Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

ABSTRACT Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are c...

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Autores principales:	André M. Comeau, Gavin M. Douglas, Morgan G. I. Langille
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	16S rRNA gene sequencing Microbiome Helper bioinformatics dual-indexing PCR education metagenomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/3e68d0895c4a47178c5a0421cd99dc03
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spelling	oai:doaj.org-article:3e68d0895c4a47178c5a0421cd99dc032021-12-02T18:39:33ZMicrobiome Helper: a Custom and Streamlined Workflow for Microbiome Research10.1128/mSystems.00127-162379-5077https://doaj.org/article/3e68d0895c4a47178c5a0421cd99dc032017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00127-16https://doaj.org/toc/2379-5077ABSTRACT Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki ). IMPORTANCE As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results. Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper. As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials.André M. ComeauGavin M. DouglasMorgan G. I. LangilleAmerican Society for Microbiologyarticle16S rRNA gene sequencingMicrobiome Helperbioinformaticsdual-indexing PCReducationmetagenomicsMicrobiologyQR1-502ENmSystems, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA gene sequencing Microbiome Helper bioinformatics dual-indexing PCR education metagenomics Microbiology QR1-502
spellingShingle	16S rRNA gene sequencing Microbiome Helper bioinformatics dual-indexing PCR education metagenomics Microbiology QR1-502 André M. Comeau Gavin M. Douglas Morgan G. I. Langille Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
description	ABSTRACT Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki ). IMPORTANCE As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results. Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper. As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials.
format	article
author	André M. Comeau Gavin M. Douglas Morgan G. I. Langille
author_facet	André M. Comeau Gavin M. Douglas Morgan G. I. Langille
author_sort	André M. Comeau
title	Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
title_short	Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
title_full	Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
title_fullStr	Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
title_full_unstemmed	Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
title_sort	microbiome helper: a custom and streamlined workflow for microbiome research
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/3e68d0895c4a47178c5a0421cd99dc03
work_keys_str_mv	AT andremcomeau microbiomehelperacustomandstreamlinedworkflowformicrobiomeresearch AT gavinmdouglas microbiomehelperacustomandstreamlinedworkflowformicrobiomeresearch AT morgangilangille microbiomehelperacustomandstreamlinedworkflowformicrobiomeresearch
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Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

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