| Title |
Exploring the genomic traits of fungus-feeding bacterial genus Collimonas
|
|---|---|
| Published in |
BMC Genomics, December 2015
|
| DOI | 10.1186/s12864-015-2289-3 |
| Pubmed ID | |
| Authors |
Chunxu Song, Ruth Schmidt, Victor de Jager, Dorota Krzyzanowska, Esmer Jongedijk, Katarina Cankar, Jules Beekwilder, Anouk van Veen, Wietse de Boer, Johannes A. van Veen, Paolina Garbeva |
| Abstract |
Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities. In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7 % of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities. Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp. |
X Demographics
The data shown below were collected from the profiles of 9 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Norway | 1 | 11% |
| France | 1 | 11% |
| Australia | 1 | 11% |
| Unknown | 6 | 67% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 9 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 82 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 82 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 16 | 20% |
| Student > Ph. D. Student | 15 | 18% |
| Student > Master | 9 | 11% |
| Student > Bachelor | 9 | 11% |
| Professor | 4 | 5% |
| Other | 17 | 21% |
| Unknown | 12 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 31 | 38% |
| Biochemistry, Genetics and Molecular Biology | 11 | 13% |
| Environmental Science | 7 | 9% |
| Immunology and Microbiology | 6 | 7% |
| Medicine and Dentistry | 4 | 5% |
| Other | 6 | 7% |
| Unknown | 17 | 21% |
Attention Score in Context
This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 September 2016.
All research outputs
#6,420,883
of 23,656,895 outputs
Outputs from BMC Genomics
#2,687
of 10,778 outputs
Outputs of similar age
#98,997
of 393,898 outputs
Outputs of similar age from BMC Genomics
#71
of 317 outputs
Altmetric has tracked 23,656,895 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 10,778 research outputs from this source. They receive a mean Attention Score of 4.8. This one has gotten more attention than average, scoring higher than 74% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 393,898 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 74% of its contemporaries.
We're also able to compare this research output to 317 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.