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Metatranscriptomics of the Human Oral Microbiome during Health and Disease
Open accessAbstract
The human microbiome plays important roles in health, but when disrupted, these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite interpatient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here, we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that health- and disease-associated communities exhibit defined differences in metabolism that are conserved between patients. In contrast, the metabolic gene expression of individual species was highly variable between patients. These results demonstrate that despite high interpatient variability in microbial composition, disease-associated communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes. IMPORTANCE The human microbiome project has shown that shifts in our microbiota are associated with many diseases, including obesity, Crohn’s disease, diabetes, and periodontitis. While changes in microbial populations are apparent during these diseases, the species associated with each disease can vary from patient to patient. Taking into account this interpatient variability, we hypothesized that specific microbiota-associated diseases would be marked by conserved microbial community behaviors. Here, we use gene expression analyses of patient-matched healthy and diseased human periodontal plaque to show that microbial communities have highly conserved metabolic gene expression profiles, whereas individual species within the community do not. Furthermore, disease-associated communities exhibit conserved changes in metabolic and virulence gene expression.
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“Culture‐independent methods have improved our understanding of microbial diversity in the oral cavity.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [14]
In the citing paper
“Application of transcriptomic approaches has proved extremely significant for delineating both microbial and host gene expression in the context of oral health and pathology.14, 68, 94”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [14]
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“However, despite dissimilar phylogeny, functional signatures among the oral microbiota are often conserved from one individual to another.13, 14”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [14]
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Metadata
- Authors
- Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., & Whiteley, M.
- Affiliations
- The University of Texas at Austin (US)
- Department of Periodontology, School of Dentistry, Ege University, Izmir, Turkey
- Ege University (TR)
- Venue
- mBio
- Publisher
- American Society for Microbiology
- Published
- 2014-05
- Volume
- 5
- Issue
- 2
- Pages
- e01012-14
- ISSN
- 2150-7511 (ISSN-L)
- 2161-2129
- PMC
- PMC3977359
- OpenAlex
- W2146975236
- Cited by
- 386
- References
- 33
- Citations by year
- 2026: 18 · 2025: 30 · 2024: 24 · 2023: 13 · 2022: 25 · 2021: 33 · 2020: 45 · 2019: 39 · 2018: 33 · 2017: 40 · 2016: 33 · 2015: 39 · 2014: 14
- FWCI
- 56.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mBio (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (5f31de021633-02)
- National Institute of Dental and Craniofacial Research (F31 DE021633, R01DE023193, 5F31DE021633-02, R01DE020100)
- 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 › Genomics and Phylogenetic Studies
- Keywords
- oral microbiota, periodontitis, metatranscriptomics, microbial community metabolism, interpatient variability, periodontal plaque, virulence gene expression
- MeSH terms
- Adult, Female, Humans, Male, Mouth, Periodontitis, Metagenome, Transcriptome, Microbiota, Dysbiosis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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