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Head & Neck Aug 2023The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome... (Review)
Review
OBJECTIVES
The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were collected from these studies to highlight similarities and account for inconsistencies. We also evaluate the possible clinical applications of the microbiome regarding screening and diagnosis of HNSCC.
METHODS
Systematic analysis of studies regarding HNSCC and the microbiome was done according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. Articles were retrieved from four databases (PubMed, ScienceDirect, CUHK Full-Text Journals, and Cochrane database) and were screened using predefined criteria.
RESULTS
Twenty studies were chosen after screening for full-text review. α-diversity comparison was inconsistent whereas β-diversity between HNSCC and normal samples showed distinct clustering. Microbial dysbiosis characterized by change in the relative abundances of several bacterial species were also seen in HNSCC patients. At a phylum level, inconsistencies were seen between studies using HNSCC tumor tissue samples and saliva samples. At a genus level, Fusobacterium, Peptostreptococcus, Alloprevotella, Capnocytophaga, Catonella, and Prevotella were differentially enriched in HNSCC while Streptococcus, Actinomyces Veillonella, and Rothia were differentially depleted. Co-occurrence network analysis revealed a positive correlation of HNSCC with periodontal pathogens and a negative correlation with commensal bacteria. Metagenomic analysis of microbiota revealed a differential enrichment of pro-inflammatory genomic pathways which was consistent across various studies. Microbial dysbiosis was applied in clinical use as a tool for HNSCC screening. Random-forest analysis was adopted to differentiate between tumor and normal tissue, at 95.7% and 70.0% accuracies respectively in two studies. Microbial dysbiosis index was also used to predict prognosis.
CONCLUSIONS
Oral microbial dysbiosis could be a promising tool for HNSCC screening and diagnosis. However, more research should be conducted pertaining to clinical applications to improve diagnostic accuracy and explore other clinical uses.
Topics: Humans; Bacteria; Dysbiosis; Head and Neck Neoplasms; Microbiota; Squamous Cell Carcinoma of Head and Neck
PubMed: 37249085
DOI: 10.1002/hed.27422 -
Molecular Ecology Resources Oct 2022Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at... (Meta-Analysis)
Meta-Analysis Review
Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study-specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta-analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for <200 bp sequences in the available literature means this relationship was not assessed with longer sequences (e.g. >800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta-analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments.
Topics: DNA; DNA, Environmental; Environmental Monitoring; Fresh Water; Temperature; Water
PubMed: 35510730
DOI: 10.1111/1755-0998.13627 -
International Journal of Molecular... Sep 2023Aging is a complex process influenced by genetics and the environment, leading to physiological decline and increased susceptibility to diseases. Cognitive decline is a... (Review)
Review
Aging is a complex process influenced by genetics and the environment, leading to physiological decline and increased susceptibility to diseases. Cognitive decline is a prominent feature of aging, with implications for different neurodegenerative disorders. The gut microbiome has gained attention for its potential impact on health and disease, including cognitive function. This systematic review and meta-analysis aimed to investigate the relationship between the gut microbiome and cognitive function in the context of aging. Following PRISMA guidelines, a comprehensive search strategy was employed in PubMed, Scopus, and Web of Science databases. Studies exploring the role of the microbiome in cognition and neurodegenerative disorders, published between 2013 and 2023, were included. Data extraction and quality assessment were performed. Quantitative synthesis using statistical analyses was performed to examine microbial diversity and relative abundance in various cognitive conditions. Sixteen studies involving a total of 1303 participants were included in the analysis. The gut microbiota's relative abundance was different in individuals with cognitive impairments such as Alzheimer's disease, Parkinson's disease, and dementia, compared to the healthy controls. The most prevalent phyla affected were Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Meta-analyses indicated substantial heterogeneity among studies focusing on Alzheimer's disease. The overall quality of evidence related to microbial analysis was moderate. The gut microbiome's role in cognitive decline and neurodegenerative disorders warrants investigation. Altered microbial abundance, particularly in specific phyla, is associated with cognitive impairments. However, variations in study findings and methodologies highlight the complexity of the relationship between the gut microbiome and cognitive function. Further studies are needed to better understand the mechanisms underlying this connection and its potential implications for aging and cognitive health.
PubMed: 37761988
DOI: 10.3390/ijms241813680 -
Helicobacter Jun 2023Empiric therapy for Helicobacter pylori infection results in significantly increased antibiotic resistance and decreased eradication efficacy. The genotypic testing of... (Meta-Analysis)
Meta-Analysis Review
Individualized diagnosis and eradication therapy for Helicobacter pylori infection based on gene detection of clarithromycin resistance in stool specimens: A systematic review and meta-analysis.
BACKGROUND
Empiric therapy for Helicobacter pylori infection results in significantly increased antibiotic resistance and decreased eradication efficacy. The genotypic testing of clarithromycin resistance from stool specimens is a promising method for individualized diagnosis and treatment. This study aimed to determine the status of research and application on this method through a systematic review and meta-analysis.
METHODS
PubMed, Embase, MEDLINE, and WAN FANG database were searched for relevant literature. The quality of included diagnostic articles was evaluated using the quality Assessment of Diagnostic Accuracy Studies-2 tool. A bivariate random-effect model was conducted to calculate the diagnostic accuracy of genotypic testing of clarithromycin resistance.
RESULTS
A total of 16 diagnostic-related were included and analyzed after exclusions. The pooled sensitivity and specificity of diagnostic meta-analysis were 0.93 (95% confidence interval [CI]: 0.90-0.96) and 0.98 (95% CI: 0.93-1.00), respectively. The area under the curve (AUC) of the summary receiver operating characteristic was 0.97 (95% CI: 0.95-0.98). The genotypic testing in stool samples had heterogeneous sensitivity (Q = 37.82, p < .01, I = 37.82) and specificity (Q = 60.34, p < .01, I = 93.72) in detecting clarithromycin resistance. Purification method, stool sample weight, real-time PCR, and antimicrobial susceptibility testing as reference accounted for the heterogeneity of pooled sensitivity, while patient age, purification method, stool sample weight, and real-time PCR for the heterogeneity of pooled specificity.
CONCLUSION
The genotypic testing of clarithromycin resistance from stool specimens is an accurate, convenient, noninvasive, and rapid detection technology, providing a definitive diagnosis of clarithromycin resistance and guiding the rational antibiotic selection.
Topics: Humans; Clarithromycin; Helicobacter Infections; Helicobacter pylori; Drug Resistance, Bacterial; Anti-Bacterial Agents; Real-Time Polymerase Chain Reaction; Microbial Sensitivity Tests
PubMed: 36828668
DOI: 10.1111/hel.12958 -
Frontiers in Public Health 2022This systematic review describes the role of the human microbiome and microbiota in healthcare-associated infections (HAIs). Studies on the microbiota of patients,...
OBJECTIVE
This systematic review describes the role of the human microbiome and microbiota in healthcare-associated infections (HAIs). Studies on the microbiota of patients, healthcare environment (HE), medical equipment, or healthcare workers (HCW) and how it could be transmitted among the different subjects will be described in order to define alarming risk factors for HAIs spreading and to identify strategies for HAIs control or prevention.
METHODS
This review was performed in adherence to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. After retrieval in databases, identification, and screening of available records, 36 published studies were considered eligible and included in the review.
RESULTS
A multifaceted approach is required and the analyses of the many factors related to human microbiota, which can influence HAIs onset, could be of paramount importance in their prevention and control. In this review, we will focus mainly on the localization, transmission, and prevention of ESKAPE (, and ) bacteria and Clostridium difficile which are the most common pathogens causing HAIs.
CONCLUSIONS
Healthcare workers' microbiota, patient's microbiota, environmental and medical equipment microbiota, ecosystem characteristics, ways of transmission, cleaning strategies, and the microbial resistome should be taken into account for future studies on more effective preventive and therapeutic strategies against HAIs.
Topics: Humans; Cross Infection; Microbiota; Delivery of Health Care
PubMed: 36530685
DOI: 10.3389/fpubh.2022.989496 -
The Science of the Total Environment Jul 2021Antibiotics and antibiotic resistance genes (ARGs) are prevalent in estuarine and coastal environments due to substantial terrestrial input, aquaculture effluent, and... (Review)
Review
Antibiotics and antibiotic resistance genes (ARGs) are prevalent in estuarine and coastal environments due to substantial terrestrial input, aquaculture effluent, and sewage discharge. In this article, based on peer-reviewed papers, the sources, spatial patterns, driving factors, and environmental implications of antibiotics and ARGs in global estuarine and coastal environments are discussed. Riverine runoff, WWTPs, sewage discharge, and aquaculture, are responsible for the prevalence of antibiotics and ARGs. Geographically, pollution due to antibiotics in low- and middle-income countries is higher than that in high-income countries, and ARGs show remarkable latitudinal variations. The distribution of antibiotics is driven by antibiotic usage and environmental variables (heavy metals, nutrients, organic pollutants, etc.), while ARGs are affected by antibiotics residues, environmental variables, microbial communities, and mobile genetic elements (MGEs). Antibiotics and ARGs alter microbial communities and biogeochemical cycles, as well as pose threats to marine organisms and human health. Our results provide comprehensive insights into the transport and environmental behaviors of antibiotics and ARGs in global estuarine and coastal environments.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; Humans; Metals, Heavy; Sewage
PubMed: 33676219
DOI: 10.1016/j.scitotenv.2021.146009 -
The British Journal of Dermatology Feb 2022Hidradenitis suppurativa (HS) is a chronic, inflammatory skin disease of the hair follicle defined by recurrent nodules, tunnels and scarring involving the... (Review)
Review
BACKGROUND
Hidradenitis suppurativa (HS) is a chronic, inflammatory skin disease of the hair follicle defined by recurrent nodules, tunnels and scarring involving the intertriginous regions. HS is associated with microbial dysbiosis and immune dysregulation. In HS, an increasing number of studies have investigated antimicrobial peptides (AMPs).
OBJECTIVES
To provide an overview of the literature on AMPs in HS, and to discuss the potential role of AMPs in the pathogenesis of HS.
METHODS
PubMed, Embase and the Cochrane Library were searched. The titles, abstracts and full texts of all articles were manually screened. Additionally, the reference lists of the included articles were screened and hand searched for relevant studies.
RESULTS
The final literature sample comprised 18 retrospective and prospective studies (no reviews or commentaries) published between 2009 and 2020.
CONCLUSIONS
This review demonstrates the multitude of AMPs in HS. Although the methodology of the studies varied, the included studies indicate a consistent overexpression of human β-defensin (hBD)-2, S100A7, S100A8 and S100A9 at both the mRNA and protein levels, and a decreased expression of hBD-1. Overall, the studies point to a dysregulation of AMPs in both lesional and nonlesional HS skin.
Topics: Antimicrobial Peptides; Hidradenitis Suppurativa; Humans; Prospective Studies; Retrospective Studies; Skin
PubMed: 34498267
DOI: 10.1111/bjd.20750 -
APMIS : Acta Pathologica,... Mar 2020Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports... (Meta-Analysis)
Meta-Analysis
Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.
Topics: Animals; Environment; Environmental Microbiology; Humans; Pseudomonas Infections; Pseudomonas aeruginosa; RNA, Ribosomal, 16S
PubMed: 31709616
DOI: 10.1111/apm.13010 -
Frontiers in Cellular and Infection... 2023For a long time, the uterus had been considered a sterile organ, meaning that under physiological conditions the uterus would not be colonized by bacteria. Based on... (Review)
Review
For a long time, the uterus had been considered a sterile organ, meaning that under physiological conditions the uterus would not be colonized by bacteria. Based on available data, it may be concluded that the gut and uterine microbiome are related, and that the role of this microbiome is greater than expected. Despite being the most common pelvic neoplasms in women of reproductive age, uterine fibroids (UFs) are still poorly understood tumors whose etiology has not been fully determined. This systematic review presents the relationship between intestinal and uterine dysbiosis and uterine fibroids. A systematic review of three medical databases was carried out: the MEDLINE/PubMed, Scopus and Cochrane. In this study, 195 titles and abstracts were reviewed, including only original articles and clinical trials of uterine microbiome criteria. Finally, 16 studies were included to the analysis. In recent years, researchers dealing with reproduction in a broad sense have focused on the microbiome in various locations to study its role in the pathogenesis and, consequently, the prevention and treatment of diseases of the genital organ. Conventional microbial detection methods are not suitable for identifying bacteria, which are difficult to culture. Next-generation sequencing (NGS) provides an easier and faster and more informative analysis of bacterial populations. It seems that gut microbiota dysbiosis has the potential to be a risk factor for uterine fibroids or affect the disease process. Some changes were shown in many types of bacteria, such as and detected in fecal samples in patients with uterine fibroids. In view of the few results on the link between the microbiome and uterine fibroids, further intensive studies in humans and animal models are necessary, including the possible use of different microbiome modulations in the prevention or treatment of uterine fibroids.
Topics: Animals; Humans; Female; Dysbiosis; Microbiota; Leiomyoma; Gastrointestinal Microbiome; Actinobacteria
PubMed: 37305407
DOI: 10.3389/fcimb.2023.1177366 -
The Journal of Investigative Dermatology May 2024Prior studies have found associations between atopic dermatitis (AD) and comorbidities, including depression, obesity, asthma, and allergic rhinitis. Although...
Prior studies have found associations between atopic dermatitis (AD) and comorbidities, including depression, obesity, asthma, and allergic rhinitis. Although observational studies often cannot establish robust causality between potential risk factors and AD, Mendelian randomization minimizes confounding when exploring causality by relying on random allelic assortment at birth. In this study, we systematically reviewed 30 Mendelian randomization studies in AD. Body mass index, gut microbial flora, the IL-18 signaling pathway, and gastroesophageal reflux disease were among the causal factors for AD, whereas AD was causal for several medical conditions, including heart failure, rheumatoid arthritis, and conjunctivitis. These insights may improve preventive counseling in AD.
Topics: Humans; Dermatitis, Atopic; Mendelian Randomization Analysis; Risk Factors; Comorbidity; Gastrointestinal Microbiome; Body Mass Index; Gastroesophageal Reflux; Interleukin-18; Genetic Predisposition to Disease
PubMed: 37977498
DOI: 10.1016/j.jid.2023.10.016