA mitigated ischemic-stroke-induced brain and intestinal damage. Mechanistically, ILA activated the aryl hydrocarbon receptor (AhR) and the nuclear transcription factor Nrf2, leading to the upregulation of SLC7A11 and GPX4 protein expression. This attenuated lipid peroxidation and intracellular iron accumulation triggered by ischemic stroke. Notably, intervention with the AhR inhibitor CH223191 abrogated the protective effects of ILA in ischemic stroke rats. These findings suggest that the therapeutic efficacy of AKK in ischemic stroke is at least partially attributable to ILA-mediated ferroptosis inhibition via AhR activation. AKK was selectively enriched by Puerariae lobatae Radix-resistant starch (PRS), promoting ILA generation more effectively than inulin and β-glucan. AKK and PRS synergistically alleviated ischemic-stroke-induced impairments, outperforming monomicrobial or prebiotic treatment alone. These findings reveal the unique mechanisms of AKK in ischemic stroke and provide a viable strategy for the clinical treatment of ischemic stroke through a novel synbiotic combination.

Precisely edited gut microbiota by tungsten-doped Prussian blue nanoparticles for the treatment of inflammatory bowel disease

Inflammatory bowel disease (IBD) is characterized by recurring gastrointestinal inflammation, accompanied by a significant rise in global prevalence and disease severity. The overaccumulation of reactive oxygen and nitrogen species (RONS) in the intestinal environment disrupts redox homeostasis and drives pathological overgrowth of Escherichia coli, which are central to IBD pathogenesis. Herein, we designed a multifunctional nanozyme (W-PB) to enable sustained and targeted regulation of intestinal homeostasis through dual mechanisms: specific inhibition of E. coli overgrowth during colitis and efficient RONS clearance. To ensure colon-specific delivery, W-PB was encapsulated in an electrostatically crosslinked hydrogel composed of alginate and chitosan. This formulation protects W-PB from degradation in harsh gastrointestinal conditions and releases the nanoparticles selectively under weakly alkaline intestinal pH. The released tungsten ions suppress E. coli growth via competitive displacement of molybdenum in the molybdopterin cofactor, while W-PB simultaneously neutralizes excess RONS to shield intestinal cells from oxidative damage. In DSS-induced colitis models, the W-PB gel demonstrated significant therapeutic efficacy, achieved through intestinal microbiota remodeling and oxidative stress mitigation.

Intestinal dysbiosis and colorectal cancer

ABSTRACT

Colorectal cancer (CRC) is one of the leading causes of cancer-related morbidity and mortality worldwide, highlighting the urgent need for novel preventive and therapeutic strategies. Emerging research highlights the crucial role of the gut microbiota, including bacteria, fungi, viruses, and their metabolites, in the pathogenesis of CRC. Dysbiosis, characterized by an imbalance in microbial composition, contributes to tumorigenesis through immune modulation, metabolic reprogramming, and genotoxicity. Specific bacterial species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis , along with fungal agents like Candida species, have been implicated in CRC progression. Moreover, viral factors, including Epstein-Barr virus and human cytomegalovirus, are increasingly recognized for their roles in promoting inflammation and immune evasion. This review synthesizes the latest evidence on host-microbiome interactions in CRC, emphasizing microbial metabolites, such as short-chain fatty acids and bile acids, which may act as both risk factors and therapeutic agents. We further discuss the latest advances in microbiota-targeted clinical applications, including biomarker-assisted diagnosis, next-generation probiotics, and microbiome-based interventions. A deeper understanding of the role of gut microbiome in CRC pathogenesis could pave the way for diagnostic, preventive, and personalized therapeutic strategies.

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.

Microbial remodeling of gut tryptophan metabolism and indole-3-lactate production regulate epithelial barrier repair and viral suppression in human and simian immunodeficiency virus infections

Gut inflammatory diseases cause microbial dysbiosis. Human immunodeficiency virus-1 (HIV) infection disrupts intestinal integrity, subverts repair/renewal pathways, impairs mucosal immunity and propels microbial dysbiosis. However, microbial metabolic mechanisms driving repair mechanisms in virally inflamed gut are not well understood. We investigated the capability and mechanisms of gut microbes to restore epithelial barriers and mucosal immunity in virally inflamed gut by using a multipronged approach: an in vivo simian immunodeficiency virus (SIV)-infected nonhuman primate model of HIV/AIDS, ex vivo HIV-exposed human colorectal explants and primary human intestinal epithelial cells. SIV infection reprogrammed tryptophan (TRP) metabolism, increasing kynurenine catabolite levels that are associated with mucosal barrier disruption and immune suppression. Administration of Lactiplantibacillus plantarum or Bifidobacterium longum subsp. infantis into the SIV-inflamed gut lumen in vivo resulted in rapid reprogramming of microbial TRP metabolism towards indole-3-lactic acid (ILA) production. This shift accelerated epithelial repair and enhanced anti-viral defenses through induction of IL-22 signaling in mucosal T cells and aryl hydrocarbon receptor activation. Additionally, ILA treatment of human colorectal tissue explants ex vivo inhibited HIV replication by reducing mucosal inflammatory cytokine production and cell activation. Our findings underscore the therapeutic potential of microbial metabolic reprogramming of TRP-to-ILA and mechanisms in mitigating viral pathogenic effects and bolstering mucosal defenses for HIV eradication.

Gut and Intratumoral microbiota: Key to lung Cancer development and immunotherapy

Lung cancer is a common malignant tumor worldwide with high incidence and mortality rates. Previous studies have claimed that the microbial community plays an integral role in the development and progression of lung cancer. Emerging evidence reveals that gut flora plays a key role in cancer formation and evolution by participating in mechanisms such as metabolism, regulation of inflammation and immune response. Not only the gut flora, but also the presence of intratumoral microbiota may influence lung cancer progression through multiple mechanisms. These research advances suggest that intestinal flora and intratumoral microbiota may not only serve as potential biomarkers for lung cancer, but may also be targets for therapy. However, current studies on both in lung cancer are still limited. Given this, this study aimed to systematically review the latest findings on the major bacterial species of the intestinal flora and their possible protective or harmful roles in the formation, progression, and metastasis of lung cancer. In addition, we analyzed the potential mechanisms by which the intratumoral microbiota affected lung cancer and elaborated on the potential roles of the gut flora and its metabolites, as well as the intratumoral microbiota, in modulating the efficacy of immunotherapy in lung cancer.

Utilizing Dual-Channel Graph and Hypergraph Convolution Network to Discover Microbes Underlying Disease Traits

Discovering microbes underlying disease traits opens up opportunities for the diagnosis and effective treatment of diseases. However, traditional methods are often based on biological experiments, which are not only time-consuming but also costly, driving the need for computational frameworks that can accelerate the discovery of these associations. Motivated by these challenges, we propose an innovative prediction algorithm named dual-channel graph and Hypergraph Convolutional Network (DCGHCN) to discover microbes underlying disease traits. First, based on the K-Nearest Neighbors (KNN) principle, we constructed attribute graphs for microbes and diseases, respectively. Next, Graph Convolutional Networks (GCNs) are used to capture homogeneous level implicit representations from attribute graphs of microbes and diseases. We used the output of the GCN layer as input to construct a hypergraph convolutional layer of microbes and diseases, to evaluate the impact of the confirmed microbes and diseases associations (MDAs) on the prediction results. Perform scalar product calculation on the microbe and disease features to determine the predicted score. The innovation of DCGHCN lies in employing the KNN algorithm to handle missing values in the correlation matrix during preprocessing and the use of a dual-channel structure to combine the advantages of GCNs and Hypergraph Convolutional Networks (HGCNs). We used 5-fold cross-validation (CV) to evaluate the performance of DCGHCN. The results showed that the DCGHCN model achieved AUC (Area Under the ROC Curve), AUPR (Area Under the PR Curve), F1-score and accuracy of 0.9415, 0.7637, 0.7515, and 0.9818. We selected two diseases for case studies, and a large number of published literature conclusions confirmed the prediction results of DCGHCN, thus proving that DCGHCN is an effective tool for discovering microbes underlying disease traits.

Indole-3-lactic acid derived from tryptophan metabolism promotes trophoblast migration and invasion by activating the AhR/VCAN pathway

BACKGROUND

Preeclampsia (PE) is a life-threatening condition that is unique to human pregnancy, and it is a leading cause of maternal and neonatal morbidity and mortality. Currently, the only definitive treatment for PE is delivery of the placenta. Several studies have suggested that the gut microbiota and its derived metabolites may be associated with PE. Our previous work indicated that the level of indole-3-lactic acid (ILA), which is a metabolite derived from tryptophan (Trp) metabolism in the gut, is increased in PE patients. However, the effects of ILA on trophoblast function and its underlying mechanisms remain largely unknown.

METHODS

Transwell assays were conducted to assess the effects of ILA on trophoblast migration and invasion. Moreover, the aryl hydrocarbon receptor (AhR) signaling pathway was examined by qRT-PCR, western blotting and siRNA transfection. Additionally, RNA-seq analysis was performed to explore the mechanism underlying the ILA-mediated effects on trophoblast function. Finally, in vivo trophoblast invasion was evaluated through immunohistochemical analysis.

RESULTS

Our data demonstrated that ILA promoted HTR-8/SVneo cell migration and invasion through AhR signaling pathway activation. Mechanistically, VCAN upregulation played a key role in mediating the effects of ILA on trophoblasts after AhR activation. Notably, ILA supplementation improved spiral artery remodeling and increased trophoblast invasion in PE-like mice, primarily by increasing VCAN levels.

CONCLUSIONS

These data strongly suggest that elevated ILA in PE serve as a protective mechanism against trophoblast dysfunction. Therefore, we propose that ILA may be a novel and promising therapeutic approach for treating PE by enhancing trophoblast functions.

Decoding the genetic and environmental forces in propelling the surge of early-onset colorectal cancer

ABSTRACT

Early-onset colorectal cancer (EOCRC) shows a different epidemiological trend compared to later-onset colorectal cancer, with its incidence rising in most regions and countries worldwide. However, the reasons behind this trend remain unclear. The etiology of EOCRC is complex and could involve both genetic and environmental factors. Apart from Lynch syndrome and Familial Adenomatous Polyposis, sporadic EOCRC exhibits a broad spectrum of pathogenic germline mutations, genetic polymorphisms, methylation changes, and chromosomal instability. Early-life exposures and environmental risk factors, including lifestyle and dietary risk factors, have been found to be associated with EOCRC risk. Meanwhile, specific chronic diseases, such as inflammatory bowel disease, diabetes, and metabolic syndrome, have been associated with EOCRC. Interactions between genetic and environmental risk factors in EOCRC have also been explored. Here we present findings from a narrative review of epidemiological studies on the assessment of early-life exposures, of EOCRC-specific environmental factors, and their interactions with susceptible loci. We also present results from EOCRC-specific genome-wide association studies that could be used to perform Mendelian randomization analyses to ascertain potential causal links between environmental factors and EOCRC.

Microbiota mechanisms in cancer progression and therapy

The composition of the microbiota in patients has been shown to correlate with cancer progression and response to therapy, highlighting unique opportunities to improve patient outcomes. In this review, we discuss the challenges and advancements in understanding the chemical mechanisms of specific microbiota species, pathways, and molecules involved in cancer progression and treatment. We also describe the modulation of cancer and immunotherapy by the microbiota, along with approaches for investigating microbiota enzymes and metabolites. Elucidating these specific microbiota mechanisms and molecules should offer new opportunities for developing enhanced diagnostics and therapeutics to improve outcomes for cancer patients. Nonetheless, many microbiota mechanisms remain to be determined and require innovative chemical genetic approaches.

Bifidobacterium bifidum 1007478 derived indole-3-lactic acid alleviates NASH via an aromatic hydrocarbon receptor-dependent pathway in zebrafish

AIMS

This study investigates the potential of Bifidobacterium bifidum 1007478 (BB478) and its metabolite indole-3-lactic acid (ILA) in alleviating non-alcoholic steatohepatitis (NASH) induced by a high-fat diet (HFD) and fructose exposure.

MATERIALS AND METHODS

A zebrafish model of NASH was established by exposure to HFD and fructose. BB478 was administered, and the effects on liver lipid accumulation, oxidative stress, and inflammation were assessed. ILA production by BB478 was confirmed, and its impact on hepatic lipogenesis and inflammatory pathways was evaluated. The involvement of the aromatic hydrocarbon receptor (AhR) was also examined using an AhR inhibitor.

KEY FINDINGS

BB478 supplementation inhibited lipid accumulation in the liver, reduced triglycerides (TG) and total cholesterol (TC), and mitigated oxidative stress, as evidenced by lower levels of reactive oxygen species (ROS) and malondialdehyde (MDA). ILA, produced by BB478, could alleviate the hepatic damage and fat deposition in liver. Mechanistically, it suppressed hepatic lipogenesis by downregulating lipogenesis-related genes, including sterol response element binding protein 1 (SREBP1) and fatty acid synthase (FASN). ILA also inhibited the expression of pro-inflammatory cytokines to suppress inflammation. The therapeutic effects of ILA were reversed by the AhR inhibitor, indicating that ILA's actions are AhR-dependent.

SIGNIFICANCE

These findings reveal the potential of ILA, produced by Bifidobacterium bifidum, as a therapeutic agent for NASH. The mechanistic insights into AhR-mediated effects provide a foundation for further exploration of ILA as a novel approach for managing liver diseases.

Nanoplastics Chronic Toxicity in Mice: Disturbing the Homeostasis of Tryptophan Metabolism in Gut-Lung-Microbiota Axis

Long-term exposure to nanoplastics causes chronic toxicity in mammals, particularly in the gut and lung tissues. The gut-lung-microbiota axis plays a pivotal role in organisms through the management of gut bacteria amino acid metabolic homeostasis. However, chronic toxicity of nanoplastics from gut to lungs have yet to be fully elucidated. In this study, nanoplastics exposure not only causes colon inflammation but also results in lung fibrosis. The abundance of Akkermansia muciniphila (AKK) is decreased after nanoplastics exposure. Interestingly, a positive correlation is observed between AKK and indole-3-lactic (ILA). Supplementation with AKK or ILA ameliorated nanoplastics-induced gut-derived lung injury by restoring the balance of tryptophan metabolism. Furthermore, knocking down indoleamine 2,3-dioxygenase 1 (ido1) upregulated ILA levels, contributing to defense against damage from nanoplastics. These results suggest that regulating ido1 expression and AKK abundance, involved in tryptophan metabolic homeostasis (especially ILA production), maybe a strategy to reduce the biological toxicity induced by nanoplastics. Mogroside V, a natural product, is found to promote AKK growth and inhibit ido1, thereby ameliorating chronic toxicity induced by nanoplastics. The study offers a new understanding of how nanoplastics cause chronic toxicity by dysregulating gut-lung-microbiota axis, as well as strategies for preventing and treating nanoplastics.

Isobutyrate Confers Resistance to Inflammatory Bowel Disease through Host-Microbiota Interactions in Pigs

Supplementation with short-chain fatty acids (SCFAs) is a potential therapeutic approach for inflammatory bowel disease (IBD). However, the therapeutic effects and mechanisms of action of isobutyrate in IBD remain unclear. Clinical data indicate that the fecal levels of isobutyrate are markedly lower in patients with Crohn's disease than in healthy controls. Compared with healthy mice and healthy pigs, mice and pigs with colitis presented significantly lower isobutyrate levels. Furthermore, the level of isobutyrate in pigs was significantly negatively correlated with the disease activity index. We speculate that isobutyrate may play a crucial role in regulating host gut homeostasis. We established a model of dextran sulfate sodium-induced colitis in pigs, which have gastrointestinal structure and function similar to those of humans; we performed multiomic analysis to investigate the therapeutic effects and potential mechanisms of isobutyrate on IBD at both the animal and cellular levels and validated the results. Phenotypically, isobutyrate can significantly alleviate diarrhea, bloody stools, weight loss, and colon shortening caused by colitis in pigs. Mechanistically, isobutyrate can increase the relative abundance of Lactobacillus reuteri, thereby increasing the production of indole-3-lactic acid, regulating aryl hydrocarbon receptor expression and downstream signaling pathways, and regulating Foxp3+ CD4+ T cell recruitment to alleviate colitis. Isobutyrate can directly activate G protein-coupled receptor 109A, promote the expression of Claudin-1, and improve intestinal barrier function. In addition, isobutyrate can increase the production of intestinal SCFAs and 3-hydroxybutyric acid and inhibit the TLR4/MyD88/NF-κB signaling pathway to suppress intestinal inflammation. In conclusion, our findings demonstrate that isobutyrate confers resistance to IBD through host-microbiota interactions, providing a theoretical basis for the use of isobutyrate in alleviating colitis.

Unpacking Food Fermentation: Clinically Relevant Tools for Fermented Food Identification and Consumption

Fermented foods have been consumed for millennia, valued for their extended shelf life, distinctive sensory properties, and potential health benefits. Emerging research suggests that fermented food consumption may contribute to gut microbiome diversity, immune modulation, and metabolic regulation; however, mechanistic insights and clinical validation remain limited. This review synthesizes current scientific evidence on the microbial and metabolite composition of fermented foods, their proposed health effects, and safety considerations for vulnerable populations. Additionally, we highlight the need for standardized definitions, serving sizes, and regulatory frameworks to enhance consumer transparency and research reproducibility. By providing a structured overview of existing data and knowledge gaps, this review establishes a foundation for integrating fermented foods into dietary recommendations and guiding future research directions.

Fecal microbiota transplantation improves growth performance of chickens by increasing the intestinal Lactobacillus and glutamine

Chicken meat is an essential source of high-quality animal protein, mainly derived from slow-growth chicken (SC) and fast-growth chicken (FC) breeds. Skeletal muscle is a highly adaptable tissue that is influenced by breed differences and the gut microbiome. Investigation whether remodeling the gut microbiota by fecal microbiota transplantation (FMT) improves chicken growth is an interesting question. We compared the gut microbial composition of eight breeds of SC (Xinghua chicken, Yangshan chicken, Zhongshan Salan chicken, Qingyuan Partridge chicken, Huiyang Bearded chicken and Huaixiang chicken) and FC (Xiaobai chicken and White rock chicken). Fecal microbiota from donor FC (Xiaobai chickens) with superior growth performance were transferred to SC (Xinghua chickens). The effects of FMT on growth performance, metabolic profile and gut microbiome of recipient chickens were evaluated. We found significant differences in gut microbial composition, with a higher abundance of Bacteroidetes in SC and a higher abundance of Firmicutes in FC. Xiaobai chickens with better growth performance and abundant Lactobacillus, and FMT significantly enhanced growth performance, the expression of mRNA (MYOG, MYF5, MYF6 and IGF1) related to breast and leg muscle development and improved the villus/crypt ratio in the jejunum. FMT altered the microbiota in the duodenum, jejunum, and ileum, increased Lactobacillus abundance, decreased the relative mRNA expression of the intestinal inflammatory factors (IL-1β, IL-6 and TNF-α), increased glutamine levels in the host, including in muscle tissues and intestinal contents, and Spearman correlation analysis indicated that the relative abundance of Lactobacillus was positively correlated with glutamine levels. Additionally, antibiotic treatment reduces glutamine levels in the intestines, blood, and muscle tissues of chickens. Glutamine can increase the expression of cyclinD1, cyclinD2, cyclinB2, MYOG, MYF5, MYF6 and IGF1 mRNA to promote chicken myoblasts proliferation and differentiation. This study found that the SC and FC gut microbes were significantly different, and the FC chicken gut microbes were able to reshape the FC gut microbiota through FMT, i.e., higher Lactobacillus, promoted chicken myoblasts proliferation and differentiation and growth performance by increasing glutamine levels.

The protective role of 3-Indoleglyoxylic acid in Bisphenol S-induced intestinal barrier dysfunction via mitochondrial ROS-Mediated IL-17/CXCL10/TNF-α signaling

Bisphenol S (BPS) has become extensively used in the manufacturing of consumer products. BPS mainly enters the body through food and water, with oral exposure targeting the gastrointestinal tract. However, its safety profile remains contentious and warrants further investigation. In this study, we aimed to assess whether BPS exerts harmful effects on the body in the absence of overt pathological damage. Our results revealed that although BPS did not lead to significant histopathological damage, it induced intestinal barrier dysfunction. Additionally, in vitro investigations utilizing NCM460 cells and human-derived colorectal organoids demonstrated that BPS exposure induced mitochondrial reactive oxygen species (ROS) levels in intestinal endocrine cells (EECs), upregulating the expression of inflammatory mediators TNF-α and CXCL10. Using a DSS-induced colitis mouse model, it was found that BPS exposure exacerbates the progression of intestinal inflammatory diseases. Analysis of single-cell databases demonstrated a significant reduction in the expression of CHGA, a functional protein of enteroendocrine cells (EECs), in patients with inflammatory bowel disease (IBD). The expression of CHGA showed a significant negative correlation with the expression of IL17. Notably, supplementation with 3-Indoleglyoxylic acid effectively mitigates the intestinal damage induced by BPS. These findings highlight the role of mitochondrial oxidative stress and IL-17/CXCL10/TNF-α signaling in BPS-induced intestinal damage and demonstrate the therapeutic potential of 3-Indoleglyoxylic acid in mitigating these effects.

Gut microbiota in cancer initiation, development and therapy

Cancer has long been associated with genetic and environmental factors, but recent studies reveal the important role of gut microbiota in its initiation and progression. Around 13% of cancers are linked to infectious agents, highlighting the need to identify the specific microorganisms involved. Gut microbiota can either promote or inhibit cancer growth by influencing oncogenic signaling pathways and altering immune responses. Dysbiosis can lead to cancer, while certain probiotics and their metabolites may help reestablish micro-ecological balance and improve anti-tumor immune responses. Research into targeted approaches that enhance therapy with probiotics is promising. However, the effects of probiotics in humans are complex and not yet fully understood. Additionally, methods to counteract harmful bacteria are still in development. Early clinical trials also indicate that modifying gut microbiota may help manage side effects of cancer treatments. Ongoing research is crucial to understand better how gut microbiota can be used to improve cancer prevention and treatment outcomes.

The Encapsulation Strategies for Targeted Delivery of Probiotics in Preventing and Treating Colorectal Cancer: A Review

Colorectal cancer (CRC) ranks as the third most prevalent cancer worldwide. It is associated with imbalanced gut microbiota. Probiotics can help restore this balance, potentially reducing the risk of CRC. However, the hostile environment and constant changes in the gastrointestinal tract pose significant challenges to the efficient delivery of probiotics to the colon. Traditional delivery methods are often insufficient due to their low viability and lack of targeting. To address these challenges, researchers are increasingly focusing on innovative encapsulation technologies. One such approach is single-cell encapsulation, which involves applying nanocoatings to individual probiotic cells. This technique can improve their resistance to the harsh gastrointestinal environment, enhance mucosal adhesion, and facilitate targeted release, thereby increasing the effectiveness of probiotic delivery. This article reviews the latest developments in probiotic encapsulation methods for targeted CRC treatment, emphasizing the potential benefits of emerging single-cell encapsulation techniques. It also analyzes and compares the advantages and disadvantages of current encapsulation technologies. Furthermore, it elucidates the underlying mechanisms through which probiotics can prevent and treat CRC, evaluates the efficacy and safety of probiotics in CRC treatment and adjuvant therapy, and discusses future directions and potential challenges in the targeted delivery of probiotics for CRC treatment and prevention.

Intestinal metabolites in colitis-associated carcinogenesis: Building a bridge between host and microbiome

ABSTRACT

Microbial-derived metabolites are important mediators of host-microbial interactions. In recent years, the role of intestinal microbial metabolites in colorectal cancer has attracted considerable attention. These metabolites, which can be derived from bacterial metabolism of dietary substrates, modification of host molecules such as bile acids, or directly from bacteria, strongly influence the progression of colitis-associated cancer (CAC) by regulating inflammation and immune response. Here, we review how microbiome metabolites short-chain fatty acids (SCFAs), secondary bile acids, polyamines, microbial tryptophan metabolites, and polyphenols are involved in the tumorigenesis and development of CAC through inflammation and immunity. Given the heated debate on the metabolites of microbiota in maintaining gut homeostasis, serving as tumor molecular markers, and affecting the efficacy of immune checkpoint inhibitors in recent years, strategies for the prevention and treatment of CAC by targeting intestinal microbial metabolites are also discussed in this review.

Intratumoral microbiota predicts the response to neoadjuvant chemoimmunotherapy in triple-negative breast cancer

BACKGROUND

Neoadjuvant immunotherapy combined with chemotherapy (Chemo-IM) is associated with significantly improved pathological complete response (pCR) rates and long-term survival outcomes in patient with early-stage triple-negative breast cancer (TNBC). However, only a small proportion of patients benefit from the addition of immunotherapy. Here, we explored and confirmed the role of intratumoral microbiota in screening patients with TNBC who are likely to benefit from neoadjuvant Chemo-IM.

METHODS

Patients with previously untreated, non-metastatic TNBC receiving neoadjuvant Chemo-IM were enrolled. Differences in the intratumoral microbiota between the pCR and non-pCR groups were explored via 16S rDNA sequencing (16S-seq). Single-cell transcriptome sequencing (scRNA-seq) was employed to profile the tumor microenvironment (TME). Moreover, correlations between the intratumor microbiota and the TME were explored. Finally, machine-learning models based on the intratumoral microbiota were constructed to predict pCR.

RESULTS

A total of 89 female patients with early-stage TNBC treated by neoadjuvant Chemo-IM were enrolled. We found that the pCR group had greater diversity and a higher load of intratumoral microbiota than the non-pCR group. Intriguingly, scRNA-seq revealed significantly increased T cell infiltration and decreased tumor-associated macrophage infiltration into tumors in the pCR group. Moreover, intratumoral microbiota load was positively associated with CD4+CXCL13+ T cell infiltration and negatively associated with CD68+SPP1+ macrophage infiltration. Combined analysis of 16S-seq and scRNA-seq data revealed that intratumoral microbiota were present in both cancer and immune cells. Finally, we developed a model incorporating intratumoral microbiota and clinicopathological characteristics, and it showed strong power for predicting pCR to neoadjuvant Chemo-IM.

CONCLUSIONS

Intratumoral microbiota may serve as a strong and specific predictor of the response of patients with early-stage TNBC to neoadjuvant Chemo-IM. Our findings could contribute to the development of individualized Chemo-IM strategies for treating TNBC.

New insights into tryptophan metabolism in cancer

Tryptophan (Trp) is an essential amino acid and key intermediate in a range of biological processes. Early studies identified altered Trp utilization in cancer cells favoring cancer survival and growth. Seminal findings linking Trp metabolism and suppression of immunity led to an explosion of interest ultimately culminating in clinical trials targeting these pathways in melanoma. The failure of these trials led to a clinical retreat in this approach; however, recent insights into the complex interplay of the various Trp circuits and between tumor cells, immune cells, and the microbiota have shown that reconsideration of Trp metabolism is needed. Here, we discuss recent developments in our understanding of Trp metabolism and apparent contradictions in the field. We also discuss adaptations that occur when Trp pathways are manipulated, which may impact therapy responses.

Safety Assessment of Lactiplantibacillus plantarum GUANKE Based on Whole-Genome Sequencing, Phenotypic, and Anti-Inflammatory Capacity Analysis

Lactiplantibacillus plantarum GUANKE (L. plantarum GUANKE) is a Gram-positive bacterium isolated from the feces of healthy volunteers. Whole-genome sequencing analysis (WGS) revealed that the genome of L. plantarum GUANKE consists of one chromosome and two plasmids, with the chromosome harbors 2955 CDS, 66 tRNAs, and 5 rRNAs. The genome is devoid of virulence factors and Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems. It contains three intact prophage regions and bacteriocin biosynthesis genes (plantaricins K, F, and E), as well as seventeen genomic islands lacking antibiotic resistance or pathogenicity determinants. Functional prediction outcomes identified that the genome of L. plantarum GUANKE is closely related to transcription, carbohydrate transport and metabolism, and amino acid transport and metabolism. Carbohydrate-active enzymes (CAZymes) analysis and GutSMASH analysis revealed that the genome of L. plantarum GUANKE contained 100 carbohydrate-active enzyme genes and two specialized metabolic gene clusters. Safety assessments confirmed that L. plantarum GUANKE neither exhibited β-hemolytic activity nor harbored detectable transferable drug resistance genes. The strain exhibited remarkable acid tolerance and bile salt resistance. Cellular adhesion assays demonstrated moderate binding capacity to Caco-2 intestinal epithelium (4.3 ± 0.007)%. In vitro analyses using lipopolysaccharide (LPS)-stimulated macrophage models demonstrated that L. plantarum GUANKE significantly suppressed the secretion of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β), exhibiting dose-dependent anti-inflammatory activity. In vivo experiments showed that L. plantarum GUANKE was involved in the regulation of the apical junction pathway and interferon pathway in colon tissue of normal mice.

The inferred modulation of correlated vaginal microbiota and metabolome by cervical differentially expressed genes across distinct CIN grades

BACKGROUND

In vitro studies have demonstrated the modulation of vaginal microbiota (VM) by cervical peptides which levels varied with the status of HPV infection and cervical intraepithelial neoplasia (CIN) grades. However, there is a deficiency in population-based studies investigating the modulation of VM compositions and metabolome by cervical differentially expressed genes (DEGs) across different grades of CIN.

METHODS

This study included 43 HPV-positive women, classified into low-grade (CIN1, n = 23) and high-grade (CIN2 + , n = 20) groups. Vaginal swabs were collected for both microbiota and metabolome analysis. Cervical exfoliated cells were collected for RNA-Seq analysis.

RESULTS

We identified 258 differentially expressed genes (DEGs), among which 176 CIN1-enriched genes were linked to immune responses, cell chemotaxis, negative regulation of cell migration, and B cell differentiation, activation, and proliferation. Eighty-two genes upregulated in CIN2 + cohorts were associated with epidermis development and keratinization. Then, we identified 5,686 paired correlations between DEGs, VM, and metabolome, with 2,320 involving Lactobacillus. Further analysis revealed Lactobacillus as the primary determinant of metabolic profiles, followed by Gardnerella, Faecalibacterium, Aerococcus and Streptococcus, such as the notable positive correlation between Lactobacillus with D-lactic acid and DL-indole-3-lactic acid. Applying mediation analysis, we found that Lactobacillus mediated the association of 14 CIN1-enriched DEGs, such as COL4A2, CCBE1 and SPON1, with the production of 57 metabolites, including D-lactic acid, oleic acid and various amino acids. Additional analysis indicated significant mediation effects of 79 metabolites on the association of DEGs with the growth of Lactobacillus, Gardnerella, Fannyhessea and Aerococcus.

CONCLUSIONS

Our findings provide valuable population-based evidence for the inferred modulation of correlated VM and metabolome by cervical DEGs across different CIN stages.

Gut microbiota-mediated gut-liver axis: a breakthrough point for understanding and treating liver cancer

The trillions of commensal microorganisms living in the gut lumen profoundly influence the physiology and pathophysiology of the liver through a unique gut-liver axis. Disruptions in the gut microbial communities, arising from environmental and genetic factors, can lead to altered microbial metabolism, impaired intestinal barrier and translocation of microbial components to the liver. These alterations collaboratively contribute to the pathogenesis of liver disease, and their continuous impact throughout the disease course plays a critical role in hepatocarcinogenesis. Persistent inflammatory responses, metabolic rearrangements and suppressed immunosurveillance induced by microbial products underlie the pro-carcinogenic mechanisms of gut microbiota. Meanwhile, intrahepatic microbiota derived from the gut also emerges as a novel player in the development and progression of liver cancer. In this review, we first discuss the causes of gut dysbiosis in liver disease, and then specify the pivotal role of gut microbiota in the malignant progression from chronic liver diseases to hepatobiliary cancers. We also delve into the cellular and molecular interactions between microbes and liver cancer microenvironment, aiming to decipher the underlying mechanism for the malignant transition processes. At last, we summarize the current progress in the clinical implications of gut microbiota for liver cancer, shedding light on microbiota-based strategies for liver cancer prevention, diagnosis and therapy.

Fucoidan exerts antitumor effects by regulating gut microbiota and tryptophan metabolism

Fucoidan, a water-soluble polysaccharide derived from marine organisms, has garnered significant attention for its ability to regulate gut microbiota and its anti-tumor properties. However, the existence of a correlation between the anti-tumor effect of fucoidan and its regulation of the gut microbiota remains unknown. In pursuit of this objective, we culled the gut microbiota of mice with broad-spectrum antibiotics to generate pseudo-sterile tumor-bearing mice. Subsequently, fecal microbial transplants were introduced into the pseudo-sterile tumor-bearing mice. The antitumor effects of fucoidan were found to be dependent on the gut microbiota. Fucoidan promoted the proliferation of Akkermansia, Bifidobacterium and Lactobacillus, which have immunomodulatory effects. Furthermore, through regulation of gut microbiota, fucoidan influenced the metabolic process of tryptophan and facilitated its conversion to indole-3-acetic acid. In addition, fucoidan decreased the kynurenine/tryptophan ratio in serum, increased the proportion of CD8+ T cells, and suppressed the expression level of IDO1 in tumor tissues. Our results confirm that fucoidan enhances anti-tumor immune responses and subsequently exhibits anti-tumor effects by modulating the gut microbiota. Our research contributes to the comprehension of the mechanism of anti-tumor effects of fucoidan and facilitates the development of fucoidan as a dietary supplement for cancer patients.

Fucoidan from Apostichopus japonicus enhances intestinal barrier function and promotes intestinal immunity via regulating the gut microbiota and tryptophan metabolism

Apostichopus japonicus is one of the most popular types of sea cucumber among consumers in Southeast Asia. Fucoidan from Apostichopus japonicus (Aj-FUC) has attracted considerable attention because of its immunomodulatory activities. Aj-FUC is indigestible in the human upper gastrointestinal tract but can be utilized by the gut microbiota. Thus, we suspect that Aj-FUC interacts with the gut to enhance immunefunction. This study showed that after a three-week intervention with Aj-FUC (100 mg/kg/d), the gut microbiota in mice developed a new homeostasis. Subsequently, in the condition of intestinal flora homeostasis, the effects of Aj-FUC on intestinal health in normal mice and the prevention of intestinal mucosal damage in cyclophosphamide-induced mice were investigated. Aj-FUC preserved intestinal structural integrity, increased the number of goblet cells, upregulated the expression of ZO-1 and Occludin, stimulated the secretion of sIgA and IgA, and maintained the Th1/Th2 balance. Importantly, beneficial bacteria were enriched, and tryptophan metabolism-related metabolites such as 5-hydroxyindole-3-acetic acid, and indole-3-lactic acid were upregulated following Aj-FUC administration. In summary, a three-week Aj-FUC intervention could result in the formation of a new homeostasis in intestinal flora, while the effect of Aj-FUC on intestinal immunity was related to the regulation of tryptophan metabolism by gut microbiota.

Survival Disparity and the Unique Genomic and Microbiome Profiles of Colon Cancer in Appalachian Kentucky

BACKGROUND

Colon cancer is a leading cause of mortality in Appalachian Kentucky. Studies suggest that the microbiome may influence cancer outcomes. We investigate differential gene expression, the tumor microbiome, and their association as potential drivers of disparities in colon cancer outcomes.

STUDY DESIGN

This study analyzed patients diagnosed with colon adenocarcinoma between 2010 and 2023. Demographic data were extracted from Kentucky Cancer Registry. Somatic mutations and significantly mutated genes were identified using Fisher's exact t -test. RNASeq data were processed for gene expression analysis and Holm-Bonferroni method was used to adjust p values for multiple comparisons. The STAR aligner (exotic), v2.1 pipeline, and KrakenUniq database were used to classify microbes in human samples. The R package (exotic) was then used to decontaminate the results.

RESULTS

The final cohort included 2,276 patients, 321 of which had available somatic mutation sequencing data. Demographic differences between Appalachian and non-Appalachian patients included marital status (p = 0.0005), race (p < 0.0001), insurance status (p = 0.0005), BMI (p = 0.001), type 2 diabetes (p < 0.0001), and Charlson Comorbidity Index (p = 0.03). There was no difference in gene mutation frequency. There was differential expression of 228 genes. Differential abundance analysis revealed differences in 381 bacterial species. Importantly, 3 microbiota significantly correlated with survival disparities between Appalachian and non-Appalachian patients: Clostridium cadaveris (adjusted p = 0.009), Ligilactobacillus salivarius (adjusted p = 0.048), and Sutterella wadsworthensis (adjusted p = 0.009).

CONCLUSIONS

This is the first report of the distinct tumor microbiome in Appalachian Kentucky and its impact on survival. Further studies are needed to better characterize the unique tumor and gut microbiome of Appalachian patients with colon cancer.

The role of TIGIT-CD226-PVR axis in mediating T cell exhaustion and apoptosis in NSCLC

The treatment of non-small cell lung cancer (NSCLC) remains a critical challenge in oncology, primarily due to the dysfunction and exhaustion of T cells within the tumor microenvironment, which greatly limits the effectiveness of immunotherapy. This study investigates the regulatory role of the T cell immunoglobulin and ITIM domain (TIGIT)-CD226-PVR signaling axis in the exhaustion and apoptosis of cluster of differentiation (CD)27+/CD127+T cells in NSCLC. Utilizing single-cell sequencing technology, we conducted a comprehensive gene expression analysis of T cells in a mouse model of NSCLC. Bioinformatics analysis revealed that the TIGIT-CD226-PVR signaling axis is highly active in the CD27+/CD127+T cell subset and is closely associated with their functional decline and exhaustion. In vitro experiments further demonstrated that inhibiting the TIGIT-PVR pathway while activating the CD226-PVR pathway significantly restored T cell proliferation and effector function. Importantly, in vivo studies showed that targeting this axis can significantly alleviate T cell exhaustion, enhance their cytotoxicity against NSCLC cells, and promote apoptosis, thereby improving the efficacy of immunotherapy.

Friends close, enemies closer: the complex role of the microbiome in antitumor immunity

Immunotherapy has achieved remarkable advances in cancer treatment by harnessing the immune system to combat tumors, yet its effectiveness remains inconsistent across patients and tumor types. The microbiota, a diverse assemblage of microorganisms residing at host barrier surfaces, is pivotal in shaping immune responses. This review explores the direct and indirect mechanisms via which the microbiota modulates antitumor immune responses both locally within the tumor microenvironment and systemically by affecting distant tumors. We discuss recent findings linking microbiota-derived metabolites and microbiota-derived antigens with antitumor immunity and immunotherapy response. Additionally, we discuss recent advances in microbiome-based therapies, including fecal microbiota transplantation. We propose the use and development of new analytical techniques to further characterize the complex functions and interactions between the microbiome and immune system. To conclude, we outline recommendations for future research and therapeutic approaches to leverage the microbiome to improve current immunotherapies.

Tumor Microenvironment: Obstacles and Opportunities for T Cell-Based Tumor Immunotherapies

The complex composition and dynamic change of the tumor microenvironment (TME), mainly consisting of tumor cells, immune cells, stromal cells, and extracellular components, significantly impede the effector function of cytotoxic T lymphocytes (CTL), thus representing a major obstacle for tumor immunotherapies. In this review, we summarize and discuss the impacts and underlying mechanisms of major elements in the TME (different cell types, extracellular matrix, nutrients and metabolites, etc.) on the infiltration, survival, and effector functions of T cells, mainly CD8+ CTLs. Moreover, we also highlight recent advances that may potentiate endogenous antitumor immunity and improve the efficacy of T cell-based immunotherapies in patients with cancer by manipulating components inside/outside of the TME. A deeper understanding of the effects and action mechanisms of TME components on the tumor-eradicating ability of CTLs may pave the way for discovering new targets to augment endogenous antitumor immunity and for designing combinational therapeutic regimens to enhance the efficacy of tumor immunotherapies in the clinic.

Programmable engineered bacteria as sustained-releasing antibody factory in situ for enhancing tumor immune checkpoint therapy

Tumor immune checkpoint therapy (ICT) aims to block immune escape signals between tumor and immune cells. However, low delivery efficiency of immune checkpoint inhibitors (ICIs), narrow single-target approach, and reduced responsiveness notably hinder clinical development of ICT. Here, we developed a nanoliposome-bacteria hybrid system that acts as an antibody (Ab) factory, enabling precise tumor targeting and macrophage activation in hypoxic environments. We reprogrammed attenuated Escherichia coli MG1655 to synthesize CD47 antibodies (aCD47) in response to hypoxic tumor microenvironments while surface conjugating with redox-responsive macrophage colony-stimulating factor-loaded liposomes. This system leverages bacterial tropism to enhance macrophage infiltration and polarization. The low oxygen levels trigger in situ aCD47 expression, blocking the "do not eat me" signal and boosting macrophage antitumor activity. In addition, macrophage antigen presentation activates CD8+CD3+ T cells, amplifying systemic antitumor immunity. Analysis of the gut microbiome shows reduced pathogenicity and improved intestinal tolerance with increased probiotics.

Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer

The incidence of colorectal cancer (CRC) has been increasing in recent decades. Current methods for CRC screening have their own drawbacks, thus there is an urgent need to identify the key microbes that drive the development of CRC for wider application in the early detection and prevention of CRC. To address this issue, we performed fecal microbiome analysis by high-throughput sequencing of 16S rRNA gene combined with blood biochemical indicators in patients with CRC stages I, II, III, and IV, healthy people, and patients with polyps. Fecal microbiota of patients with CRC was disturbed, as evidenced by significantly reduced α-diversity in patients with CRC stage IV and markedly different β-diversity. The random forest model identified the top 25 genera from 174 training data, resulting in a diagnostic accuracy of 87.95%. Further, by combining with differential genera analysis, we screened out 11 biomarkers that significantly changed in different groups. Peptostreptococcus, Parvimonas, Shewanella, Oscillibacter, Eggerthella, and Gemella associated with the development of CRC were significantly enriched, while Fenollaria, Staphylococcus, Ezakiella, Finegoldia, and Neisseria associated with the remission of CRC were significantly suppressed in patients with CRC. Importantly, carcinoembryonic antigen (CEA) was significantly correlated with these 11 microbial biomarkers, and carbohydrate antigen 19-9 (CA 19-9) was markedly correlated with Oscillibacter. Notably, co-occurrence network analysis at the genus level exhibited that the microbial co-occurrence network of CRC IV was the most complex and stable. These results suggested that CEA, CA 19-9 and 11 microbial biomarkers may be co-biomarkers for the disease occurrence and development, and non-invasive diagnosis of CRC.

IMPORTANCE

Identifying the key microbes that drive the development of colorectal cancer (CRC) has been important in this field. We delved into the research on the association between CRC and fecal microbiota in this study, providing a detailed analysis of the characteristics of fecal microbiota during the transition from normal intestine to polyps to cancer. Fecal bacterial biomarkers and blood biochemical indicators may be co-biomarkers in the development of CRC.

Butyrate-producing Faecalibacterium prausnitzii suppresses natural killer/T-cell lymphoma by dampening the JAK-STAT pathway

BACKGROUND

Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive malignancy with a dismal prognosis, and gaps remain in understanding the determinants influencing disease outcomes.

OBJECTIVE

To characterise the gut microbiota feature and identify potential probiotics that could ameliorate the development of NKTCL.

DESIGN

This cross-sectional study employed shotgun metagenomic sequencing to profile the gut microbiota in two Chinese NKTCL cohorts, with validation conducted in an independent Korean cohort. Univariable and multivariable Cox proportional hazards analyses were applied to assess associations between identified marker species and patient outcomes. Tumour-suppressing effects were investigated using comprehensive in vivo and in vitro models. In addition, metabolomics, RNA sequencing, chromatin immunoprecipitation sequencing, Western blot analysis, immunohistochemistry and lentiviral-mediated gene knockdown system were used to elucidate the underlying mechanisms.

RESULTS

We first unveiled significant gut microbiota dysbiosis in NKTCL patients, prominently marked by a notable reduction in Faecalibacterium prausnitzii which correlated strongly with shorter survival among patients. Subsequently, we substantiated the antitumour properties of F. prausnitzii in NKTCL mouse models. Furthermore, F. prausnitzii culture supernatant demonstrated significant efficacy in inhibiting NKTCL cell growth. Metabolomics analysis revealed butyrate as a critical metabolite underlying these tumour-suppressing effects, validated in three human NKTCL cell lines and multiple tumour-bearing mouse models. Mechanistically, butyrate suppressed the activation of Janus kinase-signal transducer and activator of transcription pathway through enhancing histone acetylation, promoting the expression of suppressor of cytokine signalling 1.

CONCLUSION

These findings uncover a distinctive gut microbiota profile in NKTCL and provide a novel perspective on leveraging the therapeutic potential of F. prausnitzii to ameliorate this malignancy.

AC129507.1 is a ferroptosis-related target identified by a novel mitochondria-related lncRNA signature that is involved in the tumor immune microenvironment in gastric cancer

BACKGROUND

Gastric cancer (GC) is one of the most common malignancies. Previous studies have shown that mitochondrial metabolism is associated with malignancies. However, relevant research on mitochondria-related lncRNAs in GC is lacking.

METHODS

We integrated the corresponding information of patients with GC from The Cancer Genome Atlas (TCGA) database. Mitochondria-related lncRNAs were selected based on differential expression and a correlation analysis to construct a prognostic model. The mutation data were analyzed to distinguish differences in the tumor mutation burden (TMB). Single-sample gene set enrichment analysis (ssGSEA) was performed to evaluate immunological differences. A series of cell-based experiments were adopted to evaluate the biological behavior of GC.

RESULTS

A total of 1571 mitochondria-related lncRNAs were identified. A prognostic signature incorporating nine lncRNAs was built based on 293 suitable GC cases and could predict patient prognosis. The TMB and ssGSEA indicated that the low-risk group displayed increased immune function. The enrichment analysis indicated that the differentially expressed genes were enriched in metabolic functions. AC129507.1 was significantly upregulated in GC cells and associated with a poor prognosis, and its knockdown inhibited the proliferation and migration of GC cells. Mechanistically, silencing AC129507.1 led to abnormal glycolipid metabolism and oxidative stress, thus inducing ferroptosis.

CONCLUSIONS

Our nine-lncRNA risk signature could powerfully predict patient prognosis. AC129507.1 promoted the malignant phenotypes of GC cells. AC129507.1 could play a nonnegligible role in GC by promoting the formation of a immunosuppressive tumor microenvironment by inhibiting the initiation of ferroptosis, which needs to be further explored.

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.

Preclinical Safety Assessment of the Oral Administration of Lactobacillus plantarum GUANKE in Animal Models

Probiotics have a long history as fermented food or food supplements. The health benefits and safety profiles of probiotics are strain-specific and should be evaluated individually. The aim of this study was to assess the safety of the Lactobacillus plantarum GUANKE (GUANKE) strain by conducting pharmacological studies, oral toxicity assessments, and investigating the colonization and translocation of GUANKE in experimental animal models. Three pharmacological studies were conducted to examine the effects of oral administration of GUANKE on gastric emptying, bile secretion, and gastric juice secretion. In an acute toxicity study, rats were orally administrated with different doses of GUANKE and monitored for 14 days. In the subacute toxicity study, both rats and beagles were administrated with varying doses of GUANKE for 28 consecutive days to evaluate hematologic, biochemical, and histological effects. The results showed that GUANKE administration did not result in any adverse effect on hematological parameters, biochemical parameters, urinary parameters, and organ indices. Importantly, no translocation of GUANKE to extra-intestinal organs or blood was observed following administration of the CFDA-SE labeled strain. In summary, this study demonstrated the safety of GUANKE intake, which encourages its potential application as a probiotic in clinical trials.

γ-Linolenic acid derived from Lactobacillus plantarum MM89 induces ferroptosis in colorectal cancer

Colorectal cancer (CRC) is one of the most prevalent cancers worldwide; however, current treatment options are inadequate, necessitating the exploration of new therapeutic strategies. The microbiota significantly influences the tumor microenvironment, suggesting that probiotics may serve as promising candidates for cancer treatment. We previously identified a novel probiotic, Lactobacillus plantarum MM89 (L. plantarum MM89), which was found to regulate the immune microenvironment. However, its specific role in CRC remained unclear. In this study, we employed an azoxymethane/dextran sodium sulfate-induced carcinogenesis mouse model to evaluate the therapeutic effects of L. plantarum MM89 in vivo. Transcriptome analysis was conducted to elucidate the mechanisms of action of L. plantarum MM89. Ferroptosis induction in tumor cells was assessed through cell viability assays and C11-BODIPY staining. Liquid chromatography/mass spectrometry was used to identify metabolites derived from L. plantarum MM89. MitoTracker and MitoTracker CMXRos staining and ATP content measurements were performed to assess mitochondrial damage. L. plantarum MM89 significantly inhibited tumor growth in vivo and alleviated intestinal inflammation at non-tumor foci. Transcriptome analysis and immunohistochemistry revealed that L. plantarum MM89 enhanced arachidonic acid metabolism. Small molecules present in the L. plantarum MM89 supernatant induced ferroptosis in cancer cells, as indicated by cell viability and C11-BODIPY assays. Furthermore, γ-linolenic acid (γ-LA) derived from L. plantarum MM89 was shown to induce ferroptosis via mitochondrial damage. In conclusion, γ-LA derived from L. plantarum MM89 triggers ferroptosis in tumor cells by inducing mitochondrial damage, highlighting its potential as a novel therapeutic agent for CRC treatment.

Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies

Transcriptional dysregulation is a hallmark of cancer initiation and progression, driven by genetic and epigenetic alterations. Enhancer reprogramming has emerged as a pivotal driver of carcinogenesis, with cancer cells often relying on aberrant transcriptional programs. The advent of high-throughput sequencing technologies has provided critical insights into enhancer reprogramming events and their role in malignancy. While targeting enhancers presents a promising therapeutic strategy, significant challenges remain. These include the off-target effects of enhancer-targeting technologies, the complexity and redundancy of enhancer networks, and the dynamic nature of enhancer reprogramming, which may contribute to therapeutic resistance. This review comprehensively encapsulates the structural attributes of enhancers, delineates the mechanisms underlying their dysregulation in malignant transformation, and evaluates the therapeutic opportunities and limitations associated with targeting enhancers in cancer.

The Kynurenine Pathway and Indole Pathway in Tryptophan Metabolism Influence Tumor Progression

Tryptophan (Trp), an essential amino acid, is solely acquired through dietary intake. It is vital for protein biosynthesis and acts as a precursor for numerous key bioactive compounds. The Kynurenine Pathway and the Indole Pathway are the main metabolic routes and are extensively involved in the occurrence and progression of diseases in the digestive, nervous, and urinary systems. In the Kynurenine Pathway, enzymes crucial to tryptophan metabolism, indoleamine-2,3-dioxygenase 1 (IDO1), IDO2, and Trp-2,3-dioxygenase (TDO), trigger tumor immune resistance within the tumor microenvironment and nearby lymph nodes by depleting Trp or by activating the Aromatic Hydrocarbon Receptor (AhR) through its metabolites. Furthermore, IDO1 can influence immune responses via non-enzymatic pathways. The Kynurenine Pathway exerts its effects on tumor growth through various mechanisms, including NAD+ regulation, angiogenesis promotion, tumor metastasis enhancement, and the inhibition of tumor ferroptosis. In the Indole Pathway, indole and its related metabolites are involved in gastrointestinal homeostasis, tumor immunity, and drug resistance. The gut microbiota related to indole metabolism plays a critical role in determining the effectiveness of tumor treatment strategies and can influence the efficacy of immunochemotherapy. It is worth noting that there are conflicting effects of the Kynurenine Pathway and the Indole Pathway on the same tumor phenotype. For example, different tryptophan metabolites affect the cell cycle differently, and indole metabolism has inconsistent protective effects on tumors in different regions. These differences may hold potential for enhancing therapeutic efficacy.

Quercetin-Driven Akkermansia Muciniphila Alleviates Obesity by Modulating Bile Acid Metabolism via an ILA/m6A/CYP8B1 Signaling

Global health is increasingly challenged by the growing prevalence of obesity and its associated complications. Quercetin, one of the most important dietary flavonoids, is being explored as an effective therapy for obesity with its mechanism remains understudied. Here in this study, it is demonstrated that quercetin intervention significantly reverses obesity-related phenotypes through reshaping the overall structure of microbiota, especially boosting colonization of the beneficial gut commensal Akkermansia muciniphila (A. muciniphila). Enrichment of A. muciniphila leads to generate more indole-3-lactic acid (ILA) to upregulate the expression of 12α-hydroxylase (CYP8B1) via fat mass and obesity-associated protein (FTO)/ N6-methyladenosine (m6A)/YTHDF2 manner, thereby facilitating cholesterol converts to cholic acid (CA). CA in turn drastically suppresses lipid accumulation via activating the farnesoid X receptor (FXR) in adipose tissue. This work introduces a novel therapeutic target for addressing obesity and expands upon the current limited understanding of the mediator function of m6A modifications in microorganism-influenced bile acid (BA) metabolism.

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.

Emerging insights into the gut microbiota as a key regulator of immunity and response to immunotherapy in hepatocellular carcinoma

The gut microbiota, a complex microbial ecosystem closely connected to the liver via the portal vein, has emerged as a critical regulator of liver health and disease. Numerous studies have underscored its role in the onset and progression of liver disorders, including alcoholic liver disease, metabolic dysfunction-associated steatotic liver disease (MASLD), metabolic dysfunction-associated steatohepatitis (MASH), liver fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). This review provides a comprehensive overview of current insights into the influence of the gut microbiota on HCC progression, particularly its effects on immune cells within the HCC tumor microenvironment (TME). Furthermore, we explore the potential of gut microbiota-targeted interventions, such as antibiotics, probiotics, prebiotics, and fecal microbiota transplantation (FMT), to modulate the immune response and improve outcomes of immunotherapy in HCC. By synthesizing insights from recent studies, this review aims to highlight microbiota-based strategies that may enhance immunotherapy outcomes, advancing personalized approaches in HCC treatment.

Ameba-inspired strategy enhances probiotic efficacy via prebound nutrient supply

Nutrient competition with indigenous microbes or pathogens presents a significant challenge for oral probiotic efficacy. To address this issue, we develop an ameba-inspired food-carrying strategy (AIFS) by prebinding ginger-derived exosome-like nanoparticles (GELNs) onto probiotics as food depots. AIFS enables probiotics to efficiently and exclusively consume GELNs in situ, even in the presence of competing bacteria. This results in up to 21 times higher uptake efficiency compared to unengineered probiotics, dramatically accelerating probiotic proliferation. Meanwhile, AIFS potentiates probiotics' resistance to multiple GI stressors. In a murine model of colitis, AIFS can improve the abundance of probiotics and inhibit pathogens, maintaining intestinal flora homeostasis. Additionally, it can upregulate the anti-inflammatory IL-10, reduce the proinflammatory IL-1β, and repair damaged intestinal mucus. Thereby, AIFS displays potently elevated prophylactic and therapeutic efficacy for colitis mice. This work provides a method for microbial engineering, with broad implications for microbiotherapy and gut health.

Microbiota and Radiotherapy: Unlocking the Potential for Improved Gastrointestinal Cancer Treatment

Radiotherapy (RT) is one of the major cornerstones in managing gastrointestinal (GI) cancers. However, several side effects, such as intestinal inflammation, mucosal injury, and dysbiosis, often compromise this. The gut microbiota increasingly attracts much interest as an essential modulator of RT effects influencing immune responses and tissue repair. Through short-chain fatty acids such as butyrate, representatives of certain bacterial species play a crucial role under normal conditions, keeping the mucosal integrity intact and reducing oxidative stress-mediated damage. Dysbiosis, a state where diminished microbial diversity and increased pathogenic species in the microbiota are seen, amplifies RT-induced toxicity in patients. Clinical investigations highlight that microbiota-targeted interventions, including probiotics, prebiotics, and fecal microbiota transplantation, hold the means to augment RT efficacy and lessen toxicity. Increased microflora diversity and specific microbial profiles have yielded serious patient improvements. Advanced RT methods use stereotactic body radiotherapy combined with microbiota modulation as a promising technique to shield healthy tissue and maximize immune-mediated antitumor effects. Additionally, there is an implication in tumor behavior regulated by the intratumoral microbiota regarding the response to radiotherapy. Notably, the modulation of gut and tumor microbiota provides an avenue to optimize RT benefits in GI cancers, underscoring the importance of personalized therapy.

Innovative Applications of Bacteria and Their Derivatives in Targeted Tumor Therapy

Despite significant progress in cancer treatment, traditional therapies still face considerable challenges, including poor targeting, severe toxic side effects, and the development of resistance. Recent advances in biotechnology have revealed the potential of bacteria and their derivatives as drug delivery systems for tumor therapy by leveraging their biological properties. Engineered bacteria, including Escherichia coli, Salmonella, and Listeria monocytogenes, along with their derivatives─outer membrane vesicles (OMVs), bacterial ghosts (BGs), and bacterial spores (BSPs)─can be loaded with a variety of antitumor agents, enabling precise targeting and sustained drug release within the tumor microenvironment (TME). These bacteria and their derivatives possess intrinsic properties that stimulate the immune system, enhancing both innate and adaptive immune responses to further amplify therapeutic effects. The ability of bacteria to naturally accumulate in hypoxic tumor regions and their versatility in genetic modifications allow for tailored drug delivery strategies that synergistically enhance the effectiveness of chemotherapy, immunotherapy, and targeted therapies. This review comprehensively examines the fundamental principles of bacterial therapy, focusing on the strategies employed for bacterial engineering, drug loading, and the use of bacteria and their derivatives in targeted tumor therapy. It also discusses the challenges faced in optimizing bacterial delivery systems, such as safety concerns, unintended immune responses, and scalability for clinical applications. By exploring these aspects, this review provides a theoretical framework for improving bacterial-based drug delivery systems, contributing to the development of more effective and personalized cancer treatments.

Intrahepatic levels of microbiome-derived hippurate associates with improved metabolic dysfunction-associated steatotic liver disease

OBJECTIVE

Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterised by lipid accumulation in the liver and is often associated with obesity and type 2 diabetes. The gut microbiome recently emerged as a significant player in liver metabolism and health. Hippurate, a host-microbial co-metabolite has been associated with human gut microbial gene richness and with metabolic health. However, its role on liver metabolism and homeostasis is poorly understood.

METHODS

We characterised liver biospies from 318 patients with obesity using RNAseq and metabolomics in liver and plasma to derive associations among hepatic hippurate, hepatic gene expression and MASLD and phenotypes. To test a potential beneficial role for hippurate in hepatic insulin resistance, we profile the metabolome of (IHH) using ultra-high-performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-MS/MS), and characterised intracellular triglyceride accumulation and glucose internalisation after a 24 h insulin exposure.

RESULTS

We first report significant associations among MASLD traits, plasma and hepatic hippurate. Further analysis of the hepatic transcriptome shows that liver and plasma hippurate are inversely associated with MASLD, implicating lipid metabolism and regulation of inflammatory responses pathways. Hippurate treatment inhibits lipid accumulation and rescues insulin resistance induced by 24-hour chronic insulin in IHH. Hippurate also improves hepatocyte metabolic profiles by increasing the abundance of metabolites involved in energy homeostasis that are depleted by chronic insulin treatment while decreasing those involved in inflammation.

CONCLUSIONS

Altogether, our results further highlight hippurate as a mechanistic marker of metabolic health, by its ability to improve metabolic homeostasis as a postbiotic candidate.