Co-occurrence of Anaerobes in Human Chronic Wounds
Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perf...
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| Veröffentlicht in: | Microbial ecology 2019-04, Vol.77 (3), p.808-820 |
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| creator | Choi, Yongwook Banerjee, Anirban McNish, Sean Couch, Kara S. Torralba, Manolito G. Lucas, Sarah Tovchigrechko, Andrey Madupu, Ramana Yooseph, Shibu Nelson, Karen E. Shanmugam, Victoria K. Chan, Agnes P. |
| description | Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort. |
| doi_str_mv | 10.1007/s00248-018-1231-z |
| format | Article |
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Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.</description><identifier>ISSN: 0095-3628</identifier><identifier>EISSN: 1432-184X</identifier><identifier>DOI: 10.1007/s00248-018-1231-z</identifier><identifier>PMID: 30141127</identifier><language>eng</language><publisher>New York: Springer Science + Business Media</publisher><subject>Aetiology ; Anaerobes ; Autoimmune diseases ; Bacteria ; Biomedical and Life Sciences ; Cocci ; Cohorts ; Colonization ; Communities ; Dirichlet problem ; Diseases ; Ecology ; Etiology ; Gene sequencing ; Geoecology/Natural Processes ; HUMAN MICROBIOME ; Identification ; Life Sciences ; Microbial Ecology ; Microbiology ; Microbiomes ; Microbiota ; Modelling ; Nature Conservation ; Nucleic acids ; Ribonucleic acid ; RNA ; rRNA 16S ; Trends ; Water Quality/Water Pollution ; Wound healing</subject><ispartof>Microbial ecology, 2019-04, Vol.77 (3), p.808-820</ispartof><rights>Springer Science+Business Media, LLC, part of Springer Nature 2018</rights><rights>Microbial Ecology is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c460t-bb4558b1c974f7c686a2251c8e2cb1c0ff50422f896d092dc0db7985ce80b5e53</citedby><cites>FETCH-LOGICAL-c460t-bb4558b1c974f7c686a2251c8e2cb1c0ff50422f896d092dc0db7985ce80b5e53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/48702331$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/48702331$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,27901,27902,41464,42533,51294,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30141127$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Choi, Yongwook</creatorcontrib><creatorcontrib>Banerjee, Anirban</creatorcontrib><creatorcontrib>McNish, Sean</creatorcontrib><creatorcontrib>Couch, Kara S.</creatorcontrib><creatorcontrib>Torralba, Manolito G.</creatorcontrib><creatorcontrib>Lucas, Sarah</creatorcontrib><creatorcontrib>Tovchigrechko, Andrey</creatorcontrib><creatorcontrib>Madupu, Ramana</creatorcontrib><creatorcontrib>Yooseph, Shibu</creatorcontrib><creatorcontrib>Nelson, Karen E.</creatorcontrib><creatorcontrib>Shanmugam, Victoria K.</creatorcontrib><creatorcontrib>Chan, Agnes P.</creatorcontrib><title>Co-occurrence of Anaerobes in Human Chronic Wounds</title><title>Microbial ecology</title><addtitle>Microb Ecol</addtitle><addtitle>Microb Ecol</addtitle><description>Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.</description><subject>Aetiology</subject><subject>Anaerobes</subject><subject>Autoimmune diseases</subject><subject>Bacteria</subject><subject>Biomedical and Life Sciences</subject><subject>Cocci</subject><subject>Cohorts</subject><subject>Colonization</subject><subject>Communities</subject><subject>Dirichlet problem</subject><subject>Diseases</subject><subject>Ecology</subject><subject>Etiology</subject><subject>Gene sequencing</subject><subject>Geoecology/Natural Processes</subject><subject>HUMAN MICROBIOME</subject><subject>Identification</subject><subject>Life Sciences</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Microbiomes</subject><subject>Microbiota</subject><subject>Modelling</subject><subject>Nature Conservation</subject><subject>Nucleic acids</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>rRNA 16S</subject><subject>Trends</subject><subject>Water Quality/Water Pollution</subject><subject>Wound healing</subject><issn>0095-3628</issn><issn>1432-184X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9kLFOwzAURS0EoqXwAQygSCwshudnJ3HGKgKKVIkFBJuVOA6kauxiNwP9elJSQGJgsvR87n32IeSUwRUDSK8DAApJgUnKkDO62SNjJjhSJsXLPhkDZDHlCcoROQphAcDSBPkhGXFggjFMxwRzR53WnffGahO5OprawnhXmhA1Npp1bWGj_M072-jo2XW2CsfkoC6WwZzszgl5ur15zGd0_nB3n0_nVIsE1rQsRRzLkuksFXWqE5kUiDHT0qDup1DXMQjEWmZJBRlWGqoyzWSsjYQyNjGfkMuhd-Xde2fCWrVN0Ga5LKxxXVAIGf_6SNajF3_Qheu87V-3pRC54FL0FBso7V0I3tRq5Zu28B-KgdoKVYNQ1QtVW6Fq02fOd81d2ZrqJ_FtsAdwAEJ_ZV-N_139X-vZEFqEtfM_pUKmgJwz_gkNnIfv</recordid><startdate>20190401</startdate><enddate>20190401</enddate><creator>Choi, Yongwook</creator><creator>Banerjee, Anirban</creator><creator>McNish, Sean</creator><creator>Couch, Kara 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of Anaerobes in Human Chronic Wounds</title><author>Choi, Yongwook ; Banerjee, Anirban ; McNish, Sean ; Couch, Kara S. ; Torralba, Manolito G. ; Lucas, Sarah ; Tovchigrechko, Andrey ; Madupu, Ramana ; Yooseph, Shibu ; Nelson, Karen E. ; Shanmugam, Victoria K. ; Chan, Agnes P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c460t-bb4558b1c974f7c686a2251c8e2cb1c0ff50422f896d092dc0db7985ce80b5e53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Aetiology</topic><topic>Anaerobes</topic><topic>Autoimmune diseases</topic><topic>Bacteria</topic><topic>Biomedical and Life Sciences</topic><topic>Cocci</topic><topic>Cohorts</topic><topic>Colonization</topic><topic>Communities</topic><topic>Dirichlet problem</topic><topic>Diseases</topic><topic>Ecology</topic><topic>Etiology</topic><topic>Gene sequencing</topic><topic>Geoecology/Natural Processes</topic><topic>HUMAN 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Ecol</addtitle><date>2019-04-01</date><risdate>2019</risdate><volume>77</volume><issue>3</issue><spage>808</spage><epage>820</epage><pages>808-820</pages><issn>0095-3628</issn><eissn>1432-184X</eissn><abstract>Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.</abstract><cop>New York</cop><pub>Springer Science + Business Media</pub><pmid>30141127</pmid><doi>10.1007/s00248-018-1231-z</doi><tpages>13</tpages></addata></record> |
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| ispartof | Microbial ecology, 2019-04, Vol.77 (3), p.808-820 |
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| source | Jstor Complete Legacy; Springer Nature - Complete Springer Journals |
| subjects | Aetiology Anaerobes Autoimmune diseases Bacteria Biomedical and Life Sciences Cocci Cohorts Colonization Communities Dirichlet problem Diseases Ecology Etiology Gene sequencing Geoecology/Natural Processes HUMAN MICROBIOME Identification Life Sciences Microbial Ecology Microbiology Microbiomes Microbiota Modelling Nature Conservation Nucleic acids Ribonucleic acid RNA rRNA 16S Trends Water Quality/Water Pollution Wound healing |
| title | Co-occurrence of Anaerobes in Human Chronic Wounds |
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