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Predicting prokaryotic ecological niches using genome sequence analysis.

Suen G, Goldman BS, Welch RD - PLoS ONE (2007)

Bottom Line: As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed.When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes.We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Syracuse University, Syracuse, New York, United States of America.

ABSTRACT
Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

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Related in: MedlinePlus

Clustering of prokaryotic species on the niche map.Three groups of prokaryotic species are shown, including the marine Gammaproteobacteria in NM11 that cluster according to phylogeny (a); the obligate symbionts and pathogens in NM10 and NM16 that cluster according to function (b); and the prokaryotes existing at the soil, plant, and human interface in NM14 that cluster according to environment. A high resolution view of each mountain is shown, in addition to the complete niche map labeled with the corresponding mountain (blue circles). The genus of every prokaryote in each mountain is also shown.
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pone-0000743-g005: Clustering of prokaryotic species on the niche map.Three groups of prokaryotic species are shown, including the marine Gammaproteobacteria in NM11 that cluster according to phylogeny (a); the obligate symbionts and pathogens in NM10 and NM16 that cluster according to function (b); and the prokaryotes existing at the soil, plant, and human interface in NM14 that cluster according to environment. A high resolution view of each mountain is shown, in addition to the complete niche map labeled with the corresponding mountain (blue circles). The genus of every prokaryote in each mountain is also shown.

Mentions: Perhaps the group that reveals the most about the ability of the niche map to clustering according to niche is in NM11, (Table 1 and Figure 5a) which contains several different members of the Alteromonadales, Oceanospirillales, and the Vibrionales. The members of this phylogenetically diverse group within the Gammaproteobacteria are all marine organisms, and the niche map clusters them according to a shared environment. A survey of the Pfams specific to the prokaryotes in NM11 (Table S4) reveal many membrane lipoproteins and proteins of uncharacterized function, similar to those domains observed for the Xanthomondales. Interestingly, the marine Gammaproteobacteria in NM11 (Table 1) are found adjacent to the Xanthomondales in NM01 (Table 1) on the niche map (see Figure 2).


Predicting prokaryotic ecological niches using genome sequence analysis.

Suen G, Goldman BS, Welch RD - PLoS ONE (2007)

Clustering of prokaryotic species on the niche map.Three groups of prokaryotic species are shown, including the marine Gammaproteobacteria in NM11 that cluster according to phylogeny (a); the obligate symbionts and pathogens in NM10 and NM16 that cluster according to function (b); and the prokaryotes existing at the soil, plant, and human interface in NM14 that cluster according to environment. A high resolution view of each mountain is shown, in addition to the complete niche map labeled with the corresponding mountain (blue circles). The genus of every prokaryote in each mountain is also shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1937020&req=5

pone-0000743-g005: Clustering of prokaryotic species on the niche map.Three groups of prokaryotic species are shown, including the marine Gammaproteobacteria in NM11 that cluster according to phylogeny (a); the obligate symbionts and pathogens in NM10 and NM16 that cluster according to function (b); and the prokaryotes existing at the soil, plant, and human interface in NM14 that cluster according to environment. A high resolution view of each mountain is shown, in addition to the complete niche map labeled with the corresponding mountain (blue circles). The genus of every prokaryote in each mountain is also shown.
Mentions: Perhaps the group that reveals the most about the ability of the niche map to clustering according to niche is in NM11, (Table 1 and Figure 5a) which contains several different members of the Alteromonadales, Oceanospirillales, and the Vibrionales. The members of this phylogenetically diverse group within the Gammaproteobacteria are all marine organisms, and the niche map clusters them according to a shared environment. A survey of the Pfams specific to the prokaryotes in NM11 (Table S4) reveal many membrane lipoproteins and proteins of uncharacterized function, similar to those domains observed for the Xanthomondales. Interestingly, the marine Gammaproteobacteria in NM11 (Table 1) are found adjacent to the Xanthomondales in NM01 (Table 1) on the niche map (see Figure 2).

Bottom Line: As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed.When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes.We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Syracuse University, Syracuse, New York, United States of America.

ABSTRACT
Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

Show MeSH
Related in: MedlinePlus