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

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dc.citation.volume7
dc.contributor.authorCookson AL
dc.contributor.authorBiggs PJ
dc.contributor.authorMarshall JC
dc.contributor.authorReynolds A
dc.contributor.authorCollis RM
dc.contributor.authorFrench NP
dc.contributor.authorBrightwell G
dc.date.available2017-04-12
dc.date.available2017-03-16
dc.date.issued2017-04-12
dc.description.abstractCurrent 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.
dc.description.publication-statusPublished
dc.identifierhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000399186000005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=c5bb3b2499afac691c2e3c1a83ef6fef
dc.identifierARTN 841
dc.identifier.citationSCIENTIFIC REPORTS, 2017, 7
dc.identifier.doi10.1038/s41598-017-00890-6
dc.identifier.elements-id342849
dc.identifier.harvestedMassey_Dark
dc.identifier.issn2045-2322
dc.relation.isPartOfSCIENTIFIC REPORTS
dc.rightsOpen Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
dc.titleCulture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure.
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Sciences
pubs.organisational-group/Massey University/College of Sciences/School of Mathematical and Computational Sciences
pubs.organisational-group/Massey University/College of Sciences/School of Natural Sciences
pubs.organisational-group/Massey University/College of Sciences/School of Veterinary Science
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