Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors

ABSTRACT The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bac...

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Autores principales:	Andreia B. Estrela, Toshiki G. Nakashige, Christophe Lemetre, Ian D. Woodworth, Jazz L. Weisman, Louis J. Cohen, Sean F. Brady
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	NF-κB functional screening human microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c30310d16176471586d2970fd4e6b38e
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spelling	oai:doaj.org-article:c30310d16176471586d2970fd4e6b38e2021-11-15T15:54:45ZFunctional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors10.1128/mBio.02587-192150-7511https://doaj.org/article/c30310d16176471586d2970fd4e6b38e2019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02587-19https://doaj.org/toc/2150-7511ABSTRACT The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes. IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli. NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.Andreia B. EstrelaToshiki G. NakashigeChristophe LemetreIan D. WoodworthJazz L. WeismanLouis J. CohenSean F. BradyAmerican Society for MicrobiologyarticleNF-κBfunctional screeninghuman microbiomeMicrobiologyQR1-502ENmBio, Vol 10, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	NF-κB functional screening human microbiome Microbiology QR1-502
spellingShingle	NF-κB functional screening human microbiome Microbiology QR1-502 Andreia B. Estrela Toshiki G. Nakashige Christophe Lemetre Ian D. Woodworth Jazz L. Weisman Louis J. Cohen Sean F. Brady Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
description	ABSTRACT The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes. IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli. NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.
format	article
author	Andreia B. Estrela Toshiki G. Nakashige Christophe Lemetre Ian D. Woodworth Jazz L. Weisman Louis J. Cohen Sean F. Brady
author_facet	Andreia B. Estrela Toshiki G. Nakashige Christophe Lemetre Ian D. Woodworth Jazz L. Weisman Louis J. Cohen Sean F. Brady
author_sort	Andreia B. Estrela
title	Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
title_short	Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
title_full	Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
title_fullStr	Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
title_full_unstemmed	Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors
title_sort	functional multigenomic screening of human-associated bacteria for nf-κb-inducing bioactive effectors
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/c30310d16176471586d2970fd4e6b38e
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Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors

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