ArticleApplied and environmental microbiology2012
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes.
Article in Applied and environmental microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Integrons: the hidden architects of bacterial adaptation, evolution, and the challenges of antimicrobial resistance.Antonie van Leeuwenhoek · 2025Review
- The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study.PloS one · 2024Article
- Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome.BMC oral health · 2022Article
- Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine.Scientific reports · 2020Article
- Article
- A comprehensive survey of integron-associated genes present in metagenomes.BMC genomics · 2020Article
- Identification and reconstruction of novel antibiotic resistance genes from metagenomes.Microbiome · 2019Article
- Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.Bioinformatics (Oxford, England) · 2016Article
- Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola.Frontiers in microbiology · 2016Article
- Article
- Integrons: past, present, and future.Microbiology and molecular biology reviews : MMBR · 2014Review
- Metagenomics and novel gene discovery: promise and potential for novel therapeutics.Virulence · 2014Review
- Multiple Pathways of Genome Plasticity Leading to Development of Antibiotic Resistance.Antibiotics (Basel, Switzerland) · 2013Review
- The gain and loss of chromosomal integron systems in the Treponema species.BMC evolutionary biology · 2013Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of oral spirochetes implicated in dental diseases in normal human individuals, using recombination sites associated with the chromosomal integron in Treponema genomes, taking advantage of the multiple copies of the integron recombination sites (repeats) in the genomes, and using a targeted assembly approach that we have developed. We find that integron-containing Treponema species are present in ∼80% of the normal human subjects included in the HMP. Further, we are able to de novo assemble the integron gene cassettes using our constrained assembly approach, which employs a unique application of the de Bruijn graph assembly information; most of these cassette genes were not assembled in whole-metagenome assemblies and could not be identified by mapping sequencing reads onto the known reference Treponema genomes due to the dynamic nature of integron gene cassettes. Our study significantly enriches the gene pool known to be carried by Treponema chromosomal integrons, totaling 826 (598 97% nonredundant) genes. We characterize the functions of these gene cassettes: many of these genes have unknown functions. The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes.
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