Distinct ecological niche of anal, oral, and cervical mucosal microbiomes in adolescent women

Benjamin C. Smith, Christine P. Zolnik, Mykhaylo Usyk, Zigui Chen, Katherine Kaiser, Anne Nucci-Sack, Ken Peake, Angela Diaz, Shankar Viswanathan, Howard D. Strickler, Nicolas F. Schlecht, Robert D. Burk

Research output: Contribution to journalReview articlepeer-review

13 Scopus citations


Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes, oral samples with Streptococcus and Prevotella, and cervical samples with Lactobacillus. The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.

Original languageEnglish
Pages (from-to)277-284
Number of pages8
JournalYale Journal of Biology and Medicine
Issue number3
StatePublished - Sep 2016


  • Anal microbiome
  • Cervical microbiome
  • Human microbiome
  • Massively-parallel sequencing
  • Metacommunity theory
  • Next-generation sequencing
  • Oral microbiome


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