loading page

Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus-specific primers
  • +1
  • Babak Najafpour,
  • Patricia Pinto,
  • Adelino Canario,
  • Deborah Power
Babak Najafpour
Centro de Ciencias do Mar

Corresponding Author:najafpourbabak@gmail.com

Author Profile
Patricia Pinto
Centro de Ciencias do Mar
Author Profile
Adelino Canario
Centro de Ciencias do Mar
Author Profile
Deborah Power
Centro de Ciencias do Mar
Author Profile

Abstract

The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for eleven bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.
28 Jan 2022Submitted to MicrobiologyOpen
29 Jan 2022Submission Checks Completed
29 Jan 2022Assigned to Editor
29 Jan 2022Reviewer(s) Assigned
09 Feb 2022Review(s) Completed, Editorial Evaluation Pending
09 Feb 2022Editorial Decision: Revise Minor
21 Feb 20221st Revision Received
22 Feb 2022Submission Checks Completed
22 Feb 2022Assigned to Editor
22 Feb 2022Review(s) Completed, Editorial Evaluation Pending
05 Mar 2022Editorial Decision: Accept
Jun 2022Published in MicrobiologyOpen volume 11 issue 3. 10.1002/mbo3.1274