Construction and characterization of synthetic bacterial community for experimental ecology and evolution

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.

Original languageEnglish
Article number312
JournalFrontiers in Genetics
Volume9
Number of pages12
ISSN1664-8021
DOIs
Publication statusPublished - 14 Aug 2018
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1181 Ecology, evolutionary biology
  • microbial community
  • model system
  • synthetic ecology
  • experimental evolution
  • whole-genome sequencing
  • MICROCOSM EXPERIMENTS
  • SPECIES INTERACTIONS
  • LIMITED RELEVANCE
  • ECOSYSTEM ECOLOGY
  • ESCHERICHIA-COLI
  • READ ALIGNMENT
  • SEARCH TOOL
  • IN-SITU
  • SYSTEM
  • COOPERATION

Cite this

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title = "Construction and characterization of synthetic bacterial community for experimental ecology and evolution",
abstract = "Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.",
keywords = "1181 Ecology, evolutionary biology, microbial community, model system, synthetic ecology, experimental evolution, whole-genome sequencing, MICROCOSM EXPERIMENTS, SPECIES INTERACTIONS, LIMITED RELEVANCE, ECOSYSTEM ECOLOGY, ESCHERICHIA-COLI, READ ALIGNMENT, SEARCH TOOL, IN-SITU, SYSTEM, COOPERATION",
author = "Johannes Cairns and Roosa Jokela and Jenni Hultman and Manu Tamminen and Marko Virta and Teppo Hiltunen",
year = "2018",
month = "8",
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doi = "10.3389/fgene.2018.00312",
language = "English",
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journal = "Frontiers in Genetics",
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Construction and characterization of synthetic bacterial community for experimental ecology and evolution. / Cairns, Johannes; Jokela, Roosa; Hultman, Jenni; Tamminen, Manu; Virta, Marko; Hiltunen, Teppo.

In: Frontiers in Genetics, Vol. 9, 312, 14.08.2018.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Construction and characterization of synthetic bacterial community for experimental ecology and evolution

AU - Cairns, Johannes

AU - Jokela, Roosa

AU - Hultman, Jenni

AU - Tamminen, Manu

AU - Virta, Marko

AU - Hiltunen, Teppo

PY - 2018/8/14

Y1 - 2018/8/14

N2 - Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.

AB - Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.

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KW - synthetic ecology

KW - experimental evolution

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KW - MICROCOSM EXPERIMENTS

KW - SPECIES INTERACTIONS

KW - LIMITED RELEVANCE

KW - ECOSYSTEM ECOLOGY

KW - ESCHERICHIA-COLI

KW - READ ALIGNMENT

KW - SEARCH TOOL

KW - IN-SITU

KW - SYSTEM

KW - COOPERATION

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