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Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria

Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai’i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalen...

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Autores principales: Hendrix, Jo, Epperson, L. Elaine, Tong, Eric I., Chan, Yvonne L., Hasan, Nabeeh A., Dawrs, Stephanie N., Norton, Grant J., Virdi, Ravleen, Crooks, James L., Chan, Edward D., Honda, Jennifer R., Strong, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10499228/
https://www.ncbi.nlm.nih.gov/pubmed/37703253
http://dx.doi.org/10.1371/journal.pone.0291072
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author Hendrix, Jo
Epperson, L. Elaine
Tong, Eric I.
Chan, Yvonne L.
Hasan, Nabeeh A.
Dawrs, Stephanie N.
Norton, Grant J.
Virdi, Ravleen
Crooks, James L.
Chan, Edward D.
Honda, Jennifer R.
Strong, Michael
author_facet Hendrix, Jo
Epperson, L. Elaine
Tong, Eric I.
Chan, Yvonne L.
Hasan, Nabeeh A.
Dawrs, Stephanie N.
Norton, Grant J.
Virdi, Ravleen
Crooks, James L.
Chan, Edward D.
Honda, Jennifer R.
Strong, Michael
author_sort Hendrix, Jo
collection PubMed
description Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai’i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai’i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai’i, community scientists of Hawai’i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O’ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai’i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai’i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities.
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spelling pubmed-104992282023-09-14 Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria Hendrix, Jo Epperson, L. Elaine Tong, Eric I. Chan, Yvonne L. Hasan, Nabeeh A. Dawrs, Stephanie N. Norton, Grant J. Virdi, Ravleen Crooks, James L. Chan, Edward D. Honda, Jennifer R. Strong, Michael PLoS One Research Article Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai’i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai’i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai’i, community scientists of Hawai’i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O’ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai’i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai’i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities. Public Library of Science 2023-09-13 /pmc/articles/PMC10499228/ /pubmed/37703253 http://dx.doi.org/10.1371/journal.pone.0291072 Text en © 2023 Hendrix et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hendrix, Jo
Epperson, L. Elaine
Tong, Eric I.
Chan, Yvonne L.
Hasan, Nabeeh A.
Dawrs, Stephanie N.
Norton, Grant J.
Virdi, Ravleen
Crooks, James L.
Chan, Edward D.
Honda, Jennifer R.
Strong, Michael
Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title_full Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title_fullStr Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title_full_unstemmed Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title_short Complete genome assembly of Hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
title_sort complete genome assembly of hawai’i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10499228/
https://www.ncbi.nlm.nih.gov/pubmed/37703253
http://dx.doi.org/10.1371/journal.pone.0291072
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