Table 1. Applications of transposon-insertion sequencing.

Study	Publication date	Organism	Total mutants	Unique insertion sites; Density	Application	Tn used	Name coined
Hutchison III et al., Science5	Oct 1999	M. genitalium/M. pneumoniae	1,291 918	685; ~1/850 bp 669; ~1/850 bp	Required gene sets	Tn4001	Global Transposon Mutagenesis
Goodman et al., Cell Host and Microbe7	Sep 2009	B. thetaiotaomicron	2 × 35,000	35,000;1/182 bp	Establishment in human gut as a natural habitat	Mariner	INSeq
Gawronski et al., PNAS8	Sep 2009	H. influenzae	75,000	55,935; 1/32 bp	Prolonged survival in lung in vivo	Mariner	HITS
van Opijnen et al., Nature Methods9	Oct 2009	S. pneumoniae	6 × 25,000	23,875; 1/91bp	Transcriptional regulation and carbohydrate transport	Mariner	Tn-seq
Langridge et al., Genome Research6	Dec 2009	S.Typhi 1	1.1 million	370,000; 1/13 bp	Gene requirements, bile tolerance	Tn5	TraDIS
Gallagher et al., mBio10	Jan 2011	P. aeruginosa	~100,000	95,905; 1/65 bp	Tobramycin resistance	Mariner	Tn-seq (circle method)
Eckert et al., J Bact.24	Jan 2011	E. coli	19 × 95	1,645	Colonization of bovine intestinal tract; retrospective re-evaluation of a STM study	Tn5	-
Christen et al., Mol Syst Biol.16	July 2011	C. crescentus	800,000	428,735; 1/8 bp	Gene/ncRNAs/promoter requirements	Tn5	-
Griffin et al., PLOS Pathogens27	Sept 2011	M. tuberculosis	2 × 100,000	36,488;1/120 bp	Gene requirements and cholesterol utilization	Mariner	-
Khatiwara et al., AEM35	May 2012	S. Typhimurium	16,000	~8,000; ~1/610	Bile, low nutrient and heat tolerance	Tn5	-
Mann et al., PLOS Pathogens46	July 2012	S. pnuemoniae	~9,000–24,000	~8,000‒22,000	Determining roles of sRNAs in pathogenesis	Mariner	-
van Opijnen and Camilli, Genome Research22	July 2012	S. pnuemoniae	~4,000‒30,000	Varying	Stress response and metabolism in vitro and murine in vivo colonization	Mariner	-
Brutinel and Gralnick, Molecular Microbiology51	Aug 2012	S. oneidensis	50,000	26,793; ~1/191 bp	Gene requirements and Metabolism	Mariner	-
Zhang et al., PLOS Pathogens23	Sept 2012	M. tuberculosis	2 × 100,000	36,488; ~1/120 bp	Identifying genes, regulators and ncRNAs required for growth	Mariner	-
Klein et al., BMC Genomics52	Oct. 2012	P. gingivalis	N/A	54,000; 1/43 bp	Gene requirements	Mariner	-
Pickard et al., J Bact36	Jan 2013	S.Typhi 1	1.1 million	370,000; 1/13 bp	Bacteriophage infection	Tn5	-
Barquist et al., Nuc. Acids Res15	March 2013	S. Typhi1 S. Typhimurium	1.1 million 930,000	370,000; 1/13 bp 550,000; 1/9 bp	Comparison of coding and non-coding gene requirements between two Salmonella serovars	Tn5	-

¹ The same mutant library was used in these studies. A collection of studies to date utilizing transposon-insertion sequencing. Columns: (1) study reference, (2) date of publication, (3) organism mutagenized, (4) number of mutants generated, (5) number of unique insertion sites recovered from sequencing, (6) brief description of the application, (7) transposon used, (8) method name coined, if any.