CONJUGATION Gene transfer that is mediated by certain plasmids or ICEs with relevant transfer genes. Cell–cell contact is required for conjugation, unlike transduction or transformation.

HOMOLOGOUS RECOMBINATION DNA recombination that requires extensive sequence similarity in the involved DNA segments. It is usually effected by chromosomally encoded genes, but some phages also have orthologues of such chromosomal genes.

INTEGRATIVE CONJUGATIVE ELEMENTS (ICEs). Together with conjugative transposons (CTns) and genomic islands, these are chromosomally located gene clusters that encode phage-linked integrases and conjugation proteins as well as other genes associated with an observable phenotype such as virulence or symbiosis. ICEs and CTns are gene clusters that can be transferred between cells, whereas genomic islands have not been shown to transfer. Although these gene clusters have some phage-like genes, they do not lyse the cell or form extracellular particles.

INTEGRON A genetic element that encodes an integrase enzyme, which can assemble tandem arrays of genes or gene fragments and provide them with a promoter for expression. Often associated with antibiotic multi-resistance.

METAGENOMICS Sequencing of a clone library derived from the total DNA purified from a complex microbial ecosystem. This is followed by computer assembly of the reads into multiple linkage groups assumed to represent the organisms present in the community, including those that cannot be cultured.

MOBILIZATION Transfer by a conjugative element of a plasmid or part of the bacterial cellular chromosome that cannot effect self transfer. Mediated by the trans-acting proteins of the conjugative plasmid that function on cognate mobilization (oriT) sites in the mobilized plasmid to direct it to the conjugation pore built by the conjugative element.

NON-HOMOLOGOUS RECOMBINATION DNA recombination that requires little or no similarity between the DNA segments involved. This process is carried out by specialized enzymes that are encoded by transposons and phages.

TRANSDUCTION Gene transfer that is mediated by certain types of bacteriophage.

TRANSFORMATION Gene transfer that is mediated by the uptake of free DNA.