DISCo-microbe: design of an identifiable synthetic community of microbes

PeerJ
Dana L CarperDavid J Weston

Abstract

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts' phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, includi...Continue Reading

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Citations

Nov 3, 2020·Bioinformatics·Travis J LawrenceJessy L Labbé

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Methods Mentioned

BETA
PCR
amplicon sequencing
Illumina sequencing

Software Mentioned

Biopython
QIIME2
FAST
PEAR
DISCo
dada2
fasgrep
GitHub
BLASTN
BLAST

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