Table 1 |.

Advances in techniques used to study the symbiotic associations of Euprymna scolopes

Technique	Tissues or cells analysed	Applications	References
Molecular
Whole genome	Genomes of host and 62 Vibrio fischeri strains, including ES114 and MJ11; 13 D and S strains from V. fischeri; 16 ANG symbiont strains of E. scolopes	Discovery of novel genes important for symbiosis and host range; phylogenetic comparison of ANG strains and biosynthetic potential; identification of symbiosis-related host genes	18,38,58,105–109
Microarrays	V. fischeri and light organ	Comparisons of global gene expression in host and symbiont (13,982 ESTs)	64,110,111
RNA sequencing	Light organ and V. fischeri	Identification of host and symbiont gene expression during the first hours to days of the association	35,59,112
NanoString (nCounter Analysis)	E. scolopes and V. fischeri	Resolution of multiple genes with as few as 10 juvenile animals	59
Shotgun proteomics	Light-organ exudate and haemocytes	Identification of host and symbiont proteins in exudate and first description of innate immune-related proteins from haemocytes	86,113
Quantitative proteomics (iTRAQ and spectral counting)	Haemocytes (symbiotic and cured)	Identified quantitative differences in protein abundance in haemocytes	87
16S amplicon sequencing	ANG bacteria	Characterization of the bacterial community in ANG and associated eggs	114
Metagenomics	ANG	16S rRNA gene diversity of the consortium	115
INSeq	V. fischeri	Discovery of colonization determinants	116
Gene editing	Euprymna spp.	Knockout of host genes	a
Cellular
Confocal microscopy	E. scolopes and V. fischeri	Live cell imaging of colonization; ultrastructure; cytochemistry; immunofluorescence	19,22,23,28,41,84
Transmission electron microscopy	E. scolopes and V. fischeri	Characterization of ultrastructure	6,17,115
HCR FISH	Light organ and V. fischeri	Cellular localization of gene expression in host and symbiont in time and space	47
In situ hybridization	Developing E. scolopes embryos	Allowed visualization of HOX gene expression in developing embryos	96
Imaging mass spectrometry	V. fischeri and host light organ	Imaging of small molecules in light organ	117,118
Physiological
Molecular networking	Bacteria residing in the ANG and eggs	Chemical identification and modelling of secondary metabolites	119
Model-enabled gene search	V. fischeri	Identification of metabolic function pathways	120
Metabolomics	E. scolopes	Identification of host metabolites	78
NanoSIMS	E. scolopes and V. fischeri	Transfer and localization of metabolites	49

ANG, accessory nidamental gland; EST, expressed sequence tag; HCR FISH, hybridization chain reaction fluorescence in situ hybridization; INSeq, insertion sequencing; iTRAQ, isobaric tags for relative and absolute quantification; NanoSIMS, nano secondary ion mass spectrometry.

^aC. Albertin and J. Rosenthal, personal communication.