skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

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, including taxonomic proportions, or to reach a user-specified maximum number of community members. Asmore » an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).« less

Authors:
 [1]; ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1607036
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 8; Journal Issue: NA; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; constructed community; microbiome; 16S rRNA; synthetic community; taxonomic profiling; in vivo experimentation

Citation Formats

Carper, Dana L., Lawrence, Travis J., Carrell, Alyssa A., Pelletier, Dale, and Weston, David. DISCo-microbe: design of an identifiable synthetic community of microbes. United States: N. p., 2020. Web. doi:10.7717/peerj.8534.
Carper, Dana L., Lawrence, Travis J., Carrell, Alyssa A., Pelletier, Dale, & Weston, David. DISCo-microbe: design of an identifiable synthetic community of microbes. United States. doi:10.7717/peerj.8534.
Carper, Dana L., Lawrence, Travis J., Carrell, Alyssa A., Pelletier, Dale, and Weston, David. Thu . "DISCo-microbe: design of an identifiable synthetic community of microbes". United States. doi:10.7717/peerj.8534. https://www.osti.gov/servlets/purl/1607036.
@article{osti_1607036,
title = {DISCo-microbe: design of an identifiable synthetic community of microbes},
author = {Carper, Dana L. and Lawrence, Travis J. and Carrell, Alyssa A. and Pelletier, Dale and Weston, David},
abstractNote = {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, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).},
doi = {10.7717/peerj.8534},
journal = {PeerJ},
issn = {2167-8359},
number = NA,
volume = 8,
place = {United States},
year = {2020},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Making a microbiome: the many determinants of host-associated microbial community composition
journal, February 2017


Design of synthetic bacterial communities for predictable plant phenotypes
journal, February 2018


Systematic evaluation of error rates and causes in short samples in next-generation sequencing
journal, July 2018


SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012


Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
journal, January 2017


A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota
journal, April 2014


Syntrophic exchange in synthetic microbial communities
journal, April 2014

  • Mee, M. T.; Collins, J. J.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 20
  • DOI: 10.1073/pnas.1405641111

The Plant Microbiome at Work
journal, March 2015


SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes
journal, August 2015


Top considerations for creating bioinformatics software documentation
journal, January 2017

  • Karimzadeh, Mehran; Hoffman, Michael M.
  • Briefings in Bioinformatics, Vol. 19, Issue 4
  • DOI: 10.1093/bib/bbw134

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
journal, July 2015


Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
journal, July 2019


Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass
journal, August 2013

  • Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 36
  • DOI: 10.1073/pnas.1218447110

Simplified and representative bacterial community of maize roots
journal, March 2017

  • Niu, Ben; Paulson, Joseph Nathaniel; Zheng, Xiaoqi
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
  • DOI: 10.1073/pnas.1616148114

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome
journal, April 2008


Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
journal, April 2016

  • Timm, Collin M.; Pelletier, Dale A.; Jawdy, Sara S.
  • Frontiers in Plant Science, Vol. 7
  • DOI: 10.3389/fpls.2016.00497

Biopython: freely available Python tools for computational molecular biology and bioinformatics
journal, March 2009


Niche and host-associated functional signatures of the root surface microbiome
journal, September 2014

  • Ofek-Lalzar, Maya; Sela, Noa; Goldman-Voronov, Milana
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5950

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution
journal, August 2008


Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
journal, August 2016

  • Thoendel, Matthew; Jeraldo, Patricio R.; Greenwood-Quaintance, Kerryl E.
  • Journal of Microbiological Methods, Vol. 127
  • DOI: 10.1016/j.mimet.2016.05.022

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
journal, October 2013


Design and composition of synthetic fungal-bacterial microbial consortia that improve lignocellulolytic enzyme activity
journal, March 2017


Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome
journal, February 2018


Leaf bacterial diversity mediates plant diversity and ecosystem function relationships
journal, May 2017

  • Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian
  • Nature, Vol. 546, Issue 7656
  • DOI: 10.1038/nature22399

PEAR: a fast and accurate Illumina Paired-End reAd mergeR
journal, October 2013


Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010

  • Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
  • DOI: 10.1073/pnas.1000080107

Unravelling the effects of the environment and host genotype on the gut microbiome
journal, March 2011

  • Spor, Aymé; Koren, Omry; Ley, Ruth
  • Nature Reviews Microbiology, Vol. 9, Issue 4
  • DOI: 10.1038/nrmicro2540

Research priorities for harnessing plant microbiomes in sustainable agriculture
journal, March 2017


Ten recommendations for creating usable bioinformatics command line software
journal, November 2013


Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013

  • Cole, James R.; Wang, Qiong; Fish, Jordan A.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1244

FAST: FAST Analysis of Sequences Toolbox
journal, May 2015

  • Lawrence, Travis J.; Kauffman, Kyle T.; Amrine, Katherine C. H.
  • Frontiers in Genetics, Vol. 6
  • DOI: 10.3389/fgene.2015.00172

Towards synthetic microbial consortia for bioprocessing
journal, October 2012

  • Shong, Jasmine; Jimenez Diaz, Manuel Rafael; Collins, Cynthia H.
  • Current Opinion in Biotechnology, Vol. 23, Issue 5
  • DOI: 10.1016/j.copbio.2012.02.001

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions
journal, April 2016


ART: a next-generation sequencing read simulator
journal, December 2011


Enrichment for microbes living in association with plant tissues
journal, April 2006


Impact of Polymerase Fidelity on Background Error Rates in Next-Generation Sequencing with Unique Molecular Identifiers/Barcodes
journal, March 2019


Microbes Drive Evolution of Animals and Plants: the Hologenome Concept
journal, March 2016


Improving saliva shotgun metagenomics by chemical host DNA depletion
journal, February 2018


A communal catalogue reveals Earth’s multiscale microbial diversity
journal, November 2017

  • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
  • Nature, Vol. 551, Issue 7681
  • DOI: 10.1038/nature24621