"
Team:Evry/Biology/Chassis/Pseudovibrio
From 2014.igem.org
(Difference between revisions)
| Line 17: | Line 17: | ||
<div align="justify"> | <div align="justify"> | ||
| - | At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning <i>Pseudovibrio genius</i>, only 5 mentionning <i>Pseudovibrio denitrificans, and finally none about a genetic engineering system in it. | + | At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning <i>Pseudovibrio genius</i>, only 5 mentionning <i>Pseudovibrio denitrificans</i>, and finally none about a genetic engineering system in it. |
<br><br> | <br><br> | ||
Revision as of 19:49, 12 October 2014
Pseudovibrio denitrificans the bacterium to modify.
== From a poorly known genius, a jewel emerged ==
At first glance working on the microbiome of sponges appears like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentionning Pseudovibrio genius, only 5 mentionning Pseudovibrio denitrificans, and finally none about a genetic engineering system in it.
Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of Pseudovibrio denitrificans with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (cf toxic compound) and easy to sourced at DMSZ.
On the other hand to that Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of Pseudovibrio denitrificans with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (cf toxic compound) and easy to sourced at DMSZ.
On the other hand to that Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
== A bacterium we could work with ==
In the literature Pseudovibrio denitrificans is described as a Gram-negative, motile by means of one to several lateral or subpolar flagella requiring NaCl for growth and exhibited optimal growth at about 30 degrees C, pH 8 and 3 % NaCl.
They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our RNAseq study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors.
The following section describe the protocol use to optimize (Rich media) & control(Minimal media) growth conditions
They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our RNAseq study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors.
The following section describe the protocol use to optimize (Rich media) & control(Minimal media) growth conditions
