Assessing the Potential for De Novo Reconstruction of Prokaryotic Genomes from Short Reads

Carl Kingsford, Michael Schatz, and Mihai Pop

We describe an application of de Bruijn graphs - a theoretical framework underlying several modern genome assembly programs - to analyze the global repeat structure of prokaryotic genomes. We provide the 1st survey of the repeat structure of a large number of genomes, and make publicly available the resulting simplied de Bruijn graphs. The resulting data provides an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths and/or insert sizes, thereby providing a benchmark for new software tools developed in the context of next generation sequencing data. Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely even if the genomes themselves cannot. The non-reconstructible genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages) indicating that it is at least theoretically possible to reconstruct the protein-coding genes of an organisms using very short reads.



Assembly Benchmark

Here are the compressed and simplified de Bruijn graphs constructed using the techniques described in the paper. The files are written in Graphviz ".dot" format. The node label specifies a comma separated list of offsets in the genome, followed by colon and node length. For example, the graph below has 3 nodes, with lengths 1425, 1346478, and 4305032. The sequence for node 1 occurs twice in the genome starting at offsets 2309674 and 36555581.

digraph G {
  1 [label="2309674,3655581:1425"]
  2 [label="2310101:1346478"]
  3 [label="3656008:4305032"]
  1 -> 2
  1 -> 3
  2 -> 1
  3 -> 1
}


GenomeRead Length
Acidobacteria bacterium Ellin345 25 35 50 100 250 500 1000
Acinetobacter sp ADP1 25 35 50 100 250 500 1000
Aeropyrum pernix 25 35 50 100 250 500 1000
Agrobacterium tumefaciens C58 Cereon 25 35 50 100 250 500 1000
Agrobacterium tumefaciens C58 Cereon 25 35 50 100 250 500 1000
Agrobacterium tumefaciens C58 UWash 25 35 50 100 250 500 1000
Agrobacterium tumefaciens C58 UWash 25 35 50 100 250 500 1000
Alcanivorax borkumensis SK2 25 35 50 100 250 500 1000
Alkalilimnicola ehrlichei MLHE-1 25 35 50 100 250 500 1000
Anabaena variabilis ATCC 29413 25 35 50 100 250 500 1000
Anaeromyxobacter dehalogenans 2CP-C 25 35 50 100 250 500 1000
Anaplasma marginale St Maries 25 35 50 100 250 500 1000
Anaplasma phagocytophilum HZ 25 35 50 100 250 500 1000
Aquifex aeolicus 25 35 50 100 250 500 1000
Archaeoglobus fulgidus 25 35 50 100 250 500 1000
Aster yellows witches-broom phytoplasma AYWB 25 35 50 100 250 500 1000
Azoarcus sp EbN1 25 35 50 100 250 500 1000
Bacillus anthracis Ames 0581 25 35 50 100 250 500 1000
Bacillus anthracis Ames 25 35 50 100 250 500 1000
Bacillus anthracis str Sterne 25 35 50 100 250 500 1000
Bacillus cereus ATCC 10987 25 35 50 100 250 500 1000
Bacillus cereus ATCC14579 25 35 50 100 250 500 1000
Bacillus cereus ZK 25 35 50 100 250 500 1000
Bacillus clausii KSM-K16 25 35 50 100 250 500 1000
Bacillus halodurans 25 35 50 100 250 500 1000
Bacillus licheniformis ATCC 14580 25 35 50 100 250 500 1000
Bacillus licheniformis DSM 13 25 35 50 100 250 500 1000
Bacillus subtilis 25 35 50 100 250 500 1000
Bacillus thuringiensis konkukian 25 35 50 100 250 500 1000
Bacteroides fragilis NCTC 9434 25 35 50 100 250 500 1000
Bacteroides fragilis YCH46 25 35 50 100 250 500 1000
Bacteroides thetaiotaomicron VPI-5482 25 35 50 100 250 500 1000
Bartonella henselae Houston-1 25 35 50 100 250 500 1000
Bartonella quintana Toulouse 25 35 50 100 250 500 1000
Baumannia cicadellinicola Homalodisca coagulata 25 35 50 100 250 500 1000
Bdellovibrio bacteriovorus 25 35 50 100 250 500 1000
Bifidobacterium longum 25 35 50 100 250 500 1000
Bordetella bronchiseptica 25 35 50 100 250 500 1000
Bordetella parapertussis 25 35 50 100 250 500 1000
Bordetella pertussis 25 35 50 100 250 500 1000
Borrelia afzelii PKo 25 35 50 100 250 500 1000
Borrelia burgdorferi 25 35 50 100 250 500 1000
Borrelia garinii PBi 25 35 50 100 250 500 1000
Bradyrhizobium japonicum 25 35 50 100 250 500 1000
Brucella abortus 9-941 25 35 50 100 250 500 1000
Brucella abortus 9-941 25 35 50 100 250 500 1000
Brucella melitensis biovar Abortus 25 35 50 100 250 500 1000
Brucella melitensis biovar Abortus 25 35 50 100 250 500 1000
Brucella melitensis 25 35 50 100 250 500 1000
Brucella melitensis 25 35 50 100 250 500 1000
Brucella suis 1330 25 35 50 100 250 500 1000
Brucella suis 1330 25 35 50 100 250 500 1000
Buchnera aphidicola 25 35 50 100 250 500 1000
Buchnera aphidicola Sg 25 35 50 100 250 500 1000
Buchnera sp 25 35 50 100 250 500 1000
Burkholderia 383 25 35 50 100 250 500 1000
Burkholderia 383 25 35 50 100 250 500 1000
Burkholderia 383 25 35 50 100 250 500 1000
Burkholderia cenocepacia AU 1054 25 35 50 100 250 500 1000
Burkholderia cenocepacia AU 1054 25 35 50 100 250 500 1000
Burkholderia cenocepacia AU 1054 25 35 50 100 250 500 1000
Burkholderia cepacia AMMD 25 35 50 100 250 500 1000
Burkholderia cepacia AMMD 25 35 50 100 250 500 1000
Burkholderia cepacia AMMD 25 35 50 100 250 500 1000
Burkholderia mallei ATCC 23344 25 35 50 100 250 500 1000
Burkholderia mallei ATCC 23344 25 35 50 100 250 500 1000
Burkholderia pseudomallei 1710b 25 35 50 100 250 500 1000
Burkholderia pseudomallei 1710b 25 35 50 100 250 500 1000
Burkholderia pseudomallei K96243 25 35 50 100 250 500 1000
Burkholderia pseudomallei K96243 25 35 50 100 250 500 1000
Burkholderia thailandensis E264 25 35 50 100 250 500 1000
Burkholderia thailandensis E264 25 35 50 100 250 500 1000
Burkholderia xenovorans LB400 25 35 50 100 250 500 1000
Burkholderia xenovorans LB400 25 35 50 100 250 500 1000
Burkholderia xenovorans LB400 25 35 50 100 250 500 1000
Campylobacter jejuni 25 35 50 100 250 500 1000
Campylobacter jejuni RM1221 25 35 50 100 250 500 1000
Candidatus Blochmannia floridanus 25 35 50 100 250 500 1000
Candidatus Blochmannia pennsylvanicus BPEN 25 35 50 100 250 500 1000
Candidatus Pelagibacter ubique HTCC1062 25 35 50 100 250 500 1000
Carboxydothermus hydrogenoformans Z-2901 25 35 50 100 250 500 1000
Caulobacter crescentus 25 35 50 100 250 500 1000
Chlamydia muridarum 25 35 50 100 250 500 1000
Chlamydia trachomatis A HAR-13 25 35 50 100 250 500 1000
Chlamydia trachomatis 25 35 50 100 250 500 1000
Chlamydophila abortus S26 3 25 35 50 100 250 500 1000
Chlamydophila caviae 25 35 50 100 250 500 1000
Chlamydophila felis Fe C-56 25 35 50 100 250 500 1000
Chlamydophila pneumoniae AR39 25 35 50 100 250 500 1000
Chlamydophila pneumoniae CWL029 25 35 50 100 250 500 1000
Chlamydophila pneumoniae J138 25 35 50 100 250 500 1000
Chlamydophila pneumoniae TW 183 25 35 50 100 250 500 1000
Chlorobium chlorochromatii CaD3 25 35 50 100 250 500 1000
Chlorobium tepidum TLS 25 35 50 100 250 500 1000
Chromobacterium violaceum 25 35 50 100 250 500 1000
Chromohalobacter salexigens DSM 3043 25 35 50 100 250 500 1000
Clostridium acetobutylicum 25 35 50 100 250 500 1000
Clostridium perfringens ATCC 13124 25 35 50 100 250 500 1000
Clostridium perfringens 25 35 50 100 250 500 1000
Clostridium perfringens SM101 25 35 50 100 250 500 1000
Clostridium perfringens SM101 25 35 50 100 250 500 1000
Clostridium tetani E88 25 35 50 100 250 500 1000
Colwellia psychrerythraea 34H 25 35 50 100 250 500 1000
Corynebacterium diphtheriae 25 35 50 100 250 500 1000
Corynebacterium efficiens YS-314 25 35 50 100 250 500 1000
Corynebacterium glutamicum ATCC 13032 Bielefeld 25 35 50 100 250 500 1000
Corynebacterium glutamicum ATCC 13032 Kitasato 25 35 50 100 250 500 1000
Corynebacterium jeikeium K411 25 35 50 100 250 500 1000
Coxiella burnetii 25 35 50 100 250 500 1000
Cyanobacteria bacterium Yellowstone A-Prime 25 35 50 100 250 500 1000
Cyanobacteria bacterium Yellowstone B-Prime 25 35 50 100 250 500 1000
Cytophaga hutchinsonii ATCC 33406 25 35 50 100 250 500 1000
Dechloromonas aromatica RCB 25 35 50 100 250 500 1000
Dehalococcoides CBDB1 25 35 50 100 250 500 1000
Dehalococcoides ethenogenes 195 25 35 50 100 250 500 1000
Deinococcus geothermalis DSM 11300 25 35 50 100 250 500 1000
Deinococcus radiodurans 25 35 50 100 250 500 1000
Deinococcus radiodurans 25 35 50 100 250 500 1000
Desulfitobacterium hafniense Y51 25 35 50 100 250 500 1000
Desulfotalea psychrophila LSv54 25 35 50 100 250 500 1000
Desulfovibrio desulfuricans G20 25 35 50 100 250 500 1000
Desulfovibrio vulgaris Hildenborough 25 35 50 100 250 500 1000
Ehrlichia canis Jake 25 35 50 100 250 500 1000
Ehrlichia chaffeensis Arkansas 25 35 50 100 250 500 1000
Ehrlichia ruminantium Gardel 25 35 50 100 250 500 1000
Ehrlichia ruminantium str 25 35 50 100 250 500 1000
Ehrlichia ruminantium Welgevonden 25 35 50 100 250 500 1000
Enterococcus faecalis V583 25 35 50 100 250 500 1000
Erwinia carotovora atroseptica SCRI1043 25 35 50 100 250 500 1000
Erythrobacter litoralis HTCC2594 25 35 50 100 250 500 1000
Escherichia coli 536 25 35 50 100 250 500 1000
Escherichia coli CFT073 25 35 50 100 250 500 1000
Escherichia coli K12 25 35 50 100 250 500 1000
Escherichia coli O157H7 EDL933 25 35 50 100 250 500 1000
Escherichia coli O157H7 25 35 50 100 250 500 1000
Escherichia coli UTI89 25 35 50 100 250 500 1000
Escherichia coli W3110 25 35 50 100 250 500 1000
Francisella tularensis FSC 198 25 35 50 100 250 500 1000
Francisella tularensis holarctica 25 35 50 100 250 500 1000
Francisella tularensis holarctica OSU18 25 35 50 100 250 500 1000
Francisella tularensis tularensis 25 35 50 100 250 500 1000
Frankia alni ACN14a 25 35 50 100 250 500 1000
Frankia CcI3 25 35 50 100 250 500 1000
Fusobacterium nucleatum 25 35 50 100 250 500 1000
Geobacillus kaustophilus HTA426 25 35 50 100 250 500 1000
Geobacter metallireducens GS-15 25 35 50 100 250 500 1000
Geobacter sulfurreducens 25 35 50 100 250 500 1000
Gloeobacter violaceus 25 35 50 100 250 500 1000
Gluconobacter oxydans 621H 25 35 50 100 250 500 1000
Granulobacter bethesdensis CGDNIH1 25 35 50 100 250 500 1000
Haemophilus ducreyi 35000HP 25 35 50 100 250 500 1000
Haemophilus influenzae 86 028NP 25 35 50 100 250 500 1000
Haemophilus influenzae 25 35 50 100 250 500 1000
Haemophilus somnus 129PT 25 35 50 100 250 500 1000
Hahella chejuensis KCTC 2396 25 35 50 100 250 500 1000
Haloarcula marismortui ATCC 43049 25 35 50 100 250 500 1000
Haloarcula marismortui ATCC 43049 25 35 50 100 250 500 1000
Halobacterium sp 25 35 50 100 250 500 1000
Haloquadratum walsbyi 25 35 50 100 250 500 1000
Helicobacter acinonychis Sheeba 25 35 50 100 250 500 1000
Helicobacter hepaticus 25 35 50 100 250 500 1000
Helicobacter pylori 26695 25 35 50 100 250 500 1000
Helicobacter pylori HPAG1 25 35 50 100 250 500 1000
Helicobacter pylori J99 25 35 50 100 250 500 1000
Hyphomonas neptunium ATCC 15444 25 35 50 100 250 500 1000
Idiomarina loihiensis L2TR 25 35 50 100 250 500 1000
Jannaschia CCS1 25 35 50 100 250 500 1000
Lactobacillus acidophilus NCFM 25 35 50 100 250 500 1000
Lactobacillus delbrueckii bulgaricus 25 35 50 100 250 500 1000
Lactobacillus johnsonii NCC 533 25 35 50 100 250 500 1000
Lactobacillus plantarum 25 35 50 100 250 500 1000
Lactobacillus sakei 23K 25 35 50 100 250 500 1000
Lactobacillus salivarius UCC118 25 35 50 100 250 500 1000
Lactococcus lactis 25 35 50 100 250 500 1000
Lawsonia intracellularis PHE MN1-00 25 35 50 100 250 500 1000
Legionella pneumophila Lens 25 35 50 100 250 500 1000
Legionella pneumophila Paris 25 35 50 100 250 500 1000
Legionella pneumophila Philadelphia 1 25 35 50 100 250 500 1000
Leifsonia xyli xyli CTCB0 25 35 50 100 250 500 1000
Leptospira interrogans serovar Copenhageni 25 35 50 100 250 500 1000
Leptospira interrogans serovar Copenhageni 25 35 50 100 250 500 1000
Leptospira interrogans serovar Lai 25 35 50 100 250 500 1000
Leptospira interrogans serovar Lai 25 35 50 100 250 500 1000
Listeria innocua 25 35 50 100 250 500 1000
Listeria monocytogenes 4b F2365 25 35 50 100 250 500 1000
Listeria monocytogenes 25 35 50 100 250 500 1000
Magnetospirillum magneticum AMB-1 25 35 50 100 250 500 1000
Mannheimia succiniciproducens MBEL55E 25 35 50 100 250 500 1000
Maricaulis maris MCS10 25 35 50 100 250 500 1000
Mesoplasma florum L1 25 35 50 100 250 500 1000
Mesorhizobium BNC1 25 35 50 100 250 500 1000
Mesorhizobium loti 25 35 50 100 250 500 1000
Methanobacterium thermoautotrophicum 25 35 50 100 250 500 1000
Methanococcoides burtonii DSM 6242 25 35 50 100 250 500 1000
Methanococcus jannaschii 25 35 50 100 250 500 1000
Methanococcus jannaschii 25 35 50 100 250 500 1000
Methanococcus jannaschii 25 35 50 100 250 500 1000
Methanococcus maripaludis S2 25 35 50 100 250 500 1000
Methanopyrus kandleri 25 35 50 100 250 500 1000
Methanosarcina acetivorans 25 35 50 100 250 500 1000
Methanosarcina barkeri fusaro 25 35 50 100 250 500 1000
Methanosarcina mazei 25 35 50 100 250 500 1000
Methanosphaera stadtmanae 25 35 50 100 250 500 1000
Methanospirillum hungatei JF-1 25 35 50 100 250 500 1000
Methylobacillus flagellatus KT 25 35 50 100 250 500 1000
Methylococcus capsulatus Bath 25 35 50 100 250 500 1000
Moorella thermoacetica ATCC 39073 25 35 50 100 250 500 1000
Mycobacterium avium paratuberculosis 25 35 50 100 250 500 1000
Mycobacterium bovis 25 35 50 100 250 500 1000
Mycobacterium leprae 25 35 50 100 250 500 1000
Mycobacterium MCS 25 35 50 100 250 500 1000
Mycobacterium tuberculosis CDC1551 25 35 50 100 250 500 1000
Mycobacterium tuberculosis H37Rv 25 35 50 100 250 500 1000
Mycoplasma capricolum ATCC 27343 25 35 50 100 250 500 1000
Mycoplasma gallisepticum 25 35 50 100 250 500 1000
Mycoplasma genitalium 25 35 50 100 250 500 1000
Mycoplasma hyopneumoniae 232 25 35 50 100 250 500 1000
Mycoplasma hyopneumoniae 7448 25 35 50 100 250 500 1000
Mycoplasma hyopneumoniae J 25 35 50 100 250 500 1000
Mycoplasma mobile 163K 25 35 50 100 250 500 1000
Mycoplasma mycoides 25 35 50 100 250 500 1000
Mycoplasma penetrans 25 35 50 100 250 500 1000
Mycoplasma pneumoniae 25 35 50 100 250 500 1000
Mycoplasma pulmonis 25 35 50 100 250 500 1000
Mycoplasma synoviae 53 25 35 50 100 250 500 1000
Myxococcus xanthus DK 1622 25 35 50 100 250 500 1000
Nanoarchaeum equitans 25 35 50 100 250 500 1000
Natronomonas pharaonis 25 35 50 100 250 500 1000
Neisseria gonorrhoeae FA 1090 25 35 50 100 250 500 1000
Neisseria meningitidis MC58 25 35 50 100 250 500 1000
Neisseria meningitidis Z2491 25 35 50 100 250 500 1000
Neorickettsia sennetsu Miyayama 25 35 50 100 250 500 1000
Nitrobacter hamburgensis X14 25 35 50 100 250 500 1000
Nitrobacter winogradskyi Nb-255 25 35 50 100 250 500 1000
Nitrosococcus oceani ATCC 19707 25 35 50 100 250 500 1000
Nitrosomonas europaea 25 35 50 100 250 500 1000
Nitrosomonas eutropha C71 25 35 50 100 250 500 1000
Nitrosospira multiformis ATCC 25196 25 35 50 100 250 500 1000
Nocardia farcinica IFM10152 25 35 50 100 250 500 1000
Nostoc sp 25 35 50 100 250 500 1000
Novosphingobium aromaticivorans DSM 12444 25 35 50 100 250 500 1000
Oceanobacillus iheyensis 25 35 50 100 250 500 1000
Onion yellows phytoplasma 25 35 50 100 250 500 1000
Parachlamydia sp UWE25 25 35 50 100 250 500 1000
Pasteurella multocida 25 35 50 100 250 500 1000
Pelobacter carbinolicus 25 35 50 100 250 500 1000
Pelodictyon luteolum DSM 273 25 35 50 100 250 500 1000
Photobacterium profundum SS9 25 35 50 100 250 500 1000
Photobacterium profundum SS9 25 35 50 100 250 500 1000
Photorhabdus luminescens 25 35 50 100 250 500 1000
Picrophilus torridus DSM 9790 25 35 50 100 250 500 1000
Pirellula sp 25 35 50 100 250 500 1000
Polaromonas JS666 25 35 50 100 250 500 1000
Porphyromonas gingivalis W83 25 35 50 100 250 500 1000
Prochlorococcus marinus CCMP1375 25 35 50 100 250 500 1000
Prochlorococcus marinus MED4 25 35 50 100 250 500 1000
Prochlorococcus marinus MIT 9312 25 35 50 100 250 500 1000
Prochlorococcus marinus MIT9313 25 35 50 100 250 500 1000
Prochlorococcus marinus NATL2A 25 35 50 100 250 500 1000
Propionibacterium acnes KPA171202 25 35 50 100 250 500 1000
Pseudoalteromonas atlantica T6c 25 35 50 100 250 500 1000
Pseudoalteromonas haloplanktis TAC125 25 35 50 100 250 500 1000
Pseudoalteromonas haloplanktis TAC125 25 35 50 100 250 500 1000
Pseudomonas aeruginosa 25 35 50 100 250 500 1000
Pseudomonas aeruginosa UCBPP-PA14 25 35 50 100 250 500 1000
Pseudomonas entomophila L48 25 35 50 100 250 500 1000
Pseudomonas fluorescens Pf-5 25 35 50 100 250 500 1000
Pseudomonas fluorescens PfO-1 25 35 50 100 250 500 1000
Pseudomonas putida KT2440 25 35 50 100 250 500 1000
Pseudomonas syringae phaseolicola 1448A 25 35 50 100 250 500 1000
Pseudomonas syringae pv B728a 25 35 50 100 250 500 1000
Pseudomonas syringae tomato DC3000 25 35 50 100 250 500 1000
Psychrobacter arcticum 273-4 25 35 50 100 250 500 1000
Psychrobacter cryohalolentis K5 25 35 50 100 250 500 1000
Pyrobaculum aerophilum 25 35 50 100 250 500 1000
Pyrococcus abyssi 25 35 50 100 250 500 1000
Pyrococcus furiosus 25 35 50 100 250 500 1000
Pyrococcus horikoshii 25 35 50 100 250 500 1000
Ralstonia eutropha H16 25 35 50 100 250 500 1000
Ralstonia eutropha JMP134 25 35 50 100 250 500 1000
Ralstonia eutropha JMP134 25 35 50 100 250 500 1000
Ralstonia metallidurans CH34 25 35 50 100 250 500 1000
Ralstonia metallidurans CH34 25 35 50 100 250 500 1000
Ralstonia solanacearum 25 35 50 100 250 500 1000
Rhizobium etli CFN 42 25 35 50 100 250 500 1000
Rhodobacter sphaeroides 2 4 1 25 35 50 100 250 500 1000
Rhodobacter sphaeroides 2 4 1 25 35 50 100 250 500 1000
Rhodococcus RHA1 25 35 50 100 250 500 1000
Rhodoferax ferrireducens T118 25 35 50 100 250 500 1000
Rhodopseudomonas palustris BisA53 25 35 50 100 250 500 1000
Rhodopseudomonas palustris BisB18 25 35 50 100 250 500 1000
Rhodopseudomonas palustris BisB5 25 35 50 100 250 500 1000
Rhodopseudomonas palustris CGA009 25 35 50 100 250 500 1000
Rhodopseudomonas palustris HaA2 25 35 50 100 250 500 1000
Rhodospirillum rubrum ATCC 11170 25 35 50 100 250 500 1000
Rickettsia bellii RML369-C 25 35 50 100 250 500 1000
Rickettsia conorii 25 35 50 100 250 500 1000
Rickettsia felis URRWXCal2 25 35 50 100 250 500 1000
Rickettsia prowazekii 25 35 50 100 250 500 1000
Rickettsia typhi wilmington 25 35 50 100 250 500 1000
Roseobacter denitrificans OCh 114 25 35 50 100 250 500 1000
Rubrobacter xylanophilus DSM 9941 25 35 50 100 250 500 1000
Saccharophagus degradans 2-40 25 35 50 100 250 500 1000
Salinibacter ruber DSM 13855 25 35 50 100 250 500 1000
Salmonella enterica Choleraesuis 25 35 50 100 250 500 1000
Salmonella enterica Paratypi ATCC 9150 25 35 50 100 250 500 1000
Salmonella typhimurium LT2 25 35 50 100 250 500 1000
Salmonella typhi 25 35 50 100 250 500 1000
Salmonella typhi Ty2 25 35 50 100 250 500 1000
Shewanella denitrificans OS217 25 35 50 100 250 500 1000
Shewanella frigidimarina NCIMB 400 25 35 50 100 250 500 1000
Shewanella MR-4 25 35 50 100 250 500 1000
Shewanella MR-7 25 35 50 100 250 500 1000
Shewanella oneidensis 25 35 50 100 250 500 1000
Shigella boydii Sb227 25 35 50 100 250 500 1000
Shigella dysenteriae 25 35 50 100 250 500 1000
Shigella flexneri 2a 2457T 25 35 50 100 250 500 1000
Shigella flexneri 2a 25 35 50 100 250 500 1000
Shigella flexneri 5 8401 25 35 50 100 250 500 1000
Shigella sonnei Ss046 25 35 50 100 250 500 1000
Silicibacter pomeroyi DSS-3 25 35 50 100 250 500 1000
Silicibacter TM1040 25 35 50 100 250 500 1000
Sinorhizobium meliloti 25 35 50 100 250 500 1000
Sodalis glossinidius morsitans 25 35 50 100 250 500 1000
Sphingopyxis alaskensis RB2256 25 35 50 100 250 500 1000
Staphylococcus aureus aureus MRSA252 25 35 50 100 250 500 1000
Staphylococcus aureus aureus MSSA476 25 35 50 100 250 500 1000
Staphylococcus aureus COL 25 35 50 100 250 500 1000
Staphylococcus aureus Mu50 25 35 50 100 250 500 1000
Staphylococcus aureus MW2 25 35 50 100 250 500 1000
Staphylococcus aureus N315 25 35 50 100 250 500 1000
Staphylococcus aureus NCTC 8325 25 35 50 100 250 500 1000
Staphylococcus aureus RF122 25 35 50 100 250 500 1000
Staphylococcus aureus USA300 25 35 50 100 250 500 1000
Staphylococcus epidermidis ATCC 12228 25 35 50 100 250 500 1000
Staphylococcus epidermidis RP62A 25 35 50 100 250 500 1000
Staphylococcus haemolyticus 25 35 50 100 250 500 1000
Staphylococcus saprophyticus 25 35 50 100 250 500 1000
Streptococcus agalactiae 2603 25 35 50 100 250 500 1000
Streptococcus agalactiae A909 25 35 50 100 250 500 1000
Streptococcus agalactiae NEM316 25 35 50 100 250 500 1000
Streptococcus mutans 25 35 50 100 250 500 1000
Streptococcus pneumoniae R6 25 35 50 100 250 500 1000
Streptococcus pneumoniae TIGR4 25 35 50 100 250 500 1000
Streptococcus pyogenes M1 GAS 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS10270 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS10394 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS10750 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS2096 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS315 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS5005 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS6180 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS8232 25 35 50 100 250 500 1000
Streptococcus pyogenes MGAS9429 25 35 50 100 250 500 1000
Streptococcus pyogenes SSI-1 25 35 50 100 250 500 1000
Streptococcus thermophilus CNRZ1066 25 35 50 100 250 500 1000
Streptococcus thermophilus LMG 18311 25 35 50 100 250 500 1000
Streptomyces avermitilis 25 35 50 100 250 500 1000
Streptomyces coelicolor 25 35 50 100 250 500 1000
Sulfolobus acidocaldarius DSM 639 25 35 50 100 250 500 1000
Sulfolobus solfataricus 25 35 50 100 250 500 1000
Sulfolobus tokodaii 25 35 50 100 250 500 1000
Symbiobacterium thermophilum IAM14863 25 35 50 100 250 500 1000
Synechococcus CC9311 25 35 50 100 250 500 1000
Synechococcus CC9605 25 35 50 100 250 500 1000
Synechococcus CC9902 25 35 50 100 250 500 1000
Synechococcus elongatus PCC 6301 25 35 50 100 250 500 1000
Synechococcus elongatus PCC 7942 25 35 50 100 250 500 1000
Synechococcus sp WH8102 25 35 50 100 250 500 1000
Synechocystis PCC6803 25 35 50 100 250 500 1000
Syntrophomonas wolfei Goettingen 25 35 50 100 250 500 1000
Syntrophus aciditrophicus SB 25 35 50 100 250 500 1000
Thermoanaerobacter tengcongensis 25 35 50 100 250 500 1000
Thermobifida fusca YX 25 35 50 100 250 500 1000
Thermococcus kodakaraensis KOD1 25 35 50 100 250 500 1000
Thermoplasma acidophilum 25 35 50 100 250 500 1000
Thermoplasma volcanium 25 35 50 100 250 500 1000
Thermosynechococcus elongatus 25 35 50 100 250 500 1000
Thermotoga maritima 25 35 50 100 250 500 1000
Thermus thermophilus HB27 25 35 50 100 250 500 1000
Thermus thermophilus HB8 25 35 50 100 250 500 1000
Thiobacillus denitrificans ATCC 25259 25 35 50 100 250 500 1000
Thiomicrospira crunogena XCL-2 25 35 50 100 250 500 1000
Thiomicrospira denitrificans ATCC 33889 25 35 50 100 250 500 1000
Treponema denticola ATCC 35405 25 35 50 100 250 500 1000
Treponema pallidum 25 35 50 100 250 500 1000
Trichodesmium erythraeum IMS101 25 35 50 100 250 500 1000
Tropheryma whipplei TW08 27 25 35 50 100 250 500 1000
Tropheryma whipplei Twist 25 35 50 100 250 500 1000
Ureaplasma urealyticum 25 35 50 100 250 500 1000
Vibrio cholerae 25 35 50 100 250 500 1000
Vibrio cholerae 25 35 50 100 250 500 1000
Vibrio fischeri ES114 25 35 50 100 250 500 1000
Vibrio fischeri ES114 25 35 50 100 250 500 1000
Vibrio parahaemolyticus 25 35 50 100 250 500 1000
Vibrio parahaemolyticus 25 35 50 100 250 500 1000
Vibrio vulnificus CMCP6 25 35 50 100 250 500 1000
Vibrio vulnificus CMCP6 25 35 50 100 250 500 1000
Vibrio vulnificus YJ016 25 35 50 100 250 500 1000
Vibrio vulnificus YJ016 25 35 50 100 250 500 1000
Wigglesworthia brevipalpis 25 35 50 100 250 500 1000
Wolbachia endosymbiont of Brugia malayi TRS 25 35 50 100 250 500 1000
Wolbachia endosymbiont of Drosophila melanogaster 25 35 50 100 250 500 1000
Wolinella succinogenes 25 35 50 100 250 500 1000
Xanthomonas campestris 8004 25 35 50 100 250 500 1000
Xanthomonas campestris 25 35 50 100 250 500 1000
Xanthomonas campestris vesicatoria 85-10 25 35 50 100 250 500 1000
Xanthomonas citri 25 35 50 100 250 500 1000
Xanthomonas oryzae KACC10331 25 35 50 100 250 500 1000
Xanthomonas oryzae MAFF 311018 25 35 50 100 250 500 1000
Xylella fastidiosa 25 35 50 100 250 500 1000
Xylella fastidiosa Temecula1 25 35 50 100 250 500 1000
Yersinia pestis Antiqua 25 35 50 100 250 500 1000
Yersinia pestis biovar Mediaevails 25 35 50 100 250 500 1000
Yersinia pestis CO92 25 35 50 100 250 500 1000
Yersinia pestis KIM 25 35 50 100 250 500 1000
Yersinia pestis Nepal516 25 35 50 100 250 500 1000
Yersinia pseudotuberculosis IP32953 25 35 50 100 250 500 1000
Zymomonas mobilis ZM4 25 35 50 100 250 500 1000