Open AccessA priori Considerations When Conducting High‐Throughput Amplicon‐Based Sequence Analysis
Author(s) -
Sengupta Aditi,
Dick Warren A.
Publication year - 2016
Publication title -
agricultural and environmental letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.681
H-Index - 12
ISSN - 2471-9625
DOI - 10.2134/ael2015.11.0010
Subject(s) - amplicon sequencing , data science , metagenomics , dna sequencing , throughput , computer science , popularity , metadata , microbial ecology , a priori and a posteriori , biology , ecology , world wide web , psychology , genetics , 16s ribosomal rna , dna , telecommunications , social psychology , bacteria , gene , wireless , philosophy , epistemology
Core Ideas High‐throughput sequence analysis of microbes is gaining popularity. Researchers in agronomy, soil, crop, and environmental sciences are interested in such analyses. We briefly discuss a priori considerations to guide such researchers. Developing successful research questions, experiments, and data analysis is the goal.Amplicon‐based sequencing strategies that include 16S rRNA and functional genes, alongside “meta‐omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next‐generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high‐throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high‐throughput amplicon‐based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high‐throughput microbial DNA sequencing and sequences analysis.