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Lookup NU author(s): Dr Amelie Ott, Marcos Quintela-Baluja, Dr Andrew Zealand, Dr Greg O'Donnell, Professor David GrahamORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
BackgroundUnderstanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks.ResultsHere we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation.ConclusionsMethods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.
Author(s): Ott A, Quintela M, Zealand AM, ODonnell G, Hanifah MRM, Graham DW
Publication type: Article
Publication status: Published
Journal: Environmental Microbiome
Year: 2021
Volume: 16
Print publication date: 18/11/2021
Online publication date: 18/11/2021
Acceptance date: 04/11/2021
Date deposited: 20/11/2021
ISSN (electronic): 2524-6372
Publisher: Springer Nature
URL: https://doi.org/10.1186/s40793-021-00391-0
DOI: 10.1186/s40793-021-00391-0
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