Effects of Intestinal Microbial⁻Elaborated Butyrate on Oncogenic Signaling Pathways

Sodium butyrate alleviates lipopolysaccharide-induced inflammation through JAK/STAT signalling in primary human corneal fibroblasts

BACKGROUND

Bacterial keratitis is a common cause of blindness. Antibiotic treatment leads to the rapid release of lipopolysaccharide (LPS), which can activate corneal fibroblasts and cause persistent and excessive inflammatory responses. The anti-inflammatory drugs currently used to treat keratitis have serious side effects. Therefore, the ability of sodium butyrate (NaB), which can suppress the production of proinflammatory cytokines and promote the production of anti-inflammatory cytokines, to ameliorate keratitis was assessed in the present study.

METHODS

The effect of NaB on the viability of primary human corneal fibroblasts was assayed with a CCK-8 kit. Cell migration was assessed by an in vitro scratch assay. Cell phenotypes were assessed by Western blotting and immunofluorescence staining. An antibody array was used to measure the production of proinflammatory cytokines and chemokines.

RESULTS

At 0-1 mM, NaB had no significant effect on cell viability, promoted the expression of the keratocyte marker keratocan and inhibited the fibroblast marker vimentin. Inhibition of cell migration was observed in the wound healing assay. By targeting the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signalling pathway, NaB decreased the levels of inflammation-related cytokines and chemokines whose expression was induced by LPS.

CONCLUSIONS

NaB maintained the keratocyte phenotype, inhibited cell migration, and relieved LPS-induced inflammatory responses through the JAK/STAT signalling pathway.

Probiotics and the Role of Dietary Substrates in Maintaining the Gut Health: Use of Live Microbes and Their Products for Anticancer Effects against Colorectal Cancer

The gut microbiome is an important and the largest endocrine organ linked to the microbes of the GI tract. The bacterial, viral and fungal communities are key regulators of the health and disease status in a host at hormonal, neurological, immunological, and metabolic levels. The useful microbes can compete with microbes exhibiting pathogenic behavior by maintaining resistance against their colonization, thereby maintaining eubiosis. As diagnostic tools, metagenomic, proteomic and genomic approaches can determine various microbial markers in clinic for early diagnosis of colorectal cancer (CRC). Probiotics are live non-pathogenic microorganisms such as lactic acid bacteria, Bifidobacteria, Firmicutes and Saccharomyces that can help maintain eubiosis when administered in appropriate amounts. In addition, the type of dietary intake contributes substantially to the composition of gut microbiome. The use of probiotics has been found to exert antitumor effects at preclinical levels and promote the antitumor effects of immunotherapeutic drugs at clinical levels. Also, modifying the composition of gut microbiota by Fecal Microbiota Transplantation (FMT), and using live lactic acid producing bacteria such as Lactobacillus, Bifidobacteria and their metabolites (termed postbiotics) can contribute to immunomodulation of the tumor microenvironment. This can lead to tumor-preventive effects at early stages and antitumor effects after diagnosis of CRC. To conclude, probiotics are presumably found to be safe to use in humans and are to be studied further to promote their appliance at clinical levels for management of CRC.

Altered Microbiome Promotes Pro-Inflammatory Pathways in Oesophago-Gastric Tumourigenesis

INTRODUCTION

The upper gastrointestinal microbiome is a dynamic entity that is involved in numerous processes including digestion, production of vitamins and protection against pathogens. Many external and intrinsic factors may cause changes in the proportions of bacteria within the microbial community, termed 'dysbiosis'. A number of these have been identified as risk factors for a range of diseases, including oesophago-gastric carcinoma.

MATERIALS AND METHODS

A narrative review was conducted to elucidate the current evidence on the role of the microbiome in promoting oesophago-gastric tumourigenesis. Significant causes of dysbiosis including age, medications and GORD were examined and key pro-inflammatory pathways implicated in tumourigenesis and their interaction with the microbiome were described.

RESULTS AND DISCUSSION

An association between microbial dysbiosis and development of oesophago-gastric cancer may be mediated via activation of pro-inflammatory pathways, the inflammasome and the innate immune system. Advances in sequencing technology allow microbial communities to be fingerprinted by sequencing the 16S rRNA gene, enabling a deeper understanding of the genera that may be implicated in driving tumourigenesis.

CONCLUSIONS

Developing a greater understanding of the influence of the microbiota on oesophago-gastric tumourigenesis may enable advances to be made in the early detection of malignancy and in the development of novel systemic therapies, leading to improved rates of survival.

Implementation of Machine Learning-Based System for Early Diagnosis of Feline Mammary Carcinomas through Blood Metabolite Profiling

Background: Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unspayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. The diagnosis through these methods is sometimes delayed and unreliable, leading to increased chances of mortality. Objectives: The objective of this study was to identify the biomarkers, including blood metabolites and genes, related to feline mammary carcinoma, study their relationships, and develop a machine learning (ML) model for the early diagnosis of the disease. Methods: We analyzed the blood metabolites of felines with mammary carcinoma using the pathway analysis feature in MetaboAnalyst software, v. 5.0. We utilized machine-learning (ML) methods to recognize FMC using the blood metabolites of sick patients. Results: The metabolic pathways that were elucidated to be associated with this disease include alanine, aspartate and glutamate metabolism, Glutamine and glutamate metabolism, Arginine biosynthesis, and Glycerophospholipid metabolism. Furthermore, we also elucidated several genes that play a significant role in the development of FMC, such as ERBB2, PDGFA, EGFR, FLT4, ERBB3, FIGF, PDGFC, PDGFB through STRINGdb, a database of known and predicted protein-protein interactions, and MetaboAnalyst 5.0. The best-performing ML model was able to predict metabolite class with an accuracy of 85.11%. Conclusion: Our findings demonstrate that the identification of the biomarkers associated with FMC and the affected metabolic pathways can aid in the early diagnosis of feline mammary carcinoma.

Optimal features selection in the high dimensional data based on robust technique: Application to different health database

Bio-informatics and gene expression analysis face major hurdles when dealing with high-dimensional data, where the number of variables or genes much outweighs the number of samples. These difficulties are exacerbated, particularly in microarray data processing, by redundant genes that do not significantly contribute to the response variable. To address this issue, gene selection emerges as a feasible method for identifying the most important genes, hence reducing the generalization error of classification algorithms. This paper introduces a new hybrid approach for gene selection by combining the Signal-to-Noise Ratio (SNR) score with the robust Mood median test. The Mood median test is beneficial for reducing the impact of outliers in non-normal or skewed data since it may successfully identify genes with significant changes across groups. The SNR score measures the significance of a gene's classification by comparing the gap between class means and within-class variability. By integrating both of these approaches, the suggested approach aims to find genes that are significant for classification tasks. The major objective of this study is to evaluate the effectiveness of this combination approach in choosing the optimal genes. A significant P-value is consistently identified for each gene using the Mood median test and the SNR score. By dividing the SNR value of each gene by its significant P-value, the Md score is calculated. Genes with a high signal-to-noise ratio (SNR) have been considered favorable due to their minimal noise influence and significant classification importance. To verify the effectiveness of the selected genes, the study utilizes two dependable classification techniques: Random Forest and K-Nearest Neighbors (KNN). These algorithms were chosen due to their track record of successfully completing categorization-related tasks. The performance of the selected genes is evaluated using two metrics: error reduction and classification accuracy. These metrics offer an in-depth assessment of how well the selected genes improve classification accuracy and consistency. According to the findings, the hybrid approach put out here outperforms conventional gene selection methods in high-dimensional datasets and has lower classification error rates. There are considerable improvements in classification accuracy and error reduction when specific genes are exposed to the Random Forest and KNN classifiers. The outcomes demonstrate how this hybrid technique might be a helpful tool to improve gene selection processes in bioinformatics.

Research advances in the therapy of metabolic syndrome

Metabolic syndrome refers to the pathological state of metabolic disorder of protein, fat, carbohydrate, and other substances in the human body. It is a syndrome composed of a group of complex metabolic disorders, whose pathogenesis includes multiple genetic and acquired entities falling under the category of insulin resistance and chronic low-grade inflammationand. It is a risk factor for increased prevalence and mortality from diabetes and cardiovascular disease. Cardiovascular diseases are the predominant cause of morbidity and mortality globally, thus it is imperative to investigate the impact of metabolic syndrome on alleviating this substantial disease burden. Despite the increasing number of scientists dedicating themselves to researching metabolic syndrome in recent decades, numerous aspects of this condition remain incompletely understood, leaving many questions unanswered. In this review, we present an epidemiological analysis of MetS, explore both traditional and novel pathogenesis, examine the pathophysiological repercussions of metabolic syndrome, summarize research advances, and elucidate the mechanisms underlying corresponding treatment approaches.

Microbiome in radiotherapy: an emerging approach to enhance treatment efficacy and reduce tissue injury

Radiotherapy is a widely used cancer treatment that utilizes powerful radiation to destroy cancer cells and shrink tumors. While radiation can be beneficial, it can also harm the healthy tissues surrounding the tumor. Recent research indicates that the microbiota, the collection of microorganisms in our body, may play a role in influencing the effectiveness and side effects of radiation therapy. Studies have shown that specific species of bacteria living in the stomach can influence the immune system's response to radiation, potentially increasing the effectiveness of treatment. Additionally, the microbiota may contribute to adverse effects like radiation-induced diarrhea. A potential strategy to enhance radiotherapy outcomes and capitalize on the microbiome involves using probiotics. Probiotics are living microorganisms that offer health benefits when consumed in sufficient quantities. Several studies have indicated that probiotics have the potential to alter the composition of the gut microbiota, resulting in an enhanced immune response to radiation therapy and consequently improving the efficacy of the treatment. It is important to note that radiation can disrupt the natural balance of gut bacteria, resulting in increased intestinal permeability and inflammatory conditions. These disruptions can lead to adverse effects such as diarrhea and damage to the intestinal lining. The emerging field of radiotherapy microbiome research offers a promising avenue for optimizing cancer treatment outcomes. This paper aims to provide an overview of the human microbiome and its role in augmenting radiation effectiveness while minimizing damage.

Puerariae lobatae Radix ameliorates chronic kidney disease by reshaping gut microbiota and downregulating Wnt/β‑catenin signaling

Gut microbiota dysfunction is a key factor affecting chronic kidney disease (CKD) susceptibility. Puerariae lobatae Radix (PLR), a traditional Chinese medicine and food homologous herb, is known to promote the gut microbiota homeostasis; however, its role in renoprotection remains unknown. The present study aimed to investigate the efficacy and potential mechanism of PLR to alleviate CKD. An 8‑week 2% NaCl‑feeding murine model was applied to induce CKD and evaluate the therapeutic effect of PLR supplementary. After gavage for 8 weeks, The medium and high doses of PLR significantly alleviated CKD‑associated creatinine, urine protein increasement and nephritic histopathological injury. Moreover, PLR protected kidney from fibrosis by reducing inflammatory response and downregulating the canonical Wnt/β‑catenin pathway. Furthermore, PLR rescued the gut microbiota dysbiosis and protected against high salt‑induced gut barrier dysfunction. Enrichment of Akkermansia and Bifidobacterium was found after PLR intervention, the relative abundances of which were in positive correlation with normal maintenance of renal histology and function. Next, fecal microbiota transplantation experiment verified that the positive effect of PLR on CKD was, at least partially, exerted through gut microbiota reestablishment and downregulation of the Wnt/β‑catenin pathway. The present study provided evidence for a new function of PLR on kidney protection and put forward a potential therapeutic strategy target for CKD.

The role of short-chain fatty acids in the progression of non-alcoholic fatty liver disease

Introduction. Nowadays, a multifactorial model of the pathogenesis of NAFLD is recognized. It is interesting to study the contribution of changes in the composition of the intestinal microbiota and its metabolites in the development of the disease.

Aim. To evaluate the contribution of research into the qualitative composition of the intestinal microbiota in relation to the risk of progression of NAFLD to reduce the loss of health- saving potential of the population.

Materials and methods. An open comparative study of 83 mature-aged patients (56.6 years (46–63)) suffering from NAFLD was conducted. The levels of insulin, leptin, its receptor, adiponectin in blood serum, zonulin in feces were studied, and SCFA in feces

was determined. The analysis was carried out depending on the phenotypes of NAFLD: the degree of steatosis (1 – 40 patients, degree 2 – 18 and degree 3 – 25), the presence of NASH (43 patients), the presence of fibrosis (fibrosis was found in 35 patients). The degree of steatosis and fibrosis was assessed using elastometry. The results of the study were analyzed using the Microsoft Excel, STATISTICA 12.0 software package.

Results. In patients with NAFLD, the absolute number of all SCFA in the feces was reduced. The anaerobic index was deviated towards sharply negative values (-0,711 (-0,576-(-0,830)). A high level of propionic acid was noted among the patients with fibrosis (p < 0.05). Anaerobic index, relative content of isoC4 + isoC5 + isoC6, relative content of butyric acid had a positive relationship with the St-index (rs = 0.254, rs = 0.269, rs = 0.240, p≤ 0.05). An increase in the relative amount of propionic acid was statistically significantly associated with a decrease of FLI (rs = -0.229, p ≤0.05). A positive correlation was found between the level of insulin and the absolute amount of butyric acid C4 (rs = 0.228, p ≤ 0.05). There was an inverse relationship of the absolute and relative amounts of isoC4+ isoC5 + isoC6 and Iso Cn/Cn with zonulin in the feces (rs = -0.231, p ≤ 0.05, rs = -0.380, p ≤ 0.05 and rs = -0.332, p ≤ 0.05, respectively).

Conclusion. There is the anaerobic flora among the patients with NAFLD. Modification of the content of SCFA in feces may affect to the progression of NAFLD. The effect of SCFA on the development and progression of NAFLD may be mediated by the development of insulin and leptin resistance, as well as an integrity violation of the intestinal barrier.

Butyrate as a potential therapeutic agent for neurodegenerative disorders

Maintaining an optimum microbial community within the gastrointestinal tract is intricately linked to human metabolic, immune and brain health. Disturbance to these microbial populations perturbs the production of vital bioactive compounds synthesised by the gut microbiome, such as short-chain fatty acids (SCFAs). Of the SCFAs, butyrate is known to be a major source of energy for colonocytes and has valuable effects on the maintenance of intestinal epithelium and blood brain barrier integrity, gut motility and transit, anti-inflammatory effects, and autophagy induction. Inducing endogenous butyrate production is likely to be beneficial for gut-brain homeostasis and for optimal neuronal function. For these reasons, butyrate has gained interest as a potential therapy for not only metabolic and immunological disorders, but also conditions related to the brain, including neurodegenerative diseases. While direct and indirect sources of butyrate, including prebiotics, probiotics, butyrate pro-drugs and glucosidase inhibitors, offer a promising therapeutic avenue, their efficacy and dosage in neurodegenerative conditions remain largely unknown. Here, we review current literature on effects of butyrate relevant to neuronal function, the impact of butyrate in a range of neurodegenerative diseases and related treatments that may have potential for the treatment of neurodegenerative diseases.

Enhancing cancer therapy: The role of drug delivery systems in STAT3 inhibitor efficacy and safety

The signal transducer and activator of transcription 3 (STAT3), a member of the STAT family, resides in the nucleus to regulate genes essential for vital cellular functions, including survival, proliferation, self-renewal, angiogenesis, and immune response. However, continuous STAT3 activation in tumor cells promotes their initiation, progression, and metastasis, rendering STAT3 pathway inhibitors a promising avenue for cancer therapy. Nonetheless, these inhibitors frequently encounter challenges such as cytotoxicity and suboptimal biocompatibility in clinical trials. A viable strategy to mitigate these issues involves delivering STAT3 inhibitors via drug delivery systems (DDSs). This review delineates the regulatory mechanisms of the STAT3 signaling pathway and its association with cancer. It offers a comprehensive overview of the current application of DDSs for anti-STAT3 inhibitors and investigates the role of DDSs in cancer treatment. The conclusion posits that DDSs for anti-STAT3 inhibitors exhibit enhanced efficacy and reduced adverse effects in tumor therapy compared to anti-STAT3 inhibitors alone. This paper aims to provide an outline of the ongoing research and future prospects of DDSs for STAT3 inhibitors. Additionally, it presents our insights on the merits and future outlook of DDSs in cancer treatment.

Butyrate increases methylglyoxal production through regulation of the JAK2/Stat3/Nrf2/Glo1 pathway in castration‑resistant prostate cancer cells

Cancer cells are characterized by increased glycolysis, known as the Warburg effect, which leads to increased production of cytotoxic methylglyoxal (MGO) and apoptotic cell death. Cancer cells often activate the protective nuclear factor erythroid 2‑related factor2 (Nrf2)/glyoxalase1 (Glo1) system to detoxify MGO. The effects of sodium butyrate (NaB), a product of gut microbiota, on Nrf2/Glos/MGO pathway and the underlying mechanisms in prostate cancer (PCa) cells were investigated in the present study. Treatment with NaB induced the cell death and reduced the proliferation of PCa cells (DU145 and LNCap). Moreover, the protein kinase RNA-like endoplasmic reticulum kinase/Nrf2/Glo1 pathway was greatly inhibited by NaB, thereby accumulating MGO-derived adduct hydroimidazolone (MG-H1). In response to a high amount of MGO, the expression of Nrf2 and Glo1 was attenuated, coinciding with an increased cellular death. NaB also markedly inhibited the Janus kinase 2 (JAK2)/Signal transducer and activator of transcription 3 (Stat3) pathway. Conversely, co‑treatment with Colivelin, a Stat3 activator, significantly reversed the effects of NaB on Glo1 expression, MG-H1 production, and the cell migration and viability. As expected, overexpression of Stat3 or Glo1 reduced NaB‑induced cell death. The activation of calcium/calmodulin dependent protein kinase II gamma and reactive oxygen species production also contributed to the anticancer effect of NaB. The present study, for the first time, demonstrated that NaB greatly increases MGO production through suppression of the JAK2/Stat3/Nrf2/Glo1 pathway in DU145 cells, a cell line mimicking castration‑resistant PCa (CRPC), suggesting that NaB may be a potential agent for PCa therapy.

Unlocking the gut-heart axis: exploring the role of gut microbiota in cardiovascular health and disease

Introduction

Gut microbiota has emerged as a pivotal player in cardiovascular health and disease, extending its influence beyond the gut through intricate metabolic processes and interactions with the immune system. Accumulating evidence supports a significant association between gut microbiota and cardiovascular diseases such as atherosclerosis, hypertension, and heart failure. Dietary patterns have been identified as key factors shaping the composition of the gut microbiota and exerting notable impacts on cardiovascular health. Probiotics and prebiotics have shown promise in mitigating the risks of cardiovascular disease by modulating key cardiovascular parameters. Faecal microbiota transplantation (FMT) has recently emerged as a novel and intriguing therapeutic strategy.

Aim

This review paper aims to explore and elucidate the multifaceted role of gut microbiota in cardiovascular health. It will also address the prevailing challenges and limitations in gut microbiota studies, emphasizing the importance of future research in overcoming these obstacles to expand our understanding of the gut-heart axis.

Materials and methods

A comprehensive literature search was conducted using various databases including ClinicalTrials, Google Scholar, PubMed, ScienceDirect, MEDLINE, and Ovid Resources. The search strategy included utilizing keywords such as "Gut microbiota," "Randomized controlled trials (RCTs)," "Gut-heart axis," "Dysbiosis," "Diet," "Probiotics," "Prebiotics," "Faecal Microbiota transplantation," "cardiovascular disease," "Meta-analyses," and other compatible terms thereof. Only articles written in English were considered, and selection criteria included relevance to the research objectives, reasonable sample sizes, and robust methodology. In addition to the identified articles, meta-analyses, animal models and studies, and references from the selected articles were also examined to ensure a comprehensive review of the literature.

Results

Dietary patterns exert a significant influence on the composition of the gut microbiota, and certain diets, such as the Mediterranean diet, have been associated with a favourable gut microbiota profile and a reduced risk of cardiovascular disease (CVD). Probiotics and prebiotics have emerged as potential interventions to mitigate CVD risks by modulating blood pressure, glycemic control, lipid profiles, and gut dysbiosis. Another innovative therapeutic approach is FMT, which involves transferring faecal material from a healthy donor to restore a balanced gut microbiota. FMT holds promise for improving cardiometabolic parameters in individuals with CVD, although further research is needed to elucidate its precise mechanisms and assess its effectiveness.

Conclusion

The gut microbiota is emerging as a potential therapeutic target for CVD prevention and management. However, current research has limitations, including the need for larger and more diverse studies, the challenges of establishing causality, and concerns regarding the long-term consequences and safety of gut microbiota modulation. Despite these limitations, understanding the gut-heart axis holds promise for the development of personalized therapies and interventions for cardiovascular health. Further research is needed to expand our knowledge and address the ethical and safety issues associated with gut microbiota modification.

Exploring the role of histone deacetylase and histone deacetylase inhibitors in the context of multiple myeloma: mechanisms, therapeutic implications, and future perspectives

Histone deacetylase inhibitors (HDACis) are a significant category of pharmaceuticals that have developed in the past two decades to treat multiple myeloma. Four drugs in this category have received approval from the U.S. Food and Drug Administration (FDA) for use: Panobinonstat (though canceled by the FDA in 2022), Vorinostat, Belinostat and Romidepsin. The efficacy of this group of drugs is attributed to the disruption of many processes involved in tumor growth through the inhibition of histone deacetylase, and this mode of action leads to significant anti-multiple myeloma (MM) activity. In MM, inhibition of histone deacetylase has many downstream consequences, including suppression of NF-κB signaling and HSP90, upregulation of cell cycle regulators (p21, p53), and downregulation of antiapoptotic proteins including Bcl-2. Furthermore, HDACis have a variety of direct and indirect oxidative effects on cellular DNA. HDAC inhibitors enhance normal immune function, thereby decreasing the proliferation of malignant plasma cells and promoting autophagy. The various biological effects of inhibiting histone deacetylase have a combined or additional impact when used alongside other chemotherapeutic and targeted drugs for multiple myeloma. This helps to decrease resistance to treatment. Combination treatment regimens that include HDACis have become an essential part of the therapy for multiple myeloma. These regimens incorporate drugs from other important classes of anti-myeloma agents, such as immunomodulatory drugs (IMiDs), conventional chemotherapy, monoclonal antibodies, and proteasome inhibitors. This review provides a comprehensive evaluation of the clinical efficacy and safety data pertaining to the currently approved histone deacetylase inhibitors, as well as an explanation of the crucial function of histone deacetylase in multiple myeloma and the characteristics of the different histone deacetylase inhibitors. Moreover, it provides a concise overview of the most recent developments in the use of histone deacetylase inhibitors for treating multiple myeloma, as well as potential future uses in treatment.

Host-gut microbiota derived secondary metabolite mediated regulation of Wnt/β-catenin pathway: a potential therapeutic axis in IBD and CRC

The intestinal tract encompasses one of the largest mucosal surfaces with a well-structured layer of intestinal epithelial cells supported by a network of underlying lamina propria immune cells maintaining barrier integrity. The commensal microflora in this environment is a major contributor to such functional outcomes due to its prominent role in the production of secondary metabolites. Of the several known metabolites of gut microbial origin, such as Short Chain Fatty Acids (SCFAs), amino acid derivatives, etc., secondary bile acids (BAs) are also shown to exhibit pleiotropic effects maintaining gut homeostasis in addition to their canonical role in dietary lipid digestion. However, dysbiosis in the intestine causes an imbalance in microbial diversity, resulting in alterations in the functionally effective concentration of these secondary metabolites, including BAs. This often leads to aberrant activation of the underlying lamina propria immune cells and associated signaling pathways, causing intestinal inflammation. Sustained activation of these signaling pathways drives unregulated cell proliferation and, when coupled with genotoxic stress, promotes tumorigenesis. Here, we aimed to discuss the role of secondary metabolites along with BAs in maintaining immune-gut homeostasis and regulation of inflammation-driven tumorigenesis with emphasis on the classical Wnt/β-Catenin signaling pathway in colon cancer.

Emerging clinical relevance of microbiome in cancer: promising biomarkers and therapeutic targets

The profound influence of microbiota in cancer initiation and progression has been under the spotlight for years, leading to numerous researches on cancer microbiome entering clinical evaluation. As promising biomarkers and therapeutic targets, the critical involvement of microbiota in cancer clinical practice has been increasingly appreciated. Here, recent progress in this field is reviewed. We describe the potential of tumor-associated microbiota as effective diagnostic and prognostic biomarkers, respectively. In addition, we highlight the relationship between microbiota and the therapeutic efficacy, toxicity, or side effects of commonly utilized treatments for cancer, including chemotherapy, radiotherapy, and immunotherapy. Given that microbial factors influence the cancer treatment outcome, we further summarize some dominating microbial interventions and discuss the hidden risks of these strategies. This review aims to provide an overview of the applications and advancements of microbes in cancer clinical relevance.

Postbiotic butyrate: role and its effects for being a potential drug and biomarker to pancreatic cancer

Postbiotics are produced by microbes and have recently gained importance in the field of oncology due to their beneficial effects to the host, effectiveness against cancer cells, and their ability to suppress inflammation. In particular, butyrate dominates over all other postbiotics both in quantity and anticancer properties. Pancreatic cancer (PC), being one of the most malignant and lethal cancers, reported a decreased 5-year survival rate in less than 10% of the patients. PC causes an increased mortality rate due to its inability to be detected at an early stage but still a promising strategy for its diagnosis has not been achieved yet. It is necessary to diagnose Pancreatic cancer before the metastatic progression stage. The available blood biomarkers lack accurate and proficient diagnostic results. Postbiotic butyrate is produced by gut microbiota such as Rhuminococcus and Faecalibacterium it is involved in cell signalling pathways, autophagy, and cell cycle regulation, and reduction in butyrate concentration is associated with the occurrence of pancreatic cancer. The postbiotic butyrate is a potential biomarker that could detect PC at an early stage, before the metastatic progression stage. Thus, this review focused on the gut microbiota butyrate's role in pancreatic cancer and the immuno-suppressive environment, its effects on histone deacetylase and other immune cells, microbes in major butyrate synthesis pathways, current biomarkers in use for Pancreatic Cancer.

Uncovering a novel mechanism: Butyrate induces estrogen receptor alpha activation independent of estrogen stimulation in MCF-7 breast cancer cells

Butyrate is a promising candidate for an antitumoral drug, as it promotes cancer cell apoptosis and reduces hormone receptor activity, while promoting differentiation and proliferation in normal cells. However, the effects of low-dose butyrate on breast cancer cell cultures are unclear. We explored the impact of sub-therapeutic doses of butyrate on estrogen receptor alpha (ERα) transcriptional activity in MCF-7 cells, using RT-qPCR, Western blot, wound-healing assays, and chromatin immunoprecipitation. Our results showed that sub-therapeutic doses of sodium butyrate (0.1 - 0.2 mM) increased the transcription of ESR1, TFF1, and CSTD genes, but did not affect ERα protein levels. Moreover, we observed an increase in cell migration in wound-healing assays. ChIP assays revealed that treatment with 0.1 mM of sodium butyrate resulted in estrogen-independent recruitment of ERα at the pS2 promoter and loss of NCoR. Appropriate therapeutic dosage of butyrate is essential to avoid potential adverse effects on patients' health, especially in the case of estrogen receptor-positive breast tumors. Sub-therapeutic doses of butyrate may induce undesirable cell processes, such as migration due to low-dose butyrate-mediated ERα activation. These findings shed light on the complex effects of butyrate in breast cancer and provide insights for research in the development of antitumoral drugs.

Carcinogenic effect of low doses of polycyclic and heterocyclic aromatic hydrocarbons and amines and lack of protection by inulin supplementation

Evidence suggests that meat processing and heat treatment may increase cancer risk through exposure to potentially carcinogenic compounds, polycyclic aromatic hydrocarbons (PAHs), and heterocyclic aromatic amines (HAAs). This study aims to investigate the effect of low concentrations of PAHs and HAAs (from 1 to 100 μmol/L/24h and 48h) in colorectal tumor cells (HT-29, HCT116, and LS174T) and to evaluate the effect of PAHs in the presence of inulin in mice. In vitro, the 4-PAHs have no effect on healthy colon cells but decreased the viability of the colorectal tumor cells and activated the mRNA and protein expressions of CYP1A1 and CYP1B1. In vivo, in mice with colitis induced by 3% DSS, the 4-PAHs (equimolar mix at 50,100, 150 mg/kg.bw, orally 3 times a week for 3 weeks) induced a loss of body weight and tumor formation. Inulin (10 g/L) had no effect on colon length and tumor formation. A significant decrease in the loss of b.w was observed in inulin group as compared to the fiber free group. These results underscore the importance of considering the biological association between low-dose exposure to 4-HAPs and diet-related colon tumors.

Impact of coexisting type 2 diabetes mellitus on the urinary microbiota of kidney stone patients

Objectives

Type 2 diabetes mellitus (T2DM) commonly complicates kidney stone disease (KSD). Our objective is to investigate the variations in the urinary microbiota between individuals with KSD alone and those with KSD plus T2DM. This exploration could have implications for disease diagnosis and treatment strategies.

Methods

During lithotripsy, a ureterscope was employed, and 1 mL of urine was collected from the renal pelvis after bladder disinfection. Sequencing targeting the V3-V4 hypervariable region was performed using the 16S rRNA and Illumina Novaseq platform.

Results

The Shannon index showed a significant decrease in the KSD plus T2DM group compared to the KSD-only group (false discovery rate = 0.041). Principal Coordinate Analysis (PCoA) demonstrated a distinct bacterial community in the KSD plus T2DM group compared to the KSD-only group (false discovery rate = 0.027). The abundance of Sphingomonas, Corynebacterium, and Lactobacillus was significantly higher in the KSD plus T2DM group than in the KSD-only group (false discovery rate < 0.05). Furthermore, Enhydrobacter, Chryseobacterium, and Allobaculum were positively correlated with fasting blood glucose and HbA1c values (P < 0.05).

Conclusions

The urinary microbiota in the renal pelvis exhibits differences between patients with KSD plus T2DM and those with KSD alone. Further studies employing animal models are necessary to validate these distinctions, potentially paving the way for therapeutic developments based on the urinary microbiota.

Short-chain fatty acids (SCFAs) from gastrointestinal disorders, metabolism, epigenetics, central nervous system to cancer - A mini-review

Short-chain fatty acids (SCFAs), generated through microbial fermentation of dietary fibers and proteins in the gut, play a pivotal role in maintaining intestinal integrity, cellular function, and the immune response. SCFAs, including butyrate, acetate, and propionate, are absorbed in the colon or excreted through feces, contributing to essential physiological processes. Butyrate, a primary energy source for colonocytes, exhibits anti-inflammatory properties and regulates key pathways, such as nuclear factor-κB (NF-κB) inhibition. SCFAs' impact extends beyond the intestines, influencing the gut-brain axis, systemic circulation, and folate metabolism. A decline in colonic SCFAs has been linked to gastrointestinal diseases, emphasizing their clinical relevance, while their effects on immune checkpoints, such as ipilimumab, provide intriguing prospects for cancer therapy. This mini-review explores SCFAs' diverse roles, shedding light on their significance in health and potential implications for disease management. Understanding SCFAs' intricate mechanisms enhances our knowledge of their therapeutic potential and highlights their emerging importance in various physiological contexts.

In Vitro Assessment of Postbiotic and Probiotic Commercial Dietary Supplements Recommended for Counteracting Intestinal Dysbiosis in Dogs

Many environmental aspects influence the preservation of a beneficial microbiome in dogs, and gut dysbiosis occurs when imbalances in the intestinal ecosystem cause functional changes in the microbial populations. The authors evaluated the effects of two specific commercial dietary supplements: a combination of a postbiotic and prebiotics (Microbiotal cane®) and a probiotic product (NBF 1®) recommended for counteracting intestinal dysbiosis in dogs, on the gut canine microbiota composition and its metabolic activities (production of short-chain fatty acids). The investigation was performed using an in vitro fermentation system inoculated with dog fecal samples. Microbiotal cane® promoted a more immediate increase in Lactobacillus spp. after the first 6 h of fermentation, whereas NBF 1® promoted the increase at the end of the process only. The two supplements supported an increase in the Bifidobacterium spp. counts only after 24 h. The in vitro abilities of Microbiotal cane® and NBF 1® to increase selectively beneficial bacterial groups producing acetic, propionic, and butyric acids suggest a possible positive effect on the canine gut microbiota, even if further in vivo studies are needed to confirm the beneficial effects on the intestinal health.

Epigenetic Modulations by Microbiome in Breast Cancer

Recent studies have identified a critical role of the diverse and dynamic microbiome in modulating various aspects of host physiology and intrinsic processes. However, the altered microbiome has also become a hallmark of cancer, which could influence the tumor microenvironment. Aberrations in epigenetic regulation of tumor suppressors, apoptotic genes, and oncogenes can accentuate breast cancer onset and progression. Interestingly, recent studies have established that the microbiota modulates the epigenetic mechanisms at global and gene-specific levels. While the mechanistic basis is unclear, the cross-talk between the microbiome and epigenetics influences breast cancer trajectory. Here, we review different epigenetic mechanisms of mammalian gene expression and summarize the host-associated microbiota distributed across the human body and their influence on cancer and other disease-related genes. Understanding this complex relationship between epigenetics and the microbiome holds promise for new insights into effective therapeutic strategies for breast cancer patients.

Effects of curcumin on non-alcoholic fatty liver disease: A scientific metrogy study

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases encountered in clinical practice. Curcumin can alleviate insulin resistance, inhibit oxidative stress response, reduce inflammation, reduce liver fat deposition, and effectively improve NAFLD through various modalities, inhibiting the progression into cirrhosis and fibrosis.

PURPOSE

To explore the current status, hot spots, and developing trends of curcumin in NAFLD treatment through quantitative scientific analysis to serve as a reference for subsequent studies.

STUDY DESIGN

A comprehensive analysis of the mechanism of action of curcumin in the treatment of NAFLD and methods to increase curcumin bioavailability using bibliometric analysis and literature review.

METHODS

This study used VOSviewer software to analyze the literature related to curcumin treatment of NAFLD in the Web of Science (WOS) core set database. A comprehensive and in-depth review was conducted based on the results of scientific econometric research and literature review.

RESULTS

The review observed that curcumin can activate various signaling pathways such as AMPK and NF-κB to inhibit oxidative stress and apoptosis, thereby reflecting its pharmacological effects: lowering lipid, anti-inflammatory, reducing insulin resistance, and anti-fibrosis. These mechanisms improve or even reverse the complex pathological features of lipid metabolism disorders associated with NAFLD. Curcumin also can potentially serve as a primary regulatory target for treating hepatic steatosis using gut microbiota. However, these pharmacological effects of curcumin were limited owing to its low bioavailability.

CONCLUSION

This review discusses NAFLD treatment with curcumin, analyzes the reasons for its low bioavailability, and introduces models for studying and methods for improving curcumin bioavailability. As research on NAFLD grows, future research should capture the trend of basic research, pay attention to clinical research, and continuously explore the therapeutic potential of curcumin.

Microbiome and pancreatic cancer: time to think about chemotherapy

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer characterized by late diagnosis, rapid progression, and a high mortality rate. Its complex biology, characterized by a dense, stromal tumor environment with an immunosuppressive milieu, contributes to resistance against standard treatments like chemotherapy and radiation. This comprehensive review explores the dynamic role of the microbiome in modulating chemotherapy efficacy and outcomes in PDAC. It delves into the microbiome's impact on drug metabolism and resistance, and the interaction between microbial elements, drugs, and human biology. We also highlight the significance of specific bacterial species and microbial enzymes in influencing drug action and the immune response in the tumor microenvironment. Cutting-edge methodologies, including artificial intelligence, low-biomass microbiome analysis and patient-derived organoid models, are discussed, offering insights into the nuanced interactions between microbes and cancer cells. The potential of microbiome-based interventions as adjuncts to conventional PDAC treatments are discussed, paving the way for personalized therapy approaches. This review synthesizes recent research to provide an in-depth understanding of how the microbiome affects chemotherapy efficacy. It focuses on elucidating key mechanisms and identifying existing knowledge gaps. Addressing these gaps is crucial for enhancing personalized medicine and refining cancer treatment strategies, ultimately improving patient outcomes.

Towards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors

The gut microbiota modulates immune processes both locally and systemically. This includes whether and how the immune system reacts to emerging tumours, whether antitumour immune responses are reactivated during treatment with immune-checkpoint inhibitors (ICIs), and whether unintended destructive immune pathologies accompany such treatment. Advances over the past decade have established that the gut microbiota is a promising target and that modulation of the microbiota might overcome resistance to ICIs and/or improve the safety of treatment. However, the specific mechanisms through which the microbiota modulates antitumour immunity remain unclear. Understanding the biology underpinning microbial associations with clinical outcomes in patients receiving ICIs, as well as the landscape of a 'healthy' microbiota would provide a critical foundation to facilitate opportunities to effectively manipulate the microbiota and thus improve patient outcomes. In this Review, we explore the role of diet and the gut microbiota in shaping immune responses during treatment with ICIs and highlight the key challenges in attempting to leverage the gut microbiome as a practical tool for the clinical management of patients with cancer.

Short-chain fatty acids in cancer pathogenesis

Cancer is a multi-step process that can be viewed as a cellular and immunological shift away from homeostasis in response to selected infectious agents, mutations, diet, and environmental carcinogens. Homeostasis, which contributes importantly to the definition of "health," is maintained, in part by the production of short-chain fatty acids (SCFAs), which are metabolites of specific gut bacteria. Alteration in the composition of gut bacteria, or dysbiosis, is often a major risk factor for some two dozen tumor types. Dysbiosis is often characterized by diminished levels of SCFAs in the stool, and the presence of a "leaky gut," permitting the penetration of microbes and microbial derived molecules (e.g., lipopolysaccharides) through the gut wall, thereby triggering chronic inflammation. SCFAs attenuate inflammation by inhibiting the activation of nuclear factor kappa B, by decreasing the expression of pro-inflammatory cytokines such as tumor necrosis factor alpha, by stimulating the expression of anti-inflammatory cytokines such as interleukin-10 and transforming growth factor beta, and by promoting the differentiation of naïve T cells into T regulatory cells, which down-regulate immune responses by immunomodulation. SCFA function epigenetically by inhibiting selected histone acetyltransferases that alter the expression of multiple genes and the activity of many signaling pathways (e.g., Wnt, Hedgehog, Hippo, and Notch) that contribute to the pathogenesis of cancer. SCFAs block cancer stem cell proliferation, thereby potentially delaying or inhibiting cancer development or relapse by targeting genes and pathways that are mutated in tumors (e.g., epidermal growth factor receptor, hepatocyte growth factor, and MET) and by promoting the expression of tumor suppressors (e.g., by up-regulating PTEN and p53). When administered properly, SCFAs have many advantages compared to probiotic bacteria and fecal transplants. In carcinogenesis, SCFAs are toxic against tumor cells but not to surrounding tissue due to differences in their metabolic fate. Multiple hallmarks of cancer are also targets of SCFAs. These data suggest that SCFAs may re-establish homeostasis without overt toxicity and either delay or prevent the development of various tumor types.

Short-chain fatty acids in diseases

Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fibre in the gastrointestinal tract. The absorption of SCFAs is mediated by substrate transporters, such as monocarboxylate transporter 1 and sodium-coupled monocarboxylate transporter 1, which promote cellular metabolism. An increasing number of studies have implicated metabolites produced by microorganisms as crucial executors of diet-based microbial influence on the host. SCFAs are important fuels for intestinal epithelial cells (IECs) and represent a major carbon flux from the diet, that is decomposed by the gut microbiota. SCFAs play a vital role in multiple molecular biological processes, such as promoting the secretion of glucagon-like peptide-1 by IECs to inhibit the elevation of blood glucose, increasing the expression of G protein-coupled receptors such as GPR41 and GPR43, and inhibiting histone deacetylases, which participate in the regulation of the proliferation, differentiation, and function of IECs. SCFAs affect intestinal motility, barrier function, and host metabolism. Furthermore, SCFAs play important regulatory roles in local, intermediate, and peripheral metabolisms. Acetate, propionate, and butyrate are the major SCFAs, they are involved in the regulation of immunity, apoptosis, inflammation, and lipid metabolism. Herein, we review the diverse functional roles of this major class of bacterial metabolites and reflect on their ability to affect intestine, metabolic, and other diseases. Video Abstract.

Probiotic-Derived Bioactive Compounds in Colorectal Cancer Treatment

Colorectal cancer (CRC) is a multifactorial disease with increased morbidity and mortality rates globally. Despite advanced chemotherapeutic approaches for the treatment of CRC, low survival rates due to the regular occurrence of drug resistance and deleterious side effects render the need for alternative anticancer agents imperative. Accumulating evidence supports that gut microbiota imbalance precedes the establishment of carcinogenesis, subsequently contributing to cancer progression and response to anticancer therapy. Manipulation of the gut microbiota composition via the administration of probiotic-derived bioactive compounds has gradually attained the interest of scientific communities as a novel therapeutic strategy for CRC. These compounds encompass miscellaneous metabolic secreted products of probiotics, including bacteriocins, short-chain fatty acids (SCFAs), lactate, exopolysaccharides (EPSs), biosurfactants, and bacterial peptides, with profound anti-inflammatory and antiproliferative properties. This review provides a classification of postbiotic types and a comprehensive summary of the current state of research on their biological role against CRC. It also describes how their intricate interaction with the gut microbiota regulates the proper function of the intestinal barrier, thus eliminating gut dysbiosis and CRC development. Finally, it discusses the future perspectives in precision-medicine approaches as well as the challenges of their synthesis and optimization of administration in clinical studies.

Potential role of gut microbes in the efficacy and toxicity of immune checkpoints inhibitors

In recent years, Immune checkpoint inhibitors have been extensively used in the treatment of a variety of cancers. However, the response rates ranging from 13% to 69% depending on the tumor type and the emergence of immune-related adverse events have posed significant challenges for clinical treatment. As a key environmental factor, gut microbes have a variety of important physiological functions such as regulating intestinal nutrient metabolism, promoting intestinal mucosal renewal, and maintaining intestinal mucosal immune activity. A growing number of studies have revealed that gut microbes further influence the anticancer effects of tumor patients through modulation of the efficacy and toxicity of immune checkpoint inhibitors. Currently, faecal microbiota transplantation (FMT) have been developed relatively mature and suggested as an important regulator in order to enhance the efficacy of treatment. This review is dedicated to exploring the impact of differences in flora composition on the efficacy and toxicity of immune checkpoint inhibitors as well as to summarizing the current progress of FMT.

Epigenetic effects of short-chain fatty acids from the large intestine on host cells

Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.

Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens

Objective

This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens.

Methods

The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools.

Results

Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion.

Conclusion

Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.

Changes in the chemical compositions and biological properties of kombucha beverages made from black teas and pineapple peels and cores

Several raw materials have been used as partial supplements or entire replacements for the main ingredients of kombucha to improve the biological properties of the resulting kombucha beverage. This study used pineapple peels and cores (PPC), byproducts of pineapple processing, as alternative raw materials instead of sugar for kombucha production. Kombuchas were produced from fusions of black tea and PPC at different ratios, and their chemical profiles and biological properties, including antioxidant and antimicrobial activities, were determined and compared with the control kombucha without PPC supplementation. The results showed that PPC contained high amounts of beneficial substances, including sugars, polyphenols, organic acids, vitamins, and minerals. An analysis of the microbial community in a kombucha SCOBY (Symbiotic Cultures of Bacteria and Yeasts) using next-generation sequencing revealed that Acetobacter and Komagataeibacter were the most predominant acetic acid bacteria. Furthermore, Dekkera and Bacillus were also the prominent yeast and bacteria in the kombucha SCOBY. A comparative analysis was performed for kombucha products fermented using black tea and a fusion of black tea and PPC, and the results revealed that the kombucha made from the black tea and PPC infusion exhibited a higher total phenolic content and antioxidant activity than the control kombucha. The antimicrobial properties of the kombucha products made from black tea and the PPC infusion were also greater than those of the control. Several volatile compounds that contributed to the flavor, aroma, and beneficial health properties, such as esters, carboxylic acids, phenols, alcohols, aldehydes, and ketones, were detected in kombucha products made from a fusion of black tea and PPC. This study shows that PPC exhibits high potential as a supplement to the raw material infusion used with black tea for functional kombucha production.

β-glucans: a potential source for maintaining gut microbiota and the immune system

The human gastrointestinal (GI) tract holds a complex and dynamic population of microbial communities, which exerts a marked influence on the host physiology during homeostasis and disease conditions. Diet is considered one of the main factors in structuring the gut microbiota across a lifespan. Intestinal microbial communities play a vital role in sustaining immune and metabolic homeostasis as well as protecting against pathogens. The negatively altered gut bacterial composition has related to many inflammatory diseases and infections. β-glucans are a heterogeneous assemblage of glucose polymers with a typical structure comprising a leading chain of β-(1,4) and/or β-(1,3)-glucopyranosyl units with various branches and lengths as a side chain. β-glucans bind to specific receptors on immune cells and initiate immune responses. However, β-glucans from different sources differ in their structures, conformation, physical properties, and binding affinity to receptors. How these properties modulate biological functions in terms of molecular mechanisms is not known in many examples. This review provides a critical understanding of the structures of β-glucans and their functions for modulating the gut microbiota and immune system.

Roles of Histone Acetyltransferases and Deacetylases in the Retinal Development and Diseases

The critical role of epigenetic modification of histones in maintaining the normal function of the nervous system has attracted increasing attention. Among these modifications, the level of histone acetylation, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is essential in regulating gene expression. In recent years, the research progress on the function of HDACs in retinal development and disease has advanced remarkably, while that regarding HATs remains to be investigated. Here, we overview the roles of HATs and HDACs in regulating the development of diverse retinal cells, including retinal progenitor cells, photoreceptor cells, bipolar cells, ganglion cells, and Müller glial cells. The effects of HATs and HDACs on the progression of various retinal diseases are also discussed with the highlight of the proof-of-concept research regarding the application of available HDAC inhibitors in treating retinal diseases.

Benchmarking of microbiome detection tools on RNA-seq synthetic databases according to diverse conditions

Motivation

Here, we performed a benchmarking analysis of five tools for microbe sequence detection using transcriptomics data (Kraken2, MetaPhlAn2, PathSeq, DRAC and Pandora). We built a synthetic database mimicking real-world structure with tuned conditions accounting for microbe species prevalence, base calling quality and sequence length. Sensitivity and positive predictive value (PPV) parameters, as well as computational requirements, were used for tool ranking.

Results

GATK PathSeq showed the highest sensitivity on average and across all scenarios considered. However, the main drawback of this tool was its slowness. Kraken2 was the fastest tool and displayed the second-best sensitivity, though with large variance depending on the species to be classified. There was no significant difference for the other three algorithms sensitivity. The sensitivity of MetaPhlAn2 and Pandora was affected by sequence number and DRAC by sequence quality and length. Results from this study support the use of Kraken2 for routine microbiome profiling based on its competitive sensitivity and runtime performance. Nonetheless, we strongly endorse to complement it by combining with MetaPhlAn2 for thorough taxonomic analyses.

Availability and implementation

https://github.com/fjuradorueda/MIME/ and https://github.com/lola4/DRAC/.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Design of the Building Research in CRC prevention (BRIDGE-CRC) trial: a 6-month, parallel group Mediterranean diet and weight loss randomized controlled lifestyle intervention targeting the bile acid-gut microbiome axis to reduce colorectal cancer risk among African American/Black adults with obesity

BACKGROUND

Among all racial/ethnic groups, people who identify as African American/Blacks have the second highest colorectal cancer (CRC) incidence in the USA. This disparity may exist because African American/Blacks, compared to other racial/ethnic groups, have a higher prevalence of risk factors for CRC, including obesity, low fiber consumption, and higher intakes of fat and animal protein. One unexplored, underlying mechanism of this relationship is the bile acid-gut microbiome axis. High saturated fat, low fiber diets, and obesity lead to increases in tumor promoting secondary bile acids. Diets high in fiber, such as a Mediterranean diet, and intentional weight loss may reduce CRC risk by modulating the bile acid-gut microbiome axis. The purpose of this study is to test the impact of a Mediterranean diet alone, weight loss alone, or both, compared to typical diet controls on the bile acid-gut microbiome axis and CRC risk factors among African American/Blacks with obesity. Because weight loss or a Mediterranean diet alone can reduce CRC risk, we hypothesize that weight loss plus a Mediterranean diet will reduce CRC risk the most.

METHODS

This randomized controlled lifestyle intervention will randomize 192 African American/Blacks with obesity, aged 45-75 years to one of four arms: Mediterranean diet, weight loss, weight loss plus Mediterranean diet, or typical diet controls, for 6 months (48 per arm). Data will be collected at baseline, mid-study, and study end. Primary outcomes include total circulating and fecal bile acids, taurine-conjugated bile acids, and deoxycholic acid. Secondary outcomes include body weight, body composition, dietary change, physical activity, metabolic risk, circulating cytokines, gut microbial community structure and composition, fecal short-chain fatty acids, and expression levels of genes from exfoliated intestinal cells linked to carcinogenesis.

DISCUSSION

This study will be the first randomized controlled trial to examine the effects of a Mediterranean diet, weight loss, or both on bile acid metabolism, the gut microbiome, and intestinal epithelial genes associated with carcinogenesis. This approach to CRC risk reduction may be especially important among African American/Blacks given their higher risk factor profile and increased CRC incidence.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04753359 . Registered on 15 February 2021.

Butyrate: More Than a Short Chain Fatty Acid

PURPOSE OF REVIEW

The mechanistic understanding of the importance and the potential benefits of the gut microbiome has exploded in potential roles in human health and disease. Short chain fatty acids (SCFAs), including butyrate, are one of the key metabolic end products that has been a major focus of microbiome understanding. This brief review aims to describe butyrate's relation to certain biological concepts and their clinical application.

RECENT FINDINGS

Butyrate has reportedly been described as a potent pro-resolution molecule that has a significant role in maintaining gut immunity, supporting gut barrier function, regulation of histone deacetylase (HDAC), and numerous systemic roles. Further research is needed to explore potential benefits of adding SCFAs for patients receiving total parenteral nutrition. Butyrate plays several biological roles in intestinal epithelium anti-inflammatory pathways with clear benefits in numerous acute and chronic disease states and overall human health helping to maintain homeostasis.

Effects of electroacupuncture on urinary metabolome and microbiota in presenilin1/2 conditional double knockout mice

Aim

The treatment of Alzheimer's disease (AD) is still a worldwide problem due to the unclear pathogenesis and lack of effective therapeutic targets. In recent years, metabolomic and gut microbiome changes in patients with AD have received increasing attention, and the microbiome-gut-brain (MGB) axis has been proposed as a new hypothesis for its etiology. Considering that electroacupuncture (EA) efficiently moderates cognitive deficits in AD and its mechanisms remain poorly understood, especially regarding its effects on the gut microbiota, we performed urinary metabolomic and microbial community profiling on EA-treated AD model mice, presenilin 1/2 conditional double knockout (PS cDKO) mice, to observe the effect of EA treatment on the gut microbiota in AD and find the connection between affected gut microbiota and metabolites.

Materials and methods

After 30 days of EA treatment, the recognition memory ability of PS cDKO mice was evaluated by the Y maze and the novel object recognition task. Urinary metabolomic profiling was conducted with the untargeted GC-MS method, and 16S rRNA sequence analysis was applied to analyze the microbial community. In addition, the association between differential urinary metabolites and gut microbiota was clarified by Spearman's correlation coefficient analysis.

Key findings

In addition to reversed cognitive deficits, the urinary metabolome and gut microbiota of PS cDKO mice were altered as a result of EA treatment. Notably, the increased level of isovalerylglycine and the decreased levels of glycine and threonic acid in the urine of PS cDKO mice were reversed by EA treatment, which is involved in glyoxylate and dicarboxylate metabolism, as well as glycine, serine, and threonine metabolism. In addition to significantly enhancing the diversity and richness of the microbial community, EA treatment significantly increased the abundance of the genus Mucispirillum, while displaying no remarkable effect on the other major altered gut microbiota in PS cDKO mice, norank_f_Muribaculaceae, Lactobacillus, and Lachnospiraceae_NK4A136 group. There was a significant correlation between differential urinary metabolites and differential gut microbiota.

Significance

Electroacupuncture alleviates cognitive deficits in AD by modulating gut microbiota and metabolites. Mucispirillum might play an important role in the underlying mechanism of EA treatment. Our study provides a reference for future treatment of AD from the MGB axis.

Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors

The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.

Targeted PEGylated Chitosan Nano-complex for Delivery of Sodium Butyrate to Prostate Cancer: An In Vitro Study

Introduction: Cancer remains a challenging issue against human health throughout the world; As a result, introducing novel approaches would be beneficial for cancer treatment. In this research, sodium butyrate (Sb) is one of the effective anti-cancer therapeutics (also a potent survival factor for normal cells) that was used for prostate cancer suppression in the platform of modified chitosan (CS) nano-complex (polyethylene glycol (PEG)-folic acid (FA)-Sb-CS). Methods: Different analytical devices including Fourier transform infrared, dynamic light scattering, high-performance liquid chromatography, scanning electron microscopy, and transmission electron microscopy were applied for the characterization of synthetics. On the other hand, biomedical tests including cell viability assay, molecular and functional assay of apoptosis/autophagy pathways, and cell cycle arrest analysis were potentially implemented on human PC3 (folate receptor-negative prostate cancer) and DU145 (folate receptor-positive prostate cancer) and HFF-1 normal cell lines. Results: The quality of the syntheses was effectively verified, and the size range from 140 to 170 nm was determined for the PEG-CS-FA-Sb sample. Also, 75  ±  5% of drug entrapment efficiency with controlled drug release manner (Sb release of 54.21% and 74.04% for pHs 7.4 and 5.0) were determined for nano-complex. Based on MTT results, PEG-CS-FA-Sb has indicated 72.07% and 33.53% cell viability after 24 h of treatment with 9 mM on PC3 and DU145 cell lines, respectively, which is desirable anti-cancer performance. The apoptotic and autophagy genes overexpression was 15-fold (caspase9), 2.5-fold (BAX), 11-fold (ATG5), 2-fold (BECLIN1), and 3-fold (mTORC1) genes in DU145 cancer cells. More than 50% of cell cycle arrest and 45.05% of apoptosis were obtained for DU145 cancer cells after treatment with nano-complex. Conclusion: Hence, the synthesized Sb-loaded nano-complex could specifically suppress prostate cancer cell growth and induce apoptosis and autophagy in the molecular and cellular phases.

Bacteroides fragilis strain ZY-312 promotes intestinal barrier integrity via upregulating the STAT3 pathway in a radiation-induced intestinal injury mouse model

Radiation-induced intestinal injury is characterized by intestinal barrier impairment. However, the therapeutic effects of probiotics for intestinal epithelial barrier repair in a mouse model of radiation-induced intestinal injury remain unclear. Previously, we isolated a strain of Bacteroides fragilis from the feces of a healthy infant and named it as B. fragilis strain ZY-312 (B. fragilis). In this study, we showed that B. fragilis can ameliorate radiation-induced intestinal injury in mice, manifested by decreased weight loss, intestinal length shortening, and intestinal epithelial cell (IEC) shedding. Moreover, we found that B. fragilis promoted IEC proliferation, stem cell regeneration, mucus secretion, and tight junction integrity by upregulating the STAT3 signaling pathway, through an experimental verification in Stat3 ^△IEC mice (STAT3 defects in intestinal epithelial cells). Thus, the underlying protective mechanism of B. fragilis in radiation-induced intestinal injury is related to IEC proliferation, stem cell regeneration, goblet cell secretion, and tight junction repair via activation of the STAT3 signaling pathway. In addition, the therapeutic effects of B. fragilis were studied to provide new insights into its application as a functional and clinical drug for radiation-induced intestinal injury after radiotherapy.

Characterization of Short Chain Fatty Acids Produced by Selected Potential Probiotic Lactobacillus Strains

Short-chain fatty acids (SCFAs), particularly butyrate, have received considerable attention with regard to their anti-cancer efficacy in delaying or preventing colorectal cancer. Several studies have reported that certain probiotic strains could produce SCFAs; however, different strains yielded different amounts of SCFAs. This study explored the ability to produce SCFAs of the following probiotic strains: Lacticaseibacillus paracasei SD1, Lacticaseibacillus rhamnosus SD4, Lacticaseibacillus rhamnosus SD11, and Lacticaseibacillus rhamnosus GG. L. paracasei SD1 and L. rhamnosus SD11 exhibited high butyrate production, particularly when the strains were combined. The functions of the SCFAs were further characterized; the SCFAs exerted a positive anti-cancer effect in the colon via various actions, including inhibiting the growth of the pathogens related to colon cancer, such as Fusobacterium nucleatum and Porphyromonas gingivalis; suppressing the growth of cancer cells; and stimulating the production of the anti-inflammatory cytokine IL-10 and antimicrobial peptides, especially human β-defensin-2. In addition, the SCFAs suppressed pathogen-stimulated pro-inflammatory cytokines, especially IL-8. The results of this study indicated that selected probiotic strains, particularly L. paracasei SD1 in combination with L. rhamnosus SD11, may serve as good natural sources of bio-butyrate, which may be used as biotherapy for preventing or delaying the progression of colon cancer.

Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients

BACKGROUND

Several studies suggest a role of gut microbiota in colorectal cancer (CRC) initiation and progression. Vitamin D (vitD) blood levels are also inversely correlated with CRC risk and prognosis. However, these factors' interplay remains unknown.

METHODS

74 CRC patients after standard treatment were randomized to 1-year 2000 IU/day vitD or placebo.  Baseline and post-treatment fecal microbiota for shotgun metagenomics sequencing was collected. Coda-lasso and Principal Component Analysis were used to select and summarize treatment-associated taxa and pathways. Associations between vitD and taxa/pathways were investigated with logistic regression. Mediation analysis was performed to study if treatment-associated taxa mediated the effect of supplementation on 25(OH)D levels. Cox proportional-hazards model was used for disease-free survival (DFS).

RESULTS

60 patients were analyzed. Change in alpha diversity (Shannon: p = 0.77; Simpson: p = 0.63) and post-treatment beta diversity (p = 0.70) were comparable between arms. Post-treatment abundances of 63 taxa and 32 pathways differed between arms. The 63 taxa also mediated the effect of supplementation on 25(OH)D (p = 0.02). There were sex differences in vitD levels, microbiota and pathways. Pathways of essential amino acids' biosynthesis were more abundant in supplemented women. Fusobacterium nucleatum presence at baseline was associated with worse DFS (p = 0.02). Those achieving vitD sufficiency (25(OH)D≥30 ng/ml) had lower post-treatment abundances (p = 0.05). Women were more likely to have F. nucleatum post-treatment (p = 0.02).

CONCLUSIONS

VitD supplementation may contribute shaping the gut microbiota and the microbiota may partially mediate the effect of supplementation on 25(OH)D. The observed sex-specific differences highlight the necessity of including sex/gender as a variable in microbiome studies.

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.

Microbial-Derived Tryptophan Catabolites, Kidney Disease and Gut Inflammation

Uremic metabolites, molecules either produced by the host or from the microbiota population existing in the gastrointestinal tract that gets excreted by the kidneys into urine, have significant effects on both health and disease. Tryptophan-derived catabolites are an important group of bacteria-produced metabolites with an extensive contribution to intestinal health and, eventually, chronic kidney disease (CKD) progression. The end-metabolite, indoxyl sulfate, is a key contributor to the exacerbation of CKD via the induction of an inflammatory state and oxidative stress affecting various organ systems. Contrastingly, other tryptophan catabolites positively contribute to maintaining intestinal homeostasis and preventing intestinal inflammation—activities signaled through nuclear receptors in particular—the aryl hydrocarbon receptor (AhR) and the pregnane X receptor (PXR). This review discusses the origins of these catabolites, their effect on organ systems, and how these can be manipulated therapeutically in the future as a strategy to treat CKD progression and gut inflammation management. Furthermore, the use of biotics (prebiotics, probiotics, synbiotics) as a means to increase the presence of beneficial short-chain fatty acids (SCFAs) to achieve intestinal homeostasis is discussed.

Gut Metabolites and Breast Cancer: The Continuum of Dysbiosis, Breast Cancer Risk, and Potential Breast Cancer Therapy

The complex association between the gut microbiome and cancer development has been an emerging field of study in recent years. The gut microbiome plays a crucial role in the overall maintenance of human health and interacts closely with the host immune system to prevent and fight infection. This review was designed to draw a comprehensive assessment and summary of recent research assessing the anticancer activity of the metabolites (produced by the gut microbiota) specifically against breast cancer. In this review, a total of 2701 articles were screened from different scientific databases (PubMed, Scopus, Embase and Web of Science) with 72 relevant articles included based on the predetermined inclusion and exclusion criteria. Metabolites produced by the gut microbial communities have been researched for their health benefits and potential anticancer activity. For instance, the short-chain fatty acid, butyrate, has been evaluated against multiple cancer types, including breast cancer, and has demonstrated anticancer potential via various molecular pathways. Similarly, nisin, a bacteriocin, has presented with a range of anticancer properties primarily against gastrointestinal cancers, with nominal evidence supporting its use against breast cancer. Comparatively, a natural purine nucleoside, inosine, though it has not been thoroughly investigated as a natural anticancer agent, has shown promise in recent studies. Additionally, recent studies demonstrated that gut microbial metabolites influence the efficacy of standard chemotherapeutics and potentially be implemented as a combination therapy. Despite the promising evidence supporting the anticancer action of gut metabolites on different cancer types, the molecular mechanisms of action of this activity are not well established, especially against breast cancer and warrant further investigation. As such, future research must prioritise determining the dose-response relationship, molecular mechanisms, and conducting animal and clinical studies to validate in vitro findings. This review also highlights the potential future directions of this field.

The Role of Gut Microbiota in Some Liver Diseases: From an Immunological Perspective

Gut microbiota is a microecosystem composed of various microorganisms. It plays an important role in human metabolism, and its metabolites affect different tissues and organs. Intestinal flora maintains the intestinal mucosal barrier and interacts with the immune system. The liver is closely linked to the intestine by the gut-liver axis. As the first organ that comes into contact with blood from the intestine, the liver will be deeply influenced by the gut microbiota and its metabolites, and the intestinal leakage and the imbalance of the flora are the trigger of the pathological reaction of the liver. In this paper, we discuss the role of gut microbiota and its metabolites in the pathogenesis and development of autoimmune liver diseases((including autoimmune hepatitis, primary biliary cirrhosis, primary sclerosing cholangitis), metabolic liver disease such as non-alcoholic fatty liver disease, cirrhosisits and its complications, and liver cancer from the perspective of immune mechanism. And the recent progress in the treatment of these diseases was reviewed from the perspective of gut microbiota.