Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness
It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathwa...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-12-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037024000199 |
| _version_ | 1797326341125701632 |
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| author | Eric Patridge Anmol Gorakshakar Matthew M. Molusky Oyetunji Ogundijo Angel Janevski Cristina Julian Lan Hu Momchilo Vuyisich Guruduth Banavar |
| author_facet | Eric Patridge Anmol Gorakshakar Matthew M. Molusky Oyetunji Ogundijo Angel Janevski Cristina Julian Lan Hu Momchilo Vuyisich Guruduth Banavar |
| author_sort | Eric Patridge |
| collection | DOAJ |
| description | It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129). Through this validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions. |
| first_indexed | 2024-03-08T06:21:56Z |
| format | Article |
| id | doaj.art-fe01fe84d48e4c86815a9b6c99c9e33d |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T06:21:56Z |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-fe01fe84d48e4c86815a9b6c99c9e33d2024-02-04T04:44:04ZengElsevierComputational and Structural Biotechnology Journal2001-03702024-12-0123834842Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellnessEric Patridge0Anmol Gorakshakar1Matthew M. Molusky2Oyetunji Ogundijo3Angel Janevski4Cristina Julian5Lan Hu6Momchilo Vuyisich7Guruduth Banavar8Viome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., New York City, USAViome Research Institute, Viome Life Sciences Inc., Seattle, USAViome Research Institute, Viome Life Sciences Inc., New York City, USA; Corresponding author.It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129). Through this validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions.http://www.sciencedirect.com/science/article/pii/S2001037024000199SalivaMetatranscriptomicsOral microbiomeFunctional pathwaysOropharyngeal diseasePrecision wellness |
| spellingShingle | Eric Patridge Anmol Gorakshakar Matthew M. Molusky Oyetunji Ogundijo Angel Janevski Cristina Julian Lan Hu Momchilo Vuyisich Guruduth Banavar Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness Computational and Structural Biotechnology Journal Saliva Metatranscriptomics Oral microbiome Functional pathways Oropharyngeal disease Precision wellness |
| title | Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness |
| title_full | Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness |
| title_fullStr | Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness |
| title_full_unstemmed | Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness |
| title_short | Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness |
| title_sort | microbial functional pathways based on metatranscriptomic profiling enable effective saliva based health assessments for precision wellness |
| topic | Saliva Metatranscriptomics Oral microbiome Functional pathways Oropharyngeal disease Precision wellness |
| url | http://www.sciencedirect.com/science/article/pii/S2001037024000199 |
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