Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer

Probiotics as a targeted intervention in anti-ageing: a review

CONTEXT

The age-induced disruption of gut flora, termed gut dysbiosis, is intimately tied to compromised immune function, augmented oxidative stress and a spectrum of age-linked disorders.

OBJECTIVE

This review examines the fundamental mechanisms employed by probiotic strains to modulate gut microbiota composition and metabolic profiles, mitigate cognitive decline via the gut-brain axis (GBA), modulate gene transcription and alleviate inflammatory responses and oxidative stress.

CONCLUSION

We elucidate the capacity of probiotics as a precision intervention to restore gut microbiome homeostasis and alleviate age-related conditions, thereby offering a theoretical framework for probiotics to decelerate ageing, manage age-related diseases, and elevate quality of life.

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

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

Exploring the Relationship Between Diet, Lifestyle and Gut Microbiome in Colorectal Cancer Development: A Recent Update

Colorectal cancer (CRC) is one of the major causes of cancer-related mortality worldwide. Despite advances in treatment modalities, its prevalence continues to rise, notably among younger populations. Unhealthy dietary habits, sedentary routines, and obesity have been identified as one of the key contributors to the development of colorectal cancer, apart from genetic and epigenetic modifications. Recognizing the profound impact of diet and lifestyle on the intricate gut microbiota ecosystem offers a promising avenue for understanding CRC development and its treatment. Gut dysbiosis, characterized by imbalances favoring harmful microbes over beneficial ones, has emerged as a defining feature of CRC. Changes in diet and lifestyle can profoundly alter the composition of gut microbes and the metabolites they produce, potentially contributing to CRC onset. Focusing on recent evidence, this review discussed various dietary factors, such as high consumption of red and processed meats and low fiber intake, and lifestyle factors, including obesity, lack of physical activity, smoking, and excessive alcohol consumption, that influence the gut microbiome composition and elevate CRC risk.

Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study

BACKGROUND

The relationship between intestinal obstruction due to colorectal cancer (CRC) and the gut microbiota remains largely unknown. The aim of this study was to investigate the potential association between alterations in gut microbiota and CRC in the presence of intestinal obstruction.

METHODS

Patients with CRC with or without obstruction were recruited and compared using 1:1 propensity score matching (PSM). Total DNA from tumours and adjacent normal tissues of 84 patients and 36 frozen tumour tissues was extracted and amplified. 16S RNA sequencing was used to uncover differences in microbiota composition between the two groups.

RESULTS

A total of 313 patients with CRC were recruited. Survival analysis demonstrated that patients in the obstruction group had shorter overall survival time and disease-free survival (DFS) time than those in the non-obstruction group. Microbial richness and diversity in tumour tissues of patients with obstruction were significantly higher than those of patients with no obstruction. The alpha diversity indices and beta diversity exhibited were different between the two groups (P < 0.05). At the phylum and genus levels, Bacteroidetes were significantly enriched in the tumour tissues of patients with obstruction. Alpha diversity in tumour tissues was closely related to specific microbiota. These findings were replicated in the 16S rRNA analyses from frozen samples. There were more Bacteroidetes in CRC patients with obstruction.

CONCLUSIONS

Patients with obstructed CRC have worse prognosis and have differences in their microbiota. Higher levels of Bacteroides were observed in patients with obstructed CRC.

An Update on the Pivotal Roles of Probiotics, Their Components, and Metabolites in Preventing Colon Cancer

Diet, lifestyle, and gut microbiota composition are key risk factors for the progression of colon cancer. Probiotics are living microorganisms that can offer health benefits to the parasitifer when ingested in competent quantities. Several in vivo, in vitro, and clinical studies have demonstrated that probiotics can prevent and mitigate the development of colon cancer. The anti-colon cancer mechanisms of probiotics include the suppression of cell proliferation and the promotion of cancer cell apoptosis, immunomodulation, the modulation of intestinal microorganisms and their metabolism, strengthening the intestinal barrier, and antioxidant effects. This article describes the pathogenesis of colon cancer and the available therapeutic options. In addition, this paper reviews the mechanisms by which probiotics mitigate colon cancer as well as the mitigating effects of probiotic components and metabolites on colon cancer.

Gut microbiota and microbiota-derived metabolites in colorectal cancer: enemy or friend

Colorectal cancer (CRC) is a highly prevalent gastrointestinal cancer worldwide. Recent research has shown that the gut microbiota plays a significant role in the development of CRC. There is mounting evidence supporting the crucial contributions of bacteria-derived toxins and metabolites to cancer-related inflammation, immune imbalances, and the response to therapy. Besides, some gut microbiota and microbiota-derived metabolites have protective effects against CRC. This review aims to summarize the current studies on the effects and mechanisms of gut microbiota and microbiota-produced metabolites in the initiation, progression, and drug sensitivity/resistance of CRC. Additionally, we explore the clinical implications and future prospects of utilizing gut microbiota as innovative approaches for preventing and treating CRC.

Gut microbiota, an emergent target to shape the efficiency of cancer therapy

It is now well-acknowledged that microbiota has a profound influence on both human health and illness. The gut microbiota has recently come to light as a crucial element that influences cancer through a variety of mechanisms. The connections between the microbiome and cancer therapy are further highlighted by a number of preclinical and clinical evidence, suggesting that these complicated interactions may vary by cancer type, treatment, or even by tumor stage. The paradoxical relationship between gut microbiota and cancer therapies is that in some cancers, the gut microbiota may be necessary to maintain therapeutic efficacy, whereas, in other cancers, gut microbiota depletion significantly increases efficacy. Actually, mounting research has shown that the gut microbiota plays a crucial role in regulating the host immune response and boosting the efficacy of anticancer medications like chemotherapy and immunotherapy. Therefore, gut microbiota modulation, which aims to restore gut microbial balance, is a viable technique for cancer prevention and therapy given the expanding understanding of how the gut microbiome regulates treatment response and contributes to carcinogenesis. This review will provide an outline of the gut microbiota's role in health and disease, along with a summary of the most recent research on how it may influence the effectiveness of various anticancer medicines and affect the growth of cancer. This study will next cover the newly developed microbiota-targeting strategies including prebiotics, probiotics, and fecal microbiota transplantation (FMT) to enhance anticancer therapy effectiveness, given its significance.

A pathogenicity locus of Streptococcus gallolyticus subspecies gallolyticus

Streptococcus gallolyticus subspecies gallolyticus (Sgg) is known to be strongly associated with colorectal cancer (CRC). Recent functional studies further demonstrated that Sgg actively stimulates CRC cell proliferation and promotes the development of colon tumors. However, the Sgg factors important for the pro-proliferative and pro-tumor activities of Sgg remain unclear. Here, we identified a chromosomal locus in Sgg strain TX20005. Deletion of this locus significantly reduced Sgg adherence to CRC cells and abrogated the ability of Sgg to stimulate CRC cell proliferation. Thus, we designate this locus as the Sgg pathogenicity-associated region (SPAR). More importantly, we found that SPAR is important for Sgg pathogenicity in vivo. In a gut colonization model, mice exposed to the SPAR deletion mutant showed significantly reduced Sgg load in the colonic tissues and fecal materials, suggesting that SPAR contributes to the colonization capacity of Sgg. In a mouse model of CRC, deletion of SPAR abolished the ability of Sgg to promote the development of colon tumors growth. Taken together, these results highlight SPAR as a critical pathogenicity determinant of Sgg.

Intestinal organoids: A versatile platform for modeling gastrointestinal diseases and monitoring epigenetic alterations

Considering the significant limitations of conventional 2D cell cultures and tissue in vitro models, creating intestinal organoids has burgeoned as an ideal option to recapitulate the heterogeneity of the native intestinal epithelium. Intestinal organoids can be developed from either tissue-resident adult stem cells (ADSs) or pluripotent stem cells (PSCs) in both forms induced PSCs and embryonic stem cells. Here, we review current advances in the development of intestinal organoids that have led to a better recapitulation of the complexity, physiology, morphology, function, and microenvironment of the intestine. We discuss current applications of intestinal organoids with an emphasis on disease modeling. In particular, we point out recent studies on SARS-CoV-2 infection in human intestinal organoids. We also discuss the less explored application of intestinal organoids in epigenetics by highlighting the role of epigenetic modifications in intestinal development, homeostasis, and diseases, and subsequently the power of organoids in mirroring the regulatory role of epigenetic mechanisms in these conditions and introducing novel predictive/diagnostic biomarkers. Finally, we propose 3D organoid models to evaluate the effects of novel epigenetic drugs (epi-drugs) on the treatment of GI diseases where epigenetic mechanisms play a key role in disease development and progression, particularly in colorectal cancer treatment and epigenetically acquired drug resistance.

Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.

Interaction of gut microbiota with the tumor microenvironment: A new strategy for antitumor treatment and traditional Chinese medicine in colorectal cancer

Colorectal cancer (CRC) is one of the most common malignancies worldwide and the second leading cause of cancer-related death. In recent years, the relationship between gut microbiota and CRC has attracted increasing attention from researchers. Studies reported that changes in the composition of gut microbiota, such as increase in the number of Fusobacterium nucleatum and Helicobacter hepaticus, impair the immune surveillance by affecting the intestinal mucosal immunity and increase the risk of tumor initiation and progression. The tumor microenvironment is the soil for tumor survival. Close contacts between gut microbiota and the tumor microenvironment may directly affect the progression of tumors and efficacy of antitumor drugs, thus influencing the prognosis of patients with CRC. Recently, many studies have shown that traditional Chinese medicine can safely and effectively improve the efficacy of antitumor drugs, potentially through remodeling of the tumor microenvironment by regulated gut microbiota. This article describes the effect of gut microbiota on the tumor microenvironment and possible mechanisms concerning the initiation and progression of CRC, and summarizes the potential role of traditional Chinese medicine.

Determination of biomarkers associated with neoadjuvant treatment response focusing on colibactin-producing Escherichia coli in patients with mid or low rectal cancer: a prospective clinical study protocol (MICARE)

INTRODUCTION

The management of mid and low rectal cancer is based on neoadjuvant chemoradiotherapy (CRT) followed by standardised surgery. There is no biomarker in rectal cancer to aid clinicians in foreseeing treatment response. The determination of factors associated with treatment response might allow the identification of patients who require tailored strategies (eg, therapeutic de-escalation or intensification). Colibactin-producing Escherichia coli (CoPEC) has been associated with aggressive colorectal cancer and could be a poor prognostic factor. Currently, no study has evaluated the potential association between intestinal microbiota composition and tumour response to CRT in mid and low rectal cancer. The aim of this study is to assess the association between response to neoadjuvant CRT and faecal intestinal microbiota composition and/or CoPEC prevalence in patients with mid or low rectal cancer.

METHODS AND ANALYSIS

This is a non-randomised bicentric prospective clinical study with a recruitment capacity of 200 patients. Three stool samples will be collected from participants with histological-proven adenocarcinome of mid or low rectum who meet eligibility criteria of the study protocol: one before neoadjuvant treatment start, one in the period between CRT end and surgery and one the day before surgery. In each sample, CoPEC will be detected by culture in special media and molecular (PCR) approaches. The global microbiota composition will be also assessed by the bacterial 16S rRNA gene sequencing. Neoadjuvant CRT response and tumour regression grade will be described using the Dworak system at pathological examination. Clinical data and survival outcomes will also be collected and investigated.

ETHICS AND DISSEMINATION

MICARE was approved by the local ethics committee (Comité de Protection des Personnes Sud-Est II, 18 December 2019. Reference number 2019-A02493-54 and the institutional review board. Patients will be required to provide written informed consent. Results will be published in a peer reviewed journal.

TRIAL REGISTRATION NUMBER

NCT04103567.

Microbiome insights into pediatric familial adenomatous polyposis

BACKGROUND

Individuals with familial adenomatous polyposis (FAP) harbor numerous polyps with inevitable early progression to colon cancer. Complex microbiotic-tumor microenvironment perturbations suggest a dysbiotic relationship between polyp and microbiome. In this study, we performed comprehensive analyses of stool and tissue microbiome of pediatric FAP subjects and compared with unaffected cohabiting relatives through 16S V4 region amplicon sequencing and machine learning platforms.

RESULTS

Within our FAP and control patient population, Firmicutes and Bacteroidetes were the predominant phyla in the tissue and stool samples, while Proteobacteria dominated the polyp/non-polyp mucosa. A decline in Faecalibacterium in polyps contrasted with a decline in Bacteroides in the FAP stool. The alpha- and beta-diversity indices differed significantly within the polyp/non-polyp groups, with a concurrent shift towards lower diversity in polyps. In a limited 3-year longitudinal study, the relative abundance of Proteobacteria and Fusobacteria was higher in polyps compared to non-polyp and stool specimens over time. Through machine learning, we discovered that Archaeon_enrichment_culture_clone_A13, Micrococcus_luteus, and Eubacterium_hallii in stool and PL-11B10, S1-80, and Blastocatellaceae in tissues were significantly different between patients with and without polyps.

CONCLUSIONS

Detection of certain bacterial concentrations within stool or biopsied polyps could serve as adjuncts to current screening modalities to help identify higher-risk patients.

Microbe-based therapies for colorectal cancer: Advantages and limitations

Cancer is one of the leading global causes of death in both men and women. Colorectal cancer (CRC) alone accounts for ∼10 % of total new global cases and poses an over 4% lifetime risk of developing cancer. Recent advancements in the field of biotechnology and microbiology concocted novel microbe-based therapies to treat various cancers, including CRC. Microbes have been explored for human use since centuries, especially for the treatment of various ailments. The utility of microbes in cancer therapeutics is widely explored, and various bacteria, fungi, and viruses are currently in use for the development of cancer therapeutics. The human gut hosts about 100 trillion microbes that release their metabolites in active, inactive, or dead conditions. Microbial secondary metabolites, proteins, immunotoxins, and enzymes are used to target cancer cells to induce cell cycle arrest, apoptosis, and death. Various approaches, such as dietary interventions, the use of prebiotics and probiotics, and fecal microbiota transplantation have been used to modulate the gut microbiota in order to prevent or treat CRC pathogenesis. The present review highlights the role of the gut microbiota in CRC precipitation, the potential mechanisms and use of microorganisms as CRC biomarkers, and strategies to modulate microbiota for the prevention and treatment of CRC.

Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma

The skin microbiome plays a critical role in skin homeostasis and disorders. UVR is the major cause of nonmelanoma skin cancer, but other risk factors, including immune suppression, chronic inflammation, and antibiotic usage, suggest the microbiome as an additional, unexplored risk factor and potential disease biomarker. The overarching goal was to study the skin microbiome in squamous cell carcinoma (SCC) and premalignant actinic keratosis compared with that in healthy skin to identify skin cancer‒associated changes in the skin microbiome. We performed a high-resolution analysis of shotgun metagenomes of actinic keratosis and SCC in healthy skin, revealing the microbial community shifts specific to actinic keratosis and SCC. Most prominently, the relative abundance of pathobiont Staphylococcus aureus was increased at the expense of commensal Cutibacterium acnes in SCC compared with that in healthy skin, and enrichment of functional pathways in SCC reflected this shift. Notably, C. acnes associated with lesional versus healthy skin differed at the strain level, suggesting the specific functional changes associated with its depletion in SCC. Our study revealed a transitional microbial dysbiosis from healthy skin to actinic keratosis to SCC, supporting further investigation of the skin microbiome for use as a biomarker and providing hypotheses for studies investigating how these microbes might influence skin cancer progression.

Integrated analysis of intestinal microbiota and host gene expression in colorectal cancer patients

Introduction. Colorectal cancer (CRC) is one of the most common cancers and poses heavy burden on global health. The relationship between mucosal microbiome composition and colorectal gene expression are rarely studied. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between them in colorectal cancer patients.Gap statement. Previous studies have identified the contribution of gut microbiota and DEGs to the pathogenesis of CRC, but the relationship between mucosal microbiome composition and colorectal gene expression are rarely studied.Aim. In this study, we integrated transcriptome data with microbiome data to investigate the relationship between mucosal microbiome composition and colorectal gene expression.Methodology. First, three independent CRC gene expression profiles (GSE184093, GSE156355 and GSE146587) from Gene Expression Omnibus (GEO) were used to identify differentially expressed genes (DEGs). Second, another dataset (GSE163366) was used to analyse gut mucosal microbiome differential abundance. GO (Gene Ontology) function and KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway enrichment analyses of the DEGs were performed. Protein-protein interactions (PPIs) of the DEGs were constructed. The Spearman correlation analysis was computed between host DEGs and gut microbiome abundance data.Results. A total of 1036 upregulated DEGs and 1194 downregulated DEGs between noncancerous tissues and cancerous tissues were identified based on the analysis. One significant module with a score 37.65 was selected out via MCODE including 41 upregulated DEGs, which are were mostly enriched in two pathways, including microtubule binding and tubulin binding. In particular, significant negative correlations are prevalent between Fusobacterium and the 41 DEGs with the correlation ranging between -0.54 and -0.35, and there commonly exist significant positive correlations between Blautia and the 41 DEGs with the correlation ranging between 0.42 and 0.54, indicating that Fusobacterium and Blautia are two of the most important microbes interacting with the gene regulation.Conclusion. Our results demonstrate significant correlation between some gut microbes and DEGs, providing a comprehensive bioinformatics analysis of them for future investigation into the molecular mechanisms and biomarkers.

Biological roles of toll-like receptors and gut microbiota in colorectal cancer

Colorectal cancer (CRC) is one of the most considerably common malignancies of the alimentary system, with high mortality and incidence rates.  The present study suggested that the occurrence of CRC is closely related to bacteria, as the large intestine is a gathering place for human micro-organisms. However, the nosogenesis of bacteria leading to tumorigenesis is still obscure. Recently, many studies have reported that toll-like receptors and their related molecular pathways are involved in the process of gut micro-organisms generating CRC. Gut micro-organisms can promote or inhibit the development of CRC via binding to special toll-like receptors. In this paper, the authors review the relationship among toll-like receptors, gut micro-organisms and CRC in order to provide a reference for future tumor immunotherapy and targeted therapy.

Long non-coding RNA EVADR induced by Fusobacterium nucleatum infection promotes colorectal cancer metastasis

Both Fusobacterium nucleatum (F. nucleatum) and long non-coding RNA (lncRNA) EVADR are associated with colorectal cancer (CRC), but their relationship with CRC metastasis and the mechanisms by which EVADR promotes CRC metastasis are poorly understood. Here, we report that F. nucleatum promotes colorectal cancer cell metastasis to the liver and lung and that it can be detected in CRC-metastasis colonization in mouse models. Furthermore, F. nucleatum upregulates the expression of EVADR, which can increase the metastatic ability of CRC cells in vivo and in vitro. Mechanistically, elevated EVADR serves as a modular scaffold for the Y-box binding protein 1 (YBX1) to directly enhance the translation of epithelial-mesenchymal transition (EMT)-related factors, such as Snail, Slug, and Zeb1. These findings suggest that EVADR induced by F. nucleatum promotes colorectal cancer metastasis through YBX1-dependent translation. The EVADR-YBX1 axis may be useful for the prevention and treatment of patients with F. nucleatum-associated CRC metastasis.

Roles of gastrointestinal polypeptides in intestinal barrier regulation

The intestinal barrier is a dynamic entity that is organized as a multilayer system and includes various intracellular and extracellular elements. The gut barrier functions in a coordinated manner to impede the passage of antigens, toxins, and microbiome components and simultaneously preserves the balanced development of the epithelial barrier and the immune system and the acquisition of tolerance to dietary antigens and intestinal pathogens.Numerous scientific studies have shown a significant association between gut barrier damage and gastrointestinal and extraintestinal diseases such as inflammatory bowel disease, celiac disease and hepatic fibrosis. Various internal and external factors regulate the intestinal barrier. Gastrointestinal peptides originate from enteroendocrine cells in the luminal digestive tract and are critical gut barrier regulators. Recent studies have demonstrated that gastrointestinal peptides have a therapeutic effect on digestive tract diseases, enhancing epithelial barrier activity and restoring the gut barrier. This review demonstrates the roles and mechanisms of gastrointestinal polypeptides, especially somatostatin (SST) and vasoactive intestinal peptide (VIP), in intestinal barrier regulation.

Bacterial driver-passenger model in biofilms: a new mechanism in the development of colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease of the intestinal epithelium and ranks the third largest diagnosed malignancy in the world. Many studies have shown that the high risk of CRC is believed to be related to the formation of biofilms. To prove causation, it will be significant to decipher which specific bacteria in biofilms initiate and maintain CRC and fully describe their underlying mechanisms. Here we introduce a bacterial driver-passenger model. This model added a novel and compelling angle to the role of microorganisms, putting more emphasis on the transformation of bacterial composition in biofilms which play different roles in the development of CRC. In this model, bacterial drivers can initiate the formation of CRC through genotoxicity, while bacterial passengers maintain the CRC process through metabolites. On the basis of these pathogens, we further turned our attention to strategies that can inhibit and eradicate these pathogenic biofilms, with the aim of finding new ways to hinder colorectal carcinogenesis.

Purulent Renal Papillitis Due to Streptococcus Infantarius Subsp. Infantarius in a Horse

A 6-year-old, male Arabian crossbred horse was necropsied after a 10 day history of loss of appetite, debility and weight loss. Gross and histologic examination was consistent with purulent papillitis due to Streptococcus infantarius subsp. infantarius. The isolate was sensitive to all the antibiotics tested.

Gastrointestinal Microbiota Dysbiosis Associated with SARS-CoV-2 Infection in Colorectal Cancer: The Implication of Probiotics

The complexity of coronavirus disease 2019 (COVID-19)’s pathophysiology is such that microbial dysbiosis in the lung and gastrointestinal (GI) microbiota may be involved in its pathogenic process. GI microbiota dysbiosis has been associated with respiratory disorders, including COVID-19, as well as sporadic colorectal cancer (CRC) through imbalanced microbiota and compromised immune response. It is pertinent to understand the possible role of probiotics in stabilizing the microbial environment and maintaining the integrity of the respiratory and GI tracts in SARS-CoV-2 induced dysbiosis and colorectal carcinogenesis. The long-term implication of SARS-CoV-2 in GI dysbiosis via microbiota-gut-lung cross-talk could increase the risk of new CRC diagnosis or worsen the condition of previously diagnosed individuals. Recent knowledge shows that the immune-modulatory response to probiotics is shifting the beneficial use of probiotics towards the treatment of various diseases. In this review, we highlight the potential impact of probiotics on SARS-CoV-2 infection associated with CRC through microbiota imbalance in COVID-19 patients.

Microbiomics in Collusion with the Nervous System in Carcinogenesis: Diagnosis, Pathogenesis and Treatment

The influence of the naturally occurring population of microbes on various human diseases has been a topic of much recent interest. Not surprisingly, continuously growing attention is devoted to the existence of a gut brain axis, where the microbiota present in the gut can affect the nervous system through the release of metabolites, stimulation of the immune system, changing the permeability of the blood–brain barrier or activating the vagus nerves. Many of the methods that stimulate the nervous system can also lead to the development of cancer by manipulating pathways associated with the hallmarks of cancer. Moreover, neurogenesis or the creation of new nervous tissue, is associated with the development and progression of cancer in a similar manner as the blood and lymphatic systems. Finally, microbes can secrete neurotransmitters, which can stimulate cancer growth and development. In this review we discuss the latest evidence that support the importance of microbiota and peripheral nerves in cancer development and dissemination.

A qPCR-based method for rapid quantification of six intestinal homeostasis-relevant bacterial genera in feces

Aim: Developing efficient methods for monitoring the complex microbial community to rapidly assess the health status. Materials & methods: The qPCR-based method was developed, verified and in situ applied in fecal samples. Results: Six primer pairs with high specificity were designed to perform qPCR assays under a unified reaction condition within 2.5 h. The limits of detection, amplification efficiency and feasibility of the qPCR-based method established here were verified. In situ application of 18 fecal samples showed that the amounts of Bacteroides, Streptococcus and Bifidobacterium in colorectal cancer patient feces were obviously lower than those of healthy volunteers. Conclusion: This qPCR-based method was a reliable tool for rapid quantification of the six intestinal homeostasis relevant bacterial genera in feces.

Identification, semisynthesis, and anti-inflammatory evaluation of 2,3-seco-clavine-type ergot alkaloids from human intestinal fungus Aspergillus fumigatus CY018

Intestinal commensal fungi are vital to human health, and their secondary metabolites play a key role in the reciprocal relationship. In the present study, the first example of 2,3-seco ergot alkaloids belonging to clavine-type were isolated from the fermentation of human intestinal fungus Aspergillus fumigatus CY018, including two pairs of diastereoisomers, secofumigaclavines A (3) and B (4) and secofumigaclavines C (5) and D (6), one analogue features a highly unsaturated skeleton, secofumigaclavine E (7), along with two known ones, fumigaclavines C (1) and D (2). Their structures were identified based on extensive spectroscopic data in a combination of quantum chemical calculations. Moreover, a single-step operation of semi-synthetic reaction based on riboflavin (RF)-dependent photocatalysis was performed to obtain the novel 2,3-seco ergot alkaloids 3 and 5 from their biosynthetic precursors 1 and 2. All the isolated compounds were evaluated for their anti-inflammatory activity. Among them, secofumigaclavine B (4) could bind to MD2 with a low micromole level of the equilibrium dissociation constant measured by surface plasmon resonance (SPR), and suppress TLR4-mediated NF-κB signaling pathway in RAW264.7 cells, resulting in its anti-inflammatory effect. Molecular dynamics revealed that amino acid residue Tyr131 played a key role in the interaction of secofumigaclavine B (4) with MD2. These findings suggested that secofumigaclavine B (4) could be considered as a potential candidate for the development of MD2 inhibitors.

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.

Microbiome and colorectal cancer: A review of the past, present, and future

The gastrointestinal tract is home to diverse and abundant microorganisms, collectively referred to as the microbiome. This ecosystem typically contains trillions of microbial cells that play an important role in regulation of human health. The microbiome has been implicated in host immunity, nutrient absorption, digestion, and metabolism. In recent years, researchers have shown that alteration of the microbiome is associated with disease development, such as obesity, inflammatory bowel disease, and cancer. This review discusses the five decades of research into the human microbiome and the development of colorectal cancer - the historical context including experiments that sparked interest, the explosion of research that has occurred in the last decade, and finally the future of testing and treatment.

Microbial Characteristics of Locally Advanced Rectal Cancer Patients After Neoadjuvant Chemoradiation Therapy According to Pathologic Response

Background

Intestinal microbiota play a critical role in the development of colorectal cancer. However, little is known about the structure and characteristics of gut microbial in colorectal cancer, especially in locally advanced rectal cancer after neoadjuvant chemoradiation therapy.

Methods

Here, we performed this study to evaluate microbial characteristics between pathologic complete response (pCR) (n=12) and non-pathological complete response (Non-pCR) (n=45) tumor tissues from patients with locally advanced rectal cancer after neoadjuvant chemoradiation therapy. In this study, 16S rRNA gene sequencing was used to detect the microbial diversity including Alpha diversity and Beta diversity. Moreover, we used PICRUSt from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to predict the microbial metabolism functions.

Results

There was significant statistical difference in PFS between pCR and Non-pCR group (p < 0.05). However, there was no significant difference in OS between pCR and Non-pCR group. The microbial compositions in the both groups were Proteobacteria, Actinobacteria, Firmicutes and Thermi and Bacteroidetes at the phylum level. The five most predominant genera in both pCR and Non-pCR tissue groups were Sphingobium, Acinetobacter, Cupriavidus, Thermi and Sphingomonas at the genus level. The key taxa identified in the pCR and Non-pCR tissues were Thermi and Sphingomonadaceae respectively. In addition, a series of human disease-related genes were also significantly different between pCR and Non-pCR group.

Conclusion

In summary, we demonstrated the characteristic differences in microbial communities between pCR tissues and Non-pCR tumor tissues from locally advanced rectal cancer patients after neoadjuvant chemoradiation therapy. Our results present new alterations in the microbiome in locally advanced rectal cancer after neoadjuvant chemoradiation therapy, suggesting that it will provide a new perspective for the precise treatment of neoadjuvant rectal cancer by targeting specific microbial species in the future.

Exploring the Role of Gut Microbiome in Colon Cancer

Dysbiosis of the gut microbiome has been associated with the development of colorectal cancer (CRC). Gut microbiota is involved in the metabolic transformations of dietary components into oncometabolites and tumor-suppressive metabolites that in turn affect CRC development. In a healthy colon, the major of microbial metabolism is saccharolytic fermentation pathways. The alpha-bug hypothesis suggested that oncogenic bacteria such as enterotoxigenic Bacteroides fragilis (ETBF) induce the development of CRC through direct interactions with colonic epithelial cells and alterations of microbiota composition at the colorectal site. Escherichia coli, E. faecalis, F. nucleatum, and Streptococcus gallolyticus showed higher abundance whereas Bifidobacterium, Clostridium, Faecalibacterium, and Roseburia showed reduced abundance in CRC patients. The alterations of gut microbiota may be used as potential therapeutic approaches to prevent or treat CRC. Probiotics such as Lactobacillus and Bifidobacterium inhibit the growth of CRC through inhibiting inflammation and angiogenesis and enhancing the function of the intestinal barrier through the secretion of short-chain fatty acids (SCFAs). Crosstalk between lifestyle, host genetics, and gut microbiota is well documented in the prevention and treatment of CRC. Future studies are required to understand the interaction between gut microbiota and host to the influence and prevention of CRC. However, a better understanding of bacterial dysbiosis in the heterogeneity of CRC tumors should also be considered. Metatranscriptomic and metaproteomic studies are considered a powerful omic tool to understand the anti-cancer properties of certain bacterial strains. The clinical benefits of probiotics in the CRC context remain to be determined. Metagenomic approaches along with metabolomics and immunology will open a new avenue for the treatment of CRC shortly. Dietary interventions may be suitable to modulate the growth of beneficial microbiota in the gut.

Influence of the Intestinal Microbiota on Diabetes Management

In recent decades, there has been a very rapid increase in the prevalence of diabetes globally, with serious health and economic implications. Although today there are several therapeutic treatments for this disease, these do not address the causes of the disease and have serious side effects, so it is necessary to seek new treatments to replace or complement the existing ones. Among these complementary treatments, a strong link between the intestinal microbiota and diabetes has been demonstrated, which has focused attention on the use of biotherapy to regulate the function of the intestinal microbiota and, thus, treat diabetes. In this way, the main objective of this work is to provide a review of the latest scientific evidence on diabetes, gathering information about new trends in its management, and especially, the influence of the intestinal microbiota and microbiome on this pathology. It is possible to conclude that the relationship between the intestinal microbiota and diabetes is carried out through alterations in energy metabolism, the immune system, changes in intestinal permeability, and a state of low-intensity systemic inflammation. Although, currently, most of the experimental work, using probiotics for diabetes management, has been done on experimental animals, the results obtained are promising. Thus, the modification of the microbiota through biotherapy has shown to improve the symptoms and severity of diabetes through various mechanisms related to these alterations.

A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors

Streptococcus gallolyticus subspecies gallolyticus (Sgg) has a strong clinical association with colorectal cancer (CRC) and actively promotes the development of colon tumors. However, the molecular determinants involved in Sgg pathogenicity in the gut are unknown. Bacterial type VII secretion systems (T7SS) mediate pathogen interactions with their host and are important for virulence in pathogenic mycobacteria and Staphylococcus aureus. Through genome analysis, we identified a locus in Sgg strain TX20005 that encodes a putative type VII secretion system (designated as SggT7SS^T05). We showed that core genes within the SggT7SS^T05 locus are expressed in vitro and in the colon of mice. Western blot analysis showed that SggEsxA, a protein predicted to be a T7SS secretion substrate, is detected in the bacterial culture supernatant, indicating that this SggT7SS^T05 is functional. Deletion of SggT7SS^T05 (TX20005Δesx) resulted in impaired bacterial adherence to HT29 cells and abolished the ability of Sgg to stimulate HT29 cell proliferation. Analysis of bacterial culture supernatants suggest that SggT7SS^T05-secreted factors are responsible for the pro-proliferative activity of Sgg, whereas Sgg adherence to host cells requires both SggT7SS^T05-secreted and bacterial surface-associated factors. In a murine gut colonization model, TX20005Δesx showed significantly reduced colonization compared to the parent strain. Furthermore, in a mouse model of CRC, mice exposed to TX20005 had a significantly higher tumor burden compared to saline-treated mice, whereas those exposed to TX20005Δesx did not. Examination of the Sgg load in the colon in the CRC model suggests that SggT7SS^T05-mediated activities are directly involved in the promotion of colon tumors. Taken together, these results reveal SggT7SS^T05 as a previously unrecognized pathogenicity determinant for Sgg colonization of the colon and promotion of colon tumors.

Colorectal cancer (CRC) is a leading cause of cancer-related death. The development of CRC can be strongly influenced by specific gut microbes. Understanding how gut microbes modulate CRC is critical to developing novel strategies to improve clinical diagnosis and treatment of this disease. S. gallolyticus subsp. gallolyticus (Sgg) has a strong clinical association with CRC and actively promotes the development of colon tumors. However, the specific Sgg molecules that mediate its pro-tumor activity are unknown. Here we report the first characterization of a type VII secretion system (T7SS) in Sgg, designated as SggT7SS^T05. We further demonstrate that SggT7SS^T05-mediated activities are important for Sgg to colonize the colon and to promote the development of colon tumors. These findings reveal SggT7SS^T05 as a novel pathogenicity determinant of Sgg and provide a critical breakthrough in our efforts to understand how Sgg influences the development of CRC. Future investigations of the biological activities of specific effectors of SggT7SS^T05 will likely lead to the discovery of Sgg molecules that can be used as diagnostic markers and intervention targets aimed at mitigating the harmful effect of Sgg.

Characterization of a Four-Component Regulatory System Controlling Bacteriocin Production in Streptococcus gallolyticus

Bacteriocins are natural antimicrobial peptides produced by bacteria to kill closely related competitors. The opportunistic pathogen Streptococcus gallolyticus subsp. gallolyticus was recently shown to outcompete commensal enterococci of the murine microbiota under tumoral conditions thanks to the production of a two-peptide bacteriocin named gallocin. Here, we identified four genes involved in the regulatory control of gallocin in S. gallolyticus subsp. gallolyticus UCN34 that encode a histidine kinase/response regulator two-component system (BlpH/BlpR), a secreted peptide (GSP [gallocin-stimulating peptide]), and a putative regulator of unknown function (BlpS). While BlpR is a typical 243-amino-acid (aa) response regulator possessing a phospho-receiver domain and a LytTR DNA-binding domain, BlpS is a 108-aa protein containing only a LytTR domain. Our results showed that the secreted peptide GSP activates the dedicated two-component system BlpH/BlpR to induce gallocin transcription. A genome-wide transcriptome analysis indicates that this regulatory system (GSP-BlpH/BlpR) is specific for bacteriocin production. Importantly, as opposed to BlpR, BlpS was shown to repress gallocin gene transcription. A conserved operator DNA sequence of 30 bp was found in all promoter regions regulated by BlpR and BlpS. Electrophoretic mobility shift assays (EMSA) and footprint assays showed direct and specific binding of BlpS and BlpR to various regulated promoter regions in a dose-dependent manner on this conserved sequence. Gallocin expression appears to be tightly controlled in S. gallolyticus subsp. gallolyticus by quorum sensing and antagonistic activity of 2 LytTR-containing proteins. Competition experiments in gut microbiota medium and 5% CO₂ to mimic intestinal conditions demonstrate that gallocin is functional under these in vivo-like conditions.IMPORTANCE Streptococcus gallolyticus subsp. gallolyticus, formerly known as Streptococcus bovis biotype I, is an opportunistic pathogen causing septicemia and endocarditis in the elderly often associated with asymptomatic colonic neoplasia. Recent studies indicate that S. gallolyticus subsp. gallolyticus is both a driver and a passenger of colorectal cancer. We previously showed that S. gallolyticus subsp. gallolyticus produces a bacteriocin, termed gallocin, enabling colonization of the colon under tumoral conditions by outcompeting commensal members of the murine microbiota such as Enterococcus faecalis Here, we identified and extensively characterized a four-component system that regulates gallocin production. Gallocin gene transcription is activated by a secreted peptide pheromone (GSP) and a two-component signal transduction system composed of a transmembrane histidine kinase receptor (BlpH) and a cytosolic response regulator (BlpR). Finally, a DNA-binding protein (BlpS) was found to repress gallocin genes transcription, likely by antagonizing BlpR. Understanding gallocin regulation is crucial to prevent S. gallolyticus subsp. gallolyticus colon colonization under tumoral conditions.

Clostridioides difficile antibody response of colorectal cancer patients versus clinically healthy individuals

Dysbiosis, defined as an imbalance in the gut microbiota caused by too few beneficial bacteria and an overgrowth of bad bacteria, yeast, and/or parasites, is now being associated with several diseases, including the development of colorectal carcinoma (CRC). In this study, the potential association of Clostridioides difficile (formerly Clostridium difficile) with CRC was investigated. Plasma samples obtained from preoperative histologically confirmed CRC patients (n=39) and their age- and sex-matched clinically healthy controls (n=39) were analyzed for antibodies to toxin B of C. difficile (anti-tcdB) by enzyme-linked immunosorbent assay (ELISA). A significantly greater number (p=0.012) of CRC cases (n=26/39, 66.7%) had anti-tcdB IgG levels above the cutoff value compared with controls (n=12/39, 30.8%). Eight cases (8/39, 20.5%) and none of the controls registered anti-tcdB IgA levels above the cutoff value (p=0.0039). Anti-tcdB IgG and IgA levels were not shown to be significantly associated with tumor grade or tumor stage. Anti-tcdB IgG showed 66.7% sensitivity and 69.2% specificity. For anti-tcdB IgA, sensitivity and specificity were 20.5% and 100%, respectively. The positive predictive values for anti-tcdB IgA and IgG were 100% and 68.4%, respectively. The anti-tcdB IgA and IgG negative predictive values were 55.7% and 67.5%, respectively. The results suggest the potential association of C. difficile with CRC and anti-tcdB levels, particularly the IgA level. Hence, anti-tcdB antibodies can be candidate serologic markers for CRC.

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: a systematic review and meta-analysis of observational studies

AIM

The Incidence of colorectal cancer (CRC) is increasing, and evidence suggests that maladaptation of the bowel microbiome may be associated with colorectal carcinogenesis. Consumption of antibiotics may cause imbalance of the bowel microbiome but research assessing an association between antibiotic exposure and CRC is inconsistent. The aim of this systematic review and meta-analysis was to appraise and synthesize the available evidence.

METHOD

The MEDLINE, EMBASE and CINAHL databases were searched for published observational studies. We included eight studies of 3 408 312 patients. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) for the odds of CRC following antibiotic exposure were estimated. Sensitivity analyses were performed according to exposure definition, study design and risk of bias.

RESULTS

A weak association between antibiotic exposure and CRC was demonstrated when exposure was assessed cumulatively by the number of prescriptions (OR 1.204, 95% CI 1.097-1.322, P < 0.001) or duration of antibiotic exposure (OR 1.168, 95% CI 1.087-1.256, P < 0.001). Antibiotic exposure assessed as a binary variable demonstrated no association with CRC.

CONCLUSION

The findings suggest a weak association between cumulative antibiotic consumption and risk of CRC but no causal conclusions can be made. Limitations include the heterogeneity and quality of the available research, particularly with regard to measurement of antibiotic exposure.

Diagnostic Evaluation of Streptococcus gallolyticus Infection in Patients with Colon Diseases by Polymerase Chain Reaction (PCR) and Culturing Methods

Background: Different types of Streptococcus gallolyticus are associated with malignant bowel cancer. Objectives: The aim of this study was to compare two culture and molecular methods in identifying Streptococcus gallolyticus in patients with colon diseases. Methods: A descriptive study was conducted to detect Streptococcus gallolyticus in 55 patients with colon diseases referring to hospitals in Babol and Chalus, Iran. A polymerase chain reaction and culture technique were performed. Detection of Streptococcus gallolyticus after deoxyribonucleic acid (DNA) extraction from designed primers (PCO3, PCO4) was used for SODA gene. From the general culture medium, brain heart infusion (BHI) broth and specific medium for bacterial growth and detection were used. Then, the characteristics of the two methods were evaluated. Results: Of 55 biopsy samples of patients with colon diseases, 3 samples (5.5%) with 95% confidence interval were positive and 52 (94.5%) were reported negative in terms of DNA of Streptococcus gallolyticus. According to the culture test, 9 (16.4%) were positive and 46 (83.6%) were negative for diagnosis of Streptococcus gallolyticus bacteria. Based on the diagnostic agreement between the two methods, the ratio of 9 positive cases of culture method to 3 positive cases by polymerase chain reaction (PCR) method (3.6%) were reported positive both in terms of molecular and positive culture, and 7 (12.7%) out of 9 (16.4%) were negative. To investigate the agreement between the culture and PCR methods, the Kappa test was used, which was statistically significant (P < 0.015). Other studies which have been conducted using the culture method, reported a significant relationship between the family history of colorectal cancer, diabetes, and the presence of Streptococcus gallolyticus bacteria. Conclusions: Considering the advantages, disadvantages, and the characteristics of both methods, none of them can be considered as a comprehensive, standard test at present. The simultaneous use of the two methods is recommended in cases where achieving fast results prevails, or when there is a likelihood of sample infection or late-growing microorganisms.

Metabolic models predict bacterial passengers in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found in pathogens, metagenomic studies indicate the existence of a microbiome signature, where particular bacterial taxa are enriched in the metagenomes of CRC patients. Here, we investigate to what extent the abundance of bacterial taxa in CRC metagenomes can be explained by the growth advantage resulting from the presence of specific CRC metabolites in the tumor microenvironment.

METHODS

We composed lists of metabolites and bacteria that are enriched on CRC samples by reviewing metabolomics experimental literature and integrating data from metagenomic case-control studies. We computationally evaluated the growth effect of CRC enriched metabolites on over 1500 genome-based metabolic models of human microbiome bacteria. We integrated the metabolomics data and the mechanistic models by using scores that quantify the response of bacterial biomass production to CRC-enriched metabolites and used these scores to rank bacteria as potential CRC passengers.

RESULTS

We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome.

CONCLUSION

Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome.

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMin Δ 850/+ ;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development.IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease

Tools that predict the risk of colorectal cancer are important for early diagnosis, given the high mortality rate for this cancer. The composition of the intestinal microbiota is now considered to be a risk factor for the development of colorectal cancer. This discovery has motivated a growing number of studies to identify the micro-organisms responsible for the onset and/or progression of colorectal cancer. With this in mind, this review discusses the relationship between the composition of the intestinal microbiota and colorectal cancer risk. Prospective and case-control studies indicate that the intestinal microbiota of individuals with colorectal cancer usually contains a greater proportion of bacteria responsible for gastrointestinal tract inflammatory diseases, as well as bacteria that produce toxins and carcinogenic metabolites. In contrast, there tends to be a reduced presence of butyric acid-producing bacteria, probiotic bacteria and potentially probiotic bacteria. Despite these differences, the onset and development of colorectal cancer cannot be attributed to a specific micro-organism. Thus, studies focused on the formation of the intestinal microbiota and factors that modulate its composition are important for the development of approaches for colorectal cancer prevention.

Real-time fluorescence loop-mediated isothermal amplification assay for rapid and sensitive detection of Streptococcus gallolyticus subsp. gallolyticus associated with colorectal cancer

The increasing threat of Streptococcus gallolyticus subsp. gallolyticus (SGG) infections has gained considerable attention for its strong association with colorectal cancer (CRC). Herein, we proposed real-time fluorescence loop-mediated isothermal amplification (LAMP) as a novel, simple, rapid, and highly sensitive assay for identifying SGG for the first time. This assay was capable of detecting SGG with initial DNA concentrations ranging from 10² to 10⁸ copies per microliter, under isothermal conditions within 30 min via real-time fluorescence monitoring. Our method was tested for specific identification of SGG strains without cross-reaction with other Streptococcus gallolyticus subspecies and Escherichia coli. The developed LAMP shows a superior performance with shorter time and higher sensitivity compared with conventional polymerase chain reaction (PCR). Significantly, this proposed approach was successfully applied for detecting SGG in clinical urine samples, which is non-invasive diagnosis, showing excellent accuracy and reliability to discriminate healthy controls and CRC patients. For comparison, these samples were also tested against PCR assay. These results yielded an analytical sensitivity of 100% and a specificity of 100% for SGG testing using LAMP. The findings suggest LAMP can be employed for detecting SGG infections which is useful for diagnosis and screening of CRC.

High intake of dietary fructose in overweight/obese teenagers associated with depletion of Eubacterium and Streptococcus in gut microbiome

Background: A western high fat, high carbohydrate diet has been shown to be associated with decreased gut bacterial diversity and reductions in beneficial bacteria. This gut bacteria dysbiosis could develop in early life and contribute to chronic disease risk such as obesity, type 2 diabetes and non-alcoholic fatty liver disease.Objective: To determine how dietary macronutrients are associated with the relative abundance of gut bacteria in healthy adolescents.Methods: Fifty-two obese participants (12-19 years) from two studies, many who were primarily of Hispanic background, provided fecal samples for 16S rRNA gene sequencing. Dietary macronutrients were assessed using 24-hour diet recalls and body composition was assessed using DEXA. General regression models assuming a negative binomial distribution were used to examine the associations between gut bacteria and dietary fiber, saturated fat, unsaturated fats, protein, added sugar, total sugar and free fructose after adjusting for age, gender, race/ethnicity, body fat percentage, study and caloric intake.Results: The genera Eubacterium (Benjamini-Hochberg (BH) corrected p-value = 0.10) and Streptococcus (BH corrected p-value = 0.04) were inversely associated with dietary fructose intake. There were no other significant associations between abundances of gut microbes and other dietary macronutrients, including fiber, fat, protein, total sugar or added sugar.Conclusions: High dietary fructose was associated with lower abundance of the beneficial microbes Eubacterium and Streptococcus, which are involved with carbohydrate metabolism.

Innate lymphoid cells: A potential link between microbiota and immune responses against cancer

The adaptive immune system plays a crucial role in anti-tumor surveillance. Enhancement of T cell responses through checkpoint blockade has become a major therapeutic avenue of intervention for several tumors. Because it shapes immune responses and regulates their amplitude and duration, the microbiota has a substantial impact on anti-tumor immunity. Innate lymphoid cells (ILCs) comprise a heterogeneous population of lymphocytes devoid of antigen-specific receptors that mirror T helper cells in their ability to secrete cytokines that activate immune responses. Ongoing studies suggest that ILCs contribute to anti-tumor responses. Moreover, since ILCs are present at barrier surfaces, they are stimulated by the microbiota and, reciprocally, influence the composition of the microbiota by regulating the surface barrier microenvironment. Thus, ILC-microbiota cross-talk may in part underpin the effects of the microbiota on anti-tumor responses. In this article, we review current evidence linking ILCs to cancer and discuss the potential impact of ILC-microbiota cross-talk in anti-tumor immune responses.

Differential Responses of Colorectal Cancer Cell Lines to Enterococcus faecalis' Strains Isolated from Healthy Donors and Colorectal Cancer Patients

The metabolites produced by the host’s gut microbiota have an important role in the maintenance of intestinal homeostasis, but can also act as toxins and induce DNA damage in colorectal epithelial cells increasing the colorectal cancer (CRC) chance. In this scenario, the impact of some of the components of the natural human gastrointestinal microbiota, such as Enterococcus faecalis (E. faecalis), at the onset of CRC progression remains controversial. Since under dysbiotic conditions it could turn into a pathogen, the aim of this study was to compare the effect of E. faecalis’ strains (isolated from CRC patients and healthy subjects’ stools) on the proliferation of different colorectal cells lines. First, we isolated and genotyping characterized the Enterococcus faecalis’ strains. Then, we analyzed the proliferation index (by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay) of three tumor and one normal intestinal cell lines, previously exposed to E. faecalis strains pre-cultured medium. Stool samples of CRC patients demonstrated a reduced frequency of E. faecalis compared to healthy subjects. In addition, the secreted metabolites of E. faecalis’ strains, isolated from healthy donors, decreased the human ileocecal adenocarcinoma cell line HCT-8 and human colon carcinoma cell line HCT-116 cell proliferation without effects on human colorectal adenocarcinoma cell line SW620 and on normal human diploid cell line CLR-1790. Notably, the metabolites of the strains isolated from CRC patients did not influence the cell growth of CRC cell lines. Our results demonstrated a new point of view in the investigation of E. faecalis’ role in CRC development, which raises awareness of the importance of not only associating the presence/absence of a unique microorganism, but also in defining the specific characteristics of the different investigated strains.

Current Challenges in Cancer Immunotherapy: Multimodal Approaches to Improve Efficacy and Patient Response Rates

Cancer immunotherapy is a promising innovative treatment for many forms of cancer, particularly melanoma. Although immunotherapy has been shown to be efficacious, patient response rates vary and, more often than not, only a small subset of the patients within a large cohort respond favourably to the treatment. This issue is particularly concerning and becomes a challenge of immunotherapy to improve the effectiveness and patient response rates. Here, we review the specific types of available immunotherapy options, their proposed mechanism(s) of action, and the reasons why the patient response to this treatment is variable. The potential favourable options to improve response rates to immunotherapy will be discussed with an emphasis on adopting a multimodal approach on the novel role that the gut microbiota may play in modulating the efficacy of cancer immunotherapy.

Analyzing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer

Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host-microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed. In this review article, the focus is on the roles of gut microbiome in CRC, the current findings on CRC secretome are highlighted, and the emerging challenges and strategies to drive forward this area of research are addressed.

Mechanisms underlying the effects of stress on tumorigenesis and metastasis (Review)

Stress is one of the fundamental survival mechanisms in nature. Although chronic or long-lasting stress can be detrimental to health, acute or short-term stress can have health benefits. The aim of the present review was to address the complexity and significance of stress in tumorigenesis. The review covers an evaluation of previously used and reported experimental animal models of stress, as well as the effects of stress on the neuroendocrine system, immune function, gut microbiota, and inflammation and multidrug resistance, all of which are closely associated with cancer occurrence, progression and treatment. The review concludes that understanding the efficacy of stress management (prevention and rehabilitation) is crucial to the development of comprehensive and individualized strategies for cancer prevention and treatment.

High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group

BACKGROUND & AIMS

This review examines to what extent high-protein diets (HPD), which may favor body weight loss and improve metabolic outcomes in overweight and obese individuals, may also impact the gut environment, shaping the microbiota and the host-microbe (co)metabolic pathways and products, possibly affecting large intestine mucosa homeostasis.

METHODS

PubMed-referenced publications were analyzed with an emphasis on dietary intervention studies involving human volunteers in order to clarify the beneficial vs. deleterious effects of HPD in terms of both metabolic and gut-related health parameters; taking into account the interactions with the gut microbiota.

RESULTS

HPD generally decrease body weight and improve blood metabolic parameters, but also modify the fecal and urinary contents in various bacterial metabolites and co-metabolites. The effects of HPD on the intestinal microbiota composition appear rather heterogeneous depending on the type of dietary intervention. Recently, HPD consumption was shown to modify the expression of genes playing key roles in homeostatic processes in the rectal mucosa, without evidence of intestinal inflammation. Importantly, the effects of HPD on the gut were dependent on the protein source (i.e. from plant or animal sources), a result which should be considered for further investigations.

CONCLUSION

Although HPD appear to be efficient for weight loss, the effects of HPD on microbiota-derived metabolites and gene expression in the gut raise new questions on the impact of HPD on the large intestine mucosa homeostasis leading the authors to recommend some caution regarding the utilization of HPD, notably in a recurrent and/or long-term ways.

Prediction of Microbe-Disease Associations by Graph Regularized Non-Negative Matrix Factorization

More and more evidence shows that microbes play crucial roles in human health and disease. The exploration of the relationship between microbes and diseases will help people to better understand the underlying pathogenesis and have important implications for disease diagnosis and prevention. However, the known associations between microbes and diseases are very less. We proposed a new method called non-negative matrix factorization microbe-disease associations (NMFMDA), which used Gaussian interaction profile kernel similarity measure, to calculate microbial similarity and disease similarity, and applied a logistic function to regulate disease similarity. And, based on the known microbe-disease associations, a graph-regularized non-negative matrix factorization model was utilized to simultaneously identify potential microbe-disease associations. Moreover, fivefold cross-validation was utilized to evaluate the performance of our method. It reached the reliable area under receiver operating characteristic curve (AUC) of 0.8891, higher than other state-of-the-art methods. Finally, the case studies on three complex human diseases (i.e., asthma, inflammatory bowel disease, and colon cancer) demonstrated the good performance of our method. In summary, our method can be considered as an effective computational model for predicting potential disease-microbe associations.

Fecal transplantation: digestive and extradigestive clinical applications

Background and aim

Fecal transplantation or fecal material transplantation (FMT) became a hot topic in gastroenterology in recent years. Therefore it is important to disseminate the up-to-date information on FMT. The aim of the paper is to review the knowledge on FMT and its clinical applications.

Methods

An extensive review of the literature was carried out. Titles from Pubmed were searched and analyzed. A narrative review has been written with emphasis on indications of FMT in different conditions.

Results

The guidelines recommend FMT in relapsing infection with Clostridium difficile. Several attempts to use FMT in other conditions have been analyzed. Attempts were recorded in other bowel disorders like IBD, IBS, chronic constipation and even colorectal cancer. The attempt to change the microbiota by FMT in diabetes and obesity represent challenges for the future.

Conclusions

Fecal transplantation represents an important therapeutic method, intensively investigated these years. Beside the indication for persistent and recurrent Clostridium difficile infection, several attempts were undertaken in other intestinal diseases and in metabolic conditions. The efficiency of these applications has to be demonstrated.