Sphingomonas and Phenylobacterium as Major Microbiota in Thymic Epithelial Tumors

A systematic and comprehensive review of the role of microbiota in urinary chronic pelvic pain syndrome

BACKGROUND

Many genitourinary tract disorders could be attributed partly to the microbiota. This study sought to conduct a systematic review of the role of the microbiota in urinary chronic pelvic pain syndrome (UCPPS).

METHODS

We searched Embase, Scopus, Web of Science, and PubMed with no time, language, or study type restrictions until December 1, 2023. The JBI Appraisal Tool was used to assess the quality of the studies. Study selection followed the PRISMA statement. Studies addressing microbiome variations among patients suffering from interstitial cystitis/bladder pain syndrome (IC/BPS) or chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and a control group were considered eligible.

RESULTS

A total of 21 studies (1 UCPPS, 12 IC/BPS, and 8 CP/CPPS) comprising 1125 patients were enrolled in our final data synthesis. It has been shown that the reduced diversity and discrepant composition of the gut microbiota may partly be attributed to the UCPPS pathogenesis. In terms of urine microbiota, some operational taxonomic units were shown to be elevated, while others became less abundant. Furthermore, various bacteria and fungi are linked to specific clinical features. Few investigations denied UCPPS as a dysbiotic condition.

CONCLUSIONS

Urinary and intestinal microbiota appear to be linked with UCPPS, comprising IC/BPS and CP/CPPS. However, given the substantial disparity of published studies, a battery of prospective trials is required to corroborate these findings.

Intestinal microbiota and gene expression alterations in leopard coral grouper (Plectropomus leopardus) under enteritis

Enteritis poses a significant threat to fish farming, characterized by symptoms of intestinal and hepatic inflammation, physiological dysfunction, and dysbiosis. Focused on the leopard coral grouper (Plectropomus leopardus) with an enteritis outbreak on a South China Sea farm, our prior scrutiny did not find any abnormalities in feeding or conventional water quality factors, nor were any specific pathogen infections related to enteritis identified. This study further elucidates their intestinal flora alterations, host responses, and their interactions to uncover the underlying pathogenetic mechanisms and facilitate effective prevention and management strategies. Enteritis-affected fish exhibited substantial differences in intestinal flora compared to control fish (P = 0.001). Notably, norank_f_Alcaligenaceae, which has a negative impact on fish health, predominated in enteritis-affected fish (91.76 %), while the probiotic genus Lactococcus dominated in controls (93.90 %). Additionally, certain genera with pathogenesis potentials like Achromobacter, Sphingomonas, and Streptococcus were more abundant in diseased fish, whereas Enterococcus and Clostridium_sensu_stricto with probiotic potentials were enriched in control fish. At the transcriptomic level, strong inflammatory responses, accompanied by impaired metabolic functions, tissue damage, and iron death signaling activation were observed in the intestines and liver during enteritis. Furthermore, correlation analysis highlighted that potential pathogen groups were positively associated with inflammation and tissue damage genes while presenting negatively correlated with metabolic function-related genes. In conclusion, dysbiosis in the intestinal microbiome, particularly an aberrantly high abundance of Alcaligenaceae with pathogenic potential may be the main trigger for this enteritis outbreak. Alcaligenaceae alongside Achromobacter, Sphingomonas, and Streptococcus emerged as biomarkers for enteritis, whereas some species of Lactococcus, Clostridium_sensu_stricto, and Enterococcus showed promise as probiotics to alleviate enteritis symptoms. These findings enhance our understanding of enteritis pathogenesis, highlight intestinal microbiota shifts in leopard coral grouper, and propose biomarkers for monitoring, probiotic selection, and enteritis management.

Glycolysis characteristics of intracellular polysaccharides from Agaricus bitorquis (Quél.) sacc. Chaidam and its effects on intestinal flora from different altitudes of mice in vitro fermentation

The glycolysis characteristics and effects on intestinal flora of polysaccharides from Agaricus bitorquis (Quél.) Sacc. Chaidam (ABIPs) in vitro fermentation by different altitudes of mice feces was examined, including low, medium, and high altitudes groups (LG, MG, and HG). In vitro, fermentation of ABIPs forty-eight hours resulted in a remarkable decrease in total sugar content and improvement of short-chain fatty acids (SCFAs) (mainly acetate, propionate, and butyrate), which simultaneously induced the composition of monose and uronic acids and SCFAs continuously change. Besides, ABIPs influenced the abundance and composition of the intestinal flora, generally increasing the abundance of probiotic bacteria (such as Bifidobacterium and Faecalibacterium) and decreasing the abundance of harmful bacteria (such as Phenylobacterium and Streptococcus) in all groups, with the highland biology core genus Blautia significantly enriched in LG and MG groups. It was also found that ABIPs enhanced pathways associated with biosynthesis and metabolism. In addition, correlation analysis speculated that the metabolism of SCFAs by ABIPs may be associated with genera such as Anaerostipes, Roseburia, and Weissella. ABIPs may protect organismal health by regulating hypoxic intestinal flora composition and metabolic function, and more superior fermentation performance was observed in MG compared to other groups.

Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers

INTRODUCTION

Tumor-associated bacteria and gut microbiota have gained significant attention in recent years due to their potential role in cancer development and therapeutic response. This review aims to discuss the contributions of intratumor bacteria outside the gastrointestinal tract, in addition to exploring the mechanisms, functions, and implications of these bacteria in cancer therapy.

METHODS

We reviewed current literature on intratumor bacteria and their impact on tumorigenesis, progression, metastasis, drug resistance, and anti-tumor immune modulation. Additionally, we examined techniques used to detect intratumor bacteria, precautions necessary when handling low microbial biomass tumor samples, and the recent progress in bacterial manipulation for tumor treatment.

RESULTS

Research indicates that each type of cancer uniquely interacts with its microbiome, and bacteria can be detected even in non-gastrointestinal tumors with low bacterial abundance. Intracellular bacteria have the potential to regulate tumor cells' biological behavior and contribute to critical aspects of tumor development. Furthermore, bacterial-based anti-tumor therapies have shown promising results in cancer treatment.

CONCLUSIONS

Understanding the complex interactions between intratumor bacteria and tumor cells could lead to the development of more precise cancer treatment strategies. Further research into non-gastrointestinal tumor-associated bacteria is needed to identify new therapeutic approaches and expand our knowledge of the microbiota's role in cancer biology.

Integrated microbiome and metabolome analysis reveals novel urinary microenvironmental signatures in interstitial cystitis/bladder pain syndrome patients

BACKGROUND

The pathogenesis of interstitial cystitis/bladder pain syndrome (IC/BPS) has not been elucidated, but urinary microorganisms and metabolites have been shown to be closely associated with the inflammatory response of IC/BPS. Nevertheless, the exact mechanisms related to this response have not been clarified.

METHODS

16S rRNA sequencing and untargeted metabolomics techniques were used to analyse the urinary microbial and metabolite profiles of 30 IC/BPS patients and 30 healthy controls, and correlation analyses were performed to explore the mechanisms by which they might be involved in the inflammatory response of IC/BPS.

RESULTS

Twenty-eight differential genera, such as Lactobacillus and Sphingomonas, were identified. A total of 44 differential metabolites such as 1,3,7-trimethyluric acid and theophylline were screened. The abundance of Lactobacillus and Escherichia-Shigella was significantly higher in the urine of female IC/BPS patients and healthy controls compared to males, while Bacteroides and Acinetobacter were lower than in males. The results of the Pearson correlation analysis suggested that differential microorganisms may influence the composition of metabolites. The Lactobacillus genus may be a protective bacterium against IC/BPS, whereas Sphingomonas may be a pathogenic factor. The differential metabolite theophylline, as an anti-inflammatory substance, may downregulate the inflammatory response of IC/BPS.

CONCLUSIONS

This study revealed microbial and metabolite profiles in the urine of IC/BPS patients versus healthy controls in both males and females. We also found some microorganisms and metabolites closely related to the inflammatory response of IC/BPS, which provided directions for future aetiological and therapeutic research.

Global Meta-analysis of Urine Microbiome: Colonization of Polycyclic Aromatic Hydrocarbon-degrading Bacteria Among Bladder Cancer Patients

BACKGROUND

The application of next-generation sequencing techniques has enabled characterization of urinary tract microbiome. Although many studies have demonstrated associations between the human microbiome and bladder cancer (BC), these have not always reported consistent results, thereby necessitating cross-study comparisons. Thus, the fundamental questions remain how we can utilize this knowledge.

OBJECTIVE

The aim of our study was to examine the disease-associated changes in urine microbiome communities globally utilizing a machine learning algorithm.

DESIGN, SETTING, AND PARTICIPANTS

Raw FASTQ files were downloaded for the three published studies in urinary microbiome in BC patients, in addition to our own prospectively collected cohort.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Demultiplexing and classification were performed using the QIIME 2020.8 platform. De novo operational taxonomic units were clustered using the uCLUST algorithm and defined by 97% sequence similarity and classified at the phylum level against the Silva RNA sequence database. The metadata available from the three studies included were used to evaluate the differential abundance between BC patients and controls via a random-effect meta-analysis using the metagen R function. A machine learning analysis was performed using the SIAMCAT R package.

RESULTS AND LIMITATIONS

Our study includes 129 BC urine and 60 healthy control samples across four different countries. We identified a total of 97/548 genera to be differentially abundant in the BC urine microbiome compared with that of healthy patients. Overall, while the differences in diversity metrics were clustered around the country of origin (Kruskal-Wallis, p < 0.001), collection methodology was a driver of microbiome composition. When assessing dataset from China, Hungary, and Croatia, data demonstrated no discrimination capacity to distinguish between BC patients and healthy adults (area under the curve [AUC] 0.577). However, inclusion of samples with catheterized urine improved the diagnostic accuracy of prediction for BC to AUC 0.995, with precision-recall AUC = 0.994. Through elimination of contaminants associated with the collection methodology among all cohorts, our study identified increased abundance of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria Sphingomonas, Acinetobacter, Micrococcus, Pseudomonas, and Ralstonia to be consistently present in BC patients.

CONCLUSIONS

The microbiota of the BC population may be a reflection of PAH exposure from smoking, environmental pollutants, and ingestion. Presence of PAHs in the urine of BC patients may allow for a unique metabolic niche and provide necessary metabolic resources where other bacteria are not able to flourish. Furthermore, we found that while compositional differences are associated with geography more than with disease, many are driven by the collection methodology.

PATIENT SUMMARY

The goal of our study was to compare the urine microbiome of bladder cancer patients with that of healthy controls and evaluate any potential bacteria that may be more likely to be found in patients with bladder cancer. Our study is unique as it evaluates this across multiple countries, to find a common pattern. After we removed some of the contamination, we were able to localize several key bacteria that are more likely to be found in the urine of bladder cancer patients. These bacteria all share their ability to break down tobacco carcinogens.

Investigation of putative roles of smoking-associated salivary microbiome alterations on carcinogenesis by integrative in silico analysis

Growing evidence suggests that cigarette smoking alters the salivary microbiome composition and affects the risk of various complex diseases including cancer. However, the potential role of the smoking-associated microbiome in cancer development remains unexplained. Here, the putative roles of smoking-related microbiome alterations in carcinogenesis were investigated by in silico analysis and suggested evidence can be further explored by experimental methodologies. The Disbiome database was used to extract smoking-associated microbial taxa in saliva and taxon set enrichment analysis (TSEA) was conducted to identify the gene sets associated with extracted microbial taxa. We further analyzed the expression profiles of identified genes by using RNA-sequencing data from TCGA and GTEx projects. Associations of the genes with smoking-related phenotypes in cancer datasets were analyzed to prioritize genes for their interplay between smoking-related microbiome and carcinogenesis. Thirty-eight microbial taxa associated with smoking were included in the TSEA and this revealed sixteen genes that were significantly associated with smoking-associated microbial taxa. All genes were found to be differentially expressed in at least one cancer dataset, yet the ELF3 and CTSH were the most common differentially expressed genes giving significant results for several cancer types. Moreover, C2CD3, CTSH, DSC3, ELF3, RHOT2, and WSB2 showed statistically significant associations with smoking-related phenotypes in cancer datasets. This study provides in silico evidence for the potential roles of the salivary microbiome on carcinogenesis. The results shed light on the importance of smoking cessation strategies for cancer management and interventions to stratify smokers for their risk of smoking-induced carcinogenesis.

The Microbiome Revolution: New Insights for Personalized Medicine

The availability of new culture-independent techniques to study microbes led to the explosion of the gut microbiota revolution in recent decades [...]

The Diagnostic Utility of Cell-Free DNA from Ex Vivo Bronchoalveolar Lavage Fluid in Lung Cancer

Simple Summary

This study aims to detect cell-free DNA released from lung cancer cells into the airway using the ex vivo BAL model of our own establishing. We finally demonstrated that cell-free DNA released from lung cancer cells is more abundant in the airway than in the blood, and the efficient collection of cell-free DNA derived from lung cancer in the airway by BAL and its genomic analysis could allow the accurate diagnosis of lung cancer. We believe that this approach will possibly make a breakthrough in the currently unsatisfactory diagnostic yield for lung cancer, since it is a new and constitutive diagnostic focusing on the gene mutations of lung cancer and their release into the airway in the form of cell-free DNA.

Abstract

Although bronchoscopy is generally performed to diagnose lung cancer, its diagnostic yield remains unsatisfactory. Assuming that lung cancer cells release cell-free DNA into the epithelial lining fluid, we hypothesized that lung cancer could be diagnosed by analyzing gene mutations in cell-free DNA in this fluid. This study included 32 patients with lung cancer who underwent surgery at our hospital. Bronchoalveolar lavage (BAL) was performed on the resected lung samples (ex vivo BAL model) after lobectomy. Each DNA sample (i.e., BAL fluid, primary lesion, and plasma) underwent deep targeted sequencing. Gene mutation analyses in the BAL fluid samples identified mutations identical to those in the primary lesions in 30 (93.8%) of 32 patients. In contrast, the microscopic cytology of the same BAL fluid samples yielded a diagnosis of lung cancer in only one of 32 patients, and the analysis of plasma samples revealed gene mutations identical to those in the primary lesions in only one of 32 patients. In conclusion, cell-free DNA released from lung cancer cells exists more abundantly in the airway than in the blood. The collection and analysis of the BAL fluid containing cell-free DNA derived from lung cancer can thus allow lung cancer diagnosis and the screening of driver mutations.