Table 1.

The Molecular toolkit of bacteria – eukaryote interactions: examples of bacterial target genes for screening genomes and metagenomes.

Type	Name of Pathway	Phylogenetic spread	Number of genes	Reference
Directed secretion of bacterial proteic effectors	Type 3 secretion system Type 4 secretion system Type 6 secretion system	Proteobacteria and Chlamydiae Proteobacteria Mostly proteobacteria	20–25 12 15	Galan and Wolf-Watz (2006) Backert and Selbach (2008), Bardill et al. (2005) Pukatzki et al. (2006)
Metabolic complementation on Nitrogen	Nitrogenase – diazotrophy	Proteobacteria, Cyanobacteria, Firmicutes, Euryarchaea	Operon of five genes: NifHDKEN	Raymond et al. (2004), Seefeldt et al. (2009)
Metabolic complementation on vitamin synthesis	B12 B1, B2	Euryarchea Proteobacteria Firmicutes Actinomycete Cyanobacteria	3–11 genes	Helliwell et al. (2011), Wagner-Döbler et al. (2009), Croft et al. (2005)