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Joao Gatica Arias edited AbstractImportanceIntroductionResultsDiscussionMaterials_and_methodsData_setShotgun_metagenomic__.html
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OXY, OKP and LEN protein variation databases (Gatica et al., 2016). Sequences deposited into EX-B were compared using
BioEdit 7.2.5 software and checked for non-redundant sequences; producing a
database containing 1566 non-redundant β-lactamase sequences. The EX-B
database is publically available for download at (
http://app.agri.gov.il/eddie/tools.html).
Blast searches
Homology searches among metagenomic sequences and b-lactamase sequences were performed using blastx from the BLAST suite (
class="squire-citation ltx_cite" class="ltx_cite" data-bib-text="@article{Gish_1993,
doi = {10.1038/ng0393-266},
url = {http://dx.doi.org/10.1038/ng0393-266},
year = 1993,
...
author = {Warren Gish and David J. States},
title = {Identification of protein coding regions by database similarity search},
journal = {Nature Genetics}
}" data-bib-key="Gish_1993" contenteditable="false" style="cursor: pointer"> contenteditable="false"> href="#Gish_1993">Gish 1993). Only hits with a percent of identity higher than 50%, bit scor higher than 30 and a e-value lower than 1e-4 were considered real hits. The 50% of identity was used under the consideration that the databases used to construct the EX-B database are based specially in clinical data and environmnetal data usually is not consider.
Hits analysis
Hits obteined by BLAST were analyzed in PC-ORD x.x. The hits were used to construct a matrix of present hits, according b-lactamase gene type, in each metagenome. The data was relativizated by ubiquity and traansformed by a step of power transformation. Outliers were identified and removed of analysis and a distance matrix based on Bray-Curtis distance was constructed to downstream analysis. In addition, the distance matrix produced results related to diversity indexes, multi response permutation process (MRPP), indicator especies analysis and non metric multidimensional scaling.
The Distance matrix from the previous step was used to construct a b-lactamase gene network using EDENetwork x.x (
class="squire-citation ltx_cite" class="ltx_cite" data-bib-text="@article{Kivel__2014,
doi = {10.1111/1755-0998.12290},
url = {http://dx.doi.org/10.1111/1755-0998.12290},
year = 2014,
...
title = {{EDENetworks}: A user-friendly software to build and analyse networks in biogeography,
ecology and population genetics},
journal = {Molecular Ecology Resources}
}" data-bib-key="Kivel__2014" contenteditable="false" style="cursor: pointer"> contenteditable="false"> href="#Kivel__2014">Kivelä 2014). Graphical visualization and statistical test were performed using
Cytosc ape Cytoscape x.x (). Statistical analysis included betweenness, clustering coefficient, closeness and assortativity
Supplemental material
Acknowledgments
Funding information
References
