Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis

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

The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation

Management of intramedullary tumours in children

Clinical presentation, diagnosis, surgical technique and results of 25 cases of intramedullary tumours in patients under 16 years of age are analyzed. Pre-operative spinal deformity was present in 9 patients. Surgery was performed in all. After multilaminectomy with preservation of the intervertebral joints, total removal of the lesion was achieved in 11 patients and subtotal removal in 14 others. After surgery, external immobilization lasting an average period of 5 years was instituted in all patients. Postoperative radiation therapy was performed in 11 cases (5 "high grade" astrocytomas, 5 ependymomas, 1 glioblastoma). There were 11 recurrences: 4 of which (2 ependymomas and 2 "low grade" astrocytomas) were treated surgically, 7 (5 "high grade" astrocytomas, 1 glioblastoma, 1 oligodendroglioma) with palliative radiation treatment. Six patients eventually developed postlaminectomy spinal deformities as diagnosed roentgenographically 6 to 50 months postoperatively. Of the 16 patients still alive, 7 did not present relevant neurological deficit, 1 presented a monoparesis, while the other 8 presented invalidating deficits. Surgical treatment did not differ from that employed in the intramedullary tumours in the adult: radical resection is indeed the optimal therapeutic origin. The risk of radiation therapy are greater in children: it is crucial to limit radiation therapy to only some histotypes. The incidence of spinal column deformity after multilevel laminectomy is greater in young patients. It is advisable to implement prevention of spinal deformities by postoperative external immobilization and constant follow-up so as to detect early changes of spinal stability