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Cited by 108Oral microbiology and periodontitis researchGut microbiota and healthBacterial biofilms and quorum sensing

The DOI matches its Crossref record; 95 of the 95 references it cites were found in a registry or an index.

Advancements toward a systems level understanding of the human oral microbiome

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McLean, Jeffrey S.·2014·Frontiers in Cellular and Infection Microbiology
DOI 10.3389/fcimb.2014.00098PMC PMC4114298
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Abstract

Oral microbes represent one of the most well studied microbial communities owing to the fact that they are a fundamental part of human development influencing health and disease, an easily accessible human microbiome, a highly structured and remarkably resilient biofilm as well as a model of bacteria-bacteria and bacteria-host interactions. In the last 80 years since oral plaque was first characterized for its functionally stable physiological properties such as the highly repeatable rapid pH decrease upon carbohydrate addition and subsequent recovery phase, the fundamental approaches to study the oral microbiome have cycled back and forth between community level investigations and characterizing individual model isolates. Since that time, many individual species have been well characterized and the development of the early plaque community, which involves many cell-cell binding interactions, has been carefully described. With high throughput sequencing enabling the enormous diversity of the oral cavity to be realized, a number of new challenges to progress were revealed. The large number of uncultivated oral species, the high interpersonal variability of taxonomic carriage and the possibility of multiple pathways to dysbiosis pose as major hurdles to obtain a systems level understanding from the community to the gene level. It is now possible however to start connecting the insights gained from single species with community wide approaches. This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.

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Figure 1 Overview schematic representation of the structure and complexity of oral biofilms on enamel surfaces in terms of physical heterogeneity and species diversity. Research on oral biofilms has encompassed biofilm structure and function at the macro-scale to the species diversity through 16 rRNA sequencing and their genetic potential (whole genome sequencing and metagenomics) and is now progressing to the functional activity at the molecular level (metatranscriptomics).
Figure 1 Overview schematic representation of the structure and complexity of oral biofilms on enamel surfaces in terms of physical heterogeneity and species diversity. Research on oral biofilms has encompassed biofilm structure and function at the macro-scale to the species diversity through 16 rRNA sequencing and their genetic potential (whole genome sequencing and metagenomics) and is now progressing to the functional activity at the molecular level (metatranscriptomics).CC BY · PubMed Central
Figure 2 Illustration of the hydroxyapaptite (HA) demineralization and remineralization process that occurs through the pH cycling (“Stephan Curve”) in relation to the Ecological Plaque Hypothesis (adapted from Marsh, 1994).
Figure 2 Illustration of the hydroxyapaptite (HA) demineralization and remineralization process that occurs through the pH cycling (“Stephan Curve”) in relation to the Ecological Plaque Hypothesis (adapted from Marsh, 1994).CC BY · PubMed Central
Figure 3 Workflow of the high-throughput Single Cell Genomics Platform at the J. Craig Venter Institute. Custom integrated Agilent Technologies BioCel 1200 liquid handling automated platform for high throughput single cell genomics. The BioCel platform allows processing of more than 5000 single cells per week through a multi-stage protocol that includes multiple displacement amplification (MDA) of DNA, MDA dilution and 16S rDNA PCR. After classification of 16S rRNA gene sequences, candidate genomes can be deeply sequenced followed by assembly and annotation of generated contigs. Modified from McLean et al. (2013b).
Figure 3 Workflow of the high-throughput Single Cell Genomics Platform at the J. Craig Venter Institute. Custom integrated Agilent Technologies BioCel 1200 liquid handling automated platform for high throughput single cell genomics. The BioCel platform allows processing of more than 5000 single cells per week through a multi-stage protocol that includes multiple displacement amplification (MDA) of DNA, MDA dilution and 16S rDNA PCR. After classification of 16S rRNA gene sequences, candidate genomes can be deeply sequenced followed by assembly and annotation of generated contigs. Modified from McLean et al. (2013b).CC BY · PubMed Central
Figure 4 Illustration of a NMR-SIP experimental procedure. Combining nucleic acid based Stable Isotope Probing (SIP) with in situ non-invasive Magnetic Resonance Spectroscopy (MRS) to link real-time organic acid production measurements and the specific bacterial species active in oral biofilms. The experimental procedure involves incubating plaque samples from healthy juvenile human subjects with isotopically labeled carbon sources (13C-glucose or 13C-lactate) in a defined minimal medium under various pH and buffering conditions. The temporal metabolite profiles of these live samples can then be monitored by inserting the biofilms into the NMR and performing spectroscopy with 1H MRS followed by nucleic acid isolation and SIP to determine the active species (modified from McLean et al., 2012). The * indicates a heavy isotope labeled carbon or nitrogen that can be tracked in each panel.
Figure 4 Illustration of a NMR-SIP experimental procedure. Combining nucleic acid based Stable Isotope Probing (SIP) with in situ non-invasive Magnetic Resonance Spectroscopy (MRS) to link real-time organic acid production measurements and the specific bacterial species active in oral biofilms. The experimental procedure involves incubating plaque samples from healthy juvenile human subjects with isotopically labeled carbon sources (13C-glucose or 13C-lactate) in a defined minimal medium under various pH and buffering conditions. The temporal metabolite profiles of these live samples can then be monitored by inserting the biofilms into the NMR and performing spectroscopy with 1H MRS followed by nucleic acid isolation and SIP to determine the active species (modified from McLean et al., 2012). The * indicates a heavy isotope labeled carbon or nitrogen that can be tracked in each panel.CC BY · PubMed Central
Figure 5 In vitro oral biofilm model system (Edlund et al., 2013). Schematic of in vitro model system growth and 16S rRNA gene sequencing results indicating high reproducibility of taxonomic abundance and carriage between wells.
Figure 5 In vitro oral biofilm model system (Edlund et al., 2013). Schematic of in vitro model system growth and 16S rRNA gene sequencing results indicating high reproducibility of taxonomic abundance and carriage between wells.CC BY · PubMed Central

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Metadata

Authors
McLean, J. S.
Affiliations
J. Craig Venter Institute (US)
Corresponding author
McLean, Jeffrey S.
ORCID
McLean, Jeffrey S.
Venue
Frontiers in Cellular and Infection Microbiology
Publisher
Frontiers Media SA
Published
2014-07-29
Volume
4
Pages
98-98
ISSN
2235-2988 (ISSN-L)
DOI
10.3389/fcimb.2014.00098
PMC
PMC4114298
OpenAlex
W2040159150
Cited by
108
References
95
Citations by year
2026: 11 · 2025: 8 · 2024: 5 · 2023: 20 · 2022: 6 · 2021: 6 · 2020: 9 · 2019: 6 · 2018: 12 · 2017: 8 · 2016: 6 · 2015: 10 · 2014: 1
FWCI
11.13
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Frontiers in Cellular and Infection Microbiology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institutes of Health (5r01de020102-10)
  • National Institute of Dental and Craniofacial Research (R01-DE020102)
Topics
  • Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
Keywords
oral microbiota, dental plaque, biofilm, dysbiosis, interpersonal variability, host-bacteria interactions, bacterial-bacterial interactions
MeSH terms
Bacteria, Dental Plaque, Humans, Hydrogen-Ion Concentration, Mouth, Phylogeny, Tooth Demineralization, Bacterial Physiological Phenomena, Biofilms, Host-Pathogen Interactions, Metagenome, Metagenomics, Microbial Interactions, Microbiota, Datasets as Topic

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