The genetic basis for adaptation of model-designed syntrophic co-cultures.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
03 2019
03 2019
Historique:
received:
16
05
2018
accepted:
07
02
2019
revised:
13
03
2019
pubmed:
2
3
2019
medline:
30
4
2019
entrez:
2
3
2019
Statut:
epublish
Résumé
Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains-with diverse metabolic deficiencies-were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities.
Identifiants
pubmed: 30822347
doi: 10.1371/journal.pcbi.1006213
pii: PCOMPBIOL-D-18-00756
pmc: PMC6415869
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1006213Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM057089
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI124316
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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