Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy

Unraveling the potential of bioengineered microbiome-based strategies to enhance cancer immunotherapy

The human microbiome plays a pivotal role in the field of cancer immunotherapy. The microbial communities that inhabit the gastrointestinal tract, as well as the bacterial populations within tumors, have been identified as key modulators of therapeutic outcomes, affecting immune responses and reprogramming the tumor microenvironment. Advances in synthetic biology have made it possible to reprogram and engineer these microorganisms to improve antitumor activity, enhance T-cell function, and enable targeted delivery of therapies to neoplasms. This review discusses the role of the microbiome in modulating both innate and adaptive immune mechanisms-ranging from the initiation of cytokine production and antigen presentation to the regulation of immune checkpoints-and discusses how these mechanisms improve the efficacy of immune checkpoint inhibitors. We highlight significant advances with bioengineered strains like Escherichia coli Nissle 1917, Lactococcus lactis, Bifidobacterium, and Bacteroides, which have shown promising antitumor efficacy in preclinical models. These engineered microorganisms not only efficiently colonize tumor tissues but also help overcome resistance to standard therapies by reprogramming the local immune environment. Nevertheless, several challenges remain, such as the requirement for genetic stability, effective tumor colonization, and the control of potential safety issues. In the future, the ongoing development of genetic engineering tools and the optimization of bacterial delivery systems are crucial for the translation of microbiome-based therapies into the clinic. This review highlights the potential of bioengineered microbiota as an innovative, personalized approach in cancer immunotherapy, bringing hope for more effective and personalized treatment options for patients with advanced malignancies.

The microbiota-m6A-metabolism axis: Implications for therapeutic strategies in gastrointestinal cancers

Gastrointestinal (GI) cancers remain a leading cause of cancer-related mortality worldwide, with metabolic reprogramming recognized as a central driver of tumor progression and therapeutic resistance. Among the key regulatory layers, N6-methyladenosine (m6A) RNA modification-mediated by methyltransferases (writers such as METTL3/14), RNA-binding proteins (readers like YTHDFs and IGF2BPs), and demethylases (erasers including FTO and ALKBH5), plays a pivotal role in controlling gene expression and metabolic flux in the tumor context. Concurrently, the gut microbiota profoundly influences GI tumorigenesis and immune evasion by modulating metabolite availability and remodeling the tumor microenvironment. Recent evidence has uncovered a bidirectional crosstalk between microbial metabolites and m6A methylation: microbiota-derived signals dynamically regulate m6A deposition on metabolic and immune transcripts, while m6A modifications, in turn, regulate the stability and translation of key mRNAs such as PD-L1 and FOXP3. This reciprocal interaction forms self-reinforcing epigenetic circuits that drive tumor plasticity, immune escape, and metabolic adaptation. In this review, we dissect the molecular underpinnings of the microbiota-m6A-metabolism axis in GI cancers and explore its potential to inform novel strategies in immunotherapy, metabolic intervention, and microbiome-guided precision oncology.

Exploring preventive and treatment strategies for oral cancer: Modulation of signaling pathways and microbiota by probiotics

The evidence suggests that the microbiome plays a crucial role in cancer development. The oral cavity has many microorganisms that can influence oral cancer progression. Understanding the mechanisms and signaling pathways of the oral, gum, and teeth microbiome in tumor progression can lead to new treatment strategies. Probiotics, which are friendly microorganisms, have shown potential as anti-cancer agents. These positive characteristics of probiotic strains make them suitable for cancer prevention or treatment. The oral-gut microbiome axis supports health and homeostasis, and imbalances in the oral microbiome can disrupt immune signaling pathways, epithelial barriers, cell cycles, apoptosis, genomic stability, angiogenesis, and metabolic processes. Changes in the oral microbiome in oral cancer may suggest using probiotics-based treatments for their direct or indirect positive roles in cancer development, progression, and metastasis, specifically oral squamous cell carcinoma (OSCC). Here, reported relationships between probiotics, oral microbiota, and oral cancer are summarized.

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.

Short-term microplastic exposure: A double whammy to lung metabolism and fecal microflora in diabetic SD rats

Diabetes has become a global health crisis, affecting over 800 million people, with serious complications such as vascular and neurological damage. While diabetes management has been extensively studied, the impact of environmental pollutants, particularly microplastics (PS), on diabetic health remains poorly understood. PS, defined as plastic particles smaller than 5 mm, are pervasive and can enter the body through inhalation or ingestion, posing potential risks. However, the effects of PS exposure, particularly in diabetes, have not been adequately explored. Most studies focus on high-concentration, long-term exposure, which does not reflect typical human exposure levels. This study investigates the effects of short-term PS exposure on diabetic SD rats, using histological, apoptotic, and omics techniques, including metabolomics, lipidomics, and 16S rDNA sequencing. Our results show that short-term PS exposure exacerbates lung and intestinal damage in diabetic rats, with significant alterations in the gut microbiome. We also observed correlations between differential metabolites and microbiota changes. These findings provide novel evidence that short-term PS exposure, at concentrations reflecting daily contact, worsens metabolic dysfunction and intestinal dysbiosis in diabetes. This study emphasizes the need to consider environmental pollutants in diabetes management and highlights potential strategies for prevention and therapy.

Interaction between gut microbiota and T cell immunity in colorectal cancer

This review delves into the complex and multi-layered mechanisms that govern the interaction between gut microbiota and T cells in the context of colorectal cancer (CRC), revealing a novel "microbiota-immune regulatory landscape" within the tumor microenvironment. As CRC progresses, the gut microbiota experiences a significant transformation in both its composition and metabolic patterns. On one hand, specific microbial entities within the gut microbiota can directly engage with T cells, functioning as "immunological triggers" that shape T-cell behavior. Simultaneously, microbial metabolites, such as short-chain fatty acids and bile acids, serve as "molecular regulators" that intricately govern T-cell function and differentiation, fine-tuning the immune response. On the other hand, the quorum-sensing mechanism, a recently recognized communication network among bacteria, also plays a pivotal role in orchestrating T-cell immunity. Additionally, the gut microbiota forms an intriguing connection with the neuro-immune regulatory axis, a largely unexplored "territory" in CRC research. Regarding treatment strategies, a diverse array of intervention approaches-including dietary modifications, the utilization of probiotics, bacteriophages, and targeted antibiotic therapies-offer promising prospects for restoring the equilibrium of the gut microbiota, thereby acting as "ecosystem renovators" that impede tumor initiation and progression. Nevertheless, the current research landscape in this field is fraught with challenges. These include significant variations in microbial composition, dietary preferences, and tumor microenvironments among individuals, a lack of large-scale cohort studies, and insufficient research that integrates tumor mutation analysis, gut microbiota investigations, and immune microenvironment evaluations. This review emphasizes the necessity for future research efforts to seamlessly incorporate multiple factors and utilize bioinformatics analysis to construct a more comprehensive "interactive map" of the gut microbiota-T cell relationship in CRC. The aim is to establish a solid theoretical basis for the development of highly effective and personalized treatment regimens, ultimately transforming the therapeutic approach to CRC.

Prebiotics Rescue Gut Microbiome Dysregulation and Enhance Cognitive and Gastrointestinal Function in a Mouse Model of Schizophrenia

BACKGROUND AND HYPOTHESIS

Schizophrenia is a devastating psychiatric disorder characterized by positive (eg, hallucinations) and negative (eg, reduced motivation) symptoms, and cognitive deficits. Chronic gastrointestinal tract issues exist as comorbid symptoms of schizophrenia. Recent findings indicate the involvement of the microorganisms that inhabit the gut, the microbiota (and the broader microbiome which also includes microbial genomes, etc.) in schizophrenia pathogenesis. In the present study, we hypothesized that chronic administration with prebiotics fructooligosaccharide and galactooligosaccharide (FOS and GOS; a combination used clinically for other disorders) would restore gut microbiome composition of the metabotropic glutamate receptor 5 (mGlu5) knockout (KO) mouse model of schizophrenia, which we previously demonstrated to exhibit gut dysbiosis.

STUDY DESIGN

We assessed the impact of prebiotics on gut microbiome composition and function, as well as the gastrointestinal function and schizophrenia-like phenotype of mGlu5 KO mice and wild-type littermates. We administered a combination of the prebiotics FOS and GOS, vs vehicle control administration, in both the mouse model of schizophrenia and wild-type littermates.

STUDY RESULTS

The present study firstly corroborated the altered gut microbiome composition in the mGlu5 KO mouse model of schizophrenia. Importantly, we have revealed an altered microbial metabolic profile. We have also shown that the prebiotics we administered were not only able to rescue these gut microbiome changes but also had additional beneficial effects including cognitive enhancement and improved gastrointestinal function.

CONCLUSION

These preclinical findings indicate that prebiotics, such as the combination of FOS and GOS used in the present study, may have therapeutic potential in schizophrenia as an add-on intervention with an exceptional safety profile.

TEAL-Seq: targeted expression analysis sequencing

Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.

The interplay between gut microbiota, antibiotics, and immune checkpoint inhibitors in patients with cancer: A narrative review with biological and clinical aspects

Immune checkpoint inhibitors (ICIs) targeting the programmed cell death-1 (PD-1), programmed cell death ligand-1 (PD-L1), and cytotoxic T-lymphocyte antigen 4 (CTLA-4) pathways have revolutionized cancer therapy. However, primary and secondary resistance to ICI pose significant challenges. Recent studies underscore the critical role of gut microbiota (GM) in modulating ICI efficacy by shaping host immune responses and regulating the tumor microenvironment (TME). The composition of the GM has been linked to ICI treatment outcomes, with certain microbial taxa, such as Faecalibacterium spp., Bifidobacterium spp., Eubacterium spp., Roseburia spp., and Akkermansia muciniphila, associated with favorable responses. Mechanistically, the GM affects immune responses via multiple pathways, including induction of T cell differentiation, promotion of anti- or proinflammatory cytokine environments, and enhancement of T cell priming and effector functions. Moreover, microbial-derived metabolites play a role in shaping tumor immune responses and influencing ICI efficacy. Antibiotic treatment can disrupt GM diversity and composition (gut dysbiosis), potentially diminishing ICI effectiveness. A deeper understanding of the interplay between GM, antibiotic treatment, and ICI efficacy is crucial for developing personalized therapeutic strategies to improve patient outcomes. Herein, we review current evidence on the association between specific microbial taxa and tumor immunosurveillance, the impact of antibiotics on the GM composition and immune modulation, and its implications for ICI therapy efficacy.

Gut microbiome and colorectal cancer: From pathogenesis to treatment

Colorectal cancer (CRC) continues to rank among the most prevalent cancers worldwide. A growing body of research indicates that the microbiome significantly influences the onset, development, and progression of CRC, in addition to affecting the efficacy of various systemic therapies. The composition of the microbiome, shaped by factors such as bacterial strains, geography, ethnicity, gender, and dietary habits, provides essential information for CRC screening, early diagnosis, and the prediction of treatment responses. Modulating the microbiome presents a highly promising medical strategy for improving individual health. This review aims to present a thorough overview of recent research concerning the interplay between host microbiota and CRC, along with its implications for screening and the immune response against tumors in the context of cancer treatment.

Intratumoral Fusobacterium nucleatum Recruits Tumor-Associated Neutrophils to Promote Gastric Cancer Progression and Immune Evasion

Intratumoral microbiota can affect the development and progression of many types of cancer, including gastric cancer. A better understanding of the precise mechanisms by which microbiota support gastric cancer could lead to improved therapeutic approaches. In this study, we investigated the effect of intratumoral microbiota on the tumor immune microenvironment during gastric cancer malignant progression. Analysis of human gastric cancer tissues with 16S rRNA amplicon sequencing revealed that Fusobacterium nucleatum was significantly enriched in gastric cancer tissues with lymph node metastasis and correlated with a poor prognosis. F. nucleatum infection spontaneously induced chronic gastritis and promoted gastric mucosa dysplasia in mice. Furthermore, gastric cancer cells infected with F. nucleatum showed accelerated growth in immunocompetent mice compared with immunodeficient mice. Single-cell RNA sequencing uncovered that F. nucleatum recruited tumor-associated neutrophils (TAN) to reshape the tumor immune microenvironment. Mechanistically, F. nucleatum invaded gastric cancer cells and activated IL17/NF-κB/RelB signaling, inducing TAN recruitment. F. nucleatum also stimulated TAN differentiation into the protumoral subtype and subsequent promotion of PD-L1 expression, further facilitating gastric cancer immune evasion while also enhancing the efficacy of anti-PD-L1 antibody therapy. Together, these data uncover mechanisms by which F. nucleatum affects gastric cancer immune evasion and immunotherapy efficacy, providing insights for developing effective treatment strategies. Significance: Intratumoral F. nucleatum activates NF-κB signaling to facilitate gastric cancer immune evasion by promoting tumor-associated neutrophil recruitment that sensitizes tumors to immune checkpoint blockade therapy.

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.

Roles of the gut microbiota in immune-related adverse events: mechanisms and therapeutic intervention

Immune checkpoint inhibitors (ICIs) constitute a major breakthrough in the field of cancer therapy; their use has resulted in improved outcomes across various tumour types. However, ICIs can cause a diverse range of immune-related adverse events (irAEs) that present a considerable challenge to the efficacy and safety of these treatments. The gut microbiota has been demonstrated to have a crucial role in modulating the tumour immune microenvironment and thus influences the effectiveness of ICIs. Accumulating evidence indicates that alterations in the composition and function of the gut microbiota are also associated with an increased risk of irAEs, particularly ICI-induced colitis. Indeed, these changes in the gut microbiota can contribute to the pathogenesis of irAEs. In this Review, we first summarize the current clinical challenges posed by irAEs. We then focus on reported correlations between alterations in the gut microbiota and irAEs, especially ICI-induced colitis, and postulate mechanisms by which these microbial changes influence the occurrence of irAEs. Finally, we highlight the potential value of gut microbial changes as biomarkers for predicting irAEs and discuss gut microbial interventions that might serve as new strategies for the management of irAEs, including faecal microbiota transplantation, probiotic, prebiotic and/or postbiotic supplements, and dietary modulations.

The Microbiome and Cancer: A Translational Science Review

Importance

Growing evidence suggests that microbes located within the gastrointestinal tract and other anatomical locations influence the development and progression of diseases such as cancer.

Observations

Clinical and preclinical evidence suggests that microbes in the gastrointestinal tract and other anatomical locations, such as the respiratory tract, may affect carcinogenesis, development of metastases, cancer treatment response, and cancer treatment-related adverse effects. Within tumors of patients with cancer, microbes may affect response to treatment, and therapies that reduce or eliminate these microbes may improve outcomes in patients with cancer. Modulating gastrointestinal tract (gut) microbes through fecal microbiota transplant and other strategies such as dietary intervention (eg, high-fiber diet intervention) has improved outcomes in small studies of patients treated with cancer immunotherapy. In contrast, disruption of the gut microbiota by receipt of broad-spectrum antibiotics prior to treatment with cancer immunotherapy has been associated with poorer overall survival and higher rates of adverse effects in patients treated with immune checkpoint blockade for solid tumors and also with chimeric antigen receptor T-cell therapy for hematologic malignancies.

Conclusions and Relevance

Microbes in the gut and other locations in the body may influence the development and progression of cancer and may affect the response to adverse effects from cancer therapy. Future therapies targeting microbes in the gut and other locations in the body could potentially improve outcomes in patients with cancer.

Respiratory Exposure to Agriculture Dust Extract Alters Gut Commensal Species and Key Metabolites in Mice

Exposure to agricultural dust containing antimicrobial-resistant pathogens poses significant health risks for workers in animal agriculture production. Beyond causing severe airway inflammation, pollutants are linked to intestinal diseases. Swine farm dust is rich in ultrafine particles, gram-positive and gram-negative bacteria, and bacterial components such as lipopolysaccharides (LPS; endotoxins). In our previous study, we demonstrated that intranasal exposure of male and female C57BL/6J mice to 12.5% hog dust extract (HDE, containing 22.1-91.1 EU/mL) for 3 weeks resulted in elevated total cell and neutrophil counts in bronchoalveolar lavage fluid and increased intestinal permeability compared to saline controls. Now, we report that 16S and metagenomic analyses of Week 3 stool samples from HDE-treated mice indicate a reduced abundance of the beneficial species Akkermansia muciniphila and Clostridium sp. ASF356 and Lachnospiraceae bacterium. Bacterial alpha diversity showed increased species evenness in fecal samples from HDE-treated mice (Pielou's evenness, p = 0.047, n = 5-6/group). Metabolomic analysis also indicated significant reductions in key metabolites involved in energy metabolism, including riboflavin (p = 0.027, n = 11) and nicotinic acid (p = 0.049, n = 11), as well as essential amino acids, such as inosine (p = 0.043, n = 11) and leucine (p = 0.018, n = 11). While HDE exposure does not robustly alter overall microbial abundance or community structure, it leads to specific reductions in beneficial bacterial species and critical metabolites necessary for maintaining intestinal homeostasis by supporting energy metabolism, gut barrier function, microbiota balance, and immune regulation. The results of this study underscore the potential risks for gut health posed by inhalation of agricultural dust.

Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment

The gut microbiota crucially regulates the efficacy of immune checkpoint inhibitor (ICI) based immunotherapy, but the underlying mechanisms remain unclear at the single-cell resolution. Using single-cell RNA sequencing and subsequent validations, we investigate gut microbiota-ICI synergy by profiling the tumor microenvironment (TME) and elucidating critical cellular interactions in mouse models. Our findings reveal that intact gut microbiota combined with ICIs may synergistically increase the proportions of CD8+, CD4+, and γδ T cells, reduce glycolysis metabolism, and reverse exhausted CD8+ T cells into memory/effector CD8+ T cells, enhancing antitumor response. This synergistic effect also induces macrophage reprogramming from M2 protumor Spp1+ tumor-associated macrophages (TAMs) to Cd74+ TAMs, which act as antigen-presenting cells (APCs). These macrophage subtypes show a negative correlation within tumors, particularly during fecal microbiota transplantation. Depleting Spp1+ TAMs in Spp1 conditional knockout mice boosts ICI efficacy and T cell infiltration, regardless of gut microbiota status, suggesting a potential upstream role of the gut microbiota and highlighting the crucial negative impact of Spp1+ TAMs during macrophage reprogramming on immunotherapy outcomes. Mechanistically, we propose a γδ T cell-APC-CD8+ T cell axis, where gut microbiota and ICIs enhance Cd40lg expression on γδ T cells, activating Cd40 overexpressing APCs (e.g., Cd74+ TAMs) through CD40-CD40L-related NF-κB signaling and boosting CD8+ T cell responses via CD86-CD28 interactions. These findings highlight the potential importance of γδ T cells and SPP1-related macrophage reprogramming in activating CD8+ T cells, as well as the synergistic effect of gut microbiota and ICIs in immunotherapy through modulating the TME.

The metabolic dialogue between intratumoural microbes and cancer: implications for immunotherapy

The tumour microenvironment (TME) exerts a profound influence on cancer progression and treatment outcomes. Recent investigations have elucidated the crucial role of intratumoural microbiota and their metabolites in shaping the TME and modulating anti-tumour immunity. This review critically assesses the influence of intratumoural microbial metabolites on the TME and cancer immunotherapy. We systematically analyse how microbial-derived glucose, amino acid, and lipid metabolites modulate immune cell function, cytokine secretion, and tumour growth. The roles of specific metabolites, including lactate, short-chain fatty acids, bile acids, and tryptophan derivatives, are comprehensively examined in regulating immune responses and tumour progression. Furthermore, we investigate the potential of these metabolites to augment the efficacy of cancer immunotherapies, with particular emphasis on immune checkpoint inhibitors. By delineating the mechanisms through which microbial metabolites influence the TME, this review provides insights into novel microbiome-based therapeutic strategies, thereby highlighting a promising frontier in personalised cancer medicine.

Nervous system-gut microbiota-immune system axis: future directions for preventing tumor

Tumor is one of the leading causes of death worldwide. The occurrence and development of tumors are related to multiple systems and factors such as the immune system, gut microbiota, and nervous system. The immune system plays a critical role in tumor development. Studies have also found that the gut microbiota can directly or indirectly affect tumorigenesis and tumor development. With increasing attention on the tumor microenvironment in recent years, the nervous system has emerged as a novel regulator of tumor development. Some tumor therapies based on the nervous system have also been tested in clinical trials. However, the nervous system can not only directly interact with tumor cells but also indirectly affect tumor development through the gut microbiota. The nervous system-mediated gut microbiota can regulate tumorigenesis, growth, invasion, and metastasis through the immune system. Here, we mainly explore the potential effects of the nervous system-gut microbiota-immune system axis on tumorigenesis and tumor development. The effects of the nervous system-gut microbiota-immune system axis on tumors involve the nervous system regulating immune cells through the gut microbiota, which can prevent tumor development. Meanwhile, the direct effects of the gut microbiota on tumors and the regulation of the immune system by the nervous system, which can affect tumor development, are also reviewed.

The Relationship Between Gut Microbiome Bifidobacterium and Anti-tumor Immune Responses in Esophageal Squamous Cell Carcinoma

BACKGROUND

The Bifidobacterium genus is a prominent bacterial population in the gastrointestinal tract. Previous findings suggest that Bifidobacterium is linked to tumor suppression in mouse models of melanoma. Additionally, when combined with the programmed death-ligand 1 (PD-L1) antibody, it can enhance anti-tumor treatment by increasing tumor-specific T-cell responses and promoting infiltration of antigen-specific T cells into tumors. However, there is a lack of studies on Bifidobacterium in esophageal squamous cell carcinoma (ESCC). This study aimed to investigate the potential impact of Bifidobacterium on this cancer type.

METHODS

We examined 213 samples from ESCC patients who underwent tumor resection. The presence of Bifidobacterium was confirmed using quantitative polymerase chain reaction and fluorescent in situ hybridization (FISH). Patient overall survival (OS) was analyzed with Bifidobacterium positivity. Tumor-infiltrating lymphocytes (TILs) were evaluated via hematoxylin and eosin stains, and immunohistochemistry was used to assess programmed death-1 (PD-1), PD-L1, cluster of differentiation 8 (CD8), and forkhead box P3 (FOXP3) expression. Nutritional status was evaluated via computed tomography scans.

RESULTS

Bifidobacterium positivity showed no correlation with patient OS or TIL levels; however, Bifidobacterium positivity in normal tissue was associated with lower FOXP3 levels, suggesting a potential role in upregulating anti-tumor immune responses. Patients with Bifidobacterium present in peritumor normal tissue exhibited better skeletal muscle area and volume. Conversely, Bifidobacterium positivity in tumor tissue was associated with poorer prognostic nutrition index values, likely due to decreased albumin levels.

CONCLUSION

Bifidobacterium can induce the upregulated anti-tumor immune response and is more prevalent in cases with good nutritional status.

Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome

Microbial genome-wide association studies (GWAS) have uncovered numerous host genetic variants associated with gut microbiota. However, links between host genetics, the gut microbiome and specific cellular contexts remain unclear. Here we use a computational framework, scBPS (single-cell Bacteria Polygenic Score), to integrate existing microbial GWAS and single-cell RNA-sequencing profiles of 24 human organs, including the liver, pancreas, lung and intestine, to identify host tissues and cell types relevant to gut microbes. Analysing 207 microbial taxa and 254 host cell types, scBPS-inferred cellular enrichments confirmed known biology such as dominant communications between gut microbes and the digestive tissue module and liver epithelial cell compartment. scBPS also identified a robust association between Collinsella and the central-veinal hepatocyte subpopulation. We experimentally validated the causal effects of Collinsella on cholesterol metabolism in mice through single-nuclei RNA sequencing on liver tissue to identify relevant cell subpopulations. Mechanistically, oral gavage of Collinsella modulated cholesterol pathway gene expression in central-veinal hepatocytes. We further validated our approach using independent microbial GWAS data, alongside single-cell and bulk transcriptomic analyses, demonstrating its robustness and reproducibility. Together, scBPS enables a systematic mapping of the host-microbe crosstalk by linking cell populations to their interacting gut microbes.

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.

Microbiota-Derived Inosine Suppresses Systemic Autoimmunity via Restriction of B Cell Differentiation and Migration

The role of gut microbiota dysbiosis in systemic lupus erythematosus (SLE) pathogenesis remains elusive. Here, it is shown that fecal microbiota transplantation (FMT) from healthy mice to lupus mice ameliorates lupus-like symptoms. Microbiota reconstitution effectively reduces systemic class switch recombination (CSR) and elevates immunoglobulin heavy chain (IGH) naïve isotype. Microbiota profiling reveals an enrichment of Lactobacillus johnsonii post-FMT, with a significant correlation to purine metabolites. Importantly, the L. johnsonii-derived inosine, an intermediate metabolite in purine metabolism, effectively alleviates lupus pathogenesis in mice. Inosine inhibits B cell differentiation and reduces renal B cell infiltration to protect mice from lupus. At the molecular level, inosine reprograms B cells through the extracellular signal-regulated kinase (ERK)-hypoxia-inducible factor-1alpha (HIF-1α) signaling pathway. Therefore, this study highlights the discovery of a novel microbial metabolite modulating autoimmunity and suggests its potential for innovative microbiome-based therapeutic approaches.

The gut microbiome and cancer: from tumorigenesis to therapy

The gut microbiome has a crucial role in cancer development and therapy through its interactions with the immune system and tumour microenvironment. Although evidence links gut microbiota composition to cancer progression, its precise role in modulating treatment responses remains unclear. In this Review, we summarize current knowledge on the gut microbiome's involvement in cancer, covering its role in tumour initiation and progression, interactions with chemotherapy, radiotherapy and targeted therapies, and its influence on cancer immunotherapy. We discuss the impact of microbial metabolites on immune responses, the relationship between specific bacterial species and treatment outcomes, and potential microbiota-based therapeutic strategies, including dietary interventions, probiotics and faecal microbiota transplantation. Understanding these complex microbiota-immune interactions is critical for optimizing cancer therapies. Future research should focus on defining microbial signatures associated with treatment success and developing targeted microbiome modulation strategies to enhance patient outcomes.

The Immune Regulation of Melanin From Gallus gallus domesticus Brisson Against Cyclophosphamide-Induced Immunosuppression

Black-bone silky fowl (Gallus gallus domesticus Brisson), medicinal food homology, utilizes to enhance human immunity. However, it remains unclear whether Black-bone silky fowl melanin (BSFM), one of its bioactive components, could affect immune function. The purpose of this study is to examine the immunoregulatory effect and the underlying mechanism of BSFM in the cyclophosphamide-induced immunosuppressive mice model. The findings revealed that BSFM could significantly increase white blood cells (WBC) in peripheral blood; upregulate the expression of IL-4, TNF-α, and M-CSF in the plasma; and reduce tissue damage. Mechanistically, proteomics has revealed that BSFM therapy substantially affected the quantity of 29 proteins (Mtatp6, Cst3, Pglyrp1, Igkc, and other targets), which mostly participate in the phosphatidylcholine catabolic process, positive regulation of type IIa hypersensitivity, lipid catabolic process, and neutrophil chemotaxis. Metabolomics indicated that BSFM reduced the levels of Octanoylglucuronide, Gly-Gly, and N-alpha-acetyl-ornithine and modulated arginine biosynthesis. Furthermore, BSFM treatment modified the composition of gut microbiota and increased the relative abundance of Prevotella, S24-7, Olsenella, Lactococcus, hgcl-clade, Parasutterella, and Acetobacter. A significant correlation modified the composition of gut microbiota among inflammation-associated parameters, gut microbiota, and various metabolites (DMs) through Pearson correlation analysis. These findings suggest that BSFM holds promise in enhancing the human immune system and may serve as a complementary therapy in conventional chemotherapy.

Unravelling the modified T cell receptor through Gen-Next CAR T cell therapy in Glioblastoma: Current status and future challenges

PURPOSE

Despite current technological advancements in the treatment of glioma, immediate alleviation of symptoms can be catered by therapeutic modalities, including surgery, chemotherapy, and combinatorial radiotherapy that exploit aberrations of glioma. Additionally, a small number of target antigens, their heterogeneity, and immune evasion are the potential reasons for developing targeted therapies. This oncologic milestone has catalyzed interest in developing immunotherapies against Glioblastoma to improve overall survival and cure patients with high-grade glioma. The next-gen CAR-T Cell therapy is one of the effective immunotherapeutic strategies in which autologous T cells have been modified to express receptors against GBM and it modulates cytotoxicity.

METHODS

In this review article, we examine preclinical and clinical outcomes, and limitations as well as present cutting-edge techniques to improve the function of CAR-T cell therapy and explore the possibility of combination therapy.

FINDINGS

To date, several CAR T-cell therapies are being evaluated in clinical trials for GBM and other brain malignancies and multiple preclinical studies have demonstrated encouraging outcomes.

IMPLICATIONS

CAR-T cell therapy represents a promising therapeutic paradigm in the treatment of solid tumors but a few limitations include, the blood-brain barrier (BBB), antigen escape, tumor microenvironment (TME), tumor heterogeneity, and its plasticity that suppresses immune responses weakens the ability of this therapy. Additional investigation is required that can accurately identify the targets and reflect the similar architecture of glioblastoma, thus optimizing the efficiency of CAR-T cell therapy; allowing for the selection of patients most likely to benefit from immuno-based treatments.

Regulating Intratumoral Fungi With Hydrogels: A Novel Approach to Modulating the Tumor Microbiome for Cancer Therapy

BACKGROUND

Fungi in tumors act as a double-edged sword, potentially worsening or alleviating malignancy based on the ecological balance within the tumor microenvironment (TME). Hydrogels, as innovative drug delivery systems, are poised to redefine treatment paradigms. As advanced biomaterials, they offer a versatile platform for encapsulating and releasing antifungal agents and immunomodulators, responding to the TME's unique demands.

METHODS

We have conducted and collated numerous relevant reviews and studies in recent years from three aspects: Hydrogels, intra-tumoral fungi, and tumor microbe microenvironment, in the hope of identifying the connections between hydrogels and intra-tumoral microbes.

RESULTS

This review underscores the crucial role of intra-tumoral microbes, particularly fungi, in tumorigenesis, progression, and treatment efficacy. At the same time, we concentrated on the findings of hydrogels investigations, with their remarkable adaptability to the tumor microenvironment emerge as intelligent drug delivery systems.

CONCLUSIONS

Hydrogels unique ability to precisely target and modulate the tumor microflora, including fungi, endows them with a significant edge in enhancing treatment efficacy. This innovative approach not only holds great promise for improving cancer therapy outcomes but also paves the way for developing novel strategies to control metastasis and prevent cancer recurrence.

Longitudinal Proteomic Profiling of Cognition across an Aerobic Exercise Intervention

The physiological basis of cognitive decline remains largely uncharacterized. We identified a protein panel signature, in living humans, that correlates to improvement in neurocognition over a period of 5 years. Our signature is composed of complement proteins, coagulation cascade, and extracellular matrix regulators. In our cohort, SERPINF1 is associated with greater maximal oxygen uptake after an aerobic exercise intervention. Sleep quality is also a key factor in relation to inter-alpha-trypsin inhibitor heavy chain H2, which was associated with greater sleep efficiency. Additionally, we validate that the coagulation profile of decliners' plasma contains procoagulant agonists, leading to greater platelet activation. ANN NEUROL 2025;97:1007-1018.

Cutting-Edge Advancements in the Antibiotics-Gut Microbiota-Urinary Tumour Axis

Gut microbiota regulates urological tumors. Antibiotics induce dysbiosis, altering tumor progression/therapy: reducing carcinogen metabolism but impairing immunity. Specific bacteria enhance immune responses and combat endocrine resistance. Future research should unravel microbiota-cancer links and develop microbiome-targeted therapies to optimize outcomes while preserving diversity.

Microbial metabolite ammonia disrupts TGF-β signaling to promote colon cancer

Colorectal cancer (CRC) is rising alarmingly in younger populations, potentially arising from factors such as obesity, pro-inflammatory gut microbiome and the accumulation of toxic metabolites. However, how metabolites such as ammonia impact key signaling pathways to promote CRC remains unclear. Our study investigates a critical link between gut microbiome alterations, ammonia, and their toxic effects on the TGF-β signaling pathway, driving CRC progression. We observe altered microbial populations in an obesity-induced mouse model of cancer, where ammonia promotes caspase-3-mediated cleavage of the SMAD3 adaptor βII-spectrin (SPTBN1). Cleaved SPTBN1 fragments form adducts with ammonia that induce pro-inflammatory cytokine expression and disrupt TGF-β signaling. Extending from AlphaFold docking simulations, we identified that ammonia interacts with N-terminal SPTBN1 potentially through residues D81, Y556, S663, Y666, N986, and D1177 to form hydrogen bonds that disrupt downstream SMAD3 signaling, altering TGF-β signaling to a protumorigenic phenotype. Blocking SPTBN1, through an SPTBN1-specific siRNA blocks ammonia toxicity and restores normal SMAD3/TGF-β signaling by reducing the abundance of SPTBN1 cleaved fragments in SW480 and Caco-2 (CRC) cell lines. In addition, our research establishes crosstalk between TGF-β signaling and a microbial sensor, carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), which is significantly overexpressed in CRC patients. We identified CEACAM1-SPTBN1 interactions at specific residues (E517 and Y520) within the immunoreceptor tyrosine-based inhibitory motif (ITIM) of CEACAM1 cytoplasmic domain, identifying distinguishing a potential axis that is harnessed by the altered microbiome. Our study identifies mechanistic insights into how microbial metabolites target TGF-β as a major signaling pathway to promote CRC.

A specific microbial consortium enhances Th1 immunity, improves LCMV viral clearance but aggravates LCMV disease pathology in mice

Anti-viral immunity can vary tremendously from individual to individual but mechanistic understanding is still scarce. Here, we show that a defined, low complex bacterial community (OMM12) but not the general absence of microbes in germ-free mice leads to a more potent immune response compared to the microbiome of specific-pathogen-free (SPF) mice after a systemic viral infection with LCMV Clone-13. Consequently, gnotobiotic mice colonized with OMM12 have more severe LCMV-induced disease pathology but also enhance viral clearance in the intestinal tract. Mechanistically, single-cell RNA sequencing analysis of adoptively transferred virus-specific T helper cells and endogenous T helper cells in the intestinal tract reveal a stronger pro-inflammatory Th1 profile and a more vigorous expansion in OMM12 than SPF mice. Altogether, our work highlights the causative function of the intestinal microbiome for shaping adaptive anti-viral immunity with implications for vaccination strategies and anti-cancer treatment regimens.

Expanding horizons of cancer immunotherapy: hopes and hurdles

Background

Tumor displays various forms of tumor heterogeneity including immune heterogeneity that allow cancer cells to survive during conventional anticancer drug interventions. Thus, there is a strong rationale for overcoming anticancer drug resistance by employing the components of immune cells. Using the immune system to target tumor cells has revolutionized treatment. Recently, significant progress has been achieved at preclinical and clinical levels to benefit cancer patients.

Approach

A review of literature from the past ten years across PubMed, Scopus, and Web of Science focused on immunotherapy strategies. These include immune checkpoint inhibitors (ICIs), tumor-infiltrating lymphocyte therapy, antibody-drug conjugates (ADCs), cancer vaccines, CAR T-cell therapy, and the role of the gut microbiome.

Conclusion

While immunotherapy outcomes have improved, particularly for tumor types such as melanoma and non-small cell lung cancer (NSCLC), challenges persist regarding predictive biomarker identification and better management. Ongoing research on modifiers of immune function like gut microbiome-derived metabolites, next-generation ADCs, and new classes of biologics is warranted. Overall, continued investigation toward optimizing synergistic immunotherapeutic combinations through strategic drug delivery systems is imperative for preclinical and clinical success in cancer patients.

Combinational therapeutic strategies to overcome resistance to immune checkpoint inhibitors

Over the past few years, immune checkpoint inhibitors resulted in magnificent and durable successes in treating cancer; however, only a minority of patients respond favorably to the treatment due to a broad-spectrum of tumor-intrinsic and tumor-extrinsic factors. With the recent insights gained into the mechanisms of resistance, combination treatment strategies to overcome the resistance and enhance the therapeutic potential of immune checkpoint inhibitors are emerging and showing promising results in both pre-clinical and clinical settings. This has been derived through multiple interconnected mechanisms such as enhancing tumor immunogenicity, improving neoantigen processing and presentation in addition to augmenting T cell infiltration and cytotoxic potentials. In the clinical settings, several avenues of combination treatments involving immune checkpoint inhibitors were associated with considerable improvement in the therapeutic outcome in terms of patient's survival and tumor growth control. This, in turn, increased the spectrum of cancer patients benefiting from the unprecedented and durable effects of immune checkpoint inhibitors leading to their adoption as a first-line treatment for certain cancers. Moreover, the significance of precision medicine in cancer immunotherapy and the unmet demand to develop more personalized predictive biomarkers and treatment strategies are also highlighted in this review.

METTL1-driven nucleotide metabolism reprograms the immune microenvironment in hepatocellular carcinoma: a multi-omics approach for prognostic biomarker discovery

Background

Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related mortality worldwide, partly due to an incomplete understanding of the metabolic and immune dysregulation driving its progression. Here, we uncover a novel role of METTL1 in driving nucleotide metabolism reprogramming, which significantly modulates the tumor immune microenvironment.

Methods

Utilizing an integrated multi-omics approach, we analyzed nucleotide metabolism-related genes derived from TCGA, GEO, and ICGC datasets. Non-negative matrix factorization (NMF) clustering stratified HCC patients into distinct subgroups with varied clinical features. Weighted Gene Co-expression Network Analysis (WGCNA) identified hub genes that were subsequently used to construct robust prognostic models via multiple machine learning algorithms. These computational findings were validated through in vitro experiments, immune infiltration assessments, and single-cell RNA sequencing analysis.

Results

Our analyses demonstrate that METTL1 is markedly upregulated in HCC, driving a reprogramming of nucleotide metabolism that modulates the expression of key immune checkpoints, including PD-L1 and CTLA-4. This regulation is associated with an immunosuppressive tumor microenvironment, reduced infiltration of activated T cells, and poorer clinical outcomes. Moreover, the prognostic model integrating METTL1 expression and immune checkpoint profiles shows strong predictive performance across independent cohorts, highlighting its potential clinical utility.

Conclusion

This study highlights the innovative role of METTL1-driven nucleotide metabolism reprogramming in reshaping the immune microenvironment of HCC. The findings provide novel insights into HCC pathogenesis and pave the way for developing personalized therapeutic strategies based on targeting METTL1 and its associated metabolic pathways.

Chinese yam polysaccharide enhances anti-PD-1 immunotherapy in colorectal cancer through alterations in the gut microbiota and metabolites

Immune checkpoint inhibitors (ICIs) have shown limited efficacy in colorectal cancer (CRC). Chinese yam polysaccharide (CYP), a naturally derived plant polysaccharide, demonstrates immunomodulatory and antitumour activities. This study investigated whether CYP enhances the antitumour effects of αPD-1 monoclonal antibody (mAb) by modulating gut microbiota and metabolites. In MC38 and CT26 xenograft models, CYP synergistically inhibited tumour growth when combined with αPD-1 mAb. 16S rRNA sequencing revealed that the combination therapy enriched beneficial bacteria (such as Clostridia_UCG-014 and Actinobacteria) while reducing pathogenic bacteria (including Enterorhabdus and Desulfovibrionaceae). Antibiotic-mediated gut microbiota ablation abolished therapeutic benefits, confirming microbiota-dependent mechanisms. Cytometry by Time-Of-Flight indicated that the combination therapy reshaped the tumour microenvironment by inhibiting immunosuppressive M2 macrophages (CD206+ subset) and enhancing infiltration of cytotoxic CD8+ T cells. Metabolomics analysis demonstrated that the combination therapy effectively rectified tumour-induced metabolic dysregulation, particularly in pathways related to linoleic acid, tryptophan, and purine metabolism. Significantly, the purine-associated metabolite deoxyguanosine was identified to promote M2 macrophage polarization and tumour progression in vitro, whereas its levels were markedly attenuated following combined therapeutic intervention. The results suggest that CYP enhances the efficacy of αPD-1 mAb through remodeling gut microbiota, reducing pro-tumour metabolite (deoxyguanosine), and reprogramming the tumour immune microenvironment. This provides a novel strategy for enhancing CRC patients' response to anti-PD-1 immunotherapy response.

Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model

BACKGROUND

Colorectal cancer (CRC) development is influenced by both iron and gut microbiota composition. While iron supplementation is routinely used to manage anemia in CRC patients, it may also impact gut microbiota and promote tumorigenesis. In this study, we investigated the impact of initial gut microbiota composition on iron-promoted tumorigenesis. We performed fecal microbiota transplantation (FMT) in ApcMin/+ mice using samples from healthy controls, CRC patients, and mice, followed by exposure to iron sufficient or iron excess diets.

RESULTS

We found that iron supplementation promoted CRC and resulted in distinct gut microbiota changes in ApcMin/+ mice receiving FMT from CRC patients (FMT-CRC), but not from healthy controls or mice. Oral treatment with identified bacterial strains, namely Faecalibaculum rodentium, Holdemanella biformis, Bifidobacterium pseudolongum, and Alistipes inops, protected FMT-CRC mice against iron-promoted tumorigenesis.

CONCLUSIONS

Our findings suggest that microbiota-targeted interventions may mitigate tumorigenic effects of iron supplementation in anemic patients with CRC.

Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types

Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.

Purinosomes as a therapeutic target in hepatocellular carcinoma: insights and opportunities

The formation of purinosomes, dynamic complexes involved in de novo purine biosynthesis, has been recognized as a critical process for cell growth. Although their upregulation in cancer cells suggests their potential as a therapeutic target, the specific role of purinosomes in hepatocellular carcinoma (HCC) remains uncertain. The purinosome score was found to have prognostic value. Enrichment analyses indicated a connection between purinosome-related genes and cell cycle regulation. Moreover, our research has demonstrated a correlation between the upregulation of genes associated with purinosomes and the enhanced formation of purinosomes in Huh-7 cells. Pyrimethamine has been identified as a promising therapeutic option for targeting purinosome to exert anti-cancer effects. Furthermore, the purinosome score exhibited an positive relationship with the response to immunotherapy. It may guide the stratification of liver cancer patients and screen for populations that may benefit from immunotherapy. This study examines the prognostic and predictive value of purinosome in liver cancer, suggesting that targeting purinosome formation with pyrimethamine or immunotherapy could benefit patients with high purinosome scores.

Bacillus Coagulans BC99 Protects Ionizing Radiation-Induced Intestinal Injury and Modulates Gut Microbiota and Metabolites in Mice

The gastrointestinal tract is highly sensitive to ionizing radiation (IR), which causes radiation-induced intestinal injury (RIII). There are no effective drugs available for RIII in routine clinical treatment, which is a major limiting factor during the process of radiotherapy for pelvic abdominal malignancies. In this study, we aimed to elucidate the potential of probiotic Bacillus coagulans BC99 (B.coagulans BC99) in preventing RIII. C57BL/6J mice were gavage-administered with B.coagulans BC99 for 30 days and then exposed to a single dose of 12 Gy x-ray whole abdominal irradiation (WAI). B.coagulans BC99 treatment could mitigate RIII by preventing weight loss, maintaining the integrity of intestinal structure and barrier, improving inflammatory symptoms, modulating oxidative stress, and regulating the composition of gut microbiota, thereby reestablishing intestinal homeostasis. In addition, the potential radioprotective mechanism of B.coagulans BC99 was closely related to the gut microbiota-derived metabolites. This study offers a novel perspective for advancing probiotic-based treatments for RIII and enhancing strategies for the prevention of RIII.

Regulating the Tumor Microbiome through Near-Infrared-III Light-Excited Photosynthesis

Tumor microbiomes are increasingly associated with the growth and metastasis of tumors. Exploring the regulation of the tumor microbiome through therapeutics is an area of interest in cancer therapy. In this study, the authors have investigated a biohybrid with 1550 nm light-excited photosynthetic ability to regulate the tumor microbiome. This system utilizes Er-based core-shell upconversion nanoparticles to arm microalga Chlorella, enabling the rapid evolution of Chlorella to perform oxygenic photosynthesis under 1550 nm light excitation. This biohybrid may alleviate hypoxia within the tumor microenvironment and induce significant changes in the tumor microbiome, ultimately resulting in marked inhibition of tumor growth. Benefiting from the strong tissue penetration ability of 1550 nm light, this biohybrid also exhibits clear inhibition of deep-seated tumors. The therapeutic efficacy of microbiome regulation is directly mediated by immune activation, converting "cold" tumors into "hot" tumors, which also leads to a long-lasting immune memory effect.

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.

Aged Gut Microbiota Contributes to Cognitive Impairment and Hippocampal Synapse Loss in Mice

Gut microbiota alteration during the aging process serves as a causative factor for aging-related cognitive decline, which is characterized by the early hallmark, hippocampal synaptic loss. However, the impact and mechanistic role of gut microbiota in hippocampal synapse loss during aging remains unclear. Here, we observed that the fecal microbiota of naturally aged mice successfully transferred cognitive impairment and hippocampal synapse loss to young recipients. Multi-omics analysis revealed that aged gut microbiota was characterized with obvious change in Bifidobacterium pseudolongum (B.p) and metabolite of tryptophan, indoleacetic acid (IAA) in the periphery and brain. These features were also reproduced in young recipients that were transplanted with aged gut microbiota. Fecal B.p abundance was reduced in patients with cognitive impairment compared to healthy subjects and showed a positive correlation with cognitive scores. Microbiota transplantation from patients who had fewer B.p abundances yielded worse cognitive behavior in mice than those with higher B.p abundances. Meanwhile, supplementation of B.p was capable of producing IAA and enhancing peripheral and brain IAA bioavailability, as well as improving cognitive behaviors and microglia-mediated synapse loss in 5 × FAD transgenic mice. IAA produced from B.p was shown to prevent microglia engulfment of synapses in an aryl hydrocarbon receptor-dependent manner. This study reveals that aged gut microbiota -induced cognitive decline and microglia-mediated synapse loss that is, at least partially, due to the deficiency in B.p and its metabolite, IAA. It provides a proof-of-concept strategy for preventing neurodegenerative diseases by modulating gut probionts and their tryptophan metabolites.

Multi-omics analysis of the protective effects of Platycodon grandiflorum -derived inulin-type fructan against low-concentration PM2.5-induced lung microenvironment changes in rats

In northern China, haze events frequently occur during winter, and PM2.5 is recognized as the most significant particulate matter in haze, posing a major threat to human health. Therefore, we employed a PM2.5 inhalation exposure system to investigate the protective effects of Platycodon grandiflorum inulin-type fructan (PGPI-1-a) on low-concentration PM2.5-induced lung microenvironment changes. Our findings revealed that long-term (4-month) PM2.5 exposure did not cause apparent pathological alterations in rat lungs but induced lung inflammation, which was alleviated by PGPI-1-a intervention. Multi-omics analysis demonstrated that PGPI-1-a restored abnormally expressed lung proteins, improved lung microbiota disorders, and regulated serum metabolite imbalances related to lipid and amino acid metabolism, ameliorating low-concentration PM2.5-induced lung microenvironment changes. These results suggest that Platycodon grandiflorum inulin-type fructan could serve as a potential dietary supplement for mitigating PM2.5-induced lung injury.

Gut microbiome signature in response to neoadjuvant chemoradiotherapy in patients with rectal cancer

Background

Rectal cancer remains a leading cause of cancer-associated mortality, especially in advanced cases with limited treatment options. Emerging evidence suggests that the gut microbiome may influence the therapeutic efficacy of neoadjuvant chemoradiotherapy (CRT).

Objective

This study aimed to explore the dynamic changes in gut microbiome composition and metabolic pathways in rectal cancer patients undergoing CRT.

Methods

Paired fecal samples were collected from rectal cancer patients pre- and post-CRT. 16S rRNA amplicon sequencing and proteomics analysis were conducted to investigate microbial and metabolic alterations.

Results

Significant shifts in the microbiome were observed, with Fusobacterium, Subdoligranulum, Prevotella, Alloprevotella, and Bacteroides being enriched pre-CRT, while Streptococcus, Megamonas, Megasphaera, Escherichia-Shigella, and Olsenella became dominant post-CRT. Metabolic analysis revealed upregulated carbohydrate metabolism and downregulated lipid and energy metabolism.

Conclusion

These findings identify potential microbial biomarkers and metabolic pathways associated with CRT response, offering insights into personalized treatment strategies.

Deployment of a Vibrio cholerae ordered transposon mutant library in a quorum-competent genetic background

Vibrio cholerae, the causative agent of cholera, has sparked seven pandemics in recent centuries, with the current one being the most prolonged. V. cholerae's pathogenesis hinges on its ability to switch between low- and high-cell-density gene regulatory states, enabling transmission between the host and the environment. Previously, a transposon mutant library for V. cholerae was created to support investigations aimed toward uncovering the genetic determinants of its pathogenesis. However, subsequent sequencing uncovered a mutation in the gene luxO of the parent strain, rendering mutants unable to exhibit high-cell-density behaviors. In this study, we used chitin-independent natural transformation to move transposon insertions from these low-cell-density mutants into a wild-type genomic background. Library transfer was aided by a novel gDNA extraction method we developed using thymol, which also showed high lysis specificity for Vibrio. The resulting Grant Library comprises 3,102 unique transposon mutants, covering 79.8% of V. cholerae's open reading frames. Whole-genome sequencing of randomly selected mutants demonstrates 100% precision in transposon transfer to cognate genomic positions of the recipient strain in every strain analyzed. Notably, in no instance did the luxO mutation transfer into the wild-type background. Our research uncovered density-dependent epistasis in growth on inosine, an immunomodulatory metabolite secreted by gut bacteria that is implicated in enhancing gut barrier functions. Additionally, Grant Library mutants retain the plasmid that enables rapid, scarless genomic editing. In summary, the Grant Library reintroduces organismal-relevant genetic contexts absent in the low-cell-density-locked library equivalent.Ordered transposon mutant libraries are essential tools for catalyzing research by providing access to null mutants of all non-essential genes. Such a library was previously generated for Vibrio cholerae, but whole-genome sequencing revealed that this library was made using a parent strain that is unable to exhibit cell-cell communication known as quorum sensing. Here, we utilize natural competence combined with a novel, high-throughput genomic DNA extraction method to regenerate the signaling incompetent V. cholerae ordered transposon mutant library in quorum-sensing-competent strain. Our library provides researchers with a powerful tool to understand V. cholerae biology within a genetic context that influences how it transitions from an environmentally benign organism to a disease-causing pathogen.

Gut microbiota and gastrointestinal tumors: insights from a bibliometric analysis

Introduction

Despite the growing number of studies on the role of gut microbiota in treating gastrointestinal tumors, the overall research trends in this field remain inadequately characterized.

Methods

A bibliometric analysis was conducted using publications retrieved from the Web of Science Core Collection (up to September 30, 2024). Analytical tools including VOSviewer, CiteSpace, and an online bibliometric platform were employed to evaluate trends and hotspots.

Results

Analysis of 1,421 publications revealed significant geographical disparities in research output, with China and the United States leading contributions. Institutionally, the University of Adelaide, Zhejiang University, and Shanghai Jiao Tong University were prominent contributors. Authorship analysis identified Hannah R. Wardill as the most prolific author, while the International Journal of Molecular Sciences emerged as a leading journal. Rapidly growing frontiers include "proliferation," "inhibition," "immunotherapy," "drug delivery," and "tumorigenesis."

Discussion

This study provides a comprehensive overview of research trends and highlights emerging directions, aiming to advance scientific and clinical applications of gut microbiota in gastrointestinal tumor therapy.

Optimizing Cancer Treatment Through Gut Microbiome Modulation

The gut microbiome plays a pivotal role in modulating cancer therapies, including immunotherapy and chemotherapy. Emerging evidence demonstrates its influence on treatment efficacy, immune response, and resistance mechanisms. Specific microbial taxa enhance immune checkpoint inhibitor efficacy, while dysbiosis can contribute to adverse outcomes. Chemotherapy effectiveness is also influenced by microbiome composition, with engineered probiotics and prebiotics offering promising strategies to enhance drug delivery and reduce toxicity. Moreover, microbial metabolites, such as short-chain fatty acids, and engineered microbial systems have shown potential to improve therapeutic responses. These findings underscore the importance of personalized microbiome-based approaches in optimizing cancer treatments.

Fasting-mimicking diet-enriched Bifidobacterium pseudolongum suppresses colorectal cancer by inducing memory CD8+ T cells

BACKGROUND

Fasting-mimicking diet (FMD) boosts the antitumour immune response in patients with colorectal cancer (CRC). The gut microbiota is a key host immunity regulator, affecting physiological homeostasis and disease pathogenesis.

OBJECTIVE

We aimed to investigate how FMD protects against CRC via gut microbiota modulation.

DESIGN

We assessed probiotic species enrichment in FMD-treated CRC mice using faecal metagenomic sequencing. The candidate species were verified in antibiotic-treated conventional and germ-free mouse models. Immune landscape alterations were evaluated using single-cell RNA sequencing and multicolour flow cytometry. The microbiota-derived antitumour metabolites were identified using metabolomic profiling.

RESULTS

Faecal metagenomic profiling revealed Bifidobacterium pseudolongum enrichment in FMD-treated CRC mice. B. pseudolongum mediates the FMD antitumour effects by increasing the tissue-resident memory CD8+ T-cell (TRM) population in CRC mice. The level of L-arginine, a B. pseudolongum functional metabolite, increased in FMD-treated CRC mice; furthermore, L-arginine induced the TRM phenotype in vivo and in vitro. Mechanistically, L-arginine is transported by the solute carrier family 7-member 1 (SLC7A1) receptor in CD8+ T cells. Both FMD and B. pseudolongum improved anti-CTLA-4 efficacy in the orthotopic mouse CRC model. In FMD-treated patients with CRC, the CD8+ TRM cell number increased as B. pseudolongum and L-arginine accumulated. The abundance of CD8+ TRM cells and B. pseudolongum was associated with a better prognosis in patients with CRC.

CONCLUSION

B. pseudolongum contributes to the FMD antitumour effects in CRC by producing L-arginine. This promotes CD8+ T-cell differentiation into memory cells. B. pseudolongum administration is a potential CRC therapeutic strategy.

Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses

Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.

Comprehensive MALDI mass spectrometry imaging of tumor regions post-neoadjuvant therapy

The spatial metabolic analysis of tumor tissues following neoadjuvant chemotherapy (NAC) is critical for understanding chemotherapy-induced metabolic changes. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) offers a powerful tool for revealing spatially resolved metabolic profiles within tissues. However, necrotic regions in post-NAC tissues are fragile, creating challenges for sample preparation and MALDI MSI analysis. In this study, we introduce an optimized workflow employing conductive tape to stabilize tissue samples during sectioning and MALDI MSI analysis, preserving necrotic areas while maintaining tissue integrity. Using this technique, we successfully mapped metabolic alterations across necrotic and viable regions of post-NAC tumor tissues, providing new insights into metabolic changes that occur after chemotherapy. Our findings establish MALDI MSI as a valuable tool for spatially resolved metabolomics in post-NAC tumor tissues, offering insights into chemotherapy-induced metabolic changes.

Oncobiomics: Leveraging Microbiome Translational Research in Immuno-Oncology for Clinical-Practice Changes

Growing evidence suggests that cancer should not be viewed solely as a genetic disease but also as the result of functional defects in the metaorganism, including disturbances in the gut microbiota (i.e., gut dysbiosis). The human microbiota plays a critical role in regulating epithelial barrier function in the gut, airways, and skin, along with host metabolism and systemic immune responses against microbes and cancer. Collaborative international networks, such as ONCOBIOME, are essential in advancing research equity and building microbiome resources to identify and validate microbiota-related biomarkers and therapies. In this review, we explore the intricate relationship between the microbiome, metabolism, and cancer immunity, and we propose microbiota-based strategies to improve outcomes for individuals at risk of developing cancer or living with the disease.