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Page 4 of 5 Shetty et al. Microbiome Res Rep 2023;2:14 https://dx.doi.org/10.20517/mrr.2022.18

website (https://microsud.github.io/chkMocks/) and include an example of how to compare the custom
mocks with their theoretical composition. Of note, we rely on the DECIPHER:IdTaxa function for
[23]
taxonomic assignments and chkMocks only supports bacteria and archaea .

To demonstrate the application for custom mock communities, we used data from a study investigating an
ASV profiling tool, NG-Tax and experimental samples from a previous synthetic microbiome study .
[24]
[25]
TM
Additionally, we also provide training sets for the ZymoBIOMICS Microbial Community Standard
(Catalog No. D6331) which consists of 19 of the 21 microbes. The two fungi, Candida albicans and
Saccharomyces cerevisiae, are excluded from this training set.
CONCLUSION
The chkMocks was developed for the comparison of experimental mock communities with their expected
compositions. The wet-lab protocols are often standardized depending on the target ecosystem that is
investigated. Standardization requires analysis of positive controls, which are often microbial communities
of known composition. Furthermore, a comparison of mock communities between batches when
processing a large number of samples can help identify any technical variability. We developed a simple-to-
use R package to ease the process of standardization and general quality check.

DECLARATIONS
Authors’ contributions
Conceptualized the work: Shetty SA, Fuentes S
Wrote the code: Shetty SA
Provided technical assistance: Kool J

Availability of data and materials
The chkMocks is implemented in the R statistical language and is released under the MIT license. The
source code and associated example data are available at: https://github.com/microsud/chkMocks/.

Financial support and sponsorship
This work was supported by the Dutch Ministry of Health, Welfare and Sport, and the Strategic Program of
the National Institute for Public Health and the Environment (RIVM).

Conflicts of interest
All authors declared that there are no conflicts of interest. While we use ZymoBiomics data, we, the
developers of chkMocks, are not associated with the manufacturers and this work should not be considered
as an endorsement for the said product.

Ethical approval and consent to participate
Not applicable.

Consent for publication
Not applicable.

Copyright
© The Author(s) 2023.