Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure

Abstract Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-indepen...

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Autores principales:	Adrian L. Cookson, Patrick J. Biggs, Jonathan C. Marshall, Angela Reynolds, Rose M. Collis, Nigel P. French, Gale Brightwell
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0ce253bf72004445907cb31370175ed8
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spelling	oai:doaj.org-article:0ce253bf72004445907cb31370175ed82021-12-02T11:52:55ZCulture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure10.1038/s41598-017-00890-62045-2322https://doaj.org/article/0ce253bf72004445907cb31370175ed82017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00890-6https://doaj.org/toc/2045-2322Abstract Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. ‘Animal’ was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.Adrian L. CooksonPatrick J. BiggsJonathan C. MarshallAngela ReynoldsRose M. CollisNigel P. FrenchGale BrightwellNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adrian L. Cookson Patrick J. Biggs Jonathan C. Marshall Angela Reynolds Rose M. Collis Nigel P. French Gale Brightwell Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
description	Abstract Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. ‘Animal’ was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.
format	article
author	Adrian L. Cookson Patrick J. Biggs Jonathan C. Marshall Angela Reynolds Rose M. Collis Nigel P. French Gale Brightwell
author_facet	Adrian L. Cookson Patrick J. Biggs Jonathan C. Marshall Angela Reynolds Rose M. Collis Nigel P. French Gale Brightwell
author_sort	Adrian L. Cookson
title	Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
title_short	Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
title_full	Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
title_fullStr	Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
title_full_unstemmed	Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure
title_sort	culture independent analysis using gnd as a target gene to assess escherichia coli diversity and community structure
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/0ce253bf72004445907cb31370175ed8
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Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure

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