Bioprospecting of Trichococcus species

Nikolaos Strepis

Research output: Thesisinternal PhD, WU

Abstract

Since 1928 with the discovery of penicillin, the value of microbes in our society significantly was reconsidered. Nowadays, 60% of commercial drugs and products mimic or derive from microbialmetabolites. After almost a century, can we find new compounds and where? For addressing thisquestion, we need a large-scale screening of the microbial capabilities. Trichococcus species have multiple genes for producing 1,3-propanediol (1,3-PDO), which synthesizes the partially biodegradable plastic PTT. Based on this, we developed a strategy for analyzing 90,000 bacterial genomes that eventually generated information for every microbial characteristic. The outstanding factor is that all this information is stored in a database that can be easily mined for everything. This collective andunbiased strategy resulted in identifying the key genes for efficient production of 1,3-PDO. We discovered 187 novel candidates that can produce 1,3-PDO and some were in the lab confirmed.

Another result of the screening was about Trichococcus patagoniensis. This bacterium grows in minus 5 degrees without oxygen and was discovered by NASA scientists to simulate life in other planets. When it is cold and without oxygen, T. patagoniensis “extra-terrestrial” properties allow it to create its own ”blanket” by producing exopolymer saccharides. We characterized this cryoprotectant compound as inulin, which prevents crystallization of water and many plants use it for preserving their roots in subzero temperatures. Furthermore, inulin is a commercial prebiotic and is connected with gut health. Considering the bacterial kingdom, there are limited members producing inulin and none of them wereidentified as prychrotolerant species. T. patagoniensisis produces plenty of inulin and due to its robustness, easily can be the next biofactory for the compound.The applied methods in this PhD thesis is a platform for mining every bacterial or metabolic information. All the knowledge is there and we need to dive into it. Every finding will be revolutionary and expand our perspective for microbes. Big data mining is like Zenos Dichotomy paradox, we will always know half and never everything.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Stams, Fons, Promotor
  • Machado de Sousa, Diana, Co-promotor
  • Schaap, Peter, Co-promotor
Award date16 Jan 2019
Place of PublicationWageningen
Publisher
Print ISBNs9789463433884
DOIs
Publication statusPublished - 2019

Fingerprint

Trichococcus
inulin
propanediols
Thiocystis minor
screening
microorganisms
oxygen
biodegradability
cryoprotectants
penicillins
prebiotics
crystallization
genes
digestive system
plastics
carbohydrates
drugs
genome
temperature
water

Cite this

Strepis, N. (2019). Bioprospecting of Trichococcus species. Wageningen: Wageningen University. https://doi.org/10.18174/465966
Strepis, Nikolaos. / Bioprospecting of Trichococcus species. Wageningen : Wageningen University, 2019. 228 p.
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title = "Bioprospecting of Trichococcus species",
abstract = "Since 1928 with the discovery of penicillin, the value of microbes in our society significantly was reconsidered. Nowadays, 60{\%} of commercial drugs and products mimic or derive from microbialmetabolites. After almost a century, can we find new compounds and where? For addressing thisquestion, we need a large-scale screening of the microbial capabilities. Trichococcus species have multiple genes for producing 1,3-propanediol (1,3-PDO), which synthesizes the partially biodegradable plastic PTT. Based on this, we developed a strategy for analyzing 90,000 bacterial genomes that eventually generated information for every microbial characteristic. The outstanding factor is that all this information is stored in a database that can be easily mined for everything. This collective andunbiased strategy resulted in identifying the key genes for efficient production of 1,3-PDO. We discovered 187 novel candidates that can produce 1,3-PDO and some were in the lab confirmed. Another result of the screening was about Trichococcus patagoniensis. This bacterium grows in minus 5 degrees without oxygen and was discovered by NASA scientists to simulate life in other planets. When it is cold and without oxygen, T. patagoniensis “extra-terrestrial” properties allow it to create its own ”blanket” by producing exopolymer saccharides. We characterized this cryoprotectant compound as inulin, which prevents crystallization of water and many plants use it for preserving their roots in subzero temperatures. Furthermore, inulin is a commercial prebiotic and is connected with gut health. Considering the bacterial kingdom, there are limited members producing inulin and none of them wereidentified as prychrotolerant species. T. patagoniensisis produces plenty of inulin and due to its robustness, easily can be the next biofactory for the compound.The applied methods in this PhD thesis is a platform for mining every bacterial or metabolic information. All the knowledge is there and we need to dive into it. Every finding will be revolutionary and expand our perspective for microbes. Big data mining is like Zenos Dichotomy paradox, we will always know half and never everything.",
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Strepis, N 2019, 'Bioprospecting of Trichococcus species', Doctor of Philosophy, Wageningen University, Wageningen. https://doi.org/10.18174/465966

Bioprospecting of Trichococcus species. / Strepis, Nikolaos.

Wageningen : Wageningen University, 2019. 228 p.

Research output: Thesisinternal PhD, WU

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T1 - Bioprospecting of Trichococcus species

AU - Strepis, Nikolaos

N1 - WU thesis 7136 Includes bibliographical references. - With summary in English

PY - 2019

Y1 - 2019

N2 - Since 1928 with the discovery of penicillin, the value of microbes in our society significantly was reconsidered. Nowadays, 60% of commercial drugs and products mimic or derive from microbialmetabolites. After almost a century, can we find new compounds and where? For addressing thisquestion, we need a large-scale screening of the microbial capabilities. Trichococcus species have multiple genes for producing 1,3-propanediol (1,3-PDO), which synthesizes the partially biodegradable plastic PTT. Based on this, we developed a strategy for analyzing 90,000 bacterial genomes that eventually generated information for every microbial characteristic. The outstanding factor is that all this information is stored in a database that can be easily mined for everything. This collective andunbiased strategy resulted in identifying the key genes for efficient production of 1,3-PDO. We discovered 187 novel candidates that can produce 1,3-PDO and some were in the lab confirmed. Another result of the screening was about Trichococcus patagoniensis. This bacterium grows in minus 5 degrees without oxygen and was discovered by NASA scientists to simulate life in other planets. When it is cold and without oxygen, T. patagoniensis “extra-terrestrial” properties allow it to create its own ”blanket” by producing exopolymer saccharides. We characterized this cryoprotectant compound as inulin, which prevents crystallization of water and many plants use it for preserving their roots in subzero temperatures. Furthermore, inulin is a commercial prebiotic and is connected with gut health. Considering the bacterial kingdom, there are limited members producing inulin and none of them wereidentified as prychrotolerant species. T. patagoniensisis produces plenty of inulin and due to its robustness, easily can be the next biofactory for the compound.The applied methods in this PhD thesis is a platform for mining every bacterial or metabolic information. All the knowledge is there and we need to dive into it. Every finding will be revolutionary and expand our perspective for microbes. Big data mining is like Zenos Dichotomy paradox, we will always know half and never everything.

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Strepis N. Bioprospecting of Trichococcus species. Wageningen: Wageningen University, 2019. 228 p. https://doi.org/10.18174/465966