Microbial Ecology

, Volume 77, Issue 3, pp 808–820 | Cite as

Co-occurrence of Anaerobes in Human Chronic Wounds

  • Yongwook Choi
  • Anirban Banerjee
  • Sean McNish
  • Kara S. Couch
  • Manolito G. Torralba
  • Sarah Lucas
  • Andrey Tovchigrechko
  • Ramana Madupu
  • Shibu Yooseph
  • Karen E. Nelson
  • Victoria K. ShanmugamEmail author
  • Agnes P. ChanEmail author
Human Microbiome


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.


Chronic wound Obligate anaerobe Clostridia GPAC Autoimmune disease 


Funding Information

This work was supported by award R01NR013888 from the National Institute of Nursing Research and by award number UL1 TR000075 from the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through the Clinical and Translational Science Awards Program (CTSA).

Supplementary material

248_2018_1231_MOESM1_ESM.xlsx (122 kb)
ESM 1 (XLSX 121 kb)
248_2018_1231_MOESM2_ESM.docx (49 kb)
ESM 2 (DOCX 44 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Yongwook Choi
    • 1
  • Anirban Banerjee
    • 2
  • Sean McNish
    • 2
  • Kara S. Couch
    • 2
  • Manolito G. Torralba
    • 1
  • Sarah Lucas
    • 1
  • Andrey Tovchigrechko
    • 1
  • Ramana Madupu
    • 1
  • Shibu Yooseph
    • 1
  • Karen E. Nelson
    • 1
  • Victoria K. Shanmugam
    • 2
    Email author
  • Agnes P. Chan
    • 1
    Email author
  1. 1.J. Craig Venter InstituteRockvilleUSA
  2. 2.Ideas to Health Laboratory, Division of Rheumatology, School of Medicine and Health SciencesThe George Washington UniversityWashingtonUSA

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