Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa.

DNA Primers / metabolism DNA Probes / metabolism Feces / microbiology Gastrointestinal Microbiome / genetics High-Throughput Nucleotide Sequencing Phylogeny Polymerase Chain Reaction / methods RNA, Ribosomal, 16S / genetics
Diet Gut microbiome Microbial biomarkers Nutrition assessment technique Quantitative real-time PCR Responders Taxonomic profiling

Journal

Molecular and cellular probes
ISSN: 1096-1194
Titre abrégé: Mol Cell Probes
Pays: England
ID NLM: 8709751

Informations de publication

Date de publication:
08 2020
Historique:
received: 31 01 2020
revised: 02 04 2020
accepted: 02 04 2020
pubmed: 19 4 2020
medline: 3 6 2021
entrez: 19 4 2020
Statut: ppublish

Résumé

Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods - the platform and high-throughput 16S rRNA sequencing - across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.

Identifiants

DOI: 10.1016/j.mcp.2020.101570 PMID: 32304824 PMC: PMC7158812
pubmed: 32304824
pii: S0890-8508(20)30064-5
doi: 10.1016/j.mcp.2020.101570
pmc: PMC7158812
pii:
doi:

Substances chimiques

DNA Primers 0
DNA Probes 0
RNA, Ribosomal, 16S 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

101570

Informations de copyright

Copyright © 2020 Elsevier Ltd. All rights reserved.

Déclaration de conflit d'intérêts

Decalartion of competing interest The authors declare that they have no competing interests.

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Auteurs

Irina Kurina (I)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia; Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia. Electronic address: kurina@atlas.ru.

Anna Popenko (A)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia; Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia.

Natalia Klimenko (N)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova str., 119334, Moscow, Russia.

Stanislav Koshechkin (S)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia.

Liubov Chuprikova (L)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia.

Maxim Filipenko (M)

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev ave., Novosibirsk, 630090, Russia.

Alexander Tyakht (A)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova str., 119334, Moscow, Russia. Electronic address: a.tyakht@gmail.com.

Dmitry Alexeev (D)

Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar str., building 42, premise 1, room 1639, Moscow, 143026, Russia; Atlas Biomed Group, 31 Malaya Nikitskaya str., 121069, Moscow, Russia.

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Classifications MeSH

questionsmedicales.fr › Actions chimiques et utilisations › Utilisations spécialisées de produits chimiques › Produits chimiques de laboratoire › Sondes moléculaires › Sondes d'acide nucléique › Sondes d'ADN › Amorces ADN › Development of qPCR platform with probes for...
questionsmedicales.fr › Actions chimiques et utilisations › Utilisations spécialisées de produits chimiques › Produits chimiques de laboratoire › Sondes moléculaires › Sondes d'acide nucléique › Sondes d'ADN › Development of qPCR platform with probes for...
questionsmedicales.fr › Liquides et sécrétions biologiques › Fèces › Development of qPCR platform with probes for...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Microbiome gastro-intestinal › Development of qPCR platform with probes for...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Development of qPCR platform with probes for...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Development of qPCR platform with probes for...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › Réaction de polymérisation en chaîne › Development of qPCR platform with probes for...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › ARN ribosomique 16S › Development of qPCR platform with probes for...