Supathep Tansirichaiya, Kittikun Songsomboon, Nichamon Chaianant, Wasawat Lertsivawinyu, Mohammed Al-Haroni
{"title":"Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome","authors":"Supathep Tansirichaiya, Kittikun Songsomboon, Nichamon Chaianant, Wasawat Lertsivawinyu, Mohammed Al-Haroni","doi":"10.1002/cre2.905","DOIUrl":null,"url":null,"abstract":"<div>\n \n \n <section>\n \n <h3> Objectives</h3>\n \n <p>The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.</p>\n </section>\n \n <section>\n \n <h3> Materials and Methods</h3>\n \n <p>Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.</p>\n </section>\n \n <section>\n \n <h3> Results</h3>\n \n <p>Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.</p>\n </section>\n \n <section>\n \n <h3> Conclusions</h3>\n \n <p>These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance.</p>\n </section>\n </div>","PeriodicalId":10203,"journal":{"name":"Clinical and Experimental Dental Research","volume":"10 4","pages":""},"PeriodicalIF":1.7000,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211641/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Clinical and Experimental Dental Research","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cre2.905","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"DENTISTRY, ORAL SURGERY & MEDICINE","Score":null,"Total":0}
引用次数: 0
Abstract
Objectives
The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.
Materials and Methods
Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.
Results
Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.
Conclusions
These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance.
期刊介绍:
Clinical and Experimental Dental Research aims to provide open access peer-reviewed publications of high scientific quality representing original clinical, diagnostic or experimental work within all disciplines and fields of oral medicine and dentistry. The scope of Clinical and Experimental Dental Research comprises original research material on the anatomy, physiology and pathology of oro-facial, oro-pharyngeal and maxillofacial tissues, and functions and dysfunctions within the stomatognathic system, and the epidemiology, aetiology, prevention, diagnosis, prognosis and therapy of diseases and conditions that have an effect on the homeostasis of the mouth, jaws, and closely associated structures, as well as the healing and regeneration and the clinical aspects of replacement of hard and soft tissues with biomaterials, and the rehabilitation of stomatognathic functions. Studies that bring new knowledge on how to advance health on the individual or public health levels, including interactions between oral and general health and ill-health are welcome.