Sinonasal microbiome sampling: a comparison of techniques
The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investiga...
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| Veröffentlicht in: | PloS one 2015-04, Vol.10 (4), p.e0123216-e0123216 |
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| creator | Bassiouni, Ahmed Cleland, Edward John Psaltis, Alkis James Vreugde, Sarah Wormald, Peter-John |
| description | The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample.
Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package.
At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05).
We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies. |
| doi_str_mv | 10.1371/journal.pone.0123216 |
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Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package.
At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05).
We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0123216</identifier><identifier>PMID: 25876035</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Biofilms ; Biopsy ; Cross-Sectional Studies ; Data processing ; Deoxyribonucleic acid ; DNA ; Floating ; Humans ; Methods ; Microbiota ; Microbiota (Symbiotic organisms) ; Mucosa ; Nucleotide sequence ; Paranasal Sinuses - microbiology ; Phylogeny ; Plant diversity ; Primers ; Principal Component Analysis ; RNA ; RNA, Ribosomal, 16S - analysis ; rRNA 16S ; Sampling ; Sampling methods ; Sequence Analysis, RNA ; Sinus ; Sinuses ; Species richness ; Specimen Handling - methods</subject><ispartof>PloS one, 2015-04, Vol.10 (4), p.e0123216-e0123216</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Bassiouni et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Bassiouni et al 2015 Bassiouni et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-f241dab87699bf26fac2514a4469e205f4868f954eb676569427f058adee7e783</citedby><cites>FETCH-LOGICAL-c692t-f241dab87699bf26fac2514a4469e205f4868f954eb676569427f058adee7e783</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396979/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396979/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25876035$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cohen, Noam A.</contributor><creatorcontrib>Bassiouni, Ahmed</creatorcontrib><creatorcontrib>Cleland, Edward John</creatorcontrib><creatorcontrib>Psaltis, Alkis James</creatorcontrib><creatorcontrib>Vreugde, Sarah</creatorcontrib><creatorcontrib>Wormald, Peter-John</creatorcontrib><title>Sinonasal microbiome sampling: a comparison of techniques</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample.
Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package.
At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05).
We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.</description><subject>Analysis</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Biofilms</subject><subject>Biopsy</subject><subject>Cross-Sectional Studies</subject><subject>Data processing</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Floating</subject><subject>Humans</subject><subject>Methods</subject><subject>Microbiota</subject><subject>Microbiota (Symbiotic organisms)</subject><subject>Mucosa</subject><subject>Nucleotide sequence</subject><subject>Paranasal Sinuses - microbiology</subject><subject>Phylogeny</subject><subject>Plant diversity</subject><subject>Primers</subject><subject>Principal Component Analysis</subject><subject>RNA</subject><subject>RNA, Ribosomal, 16S - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bassiouni, Ahmed</au><au>Cleland, Edward John</au><au>Psaltis, Alkis James</au><au>Vreugde, Sarah</au><au>Wormald, Peter-John</au><au>Cohen, Noam A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sinonasal microbiome sampling: a comparison of techniques</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-04-14</date><risdate>2015</risdate><volume>10</volume><issue>4</issue><spage>e0123216</spage><epage>e0123216</epage><pages>e0123216-e0123216</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample.
Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package.
At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05).
We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25876035</pmid><doi>10.1371/journal.pone.0123216</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Biofilms Biopsy Cross-Sectional Studies Data processing Deoxyribonucleic acid DNA Floating Humans Methods Microbiota Microbiota (Symbiotic organisms) Mucosa Nucleotide sequence Paranasal Sinuses - microbiology Phylogeny Plant diversity Primers Principal Component Analysis RNA RNA, Ribosomal, 16S - analysis rRNA 16S Sampling Sampling methods Sequence Analysis, RNA Sinus Sinuses Species richness Specimen Handling - methods |
| title | Sinonasal microbiome sampling: a comparison of techniques |
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