The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

ABSTRACT In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this o...

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Autores principales:	Matthew R. Olm, Cristina N. Butterfield, Alex Copeland, T. Christian Boles, Brian C. Thomas, Jillian F. Banfield
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/131b6608c9964b34aaf3fa17cf8896f5
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spelling	oai:doaj.org-article:131b6608c9964b34aaf3fa17cf8896f52021-11-15T15:51:06ZThe Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis10.1128/mBio.01969-162150-7511https://doaj.org/article/131b6608c9964b34aaf3fa17cf8896f52017-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01969-16https://doaj.org/toc/2150-7511ABSTRACT In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods. IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.Matthew R. OlmCristina N. ButterfieldAlex CopelandT. Christian BolesBrian C. ThomasJillian F. BanfieldAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 8, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Matthew R. Olm Cristina N. Butterfield Alex Copeland T. Christian Boles Brian C. Thomas Jillian F. Banfield The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
description	ABSTRACT In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods. IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.
format	article
author	Matthew R. Olm Cristina N. Butterfield Alex Copeland T. Christian Boles Brian C. Thomas Jillian F. Banfield
author_facet	Matthew R. Olm Cristina N. Butterfield Alex Copeland T. Christian Boles Brian C. Thomas Jillian F. Banfield
author_sort	Matthew R. Olm
title	The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
title_short	The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
title_full	The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
title_fullStr	The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
title_full_unstemmed	The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
title_sort	source and evolutionary history of a microbial contaminant identified through soil metagenomic analysis
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/131b6608c9964b34aaf3fa17cf8896f5
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The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

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