PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Gouret, Philippe; Thompson, Julie; Pontarotti, Pierre

doi:10.1186/1471-2105-10-298

Cited by 58 publications

(54 citation statements)

References 23 publications

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“…Comparator species for genomic comparison were identified in the 16S RNA tree using Phylopattern software [28]. The genome of strain mt6 T was compared to those of Alkaliphilus metalliredigens strain QYMF, Clostridium aceticum strain DSM 1496, Alkaliphilus transvaalensis strain SAGM1 and Alkaliphilus oremlandii strain OhILAs.…”

Section: Methodsmentioning

confidence: 99%

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Alou

Rathored

Lagier

et al. 2017

New Microbes and New Infections

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Rubeoparvulum massiliense strain mt6T was isolated from the gut microbiota of a severely malnourished boy from Senegal and consisted of facultative anaerobic, spore-forming, nonmotile and Gram-negative rods. R. massiliense showed a 92% similarity with the 16S rRNA of Bacillus mannanilyticus. The genome of strain mt6T is 2 843 796 bp long with a 43.75% G+C content. It contains 2735 protein-coding genes and 76 RNA genes, among which are nine rRNA genes.

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Section: Methodsmentioning

confidence: 99%

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Alou

Rathored

Lagier

et al. 2017

New Microbes and New Infections

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show abstract

“…Genomes were automatically retrieved from the 16S RNA tree using Xegen software (PhyloPattern) [17]. For each selected genome, the complete genome sequence, proteome genome sequence and ORFeome genome sequence were retrieved from the NCBI's FTP site.…”

Section: Methodsmentioning

confidence: 99%

Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile

Afouda

Ndongo

Khelaifia

et al. 2017

New Microbes and New Infections

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Prevotella phocaeensis sp. nov. strain SN19T (= DSM 103364) is a new species isolated from the gut microbiota of patient with colitis due to Clostridium difficile. Strain SN19T is Gram-negative rod-shaped bacteria, strictly anaerobic, nonmotile and non–endospore forming. The predominance fatty acid is hexadecanoic acid. Its 16S rRNA showed a 97.70% sequence identity with its phylogenetically closest species, Prevotella oralis. The genome is 2 922 117 bp long and contains 2486 predicted genes including 56 RNA genes.

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“…Genomes were automatically retrieved from the 16S RNA tree using XEGEN software (Phylopattern) [26]. For each selected genome, the complete genome sequence, proteome genome sequence (all gene sequences encoding proteins in a genome) and Orfeome genome sequence (all gene sequences encoding orphan proteins in a genome) were retrieved from the FTP of NCBI.…”

Section: Genome Annotation and Analysismentioning

confidence: 99%

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

Alou¹,

Khelaifia²,

Michelle³

et al. 2016

Anaerobe

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Anaerococcus rubiinfantis sp. nov. strain mt16(T) is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16(T) showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease.

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PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Cited by 58 publications

References 23 publications

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Rubeoparvulum massiliense gen. nov., sp. nov., a new bacterial genus isolated from the human gut of a Senegalese infant with severe acute malnutrition

Noncontiguous finished genome sequence and description of Prevotella phocaeensis sp. nov., a new anaerobic species isolated from human gut infected by Clostridium difficile

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

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