Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

ABSTRACT Microbiome community composition plays an important role in human health, and while most research to date has focused on high-microbial-biomass communities, low-biomass communities are also important. However, contamination and technical noise make determining the true community signal diff...

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Autores principales:	Vincent Caruso, Xubo Song, Mark Asquith, Lisa Karstens
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	ASV methods OTU clustering bioinformatics microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a3e061abb7754cf286edd06905aa809f
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spelling	oai:doaj.org-article:a3e061abb7754cf286edd06905aa809f2021-12-02T19:46:18ZPerformance of Microbiome Sequence Inference Methods in Environments with Varying Biomass10.1128/mSystems.00163-182379-5077https://doaj.org/article/a3e061abb7754cf286edd06905aa809f2019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00163-18https://doaj.org/toc/2379-5077ABSTRACT Microbiome community composition plays an important role in human health, and while most research to date has focused on high-microbial-biomass communities, low-biomass communities are also important. However, contamination and technical noise make determining the true community signal difficult when biomass levels are low, and the influence of varying biomass on sequence processing methods has received little attention. Here, we benchmarked six methods that infer community composition from 16S rRNA sequence reads, using samples of varying biomass. We included two operational taxonomic unit (OTU) clustering algorithms, one entropy-based method, and three more-recent amplicon sequence variant (ASV) methods. We first compared inference results from high-biomass mock communities to assess baseline performance. We then benchmarked the methods on a dilution series made from a single mock community—samples that varied only in biomass. ASVs/OTUs inferred by each method were classified as representing expected community, technical noise, or contamination. With the high-biomass data, we found that the ASV methods had good sensitivity and precision, whereas the other methods suffered in one area or in both. Inferred contamination was present only in small proportions. With the dilution series, contamination represented an increasing proportion of the data from the inferred communities, regardless of the inference method used. However, correlation between inferred contaminants and sample biomass was strongest for the ASV methods and weakest for the OTU methods. Thus, no inference method on its own can distinguish true community sequences from contaminant sequences, but ASV methods provide the most accurate characterization of community and contaminants. IMPORTANCE Microbial communities have important ramifications for human health, but determining their impact requires accurate characterization. Current technology makes microbiome sequence data more accessible than ever. However, popular software methods for analyzing these data are based on algorithms developed alongside older sequencing technology and smaller data sets and thus may not be adequate for modern, high-throughput data sets. Additionally, samples from environments where microbes are scarce present additional challenges to community characterization relative to high-biomass environments, an issue that is often ignored. We found that a new class of microbiome sequence processing tools, called amplicon sequence variant (ASV) methods, outperformed conventional methods. In samples representing low-biomass communities, where sample contamination becomes a significant confounding factor, the improved accuracy of ASV methods may allow more-robust computational identification of contaminants.Vincent CarusoXubo SongMark AsquithLisa KarstensAmerican Society for MicrobiologyarticleASV methodsOTU clusteringbioinformaticsmicrobiomeMicrobiologyQR1-502ENmSystems, Vol 4, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	ASV methods OTU clustering bioinformatics microbiome Microbiology QR1-502
spellingShingle	ASV methods OTU clustering bioinformatics microbiome Microbiology QR1-502 Vincent Caruso Xubo Song Mark Asquith Lisa Karstens Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
description	ABSTRACT Microbiome community composition plays an important role in human health, and while most research to date has focused on high-microbial-biomass communities, low-biomass communities are also important. However, contamination and technical noise make determining the true community signal difficult when biomass levels are low, and the influence of varying biomass on sequence processing methods has received little attention. Here, we benchmarked six methods that infer community composition from 16S rRNA sequence reads, using samples of varying biomass. We included two operational taxonomic unit (OTU) clustering algorithms, one entropy-based method, and three more-recent amplicon sequence variant (ASV) methods. We first compared inference results from high-biomass mock communities to assess baseline performance. We then benchmarked the methods on a dilution series made from a single mock community—samples that varied only in biomass. ASVs/OTUs inferred by each method were classified as representing expected community, technical noise, or contamination. With the high-biomass data, we found that the ASV methods had good sensitivity and precision, whereas the other methods suffered in one area or in both. Inferred contamination was present only in small proportions. With the dilution series, contamination represented an increasing proportion of the data from the inferred communities, regardless of the inference method used. However, correlation between inferred contaminants and sample biomass was strongest for the ASV methods and weakest for the OTU methods. Thus, no inference method on its own can distinguish true community sequences from contaminant sequences, but ASV methods provide the most accurate characterization of community and contaminants. IMPORTANCE Microbial communities have important ramifications for human health, but determining their impact requires accurate characterization. Current technology makes microbiome sequence data more accessible than ever. However, popular software methods for analyzing these data are based on algorithms developed alongside older sequencing technology and smaller data sets and thus may not be adequate for modern, high-throughput data sets. Additionally, samples from environments where microbes are scarce present additional challenges to community characterization relative to high-biomass environments, an issue that is often ignored. We found that a new class of microbiome sequence processing tools, called amplicon sequence variant (ASV) methods, outperformed conventional methods. In samples representing low-biomass communities, where sample contamination becomes a significant confounding factor, the improved accuracy of ASV methods may allow more-robust computational identification of contaminants.
format	article
author	Vincent Caruso Xubo Song Mark Asquith Lisa Karstens
author_facet	Vincent Caruso Xubo Song Mark Asquith Lisa Karstens
author_sort	Vincent Caruso
title	Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
title_short	Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
title_full	Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
title_fullStr	Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
title_full_unstemmed	Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
title_sort	performance of microbiome sequence inference methods in environments with varying biomass
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/a3e061abb7754cf286edd06905aa809f
work_keys_str_mv	AT vincentcaruso performanceofmicrobiomesequenceinferencemethodsinenvironmentswithvaryingbiomass AT xubosong performanceofmicrobiomesequenceinferencemethodsinenvironmentswithvaryingbiomass AT markasquith performanceofmicrobiomesequenceinferencemethodsinenvironmentswithvaryingbiomass AT lisakarstens performanceofmicrobiomesequenceinferencemethodsinenvironmentswithvaryingbiomass
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Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

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