Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome

IF 1.7 Q3 DENTISTRY, ORAL SURGERY & MEDICINE Clinical and Experimental Dental Research Pub Date : 2024-06-28 DOI:10.1002/cre2.905
Supathep Tansirichaiya, Kittikun Songsomboon, Nichamon Chaianant, Wasawat Lertsivawinyu, Mohammed Al-Haroni
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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.

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唾液元基因组 DNA 提取前的细胞裂解处理对口腔微生物组和相关抗药性组的影响。
目的:人类口腔微生物组是一个复杂的生态系统,与口腔和全身健康息息相关,其中蕴藏着各种各样的微生物种群,包括抗菌药耐药性基因 (ARGs)。作为应对抗生素耐药性的 "一体健康 "方法的重要组成部分,了解口腔耐药基因组的组成和多样性势在必行。本研究的目的是调查使用 MetaPolyzyme 进行化学细胞裂解处理对口腔微生物组、耐药性组以及 DNA 质量和数量的影响:从五名健康人口中采集唾液样本,对每个样本进行DNA提取,并分别使用MetaPolyzyme处理和不使用MetaPolyzyme处理。通过元基因组测序,我们分析、评估和比较了两组提取DNA的微生物组成、抗性组和DNA特征:结果:我们的研究发现,MetaPolyzyme 处理导致微生物组成的可检测性发生了显著变化,革兰氏阳性菌(尤其是链球菌)比革兰氏阴性菌更受青睐。此外,MetaPolyzyme 处理还导致 ARG 分布发生明显变化。与未处理组相比,这种变化的特点是与氟喹诺酮类药物和外排泵相关的ARG比例上升,同时四环素和β-内酰胺耐药基因的流行率下降。阿尔法多样性分析表明,物种和 ARG 分布发生了改变,但不影响总体多样性,而贝塔多样性分析则证实,治疗组和非治疗组之间的分类组成和口腔耐药性组存在显著差异:这些发现强调了细胞裂解处理在优化口腔元基因组研究中的关键作用,并加深了我们对抗菌药耐药性背景下口腔耐药性组动态的了解。
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来源期刊
Clinical and Experimental Dental Research
Clinical and Experimental Dental Research DENTISTRY, ORAL SURGERY & MEDICINE-
CiteScore
3.30
自引率
5.60%
发文量
165
审稿时长
26 weeks
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.
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