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Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

Soto-Girón MJ, Ospina OE, Massey SE - Evol Med Public Health (2015)

Bottom Line: H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa.Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host.Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis of 37 H.pylori strains with complete genomes. Bayesian phylogenetic inference of 37 H.pylori strains was conducted as described in Methods. Colors indicate the region from which each strain was isolated. Numbers at nodes represent posterior probabilities
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eov005-F1: Phylogenetic analysis of 37 H.pylori strains with complete genomes. Bayesian phylogenetic inference of 37 H.pylori strains was conducted as described in Methods. Colors indicate the region from which each strain was isolated. Numbers at nodes represent posterior probabilities

Mentions: A phylogenetic tree of 37 H.pylori strains with complete genomes available was constructed (Fig. 1). The strains, with NCBI Refseq ID, country of origin and associated disease status where available (Ga; gastritis, PUD; peptic ulcer disease, ML; MALT lymphoma, GC; gastric cancer, C; commensal) were as follows. SouthAfrica7 (NC_017361.1; South Africa; C), Gambia94/24 (NC_017371.1; Gambia; C), J99 (NC_000921.1; USA; PUD), PeCan18 (NC_017742; Peru; GC), 908 (NC_017357.1; West Africa; PUD), 2017 (NC_017374.1; West Africa; PUD), 2018 (NC_017381.1; West Africa; PUD), ELS37 (NC_017063.1; El Salvador; GC), SJM180 (NC_014560.1; Peru; Ga), Lithuania75 (NC_017362.1; Lithuania; C), G27 (NC_011333.1; Italy; PUD), B38 (NC_012973.1; France; ML), HUP-B14 (NC_017733.1, Spain; C), P12 (NC_011498.1, Germany, PUD), 26695 (NC_000915.1; UK; Ga), HPAG1 (NC_008086.1; Sweden; Ga), B8 (NC_014256.1; USA; PUD), India7 (NC_017372.1; India; PUD), SNT49 (NC_017376.1; India; C), PeCan4 (NC_014555.1; Peru; GC), Puno135 (NC_017379.1; Peru; Ga), Puno120 (NC_017378.1; Peru; Ga), Shi169 (NC_017740.1; Peru; C), Sat464 (NC_017359.1; Peru; C), Shi470 (NC_010698.2; Peru; Ga), v225d (NC_017355.1; Venezuela; Ga), Shi417 (NC_017739.1; Peru; C), Shi112 (NC_017741.1; Peru; C), Cuz20 (NC_017358.1; Peru; C), 51 (NC_017382.1; South Korea; PUD), F30 (NC_017365.1; Japan; PUD), F32 (NC_017366.1; Japan; GC), F16 (NC_017368.1; Japan; Ga), F57 (NC_017367.1; Japan; GC), 52 (NC_017354.1; South Korea), 83 (NC_017375.1; Japan; GC), 35A (NC_017360.1: Japan; PUD). Sequences from the H.acinonychis genome (NC_008229.1) were used as an outgroup.Figure 1.


Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

Soto-Girón MJ, Ospina OE, Massey SE - Evol Med Public Health (2015)

Phylogenetic analysis of 37 H.pylori strains with complete genomes. Bayesian phylogenetic inference of 37 H.pylori strains was conducted as described in Methods. Colors indicate the region from which each strain was isolated. Numbers at nodes represent posterior probabilities
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4419197&req=5

eov005-F1: Phylogenetic analysis of 37 H.pylori strains with complete genomes. Bayesian phylogenetic inference of 37 H.pylori strains was conducted as described in Methods. Colors indicate the region from which each strain was isolated. Numbers at nodes represent posterior probabilities
Mentions: A phylogenetic tree of 37 H.pylori strains with complete genomes available was constructed (Fig. 1). The strains, with NCBI Refseq ID, country of origin and associated disease status where available (Ga; gastritis, PUD; peptic ulcer disease, ML; MALT lymphoma, GC; gastric cancer, C; commensal) were as follows. SouthAfrica7 (NC_017361.1; South Africa; C), Gambia94/24 (NC_017371.1; Gambia; C), J99 (NC_000921.1; USA; PUD), PeCan18 (NC_017742; Peru; GC), 908 (NC_017357.1; West Africa; PUD), 2017 (NC_017374.1; West Africa; PUD), 2018 (NC_017381.1; West Africa; PUD), ELS37 (NC_017063.1; El Salvador; GC), SJM180 (NC_014560.1; Peru; Ga), Lithuania75 (NC_017362.1; Lithuania; C), G27 (NC_011333.1; Italy; PUD), B38 (NC_012973.1; France; ML), HUP-B14 (NC_017733.1, Spain; C), P12 (NC_011498.1, Germany, PUD), 26695 (NC_000915.1; UK; Ga), HPAG1 (NC_008086.1; Sweden; Ga), B8 (NC_014256.1; USA; PUD), India7 (NC_017372.1; India; PUD), SNT49 (NC_017376.1; India; C), PeCan4 (NC_014555.1; Peru; GC), Puno135 (NC_017379.1; Peru; Ga), Puno120 (NC_017378.1; Peru; Ga), Shi169 (NC_017740.1; Peru; C), Sat464 (NC_017359.1; Peru; C), Shi470 (NC_010698.2; Peru; Ga), v225d (NC_017355.1; Venezuela; Ga), Shi417 (NC_017739.1; Peru; C), Shi112 (NC_017741.1; Peru; C), Cuz20 (NC_017358.1; Peru; C), 51 (NC_017382.1; South Korea; PUD), F30 (NC_017365.1; Japan; PUD), F32 (NC_017366.1; Japan; GC), F16 (NC_017368.1; Japan; Ga), F57 (NC_017367.1; Japan; GC), 52 (NC_017354.1; South Korea), 83 (NC_017375.1; Japan; GC), 35A (NC_017360.1: Japan; PUD). Sequences from the H.acinonychis genome (NC_008229.1) were used as an outgroup.Figure 1.

Bottom Line: H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa.Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host.Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.

No MeSH data available.


Related in: MedlinePlus