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Updated: May 6, 2026
Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
16S rRNA Amplicon Sequencing of the Intraoperative Surgical Site Demonstrates an Aberrant Microbiota Which Can
Veral Vishnoi1,2,3, Emily C Hoedt1,2,4, Michelle Zhao3
1School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia.
Introduction:
Surgical Site Infection (SSI) of an abdominal incision is a dreaded infectious complication following colorectal surgery. Understanding the intraoperative microbiology holds the key to prevention. Genomic sequencing has revolutionised culture-independent techniques, allowing for a more sensitive tool in microbial detection. The purpose of this study is to determine whether an aberrant microbiota is present within the intraoperative surgical site in patients that develop an SSI.
Methods:
The subcutaneous abdominal surgical site of patients undergoing elective bowel resection was opportunistically sampled, following fascial closure. DNA was recovered from the swabs and used for 16S rRNA gene amplicon sequencing. The intraoperative microbiota was compared in those with and without a subsequent SSI with focus on alpha diversity and beta diversity, as well as taxonomic composition.
Results:
16/123 patients developed an SSI. The bacterial profile within the surgical site showed a strong presence of obligate anaerobes in all patients. Chao1, Shannon, and Simpson measures of alpha diversity from the intraoperative swabs were all significantly increased in SSI patients (p = 0.05, 0.05 and 0.05, respectively). Beta diversity demonstrated no significant separation between patients (Bray-Curtis dissimilarity index, PERMANOVA p = 0.394).
Conclusions:
To the best of our knowledge this is the first study to demonstrate an aberrant intraoperative microbiota of the surgical site associated with subsequent infection. Pending validation studies, this provides a target for the strategic manipulation of the surgical site to reduce the burden of infection.
