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

Tansirichaiya, S; Songsomboon, K; Chaianant, N; Lertsivawinyu, W; Al-Haroni, M

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

Tansirichaiya, S Songsomboon, K

Chaianant, N Lertsivawinyu, W Al-Haroni, M

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Publisher:: WILEY
Publication Type:: Journal Article
Citation:: Clin Exp Dent Res, 2024, 10, (4), pp. e905
Issue Date:: 2024-08

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Field	Value	Language
dc.contributor.author	Tansirichaiya, S
dc.contributor.author	Songsomboon, K https://orcid.org/0000-0002-3189-2318
dc.contributor.author	Chaianant, N
dc.contributor.author	Lertsivawinyu, W
dc.contributor.author	Al-Haroni, M
dc.date.accessioned	2025-05-05T03:00:03Z
dc.date.available	2024-05-13
dc.date.available	2025-05-05T03:00:03Z
dc.date.issued	2024-08
dc.identifier.citation	Clin Exp Dent Res, 2024, 10, (4), pp. e905
dc.identifier.issn	2057-4347
dc.identifier.issn	2057-4347
dc.identifier.uri	http://hdl.handle.net/10453/187183
dc.description.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.
dc.format	Print
dc.language	eng
dc.publisher	WILEY
dc.relation.ispartof	Clin Exp Dent Res
dc.relation.isbasedon	10.1002/cre2.905
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	1105 Dentistry
dc.subject.classification	3203 Dentistry
dc.subject.mesh	Saliva
dc.subject.mesh	Humans
dc.subject.mesh	Microbiota
dc.subject.mesh	DNA, Bacterial
dc.subject.mesh	Metagenomics
dc.subject.mesh	Metagenome
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Mouth
dc.subject.mesh	Adult
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	Male
dc.subject.mesh	Female
dc.subject.mesh	Healthy Volunteers
dc.subject.mesh	Mouth
dc.subject.mesh	Saliva
dc.subject.mesh	Humans
dc.subject.mesh	DNA, Bacterial
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Adult
dc.subject.mesh	Female
dc.subject.mesh	Male
dc.subject.mesh	Metagenome
dc.subject.mesh	Metagenomics
dc.subject.mesh	Healthy Volunteers
dc.subject.mesh	Microbiota
dc.subject.mesh	Saliva
dc.subject.mesh	Humans
dc.subject.mesh	Microbiota
dc.subject.mesh	DNA, Bacterial
dc.subject.mesh	Metagenomics
dc.subject.mesh	Metagenome
dc.subject.mesh	Drug Resistance, Bacterial
dc.subject.mesh	Mouth
dc.subject.mesh	Adult
dc.subject.mesh	Anti-Bacterial Agents
dc.subject.mesh	Male
dc.subject.mesh	Female
dc.subject.mesh	Healthy Volunteers
dc.title	Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome.
dc.type	Journal Article
utslib.citation.volume	10
utslib.location.activity	United States
utslib.for	1105 Dentistry
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Science
pubs.organisational-group	University of Technology Sydney/UTS Groups
pubs.organisational-group	University of Technology Sydney/UTS Groups/Climate Change Cluster Research Strength (C3)
utslib.copyright.status	open_access	*
dc.rights.license	This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
dc.date.updated	2025-05-05T03:00:00Z
pubs.issue	4
pubs.publication-status	Published
pubs.volume	10
utslib.citation.issue	4

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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http://hdl.handle.net/10453/187183