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...
publically-available databases: The Lahey β-lactamase database,
The Lactamase Engineering Database (LACED), The Comprehensive
Antibiotic Resistance Database (CARD) and The Pasteur Institute’s
OXY, OKP and LEN protein variation databases
(Gatica (Gatica et al., 2016). 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 (
...
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">Gish 1993). Only hits with a percent of identity higher than 50%, bit
scor score 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
highly based
specially in clinical data and
environmnetal data usually is generally it not
consider.
Hits consider environmental data.
Hits analysis
Hits obteined obtained by BLAST were analyzed in PC-ORD 5.0. The 5.0 (McCune and Mefford, 2011).The hits were used to construct a matrix of present hits, according b-lactamase gene type, in each metagenome. The data was relativizated by weighting by ubiquity and traansformed transformed by a step of power transformation. square root. 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 constructed was used to obtain diversity indexes, multi response permutation process (MRPP), indicator especies species analysis and non metric multidimensional scaling.
The Distance matrix from the previous step was used to construct a b-lactamase gene network using EDENetwork 2.18 (
...
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">Kivelä 2014). Graphical visualization and statistical test were performed using Cytoscape 3.4.0
(). (Shannon 2003). Statistical analysis included betweenness, clustering coefficient, closeness and assortativity. In addition cluster identification was performed with NetworkAnalyzer and AutoAnnottate tools in cytoscape.
Supplemental material
Acknowledgments
Funding information
References
information
References
McCune, B. and M. J. Mefford. 2011. PC-ORD. Multivariate Analysis of
Ecological Data. Version 6. MjM Software, Gleneden Beach, Oregon, U.S.A.
