16S rRNA gene primer choice impacts of‑target amplifcation in human gastrointestinal tract biopsies and microbiome profling
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F23%3A00078302" target="_blank" >RIV/65269705:_____/23:00078302 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41598-023-39575-8.pdf" target="_blank" >https://www.nature.com/articles/s41598-023-39575-8.pdf</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 of‑target amplifcation in human gastrointestinal tract biopsies and microbiome profling
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
<a href="/en/project/NU20-03-00126" target="_blank" >NU20-03-00126: Host microbiome in relation to Barrett´s esophagus and esophageal adenocarcinoma development</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
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
Scientific Reports
ISSN
2045-2322
e-ISSN
2045-2322
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
—
UT code for WoS article
001042854100051
EID of the result in the Scopus database
2-s2.0-85166745396