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PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification Ghezzi, Hans; Fan, M. Yiyun; Ng, M. Katharine; Burckhardt, C. Juan; Pepin, M. Deanna; Lin, Xuan; Ziels, M. Ryan; Tropini, Carolina

Description

Characterizing microbial communities at high-resolution is crucial to unravel the complexity and functional diversity of microbial ecosystems, providing valuable insights into human health and ecology. Over the last decades, advances in bulk sequencing assays, such as 16S rRNA and shotgun sequencing, have enabled unparalleled qualitative and quantitative investigations of microbial communities. However, these methods generally do not provide resolution beyond the genus- or species-level, only measure relative abundance, and do not account for spatial organization, overlooking intricate details and functional insights on the real gut microbial heterogeneity. PUPpy (Phylogenetically Unique Primers in python) is a fully automated pipeline to design taxon-specific primers for any defined bacterial community. PUPpy-designed primers can be used to detect individual microbes and quantify absolute microbial abundance, providing more resolved and accurate quantification in gnotobiotic communities than 16S and shotgun sequencing.

Item Metadata

Title	PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification
Creator	Ghezzi, Hans; Fan, M. Yiyun; Ng, M. Katharine; Burckhardt, C. Juan; Pepin, M. Deanna; Lin, Xuan; Ziels, M. Ryan; Tropini, Carolina
Contributor	Ghezzi, Hans; University of British Columbia; University of British Columbia Four Year Doctoral Fellowship
Date Issued	2024-01-29
Description	Characterizing microbial communities at high-resolution is crucial to unravel the complexity and functional diversity of microbial ecosystems, providing valuable insights into human health and ecology. Over the last decades, advances in bulk sequencing assays, such as 16S rRNA and shotgun sequencing, have enabled unparalleled qualitative and quantitative investigations of microbial communities. However, these methods generally do not provide resolution beyond the genus- or species-level, only measure relative abundance, and do not account for spatial organization, overlooking intricate details and functional insights on the real gut microbial heterogeneity. PUPpy (Phylogenetically Unique Primers in python) is a fully automated pipeline to design taxon-specific primers for any defined bacterial community. PUPpy-designed primers can be used to detect individual microbes and quantify absolute microbial abundance, providing more resolved and accurate quantification in gnotobiotic communities than 16S and shotgun sequencing.
Subject	Computer and Information Science; Medicine, Health and Life Sciences; Pipeline; taxon-specific primers; resolution; microbiome
Geographic Location	Vancouver; British Columbia
Type	Dataset
Language	English
Date Available	2023-10-11
Provider	University of British Columbia Library
License	CC-BY 4.0
DOI	10.14288/1.0438913
URI	https://doi.org/10.5683/SP3/HWXPV3
Publisher DOI	https://doi.org/10.5683/SP3/HWXPV3
Rights URI	http://creativecommons.org/licenses/by/4.0
Country	Canada
Aggregated Source Repository	Dataverse

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CC-BY 4.0