Computational protocol: Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics

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Protocol publication

[…] The evolutionary relationship of β-lactamases was inferred using the maximum likelihood method in the MEGA5 software tool. Amino acid sequences were aligned with PRANK, and highly variable regions removed from the dataset. The Whelan and Goldman model of evolution was used and initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100, or otherwise less than one-fourth of the total number of sites, the maximum parsimony method was used; otherwise the BIONJ method, with maximum composite likelihood (MCL) distance matrix, was used. To provide statistical support for each node on the tree, a consensus tree was generated from 1000 bootstrap datasets. […]

Pipeline specifications

Software tools MEGA, PRANK, BIONJ
Application Phylogenetics
Organisms Salmonella enterica subsp. enterica serovar Typhimurium, Bacteroides thetaiotaomicron, Homo sapiens, Bifidobacterium breve, Bacteroides fragilis, Bacteroides ovatus
Chemicals Cefotaxime