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Shetty et al. Microbiome Res Rep 2023;2:14 Microbiome Research
DOI: 10.20517/mrr.2022.18
Reports

Technical Note Open Access

A tool to assess the mock community samples in
16S rRNA gene-based microbiota profiling studies

1
Sudarshan A. Shetty 1,2 , Jolanda Kool , Susana Fuentes 1
1
Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan
9, Bilthoven 3721 MA, Netherlands.
2
Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical
Center Groningen, Hanzeplein 1, Groningen 9713 GZ, Netherlands.
Correspondence to: Dr. Sudarshan A. Shetty. Center for Infectious Disease Control, National Institute for Public Health and the
Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands. E-mail: sudarshanshetty9@gmail.com; Dr.
Susana Fuentes. Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van
Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands. E-mail: susana.fuentes@rivm.nl

How to cite this article: Shetty SA, Kool J, Fuentes S. A tool to assess the mock community samples in 16S rRNA gene-based
microbiota profiling studies. Microbiome Res Rep 2023;2:14. https://dx.doi.org/10.20517/mrr.2022.18

Received: 23 Nov 2022 First Decision: 13 Feb 2023 Revised: 24 Mar 2023 Accepted: 17 Apr 2023 Published: 27 Apr 2023

Academic Editors: Jennifer Mahony, Marco Ventura Copy Editor: Ke-Cui Yang Production Editor: Ke-Cui Yang

Abstract
Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding
technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare
the composition of mock communities that are processed along with samples to their theoretical composition. A
visual comparison between experimental and theoretical community composition and their correlation is provided
for researchers to assess the quality of their sample processing workflows.

Keywords: Mock community, microbiome profiling, positive control

INTRODUCTION
Microbiota profiling of diverse environments is widely done using 16S rRNA gene sequencing. Preparation
of samples for microbiota profiling consists of sampling, storage, DNA extraction, PCR, library preparation,
[1-4]
sequencing, and downstream bioinformatics analysis . At every step, technical variability is a major factor
that can ultimately affect the observed microbiota profiles . Including negative and positive controls,
[5-8]

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing,
adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as
long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and
indicate if changes were made.

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