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Bacterial diversity within the human subgingival crevice
I Kroes1, P W Lepp, D A Relman
1Department of Microbiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Summary
Molecular surveys reveal extensive uncharacterized bacterial diversity in the human subgingival crevice. Cultivation methods underestimate this microbial diversity, highlighting gaps in our understanding of the human microbiome.
Area of Science:
- Microbiology
- Molecular Biology
- Human Microbiome Research
Background:
- Human endogenous bacterial flora studies traditionally rely on cultivation.
- Molecular methods have uncovered vast microbial diversity in environmental samples.
- Previous studies of the human microbiome primarily used cultivation techniques.
Purpose of the Study:
- To molecularly characterize bacterial diversity in the human subgingival crevice.
- To compare molecular diversity with cultivation-based diversity assessments.
- To identify previously uncharacterized bacterial species in subgingival plaque.
Main Methods:
- Direct amplification of 16S ribosomal DNA (rDNA) from subgingival plaque.
- Creation of 21 clone libraries from amplified products.
- Comparison of sequences with cultivated bacteria and public databases.
Main Results:
- Over 52% of directly amplified 16S rRNA sequences showed <99% identity to public databases.
- Only 21.4% of cultivated sequences exhibited similar variability.
- 13.5% of amplified sequences were >5% dissimilar to known sequences, indicating novel genera.
Conclusions:
- Direct molecular amplification reveals significantly greater bacterial diversity than cultivation.
- A substantial portion of the human subgingival flora remains poorly characterized.
- Current cultivation-dependent methods likely underestimate the true microbial diversity within the human body.