Journal ArticleDOI
Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers
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TLDR
A pair of PCR primers were designed which, when used in combination with the previously developed degenerate, universal cpn60 primers, improve the representation of templates with high G+C content and represents an improvement of established methods and a significant advance in the ability to generate cPN60 PCR product libraries that more closely represent the sequence diversity in complex templates.Abstract:
Some classes of high G+C content organisms such as the Actinobacteria, which are known through culture-based studies to be present in large numbers in particular microbial communities, are under-represented or even absent from 16S rRNA or cpn60 polymerase chain reaction (PCR) product libraries derived from these templates. Using reference cpn60 sequence data from organisms with high G+C content genomes, a pair of PCR primers were designed which, when used in combination with the previously developed degenerate, universal cpn60 primers, improve the representation of templates with high G+C content. The primers were validated using a combination of traditional and quantitative real-time PCR on both manufactured template mixtures and biological samples. The development and optimization of this specific primer mixture represents an improvement of established methods and a significant advance in the ability to generate cpn60 PCR product libraries that more closely represent the sequence diversity in complex templates.read more
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Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle
Bonnie Chaban,Matthew G. Links,Matthew G. Links,Teenus Paramel Jayaprakash,Emily C. Wagner,Danielle K Bourque,Zoe Lohn,Arianne Albert,Julie van Schalkwyk,Gregor Reid,Sean M. Hemmingsen,Sean M. Hemmingsen,Janet E. Hill,Deborah Money +13 more
TL;DR: The cpn 60-based investigation of the vaginal microbiome demonstrated that in healthy women most vaginal microbiomes remained stable through their menstrual cycle, with little variation in diversity and only modest fluctuations in species richness.
Journal ArticleDOI
The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data.
Matthew G. Links,Matthew G. Links,Tim J. Dumonceaux,Tim J. Dumonceaux,Sean M. Hemmingsen,Sean M. Hemmingsen,Janet E. Hill +6 more
TL;DR: The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies and a large barcode gap for cpn60 provided a robust target for species-level characterization of data.
Journal ArticleDOI
The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women
Aline C. Freitas,Bonnie Chaban,Bonnie Chaban,Alan D. Bocking,Alan D. Bocking,Maria Rocco,Siwen Yang,Siwen Yang,Janet E. Hill,Deborah Money +9 more
TL;DR: This study characterized the vaginal microbiomes of healthy pregnant women at 11–16 weeks of gestational age and compared them to those of non-pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.
Journal ArticleDOI
Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds.
Matthew G. Links,Matthew G. Links,Tigst Demeke,Tom Gräfenhan,Janet E. Hill,Sean M. Hemmingsen,Tim J. Dumonceaux,Tim J. Dumonceaux +7 more
TL;DR: A core seed-associated microbiota shared between diverse plant genera is revealed, providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds.
Journal ArticleDOI
Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers.
M.H. Farris,J.B. Olson +1 more
TL;DR: The aims of this study were to develop media to cultivate actinomycetes, screen the resulting isolates with Actinobacteria‐specific primers, and examine the efficacy of detection of the actinobacterial isolate with universal primers.
References
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Journal ArticleDOI
Base pairing involving deoxyinosine: implications for probe design
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