Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis
Bacteria that infect the airways of persons with cystic fibrosis (CF) include a group of well-described opportunistic pathogens as well as numerous, mainly obligate or facultative anaerobic species typically not reported by standard sputum culture. We sequenced the V3-V5 hypervariable region of the...
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| creator | Carmody, Lisa A Caverly, Lindsay J Foster, Bridget K Rogers, Mary A M Kalikin, Linda M Simon, Richard H VanDevanter, Donald R LiPuma, John J |
| description | Bacteria that infect the airways of persons with cystic fibrosis (CF) include a group of well-described opportunistic pathogens as well as numerous, mainly obligate or facultative anaerobic species typically not reported by standard sputum culture. We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 sputum specimens collected from 111 CF patients over 10 years. We describe fluctuations in the relative abundances of typical CF pathogens, as well as anaerobic species, in relation to changes in patients' clinical state and lung disease stage. Both bacterial community diversity and the relative abundance of anaerobes increased during exacerbation of symptoms (prior to antibiotic treatment), although this trend was not observed uniformly across disease stages. Community diversity and the relative abundance of anaerobic species decreased during antibiotic treatment. These results support current hypotheses regarding the role of anaerobes in CF pulmonary exacerbations and lung disease progression. |
| doi_str_mv | 10.1371/journal.pone.0194060 |
| format | Article |
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We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 sputum specimens collected from 111 CF patients over 10 years. We describe fluctuations in the relative abundances of typical CF pathogens, as well as anaerobic species, in relation to changes in patients' clinical state and lung disease stage. Both bacterial community diversity and the relative abundance of anaerobes increased during exacerbation of symptoms (prior to antibiotic treatment), although this trend was not observed uniformly across disease stages. Community diversity and the relative abundance of anaerobic species decreased during antibiotic treatment. These results support current hypotheses regarding the role of anaerobes in CF pulmonary exacerbations and lung disease progression.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0194060</identifier><identifier>PMID: 29522532</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abundance ; Adolescent ; Adult ; Aggressiveness ; Anaerobes ; Anaerobic treatment ; Antibiotics ; Archives & records ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteria, Anaerobic - genetics ; Bacteria, Anaerobic - isolation & purification ; Biodiversity ; Biology and Life Sciences ; Child ; Communities ; Cystic fibrosis ; Cystic Fibrosis - microbiology ; Deoxyribonucleic acid ; Development and progression ; Disease Progression ; DNA ; DNA sequencing ; Ecology and Environmental Sciences ; Female ; Fluctuations ; Forced Expiratory Volume ; Genotype & phenotype ; Humans ; Internal medicine ; Laboratories ; Lung diseases ; Male ; Medical records ; Medical schools ; Medicine ; Medicine and Health Sciences ; Microbial colonies ; Microbiota ; Middle Aged ; Opportunist infection ; Pathogens ; Patients ; Pediatrics ; Relative abundance ; Respiratory tract ; Ribotyping ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Species ; Species diversity ; Sputum ; Sputum - microbiology ; Young Adult</subject><ispartof>PloS one, 2018-03, Vol.13 (3), p.e0194060-e0194060</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Carmody 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>2018 Carmody et al 2018 Carmody et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-39ec0a3af75a9d4cd16bc2a4635e8096b5dc68f52a030a253495dbfcdbaf39423</citedby><cites>FETCH-LOGICAL-c692t-39ec0a3af75a9d4cd16bc2a4635e8096b5dc68f52a030a253495dbfcdbaf39423</cites><orcidid>0000-0003-4033-7794</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844593/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844593/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29522532$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Carmody, Lisa A</creatorcontrib><creatorcontrib>Caverly, Lindsay J</creatorcontrib><creatorcontrib>Foster, Bridget K</creatorcontrib><creatorcontrib>Rogers, Mary A M</creatorcontrib><creatorcontrib>Kalikin, Linda M</creatorcontrib><creatorcontrib>Simon, Richard H</creatorcontrib><creatorcontrib>VanDevanter, Donald R</creatorcontrib><creatorcontrib>LiPuma, John J</creatorcontrib><title>Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Bacteria that infect the airways of persons with cystic fibrosis (CF) include a group of well-described opportunistic pathogens as well as numerous, mainly obligate or facultative anaerobic species typically not reported by standard sputum culture. We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 sputum specimens collected from 111 CF patients over 10 years. We describe fluctuations in the relative abundances of typical CF pathogens, as well as anaerobic species, in relation to changes in patients' clinical state and lung disease stage. Both bacterial community diversity and the relative abundance of anaerobes increased during exacerbation of symptoms (prior to antibiotic treatment), although this trend was not observed uniformly across disease stages. Community diversity and the relative abundance of anaerobic species decreased during antibiotic treatment. These results support current hypotheses regarding the role of anaerobes in CF pulmonary exacerbations and lung disease progression.</description><subject>Abundance</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Aggressiveness</subject><subject>Anaerobes</subject><subject>Anaerobic treatment</subject><subject>Antibiotics</subject><subject>Archives & records</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteria, Anaerobic - genetics</subject><subject>Bacteria, Anaerobic - isolation & purification</subject><subject>Biodiversity</subject><subject>Biology and Life Sciences</subject><subject>Child</subject><subject>Communities</subject><subject>Cystic fibrosis</subject><subject>Cystic Fibrosis - microbiology</subject><subject>Deoxyribonucleic acid</subject><subject>Development and progression</subject><subject>Disease Progression</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Ecology and Environmental Sciences</subject><subject>Female</subject><subject>Fluctuations</subject><subject>Forced Expiratory Volume</subject><subject>Genotype & phenotype</subject><subject>Humans</subject><subject>Internal medicine</subject><subject>Laboratories</subject><subject>Lung diseases</subject><subject>Male</subject><subject>Medical records</subject><subject>Medical schools</subject><subject>Medicine</subject><subject>Medicine and Health Sciences</subject><subject>Microbial colonies</subject><subject>Microbiota</subject><subject>Middle Aged</subject><subject>Opportunist infection</subject><subject>Pathogens</subject><subject>Patients</subject><subject>Pediatrics</subject><subject>Relative abundance</subject><subject>Respiratory tract</subject><subject>Ribotyping</subject><subject>RNA, Ribosomal, 16S - 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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abundance Adolescent Adult Aggressiveness Anaerobes Anaerobic treatment Antibiotics Archives & records Bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteria, Anaerobic - genetics Bacteria, Anaerobic - isolation & purification Biodiversity Biology and Life Sciences Child Communities Cystic fibrosis Cystic Fibrosis - microbiology Deoxyribonucleic acid Development and progression Disease Progression DNA DNA sequencing Ecology and Environmental Sciences Female Fluctuations Forced Expiratory Volume Genotype & phenotype Humans Internal medicine Laboratories Lung diseases Male Medical records Medical schools Medicine Medicine and Health Sciences Microbial colonies Microbiota Middle Aged Opportunist infection Pathogens Patients Pediatrics Relative abundance Respiratory tract Ribotyping RNA, Ribosomal, 16S - genetics rRNA 16S Species Species diversity Sputum Sputum - microbiology Young Adult |
| title | Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis |
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