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Presence of Archaea in dental caries biofilms
•Archaeal sequences were detected in dental caries for the first time.•Archaeal diversity in the mouth is currently underestimated.•Archaeal diversity in caries does not seem to be a restriction on methanogens.•Primers direct to archaeal 16S rRNA could be better for archaeal taxonomy in dental carie...
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| Published in: | Archives of oral biology 2020-02, Vol.110, p.104606-104606, Article 104606 |
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| container_title | Archives of oral biology |
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| creator | Dame-Teixeira, Naile de Cena, Jéssica Alves Côrtes, Débora Azevedo Belmok, Aline dos Anjos Borges, Luiz Gustavo Marconatto, Letícia Giongo, Adriana Kyaw, Cynthia Maria |
| description | •Archaeal sequences were detected in dental caries for the first time.•Archaeal diversity in the mouth is currently underestimated.•Archaeal diversity in caries does not seem to be a restriction on methanogens.•Primers direct to archaeal 16S rRNA could be better for archaeal taxonomy in dental caries.
Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.
To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.
The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.
Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens. |
| doi_str_mv | 10.1016/j.archoralbio.2019.104606 |
| format | article |
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Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.
To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.
The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.
Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.</description><identifier>ISSN: 0003-9969</identifier><identifier>EISSN: 1879-1506</identifier><identifier>DOI: 10.1016/j.archoralbio.2019.104606</identifier><identifier>PMID: 31739075</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Archaea ; Archaea - genetics ; Archaea - isolation & purification ; Bacteria ; Biofilms ; Dental caries ; Dental Caries - microbiology ; Dentistry ; DNA, Bacterial - analysis ; High-throughput DNA sequencing ; Humans ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence analysis ; Sequence Analysis, DNA</subject><ispartof>Archives of oral biology, 2020-02, Vol.110, p.104606-104606, Article 104606</ispartof><rights>2019 Elsevier Ltd</rights><rights>Copyright © 2019 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c443t-a5f709841833fc1d0814ead29b5a81d2edbb0641dadc96463523b036934878273</citedby><cites>FETCH-LOGICAL-c443t-a5f709841833fc1d0814ead29b5a81d2edbb0641dadc96463523b036934878273</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31739075$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dame-Teixeira, Naile</creatorcontrib><creatorcontrib>de Cena, Jéssica Alves</creatorcontrib><creatorcontrib>Côrtes, Débora Azevedo</creatorcontrib><creatorcontrib>Belmok, Aline</creatorcontrib><creatorcontrib>dos Anjos Borges, Luiz Gustavo</creatorcontrib><creatorcontrib>Marconatto, Letícia</creatorcontrib><creatorcontrib>Giongo, Adriana</creatorcontrib><creatorcontrib>Kyaw, Cynthia Maria</creatorcontrib><title>Presence of Archaea in dental caries biofilms</title><title>Archives of oral biology</title><addtitle>Arch Oral Biol</addtitle><description>•Archaeal sequences were detected in dental caries for the first time.•Archaeal diversity in the mouth is currently underestimated.•Archaeal diversity in caries does not seem to be a restriction on methanogens.•Primers direct to archaeal 16S rRNA could be better for archaeal taxonomy in dental caries.
Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.
To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.
The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.
Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.</description><subject>Archaea</subject><subject>Archaea - genetics</subject><subject>Archaea - isolation & purification</subject><subject>Bacteria</subject><subject>Biofilms</subject><subject>Dental caries</subject><subject>Dental Caries - microbiology</subject><subject>Dentistry</subject><subject>DNA, Bacterial - analysis</subject><subject>High-throughput DNA sequencing</subject><subject>Humans</subject><subject>Microbiota</subject><subject>Phylogeny</subject><subject>RNA, Ribosomal, 16S</subject><subject>Sequence analysis</subject><subject>Sequence Analysis, DNA</subject><issn>0003-9969</issn><issn>1879-1506</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNqNkEtLAzEQx4Motla_gqw3L1szm2w2OUrxBQU96Dlkk1lM2UdNtoLf3pSt4tHTMMP_wfwIuQK6BAriZrM0wb4PwbS1H5YFBZXuXFBxROYgK5VDScUxmVNKWa6UUDNyFuMmraUQcEpmDCqmaFXOSf4SMGJvMRua7DalGjSZ7zOH_WjazJrgMWappvFtF8_JSWPaiBeHuSBv93evq8d8_fzwtLpd55ZzNuambCqqJAfJWGPBUQkcjStUXRoJrkBX11RwcMZZJbhgZcFqyoRiXFayqNiCXE-52zB87DCOuvPRYtuaHodd1AWDUlWMA01SNUltGGIM2Oht8J0JXxqo3tPSG_2Hlt7T0hOt5L081OzqDt2v8wdPEqwmAaZnPz0GHa3f03I-oB21G_w_ar4B29R-xQ</recordid><startdate>202002</startdate><enddate>202002</enddate><creator>Dame-Teixeira, Naile</creator><creator>de Cena, Jéssica Alves</creator><creator>Côrtes, Débora Azevedo</creator><creator>Belmok, Aline</creator><creator>dos Anjos Borges, Luiz Gustavo</creator><creator>Marconatto, Letícia</creator><creator>Giongo, Adriana</creator><creator>Kyaw, Cynthia Maria</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>202002</creationdate><title>Presence of Archaea in dental caries biofilms</title><author>Dame-Teixeira, Naile ; de Cena, Jéssica Alves ; Côrtes, Débora Azevedo ; Belmok, Aline ; dos Anjos Borges, Luiz Gustavo ; Marconatto, Letícia ; Giongo, Adriana ; Kyaw, Cynthia Maria</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c443t-a5f709841833fc1d0814ead29b5a81d2edbb0641dadc96463523b036934878273</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Archaea</topic><topic>Archaea - genetics</topic><topic>Archaea - isolation & purification</topic><topic>Bacteria</topic><topic>Biofilms</topic><topic>Dental caries</topic><topic>Dental Caries - microbiology</topic><topic>Dentistry</topic><topic>DNA, Bacterial - analysis</topic><topic>High-throughput DNA sequencing</topic><topic>Humans</topic><topic>Microbiota</topic><topic>Phylogeny</topic><topic>RNA, Ribosomal, 16S</topic><topic>Sequence analysis</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dame-Teixeira, Naile</creatorcontrib><creatorcontrib>de Cena, Jéssica Alves</creatorcontrib><creatorcontrib>Côrtes, Débora Azevedo</creatorcontrib><creatorcontrib>Belmok, Aline</creatorcontrib><creatorcontrib>dos Anjos Borges, Luiz Gustavo</creatorcontrib><creatorcontrib>Marconatto, Letícia</creatorcontrib><creatorcontrib>Giongo, Adriana</creatorcontrib><creatorcontrib>Kyaw, Cynthia Maria</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Archives of oral biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dame-Teixeira, Naile</au><au>de Cena, Jéssica Alves</au><au>Côrtes, Débora Azevedo</au><au>Belmok, Aline</au><au>dos Anjos Borges, Luiz Gustavo</au><au>Marconatto, Letícia</au><au>Giongo, Adriana</au><au>Kyaw, Cynthia Maria</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Presence of Archaea in dental caries biofilms</atitle><jtitle>Archives of oral biology</jtitle><addtitle>Arch Oral Biol</addtitle><date>2020-02</date><risdate>2020</risdate><volume>110</volume><spage>104606</spage><epage>104606</epage><pages>104606-104606</pages><artnum>104606</artnum><issn>0003-9969</issn><eissn>1879-1506</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>•Archaeal sequences were detected in dental caries for the first time.•Archaeal diversity in the mouth is currently underestimated.•Archaeal diversity in caries does not seem to be a restriction on methanogens.•Primers direct to archaeal 16S rRNA could be better for archaeal taxonomy in dental caries.
Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet.
To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated.
The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota.
Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>31739075</pmid><doi>10.1016/j.archoralbio.2019.104606</doi><tpages>1</tpages></addata></record> |
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| ispartof | Archives of oral biology, 2020-02, Vol.110, p.104606-104606, Article 104606 |
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| source | ScienceDirect Journals |
| subjects | Archaea Archaea - genetics Archaea - isolation & purification Bacteria Biofilms Dental caries Dental Caries - microbiology Dentistry DNA, Bacterial - analysis High-throughput DNA sequencing Humans Microbiota Phylogeny RNA, Ribosomal, 16S Sequence analysis Sequence Analysis, DNA |
| title | Presence of Archaea in dental caries biofilms |
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