Apr 23, 2020

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota

BioRxiv : the Preprint Server for Biology
Shirin MoossaviM. Azad

Abstract

Background: Quality control including assessment of batch variabilities and confirmation of repeatability and reproducibility are integral component of high throughput omics studies including microbiome research. Batch effects can mask true biological results and/or result in irreproducible conclusions and interpretations. Low biomass samples in microbiome research are prone to reagent contamination; yet, quality control procedures for low biomass samples in large-scale microbiome studies are not well established. Results: In this study we have proposed a framework for an in-depth step-by-step approach to address this gap. The framework consists of three independent stages: 1) verification of sequencing accuracy by assessing technical repeatability and reproducibility of the results using mock communities and biological controls; 2) contaminant removal and batch variability correction by applying a two-tier strategy using statistical algorithms (e.g. decontam) followed by comparison of the data structure between batches; and 3) corroborating the repeatability and reproducibility of microbiome composition and downstream statistical analysis. Using this approach on the milk microbiota data from the CHILD Cohort generated in two b...Continue Reading

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Mentioned in this Paper

Metabolic Process, Cellular
Establishment and Maintenance of Localization
Transcription Cofactor Activity
Enzymes, antithrombotic
Bacteriophages
Fluorescent stain
Enzymes for Treatment of Wounds and Ulcers
Tracking
Cellular Component Organization
Analysis

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