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16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14110%2F23%3A00132245" target="_blank" >RIV/00216224:14110/23:00132245 - isvavai.cz</a>

  • Result on the web

    <a href="https://www.nature.com/articles/s41598-023-39575-8" target="_blank" >https://www.nature.com/articles/s41598-023-39575-8</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1038/s41598-023-39575-8" target="_blank" >10.1038/s41598-023-39575-8</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

  • Original language description

    16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1-V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1-V2M primers. Moreover, the V1-V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1-V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10700 - Other natural sciences

Result continuities

  • Project

    Result was created during the realization of more than one project. More information in the Projects tab.

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2023

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Nature Scientific Reports

  • ISSN

    2045-2322

  • e-ISSN

  • Volume of the periodical

    13

  • Issue of the periodical within the volume

    1

  • Country of publishing house

    DE - GERMANY

  • Number of pages

    10

  • Pages from-to

    1-10

  • UT code for WoS article

    001042854100051

  • EID of the result in the Scopus database

    2-s2.0-85166745396