| Abelson murine leukemia virus | 3 | 3 | 1 |
| Abutilon mosaic virus | 1 | 1 | 1 |
| Acanthamoeba castellanii str. Neff | 5 | 4 | 5 |
| Acanthamoeba polyphaga mimivirus | 10 | 10 | 9 |
| Acaryochloris marina MBIC11017 | 1 | 1 | 1 |
| Acetobacter aceti | 1 | 1 | 1 |
| Acetobacter pasteurianus IFO 3283-01 | 2 | 2 | 2 |
| Acetobacterium woodii DSM 1030 | 1 | 1 | 1 |
| Acholeplasma laidlawii PG-8A | 1 | 1 | 1 |
| Achromobacter xylosoxidans A8 | 1 | 1 | 1 |
| Acidianus filamentous virus 1 | 3 | 3 | 3 |
| Acidianus filamentous virus 6 | 1 | 1 | 1 |
| Acidianus two-tailed virus | 2 | 2 | 2 |
| Acidilobus saccharovorans 345-15 | 1 | 1 | 1 |
| Acidithiobacillus ferridurans | 1 | 1 | 1 |
| Acidithiobacillus ferrooxidans ATCC 23270 | 16 | 15 | 15 |
| Acidithiobacillus ferrooxidans ATCC 53993 | 1 | 1 | 1 |
| Acidobacterium capsulatum ATCC 51196 | 1 | 1 | 1 |
| Aciduliprofundum boonei T469 | 1 | 1 | 1 |
| Acinetobacter baumannii | 42 | 36 | 28 |
| Acinetobacter baumannii AB0057 | 7 | 5 | 6 |
| Acinetobacter baumannii AB307-0294 | 2 | 2 | 2 |
| Acinetobacter baumannii ACICU | 2 | 2 | 2 |
| Acinetobacter baumannii ATCC 17978 | 15 | 11 | 12 |
| Acinetobacter baumannii AYE | 3 | 2 | 3 |
| Acinetobacter baumannii SDF | 1 | 1 | 1 |
| Acinetobacter baylyi ADP1 | 5 | 3 | 5 |
| Acinetobacter calcoaceticus | 2 | 2 | 1 |
| Acinetobacter phage AP205 | 1 | 1 | 1 |
| Acinetobacter pittii PHEA-2 | 2 | 1 | 2 |
| Acropora digitifera | 1 | 1 | 1 |
| Actinobacillus pleuropneumoniae serovar 3 str. JL03 | 6 | 6 | 6 |
| Actinobacillus pleuropneumoniae serovar 5b str. L20 | 10 | 9 | 8 |
| Actinobacillus pleuropneumoniae serovar 7 str. AP76 | 1 | 1 | 1 |
| Acyrthosiphon pisum (pea aphid) | 12 | 9 | 12 |
| Adeno-associated virus - 1 | 3 | 3 | 1 |
| Adeno-associated virus - 2 | 28 | 20 | 10 |
| Adeno-associated virus - 8 | 2 | 2 | 1 |
| Advenella kashmirensis WT001 | 1 | 1 | 1 |
| Aedes aegypti (yellow fever mosquito) | 104 | 79 | 90 |
| Aedes albopictus (Asian tiger mosquito) | 4 | 2 | 4 |
| Aerococcus viridans | 1 | 1 | 1 |
| Aeromonas hydrophila | 1 | 1 | 1 |
| Aeromonas hydrophila subsp. hydrophila ATCC 7966 | 11 | 11 | 10 |
| Aeromonas salmonicida subsp. salmonicida | 2 | 2 | 1 |
| Aeromonas salmonicida subsp. salmonicida A449 | 3 | 3 | 3 |
| Aeromonas veronii | 3 | 3 | 3 |
| Aeromonas virus Aeh1 | 3 | 2 | 2 |
| Aeropyrum pernix K1 | 29 | 28 | 25 |
| African cassava mosaic virus | 3 | 3 | 1 |
| African green monkey simian foamy virus | 2 | 2 | 1 |
| African horse sickness virus | 5 | 5 | 4 |
| African swine fever virus | 35 | 33 | 28 |
| Agaricus bisporus var. bisporus H97 | 1 | 1 | 1 |
| Aggregatibacter actinomycetemcomitans | 5 | 5 | 3 |
| Aggregatibacter actinomycetemcomitans D11S-1 | 1 | 1 | 1 |
| Aggregatibacter actinomycetemcomitans NUM4039 | 1 | 1 | 1 |
| Agrobacterium fabrum str. C58 | 109 | 82 | 87 |
| Agrobacterium radiobacter K84 | 1 | 1 | 1 |
| Agrobacterium rhizogenes | 1 | 1 | 1 |
| Agrobacterium tumefaciens | 52 | 38 | 26 |
| Agrobacterium tumefaciens F2 | 2 | 2 | 2 |
| Agrotis segetum granulovirus | 1 | 1 | 1 |
| Aichi virus 1 | 3 | 3 | 1 |
| Ailuropoda melanoleuca (giant panda) | 12 | 10 | 12 |
| Alcaligenes faecalis | 1 | 1 | 1 |
| Alcanivorax borkumensis SK2 | 2 | 1 | 2 |
| Alcelaphine gammaherpesvirus 1 (wildebeest herpesvirus) | 2 | 2 | 2 |
| Alfalfa dwarf virus | 1 | 1 | 1 |
| Alfalfa mosaic virus | 3 | 3 | 1 |
| Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 | 2 | 2 | 1 |
| Aliivibrio fischeri ES114 | 50 | 37 | 37 |
| Aliivibrio fischeri MJ11 | 2 | 2 | 2 |
| Alkalilimnicola ehrlichii MLHE-1 | 2 | 2 | 2 |
| Alkaliphilus oremlandii OhILAs | 1 | 1 | 1 |
| Alligator mississippiensis (American alligator) | 5 | 3 | 5 |
| Alligator sinensis (Chinese alligator) | 8 | 5 | 8 |
| Allochromatium vinosum DSM 180 | 5 | 3 | 5 |
| Alphapapillomavirus 4 | 1 | 1 | 1 |
| Alphapapillomavirus 7 | 101 | 82 | 7 |
| Alternanthera mosaic virus | 2 | 2 | 2 |
| Alternaria alternata | 2 | 1 | 2 |
| Ambystoma tigrinum virus | 2 | 2 | 2 |
| American grass carp reovirus | 4 | 4 | 4 |
| Amsacta moorei entomopoxvirus | 3 | 3 | 2 |
| Amycolatopsis mediterranei U32 | 4 | 4 | 3 |
| Anaerolinea thermophila UNI-1 | 1 | 1 | 1 |
| Ananas comosus (pineapple) | 2 | 1 | 2 |
| Anaplasma phagocytophilum str. HZ | 6 | 5 | 5 |
| Anas platyrhynchos (mallard) | 64 | 52 | 56 |
| Anatid alphaherpesvirus 1 | 14 | 14 | 13 |
| Andes orthohantavirus | 9 | 9 | 4 |
| Anolis carolinensis (green anole) | 14 | 9 | 14 |
| Anopheles gambiae str. PEST | 100 | 80 | 72 |
| Anser cygnoides domesticus | 24 | 20 | 23 |
| Anticarsia gemmatalis nucleopolyhedrovirus | 1 | 1 | 1 |
| Apis cerana (Asiatic honeybee) | 5 | 4 | 5 |
| Apis mellifera (honey bee) | 179 | 135 | 126 |
| Apis mellifera ligustica (common honey bee) | 1 | 1 | 1 |
| Aplysia californica (California sea hare) | 16 | 14 | 12 |
| Apple chlorotic leaf spot virus | 2 | 2 | 1 |
| Apple geminivirus PL-2015 | 3 | 1 | 3 |
| Apple latent spherical virus | 1 | 1 | 1 |
| Apple stem grooving virus | 1 | 1 | 1 |
| Aquareovirus C | 1 | 1 | 1 |
| Aquifex aeolicus VF5 | 44 | 41 | 34 |
| Aquila chrysaetos canadensis | 1 | 1 | 1 |
| Arabidopsis lyrata subsp. lyrata | 27 | 26 | 27 |
| Arabidopsis thaliana (thale cress) | 21026 | 13880 | 6892 |
| Arachis hypogaea (peanut) | 3 | 2 | 3 |
| Arcanobacterium haemolyticum DSM 20595 | 1 | 1 | 1 |
| Archaeoglobus fulgidus DSM 4304 | 45 | 43 | 40 |
| Archaeoglobus veneficus SNP6 | 1 | 1 | 1 |
| Argentinian mammarenavirus | 10 | 10 | 2 |
| Aromatoleum aromaticum EbN1 | 2 | 1 | 2 |
| Arthrobacter sp. Rue61a | 3 | 3 | 3 |
| Arthrobotrys oligospora ATCC 24927 | 2 | 2 | 2 |
| Artibeus jamaicensis (Jamaican fruit-eating bat) | 1 | 1 | 1 |
| Asparagus officinalis (garden asparagus) | 2 | 1 | 2 |
| Asparagus virus 2 | 1 | 1 | 1 |
| Aspergillus clavatus NRRL 1 | 3 | 2 | 3 |
| Aspergillus fischeri NRRL 181 | 1 | 1 | 1 |
| Aspergillus flavus NRRL3357 | 27 | 27 | 20 |
| Aspergillus fumigatus Af293 | 171 | 143 | 123 |
| Aspergillus nidulans FGSC A4 | 86 | 69 | 66 |
| Aspergillus niger CBS 513.88 | 29 | 26 | 22 |
| Aspergillus oryzae RIB40 | 40 | 32 | 34 |
| Aspergillus terreus NIH2624 | 1 | 1 | 1 |
| Aspergillus thermomutatus | 2 | 2 | 2 |
| Astyanax mexicanus (Mexican tetra) | 1 | 1 | 1 |
| Athalia rosae (coleseed sawfly) | 3 | 1 | 3 |
| Australian bat lyssavirus | 1 | 1 | 1 |
| Autographa californica nucleopolyhedrovirus | 98 | 87 | 46 |
| Avian avulavirus 1 | 3 | 3 | 3 |
| Avian avulavirus 5 | 1 | 1 | 1 |
| Avian leukosis virus - RSA | 6 | 6 | 2 |
| Avian metapneumovirus | 9 | 9 | 4 |
| Avian orthoreovirus | 6 | 5 | 3 |
| Avian paramyxovirus 4 | 1 | 1 | 1 |
| Azoarcus sp. BH72 | 3 | 3 | 3 |
| Azorhizobium caulinodans ORS 571 | 3 | 3 | 3 |
| Azospirillum brasilense | 5 | 2 | 5 |
| Azospirillum brasilense Sp245 | 2 | 2 | 2 |
| Azotobacter vinelandii DJ | 34 | 19 | 27 |
| BK polyomavirus | 12 | 11 | 5 |
| Babesia bovis T2Bo | 8 | 7 | 8 |
| Babesia microti strain RI | 1 | 1 | 1 |
| Bacillus amyloliquefaciens DSM 7 = ATCC 23350 | 2 | 2 | 2 |
| Bacillus anthracis (anthrax) | 9 | 9 | 3 |
| Bacillus anthracis str. 'Ames Ancestor' | 86 | 73 | 37 |
| Bacillus anthracis str. A0248 | 6 | 5 | 5 |
| Bacillus anthracis str. A2012 | 2 | 2 | 2 |
| Bacillus anthracis str. Ames | 46 | 38 | 41 |
| Bacillus anthracis str. CDC 684 | 1 | 1 | 1 |
| Bacillus anthracis str. Sterne | 27 | 22 | 25 |
| Bacillus cereus | 1 | 1 | 1 |
| Bacillus cereus 03BB102 | 3 | 2 | 3 |
| Bacillus cereus AH187 | 1 | 1 | 1 |
| Bacillus cereus AH621 | 1 | 1 | 1 |
| Bacillus cereus AH820 | 1 | 1 | 1 |
| Bacillus cereus ATCC 10987 | 7 | 7 | 5 |
| Bacillus cereus ATCC 14579 | 56 | 50 | 43 |
| Bacillus cereus E33L | 17 | 16 | 15 |
| Bacillus cereus F837/76 | 1 | 1 | 1 |
| Bacillus cereus G9842 | 1 | 1 | 1 |
| Bacillus cereus NC7401 | 1 | 1 | 1 |
| Bacillus cereus biovar anthracis str. CI | 2 | 2 | 2 |
| Bacillus cytotoxicus NVH 391-98 | 1 | 1 | 1 |
| Bacillus halodurans C-125 | 15 | 14 | 15 |
| Bacillus licheniformis DSM 13 = ATCC 14580 | 25 | 25 | 18 |
| Bacillus megaterium DSM 319 | 5 | 4 | 5 |
| Bacillus megaterium QM B1551 | 1 | 1 | 1 |
| Bacillus megaterium WSH-002 | 1 | 1 | 1 |
| Bacillus methanolicus MGA3 | 2 | 2 | 2 |
| Bacillus mycoides KBAB4 | 1 | 1 | 1 |
| Bacillus phage PZA | 7 | 6 | 6 |
| Bacillus phage SPP1 | 1 | 1 | 1 |
| Bacillus pseudofirmus OF4 | 3 | 1 | 3 |
| Bacillus pumilus SAFR-032 | 4 | 3 | 4 |
| Bacillus subtilis | 21 | 18 | 21 |
| Bacillus subtilis BEST7613 | 1 | 1 | 1 |
| Bacillus subtilis BSn5 | 1 | 1 | 1 |
| Bacillus subtilis PY79 | 9 | 6 | 9 |
| Bacillus subtilis QB928 | 2 | 2 | 2 |
| Bacillus subtilis XF-1 | 1 | 1 | 1 |
| Bacillus subtilis subsp. natto | 1 | 1 | 1 |
| Bacillus subtilis subsp. natto BEST195 | 2 | 2 | 2 |
| Bacillus subtilis subsp. spizizenii TU-B-10 | 7 | 7 | 6 |
| Bacillus subtilis subsp. spizizenii str. W23 | 9 | 9 | 9 |
| Bacillus subtilis subsp. subtilis 6051-HGW | 1 | 1 | 1 |
| Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 | 2 | 2 | 2 |
| Bacillus subtilis subsp. subtilis str. 168 | 1279 | 911 | 690 |
| Bacillus subtilis subsp. subtilis str. RO-NN-1 | 3 | 3 | 3 |
| Bacillus thuringiensis | 6 | 6 | 4 |
| Bacillus thuringiensis BMB171 | 3 | 3 | 3 |
| Bacillus thuringiensis Bt407 | 2 | 2 | 2 |
| Bacillus thuringiensis MC28 | 1 | 1 | 1 |
| Bacillus thuringiensis YBT-1518 | 1 | 1 | 1 |
| Bacillus thuringiensis serovar israelensis | 30 | 27 | 10 |
| Bacillus thuringiensis serovar kurstaki str. HD73 | 3 | 2 | 3 |
| Bacillus velezensis FZB42 | 10 | 8 | 9 |
| Bacillus velezensis YAU B9601-Y2 | 1 | 1 | 1 |
| Bacillus virus GA1 | 1 | 1 | 1 |
| Bacillus virus SPO1 | 1 | 1 | 1 |
| Bacillus virus phi29 | 18 | 18 | 8 |
| Bacteroides fragilis NCTC 9343 | 98 | 22 | 94 |
| Bacteroides fragilis YCH46 | 5 | 5 | 4 |
| Bacteroides helcogenes P 36-108 | 1 | 1 | 1 |
| Bacteroides thetaiotaomicron | 5 | 4 | 5 |
| Bacteroides thetaiotaomicron VPI-5482 | 17 | 16 | 17 |
| Bacteroides vulgatus ATCC 8482 | 4 | 4 | 3 |
| Bactrocera dorsalis (oriental fruit fly) | 11 | 10 | 11 |
| Bactrocera latifrons | 1 | 1 | 1 |
| Bamboo mosaic virus | 6 | 4 | 3 |
| Banana streak virus Acuminata Yunnan | 1 | 1 | 1 |
| Banna virus strain JKT-6423 | 1 | 1 | 1 |
| Barley stripe mosaic virus | 2 | 2 | 1 |
| Barley yellow dwarf virus PAV | 1 | 1 | 1 |
| Barley yellow mosaic virus | 1 | 1 | 1 |
| Bartonella henselae str. Houston-1 | 11 | 7 | 11 |
| Bartonella quintana RM-11 | 1 | 1 | 1 |
| Bartonella quintana str. Toulouse | 3 | 1 | 3 |
| Bat SARS CoV Rp3/2004 | 1 | 1 | 1 |
| Bat SARS coronavirus HKU3 | 1 | 1 | 1 |
| Bdellovibrio bacteriovorus HD100 | 17 | 8 | 17 |
| Beak and feather disease virus | 1 | 1 | 1 |
| Bean dwarf mosaic virus | 1 | 1 | 1 |
| Bean pod mottle virus | 1 | 1 | 1 |
| Beauveria bassiana ARSEF 2860 | 15 | 12 | 15 |
| Beet black scorch virus | 1 | 1 | 1 |
| Beet curly top virus | 4 | 4 | 2 |
| Beet necrotic yellow vein virus | 4 | 4 | 2 |
| Beet yellows virus | 2 | 2 | 1 |
| Beilong virus | 1 | 1 | 1 |
| Bemisia tabaci (sweet potato whitefly) | 1 | 1 | 1 |
| Beta vulgaris subsp. vulgaris (Swiss chard) | 8 | 6 | 8 |
| Bhendi yellow vein betasatellite | 1 | 1 | 1 |
| Bhendi yellow vein mosaic virus | 3 | 3 | 2 |
| Bifidobacterium adolescentis ATCC 15703 | 7 | 7 | 4 |
| Bifidobacterium bifidum PRL2010 | 4 | 4 | 4 |
| Bifidobacterium breve UCC2003 | 3 | 1 | 3 |
| Bifidobacterium longum NCC2705 | 5 | 4 | 5 |
| Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 | 2 | 1 | 2 |
| Bifidobacterium longum subsp. longum JCM 1217 | 1 | 1 | 1 |
| Biomphalaria glabrata (bloodfluke planorb) | 1 | 1 | 1 |
| Bison bison bison | 3 | 2 | 3 |
| Blackcurrant reversion virus | 1 | 1 | 1 |
| Blattella germanica densovirus 1 | 1 | 1 | 1 |
| Bluetongue virus | 15 | 14 | 10 |
| Boleophthalmus pectinirostris (great blue-spotted mudskipper) | 1 | 1 | 1 |
| Bombus terrestris (buff-tailed bumblebee) | 6 | 4 | 6 |
| Bombyx mandarina nucleopolyhedrovirus | 2 | 1 | 2 |
| Bombyx mori (domestic silkworm) | 545 | 421 | 371 |
| Bombyx mori nucleopolyhedrovirus | 60 | 56 | 42 |
| Bordetella avium 197N | 2 | 1 | 2 |
| Bordetella bronchiseptica | 3 | 1 | 3 |
| Bordetella bronchiseptica RB50 | 25 | 18 | 22 |
| Bordetella parapertussis 12822 | 2 | 1 | 2 |
| Bordetella pertussis 18323 | 1 | 1 | 1 |
| Bordetella pertussis Tohama I | 62 | 54 | 30 |
| Bordetella petrii DSM 12804 | 1 | 1 | 1 |
| Borrelia hermsii | 1 | 1 | 1 |
| Borrelia turicatae 91E135 | 1 | 1 | 1 |
| Borreliella afzelii ACA-1 | 1 | 1 | 1 |
| Borreliella afzelii PKo | 2 | 2 | 2 |
| Borreliella bavariensis PBi | 2 | 2 | 1 |
| Borreliella bissettii DN127 | 1 | 1 | 1 |
| Borreliella burgdorferi (Lyme disease spirochete) | 7 | 7 | 2 |
| Borreliella burgdorferi 118a | 1 | 1 | 1 |
| Borreliella burgdorferi 156a | 2 | 2 | 2 |
| Borreliella burgdorferi 297 | 7 | 6 | 4 |
| Borreliella burgdorferi 64b | 2 | 2 | 1 |
| Borreliella burgdorferi B31 | 204 | 161 | 96 |
| Borreliella burgdorferi ZS7 | 6 | 4 | 6 |
| Bos indicus (zebu cattle) | 9 | 9 | 9 |
| Bos indicus x Bos taurus (hybrid cattle) | 1 | 1 | 1 |
| Bos mutus (wild yak) | 5 | 5 | 5 |
| Bos taurus (cattle) | 6785 | 5051 | 2272 |
| Bos taurus papillomavirus 7 | 2 | 2 | 1 |
| Botrytis cinerea B05.10 | 13 | 12 | 13 |
| Bovine adenovirus 3 | 7 | 6 | 6 |
| Bovine alphaherpesvirus 1 | 45 | 39 | 12 |
| Bovine alphaherpesvirus 5 | 3 | 3 | 2 |
| Bovine coronavirus | 6 | 4 | 5 |
| Bovine ephemeral fever virus | 2 | 1 | 2 |
| Bovine gammaherpesvirus 4 | 2 | 2 | 2 |
| Bovine immunodeficiency virus | 5 | 5 | 4 |
| Bovine leukemia virus | 5 | 5 | 3 |
| Bovine orthopneumovirus | 2 | 2 | 2 |
| Bovine papular stomatitis virus | 2 | 2 | 2 |
| Bovine viral diarrhea virus 1 | 14 | 14 | 1 |
| Bovine viral diarrhea virus 2 (BVDV-2) | 1 | 1 | 1 |
| Brachypodium distachyon (stiff brome) | 11 | 11 | 11 |
| Brachyspira hyodysenteriae WA1 | 2 | 1 | 2 |
| Bradyrhizobium diazoefficiens USDA 110 | 62 | 44 | 47 |
| Bradyrhizobium japonicum USDA 6 | 8 | 6 | 7 |
| Bradyrhizobium sp. | 1 | 1 | 1 |
| Bradyrhizobium sp. BTAi1 | 1 | 1 | 1 |
| Bradyrhizobium sp. ORS 278 | 3 | 2 | 3 |
| Branchiostoma belcheri (Belcher's lancelet) | 1 | 1 | 1 |
| Branchiostoma floridae (Florida lancelet) | 3 | 3 | 2 |
| Brassica napus (rape) | 32 | 26 | 31 |
| Brassica oleracea (wild cabbage) | 10 | 10 | 10 |
| Brassica rapa (field mustard) | 26 | 24 | 22 |
| Brevibacillus brevis NBRC 100599 | 1 | 1 | 1 |
| Brome mosaic virus | 11 | 9 | 4 |
| Brucella abortus 2308 | 45 | 28 | 41 |
| Brucella abortus bv. 1 str. 9-941 | 12 | 10 | 10 |
| Brucella melitensis ATCC 23457 | 2 | 1 | 2 |
| Brucella melitensis M28 | 1 | 1 | 1 |
| Brucella melitensis M5-90 | 1 | 1 | 1 |
| Brucella melitensis NI | 1 | 1 | 1 |
| Brucella melitensis bv. 1 str. 16M | 19 | 17 | 15 |
| Brucella microti CCM 4915 | 1 | 1 | 1 |
| Brucella ovis ATCC 25840 | 1 | 1 | 1 |
| Brucella suis 1330 | 18 | 11 | 15 |
| Brugia malayi (agent of lymphatic filariasis) | 14 | 14 | 13 |
| Bubalus bubalis (water buffalo) | 77 | 62 | 69 |
| Bunyamwera virus | 7 | 7 | 3 |
| Burkholderia ambifaria AMMD | 1 | 1 | 1 |
| Burkholderia cenocepacia AU 1054 | 2 | 2 | 2 |
| Burkholderia cenocepacia J2315 | 20 | 14 | 19 |
| Burkholderia cenocepacia MC0-3 | 1 | 1 | 1 |
| Burkholderia gladioli BSR3 | 1 | 1 | 1 |
| Burkholderia glumae BGR1 | 1 | 1 | 1 |
| Burkholderia mallei ATCC 23344 | 7 | 6 | 7 |
| Burkholderia multivorans ATCC 17616 | 5 | 4 | 4 |
| Burkholderia pseudomallei 1026b | 1 | 1 | 1 |
| Burkholderia pseudomallei 1710b | 9 | 9 | 9 |
| Burkholderia pseudomallei 406e | 1 | 1 | 1 |
| Burkholderia pseudomallei K96243 | 52 | 48 | 43 |
| Burkholderia pseudomallei MSHR2543 | 2 | 1 | 2 |
| Burkholderia pseudomallei MSHR346 | 2 | 2 | 2 |
| Burkholderia thailandensis E264 | 8 | 7 | 8 |
| Butyrivibrio proteoclasticus B316 | 1 | 1 | 1 |
| Cabbage leaf curl virus | 3 | 3 | 1 |
| Caenorhabditis briggsae | 3 | 3 | 3 |
| Caenorhabditis elegans (roundworm) | 6118 | 4201 | 2432 |
| Caenorhabditis remanei | 3 | 3 | 3 |
| Caldanaerobacter subterraneus subsp. tengcongensis MB4 | 25 | 23 | 23 |
| Caldicellulosiruptor bescii DSM 6725 | 2 | 2 | 2 |
| Caldicellulosiruptor saccharolyticus DSM 8903 | 4 | 3 | 4 |
| Caldivirga maquilingensis IC-167 | 1 | 1 | 1 |
| Cali mammarenavirus | 1 | 1 | 1 |
| Callithrix jacchus (white-tufted-ear marmoset) | 28 | 24 | 27 |
| Camelina sativa (false flax) | 2 | 1 | 2 |
| Camellia sinensis (black tea) | 7 | 4 | 7 |
| Camelus bactrianus (Bactrian camel) | 2 | 2 | 2 |
| Camelus dromedarius (Arabian camel) | 6 | 5 | 6 |
| Campoletis sonorensis ichnovirus | 1 | 1 | 1 |
| Camponotus floridanus (Florida carpenter ant) | 1 | 1 | 1 |
| Campylobacter coli | 1 | 1 | 1 |
| Campylobacter coli CVM N29710 | 1 | 1 | 1 |
| Campylobacter jejuni 4031 | 3 | 1 | 3 |
| Campylobacter jejuni RM1221 | 4 | 4 | 4 |
| Campylobacter jejuni subsp. jejuni 00-2425 | 1 | 1 | 1 |
| Campylobacter jejuni subsp. jejuni 81-176 | 25 | 21 | 24 |
| Campylobacter jejuni subsp. jejuni 81116 | 6 | 5 | 6 |
| Campylobacter jejuni subsp. jejuni IA3902 | 1 | 1 | 1 |
| Campylobacter jejuni subsp. jejuni ICDCCJ07001 | 1 | 1 | 1 |
| Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 | 148 | 116 | 115 |
| Campylobacter lari RM2100 | 8 | 8 | 5 |
| Campylobacter virus NCTC12673 | 1 | 1 | 1 |
| Candida albicans SC5314 | 677 | 512 | 412 |
| Candida dubliniensis CD36 | 6 | 5 | 6 |
| Candida orthopsilosis Co 90-125 | 2 | 2 | 2 |
| Candida tropicalis MYA-3404 | 3 | 2 | 3 |
| Candidatus Pelagibacter ubique HTCC1062 | 1 | 1 | 1 |
| Candidatus Protochlamydia amoebophila UWE25 | 1 | 1 | 1 |
| Canine bocavirus 1 | 1 | 1 | 1 |
| Canine minute virus | 3 | 3 | 1 |
| Canine morbillivirus | 17 | 15 | 5 |
| Canine parvovirus | 6 | 6 | 2 |
| Canis lupus dingo (dingo) | 1 | 1 | 1 |
| Canis lupus familiaris (dog) | 3033 | 2225 | 1367 |
| Capra hircus (goat) | 311 | 232 | 217 |
| Capsicum annuum | 15 | 12 | 15 |
| Carassius auratus (goldfish) | 2 | 2 | 2 |
| Carboxydothermus hydrogenoformans Z-2901 | 2 | 2 | 2 |
| Carica papaya (papaya) | 4 | 4 | 4 |
| Carlito syrichta (Philippine tarsier) | 3 | 3 | 3 |
| Carnation Italian ringspot virus | 1 | 1 | 1 |
| Cauliflower mosaic virus | 7 | 6 | 3 |
| Caulobacter vibrioides CB15 | 98 | 60 | 65 |
| Caulobacter vibrioides NA1000 | 85 | 63 | 60 |
| Cavenderia fasciculata | 1 | 1 | 1 |
| Cavia porcellus (domestic guinea pig) | 187 | 147 | 147 |
| Caviid betaherpesvirus 2 | 9 | 4 | 4 |
| Cedecea neteri | 1 | 1 | 1 |
| Cellulomonas gilvus ATCC 13127 | 1 | 1 | 1 |
| Cellulosimicrobium cellulans | 1 | 1 | 1 |
| Cellvibrio japonicus Ueda107 | 2 | 2 | 2 |
| Ceratitis capitata (Mediterranean fruit fly) | 2 | 2 | 2 |
| Cercocebus atys (sooty mangabey) | 1 | 1 | 1 |
| Cercopithecine alphaherpesvirus 9 (Simian varicella virus) | 5 | 4 | 4 |
| Cereal yellow dwarf virus RPS | 2 | 2 | 2 |
| Cereal yellow dwarf virus RPV | 2 | 2 | 1 |
| Chaetomium thermophilum var. thermophilum DSM 1495 | 13 | 12 | 13 |
| Chandipura virus | 2 | 2 | 2 |
| Chelonia mydas (Green sea turtle) | 1 | 1 | 1 |
| Chicken anemia virus | 22 | 22 | 1 |
| Chikungunya virus | 42 | 42 | 2 |
| Chili leaf curl betasatellite | 1 | 1 | 1 |
| Chinchilla lanigera (long-tailed chinchilla) | 2 | 2 | 2 |
| Chinese wheat mosaic virus | 4 | 3 | 4 |
| Chlamydia abortus S26/3 | 2 | 2 | 2 |
| Chlamydia muridarum str. Nigg | 7 | 6 | 5 |
| Chlamydia pneumoniae AR39 | 12 | 10 | 9 |
| Chlamydia pneumoniae CWL029 | 12 | 12 | 11 |
| Chlamydia pneumoniae TW-183 | 6 | 6 | 5 |
| Chlamydia psittaci 6BC | 2 | 2 | 2 |
| Chlamydia trachomatis | 4 | 4 | 1 |
| Chlamydia trachomatis 434/Bu | 16 | 11 | 16 |
| Chlamydia trachomatis A/HAR-13 | 4 | 4 | 3 |
| Chlamydia trachomatis B/Jali20/OT | 1 | 1 | 1 |
| Chlamydia trachomatis B/TZ1A828/OT | 3 | 2 | 3 |
| Chlamydia trachomatis D/UW-3/CX | 39 | 35 | 30 |
| Chlamydia trachomatis L1/440/LN | 1 | 1 | 1 |
| Chlamydia trachomatis L2b/UCH-1/proctitis | 5 | 5 | 4 |
| Chlamydia trachomatis L2c | 3 | 3 | 3 |
| Chlamydomonas reinhardtii | 351 | 280 | 233 |
| Chlorobaculum tepidum TLS | 38 | 26 | 32 |
| Chlorocebus sabaeus (green monkey) | 23 | 18 | 23 |
| Chloroherpeton thalassium ATCC 35110 | 1 | 1 | 1 |
| Choristoneura fumiferana DEF multiple nucleopolyhedrovirus | 1 | 1 | 1 |
| Chromobacterium violaceum ATCC 12472 | 6 | 4 | 6 |
| Chromohalobacter salexigens DSM 3043 | 1 | 1 | 1 |
| Chrysemys picta (Painted turtle) | 2 | 2 | 2 |
| Chrysodeixis chalcites nucleopolyhedrovirus | 1 | 1 | 1 |
| Cicer arietinum (chickpea) | 18 | 14 | 18 |
| Cimex lectularius (bed bug) | 2 | 2 | 2 |
| Ciona intestinalis (vase tunicate) | 126 | 98 | 76 |
| Citrobacter freundii | 3 | 2 | 2 |
| Citrobacter freundii CFNIH1 | 3 | 3 | 2 |
| Citrobacter koseri ATCC BAA-895 | 1 | 1 | 1 |
| Citrobacter rodentium ICC168 | 2 | 2 | 2 |
| Citrus leaf blotch virus | 1 | 1 | 1 |
| Citrus psorosis virus | 2 | 1 | 2 |
| Citrus sinensis (sweet orange) | 9 | 9 | 9 |
| Citrus tristeza virus | 16 | 11 | 7 |
| Classical swine fever virus | 62 | 62 | 1 |
| Clavibacter michiganensis subsp. michiganensis NCPPB 382 | 2 | 1 | 2 |
| Clavispora lusitaniae ATCC 42720 | 1 | 1 | 1 |
| Clostridioides difficile | 9 | 7 | 8 |
| Clostridioides difficile 630 | 100 | 76 | 43 |
| Clostridioides difficile CD196 | 2 | 2 | 2 |
| Clostridioides difficile R20291 | 7 | 6 | 6 |
| Clostridium acetobutylicum ATCC 824 | 45 | 29 | 36 |
| Clostridium acetobutylicum DSM 1731 | 1 | 1 | 1 |
| Clostridium beijerinckii NCIMB 8052 | 1 | 1 | 1 |
| Clostridium botulinum | 2 | 2 | 1 |
| Clostridium botulinum A str. ATCC 19397 | 1 | 1 | 1 |
| Clostridium botulinum A str. ATCC 3502 | 38 | 30 | 18 |
| Clostridium botulinum A str. Hall | 2 | 2 | 1 |
| Clostridium botulinum B str. Eklund 17B | 2 | 2 | 1 |
| Clostridium botulinum B1 str. Okra | 2 | 2 | 1 |
| Clostridium botulinum BKT015925 | 2 | 2 | 2 |
| Clostridium botulinum Ba4 str. 657 | 2 | 2 | 1 |
| Clostridium botulinum F str. Langeland | 1 | 1 | 1 |
| Clostridium botulinum H04402 065 | 1 | 1 | 1 |
| Clostridium cellulovorans 743B | 1 | 1 | 1 |
| Clostridium kluyveri DSM 555 | 2 | 2 | 2 |
| Clostridium pasteurianum BC1 | 1 | 1 | 1 |
| Clostridium perfringens | 27 | 23 | 15 |
| Clostridium perfringens ATCC 13124 | 12 | 12 | 9 |
| Clostridium perfringens SM101 | 11 | 8 | 11 |
| Clostridium perfringens str. 13 | 43 | 33 | 27 |
| Clostridium tetani E88 | 5 | 5 | 4 |
| Clover yellow vein virus | 2 | 1 | 2 |
| Clupea harengus (Atlantic herring) | 2 | 2 | 2 |
| Coccidioides immitis RS | 2 | 2 | 2 |
| Coccomyxa subellipsoidea C-169 | 1 | 1 | 1 |
| Cocksfoot mottle virus | 1 | 1 | 1 |
| Colletotrichum fructicola | 1 | 1 | 1 |
| Colletotrichum fructicola Nara gc5 | 1 | 1 | 1 |
| Columba livia (rock pigeon) | 25 | 20 | 23 |
| Colwellia psychrerythraea 34H | 2 | 2 | 2 |
| Comamonas testosteroni TK102 | 4 | 4 | 4 |
| Condylura cristata (star-nosed mole) | 1 | 1 | 1 |
| Coprinopsis cinerea okayama7#130 | 10 | 9 | 10 |
| Cordyceps militaris CM01 | 1 | 1 | 1 |
| Corynebacterium diphtheriae | 4 | 4 | 3 |
| Corynebacterium diphtheriae C7 (beta) | 2 | 1 | 2 |
| Corynebacterium diphtheriae NCTC 13129 | 22 | 19 | 11 |
| Corynebacterium glutamicum | 2 | 2 | 2 |
| Corynebacterium glutamicum ATCC 13032 | 201 | 149 | 161 |
| Corynebacterium glutamicum MB001 | 3 | 3 | 3 |
| Corynebacterium glutamicum R | 14 | 10 | 14 |
| Corynebacterium jeikeium | 1 | 1 | 1 |
| Corynebacterium jeikeium K411 | 3 | 2 | 3 |
| Corynebacterium phage BFK20 | 2 | 2 | 2 |
| Corynebacterium pseudotuberculosis 31 | 1 | 1 | 1 |
| Corynebacterium pseudotuberculosis C231 | 1 | 1 | 1 |
| Cotton leaf curl Multan betasatellite | 1 | 1 | 1 |
| Cotton leafroll dwarf virus | 1 | 1 | 1 |
| Coturnix japonica (Japanese quail) | 27 | 20 | 22 |
| Cowpea chlorotic mottle virus | 1 | 1 | 1 |
| Cowpea mosaic virus | 1 | 1 | 1 |
| Cowpox virus | 11 | 11 | 7 |
| Coxiella burnetii RSA 493 | 14 | 11 | 14 |
| Crassostrea gigas (Pacific oyster) | 25 | 22 | 25 |
| Cricetulus griseus (Chinese hamster) | 79 | 67 | 72 |
| Crimean-Congo hemorrhagic fever orthonairovirus | 6 | 6 | 3 |
| Crocosphaera subtropica ATCC 51142 | 2 | 1 | 2 |
| Cronobacter sakazakii | 4 | 4 | 3 |
| Cronobacter sakazakii ATCC BAA-894 | 3 | 3 | 3 |
| Cryptococcus gattii WM276 | 3 | 3 | 3 |
| Cryptococcus neoformans var. grubii H99 | 21 | 18 | 20 |
| Cryptococcus neoformans var. neoformans B-3501A | 1 | 1 | 1 |
| Cryptococcus neoformans var. neoformans JEC21 | 31 | 29 | 21 |
| Cryptomeria japonica (Japanese cedar) | 1 | 1 | 1 |
| Cryptosporidium hominis TU502 | 1 | 1 | 1 |
| Cryptosporidium parvum Iowa II | 25 | 24 | 23 |
| Cucumber mosaic virus (cucumber mosaic cucumovirus) | 22 | 20 | 4 |
| Cucumber necrosis virus | 5 | 5 | 2 |
| Cucumber vein yellowing virus | 2 | 2 | 1 |
| Cucumis melo (muskmelon) | 5 | 4 | 5 |
| Cucumis sativus (cucumber) | 31 | 30 | 31 |
| Cucurbit yellow stunting disorder virus | 1 | 1 | 1 |
| Cucurbita maxima (winter squash) | 1 | 1 | 1 |
| Cucurbita moschata (crookneck pumpkin) | 1 | 1 | 1 |
| Culex quinquefasciatus (southern house mosquito) | 22 | 16 | 20 |
| Cupriavidus metallidurans CH34 | 20 | 19 | 17 |
| Cupriavidus necator H16 | 51 | 35 | 41 |
| Cupriavidus necator N-1 | 2 | 2 | 2 |
| Cutibacterium acnes KPA171202 | 4 | 4 | 4 |
| Cyanidioschyzon merolae strain 10D | 2 | 2 | 2 |
| Cymbidium mosaic virus | 1 | 1 | 1 |
| Cymbidium ringspot virus | 1 | 1 | 1 |
| Cynoglossus semilaevis (tongue sole) | 21 | 19 | 20 |
| Cypovirus 1 | 2 | 2 | 2 |
| Cyprinid herpesvirus 3 | 6 | 6 | 5 |
| Cyprinodon variegatus (sheepshead minnow) | 1 | 1 | 1 |
| Cyprinus carpio (common carp) | 16 | 13 | 16 |
| Cytophaga hutchinsonii ATCC 33406 | 2 | 2 | 2 |
| Danio rerio (zebrafish) | 8357 | 5918 | 3762 |
| Daucus carota subsp. sativus | 1 | 1 | 1 |
| Debaryomyces hansenii CBS767 | 2 | 2 | 2 |
| Dechloromonas aromatica RCB | 1 | 1 | 1 |
| Dehalococcoides mccartyi CBDB1 | 1 | 1 | 1 |
| Deinococcus deserti VCD115 | 3 | 2 | 3 |
| Deinococcus geothermalis DSM 11300 | 7 | 7 | 6 |
| Deinococcus radiodurans R1 | 110 | 91 | 83 |
| Deltapapillomavirus 4 | 38 | 33 | 6 |
| Dendrolimus punctatus cypovirus 22 | 1 | 1 | 1 |
| Dendrolimus punctatus virus | 1 | 1 | 1 |
| Dengue virus 1 | 35 | 35 | 1 |
| Dengue virus 2 | 98 | 98 | 1 |
| Dengue virus 3 | 15 | 15 | 1 |
| Dengue virus 4 | 9 | 9 | 1 |
| Denitrovibrio acetiphilus DSM 12809 | 1 | 1 | 1 |
| Desmodus rotundus (common vampire bat) | 3 | 3 | 3 |
| Desulfitobacterium hafniense DCB-2 | 2 | 2 | 2 |
| Desulfitobacterium hafniense Y51 | 1 | 1 | 1 |
| Desulfovibrio alaskensis G20 | 4 | 4 | 4 |
| Desulfovibrio desulfuricans ATCC 27774 | 1 | 1 | 1 |
| Desulfovibrio gigas DSM 1382 = ATCC 19364 | 2 | 1 | 2 |
| Desulfovibrio vulgaris DP4 | 1 | 1 | 1 |
| Desulfovibrio vulgaris str. 'Miyazaki F' | 1 | 1 | 1 |
| Desulfovibrio vulgaris str. Hildenborough | 35 | 26 | 31 |
| Desulfurococcus amylolyticus 1221n | 1 | 1 | 1 |
| Diaphorina citri (Asian citrus psyllid) | 2 | 2 | 2 |
| Dichelobacter nodosus VCS1703A | 7 | 5 | 7 |
| Dickeya dadantii 3937 | 9 | 7 | 9 |
| Dictyostelium discoideum AX4 | 287 | 238 | 225 |
| Drosophila ananassae | 2 | 2 | 2 |
| Drosophila erecta | 2 | 2 | 2 |
| Drosophila ficusphila | 2 | 2 | 2 |
| Drosophila grimshawi | 2 | 2 | 2 |
| Drosophila hydei | 2 | 2 | 2 |
| Drosophila melanogaster (fruit fly) | 18781 | 12804 | 3938 |
| Drosophila mojavensis | 4 | 4 | 3 |
| Drosophila navojoa | 1 | 1 | 1 |
| Drosophila novamexicana | 1 | 1 | 1 |
| Drosophila persimilis | 1 | 1 | 1 |
| Drosophila pseudoobscura | 3 | 3 | 3 |
| Drosophila sechellia | 2 | 2 | 2 |
| Drosophila simulans | 6 | 6 | 5 |
| Drosophila takahashii | 1 | 1 | 1 |
| Drosophila virilis | 21 | 20 | 21 |
| Drosophila willistoni | 1 | 1 | 1 |
| Drosophila yakuba | 2 | 2 | 2 |
| Duck circovirus | 2 | 2 | 2 |
| Duck hepatitis A virus 3 | 1 | 1 | 1 |
| Duck hepatitis B virus | 4 | 4 | 2 |
| East African cassava mosaic Cameroon virus | 2 | 2 | 2 |
| East African cassava mosaic Zanzibar virus | 1 | 1 | 1 |
| Eastern equine encephalitis virus | 2 | 2 | 1 |
| Echinococcus granulosus | 4 | 3 | 4 |
| Echinops telfairi (small Madagascar hedgehog) | 2 | 2 | 2 |
| Ectocarpus siliculosus virus 1 | 1 | 1 | 1 |
| Ectromelia virus | 4 | 3 | 3 |
| Ectropis obliqua picorna-like virus | 1 | 1 | 1 |
| Edwardsiella anguillarum ET080813 | 1 | 1 | 1 |
| Edwardsiella ictaluri | 3 | 1 | 3 |
| Edwardsiella ictaluri 93-146 | 4 | 2 | 4 |
| Edwardsiella tarda EIB202 | 12 | 10 | 12 |
| Ehrlichia chaffeensis str. Arkansas | 1 | 1 | 1 |
| Ehrlichia ruminantium str. Welgevonden | 2 | 2 | 2 |
| Eimeria maxima | 1 | 1 | 1 |
| Eimeria tenella | 1 | 1 | 1 |
| Elaeis guineensis (African oil palm) | 1 | 1 | 1 |
| Emiliania huxleyi virus 86 | 1 | 1 | 1 |
| Encephalitozoon cuniculi GB-M1 | 9 | 9 | 8 |
| Encephalomyocarditis virus | 12 | 12 | 1 |
| Entamoeba histolytica HM-1:IMSS | 72 | 62 | 65 |
| Entamoeba invadens IP1 | 4 | 2 | 4 |
| Enterobacter cloacae | 6 | 6 | 4 |
| Enterobacter cloacae subsp. cloacae ATCC 13047 | 11 | 7 | 9 |
| Enterobacteria phage Ike | 1 | 1 | 1 |
| Enterobacteria phage MS2 | 5 | 5 | 2 |
| Enterobacteria phage P4 | 4 | 3 | 3 |
| Enterobacteria phage PRD1 | 2 | 1 | 2 |
| Enterobacteria phage T3 | 1 | 1 | 1 |
| Enterobacteria phage phi92 | 1 | 1 | 1 |
| Enterobacteria phage phiP27 | 1 | 1 | 1 |
| Enterococcus faecalis | 34 | 27 | 20 |
| Enterococcus faecalis 62 | 6 | 5 | 5 |
| Enterococcus faecalis OG1RF | 4 | 4 | 3 |
| Enterococcus faecalis V583 | 51 | 41 | 43 |
| Enterococcus faecium | 17 | 13 | 10 |
| Enterococcus faecium DO | 6 | 6 | 6 |
| Enterococcus hirae ATCC 9790 | 2 | 2 | 2 |
| Enterococcus phage BC611 | 2 | 2 | 2 |
| Enterovirus A | 38 | 38 | 1 |
| Enterovirus B | 5 | 5 | 1 |
| Enterovirus C | 29 | 29 | 1 |
| Enterovirus D | 5 | 5 | 1 |
| Enzootic nasal tumour virus of goats | 1 | 1 | 1 |
| Epiphyas postvittana nucleopolyhedrovirus | 1 | 1 | 1 |
| Eptesicus fuscus (big brown bat) | 2 | 2 | 2 |
| Equid alphaherpesvirus 1 (Equine herpesvirus 1) | 31 | 28 | 19 |
| Equid alphaherpesvirus 4 (Equine herpesvirus 4) | 6 | 6 | 6 |
| Equine arteritis virus | 8 | 8 | 3 |
| Equine hepacivirus JPN3/JAPAN/2013 | 1 | 1 | 1 |
| Equine infectious anemia virus | 7 | 7 | 2 |
| Equus asinus (ass) | 9 | 8 | 9 |
| Equus caballus (horse) | 716 | 535 | 390 |
| Equus przewalskii (Przewalski's horse) | 1 | 1 | 1 |
| Eremothecium gossypii ATCC 10895 | 17 | 13 | 17 |
| Erinaceus europaeus (western European hedgehog) | 1 | 1 | 1 |
| Erwinia amylovora ATCC 49946 | 5 | 4 | 5 |
| Erwinia amylovora CFBP1430 | 14 | 13 | 7 |
| Erythrobacter litoralis HTCC2594 | 1 | 1 | 1 |
| Escherichia coli (E. coli) | 332 | 298 | 174 |
| Escherichia coli 'BL21-Gold(DE3)pLysS AG' | 15 | 15 | 14 |
| Escherichia coli 042 | 5 | 3 | 4 |
| Escherichia coli 536 | 2 | 2 | 2 |
| Escherichia coli ABU 83972 | 1 | 1 | 1 |
| Escherichia coli APEC O1 | 15 | 14 | 15 |
| Escherichia coli ATCC 8739 | 1 | 1 | 1 |
| Escherichia coli B str. REL606 | 4 | 2 | 4 |
| Escherichia coli B171 | 2 | 2 | 2 |
| Escherichia coli BL21(DE3) | 75 | 50 | 71 |
| Escherichia coli BW2952 | 11 | 11 | 11 |
| Escherichia coli CFT073 | 105 | 95 | 90 |
| Escherichia coli ED1a | 1 | 1 | 1 |
| Escherichia coli ETEC 1392/75 | 1 | 1 | 1 |
| Escherichia coli ETEC H10407 | 5 | 5 | 3 |
| Escherichia coli F18+ | 1 | 1 | 1 |
| Escherichia coli HS | 11 | 10 | 10 |
| Escherichia coli IAI1 | 1 | 1 | 1 |
| Escherichia coli IAI39 | 6 | 6 | 6 |
| Escherichia coli IHE3034 | 4 | 2 | 4 |
| Escherichia coli K-12 | 14 | 12 | 13 |
| Escherichia coli LF82 | 4 | 4 | 4 |
| Escherichia coli O103:H2 str. 12009 | 5 | 4 | 4 |
| Escherichia coli O104:H4 str. 2011C-3493 | 8 | 7 | 8 |
| Escherichia coli O111:H- str. 11128 | 6 | 5 | 6 |
| Escherichia coli O127:H6 str. E2348/69 | 34 | 25 | 27 |
| Escherichia coli O139:H28 str. E24377A | 7 | 7 | 7 |
| Escherichia coli O157:H7 | 1 | 1 | 1 |
| Escherichia coli O157:H7 str. EC4115 | 7 | 4 | 7 |
| Escherichia coli O157:H7 str. EDL933 | 91 | 77 | 67 |
| Escherichia coli O157:H7 str. Sakai | 89 | 72 | 63 |
| Escherichia coli O157:H7 str. TW14359 | 16 | 12 | 15 |
| Escherichia coli O18:H1 | 1 | 1 | 1 |
| Escherichia coli O25b:H4-ST131 | 1 | 1 | 1 |
| Escherichia coli O26:H11 str. 11368 | 4 | 2 | 3 |
| Escherichia coli O55:H7 str. CB9615 | 2 | 2 | 2 |
| Escherichia coli O7:K1 str. CE10 | 1 | 1 | 1 |
| Escherichia coli O83:H1 str. NRG 857C | 1 | 1 | 1 |
| Escherichia coli PMV-1 | 1 | 1 | 1 |
| Escherichia coli S88 | 2 | 2 | 2 |
| Escherichia coli SMS-3-5 | 2 | 2 | 2 |
| Escherichia coli UMN026 | 10 | 8 | 10 |
| Escherichia coli UTI89 | 30 | 28 | 23 |
| Escherichia coli W | 2 | 2 | 2 |
| Escherichia coli str. K-12 substr. DH10B | 239 | 202 | 181 |
| Escherichia coli str. K-12 substr. MG1655 | 8653 | 6396 | 2051 |
| Escherichia coli str. K-12 substr. W3110 | 142 | 109 | 126 |
| Escherichia phage 933W | 4 | 4 | 3 |
| Escherichia phage JS98 | 1 | 1 | 1 |
| Escherichia phage Mu | 7 | 6 | 6 |
| Escherichia phage NJ01 | 1 | 1 | 1 |
| Escherichia phage RB69 | 17 | 17 | 1 |
| Escherichia phage T7 | 57 | 50 | 14 |
| Escherichia phage vB_EcoP_24B | 1 | 1 | 1 |
| Escherichia virus HK022 | 1 | 1 | 1 |
| Escherichia virus HK97 | 6 | 6 | 5 |
| Escherichia virus Lambda | 43 | 37 | 21 |
| Escherichia virus M13 | 4 | 4 | 3 |
| Escherichia virus N15 | 5 | 5 | 4 |
| Escherichia virus N4 | 3 | 3 | 3 |
| Escherichia virus P1 | 13 | 11 | 6 |
| Escherichia virus P2 | 5 | 5 | 5 |
| Escherichia virus Qbeta | 8 | 8 | 2 |
| Escherichia virus T4 | 131 | 107 | 55 |
| Escherichia virus T5 | 4 | 4 | 4 |
| Escherichia virus phiX174 | 1 | 1 | 1 |
| Esox lucius (northern pike) | 1 | 1 | 1 |
| Eucalyptus grandis (rose gum) | 4 | 2 | 4 |
| Euglena gracilis | 2 | 1 | 2 |
| Euglena longa | 1 | 1 | 1 |
| Eutrema salsugineum (saltwater cress) | 2 | 2 | 2 |
| Exiguobacterium sibiricum 255-15 | 2 | 2 | 2 |
| Falco cherrug (Saker falcon) | 1 | 1 | 1 |
| Fasciola hepatica (liver fluke) | 1 | 1 | 1 |
| Feline calicivirus | 5 | 5 | 2 |
| Feline coronavirus | 2 | 2 | 2 |
| Feline foamy virus | 5 | 5 | 4 |
| Feline immunodeficiency virus | 15 | 15 | 3 |
| Feline infectious peritonitis virus (FIPV) | 9 | 8 | 6 |
| Feline leukemia virus | 4 | 4 | 1 |
| Felis catus (domestic cat) | 392 | 299 | 254 |
| Fibrobacter succinogenes subsp. succinogenes S85 | 2 | 2 | 1 |
| Ficedula albicollis (Collared flycatcher) | 3 | 3 | 2 |
| Finegoldia magna ATCC 29328 | 1 | 1 | 1 |
| Flavobacterium johnsoniae UW101 | 2 | 2 | 2 |
| Flavobacterium psychrophilum JIP02/86 | 4 | 3 | 4 |
| Flock House virus | 5 | 5 | 2 |
| Foot-and-mouth disease virus - type A | 6 | 6 | 1 |
| Foot-and-mouth disease virus - type Asia 1 | 3 | 3 | 1 |
| Foot-and-mouth disease virus - type C | 5 | 5 | 1 |
| Foot-and-mouth disease virus - type O | 18 | 18 | 2 |
| Fowl aviadenovirus C | 1 | 1 | 1 |
| Fowlpox virus | 6 | 5 | 5 |
| Fragaria vesca (wild strawberry) | 7 | 6 | 6 |
| Francisella tularensis subsp. holarctica LVS | 12 | 9 | 11 |
| Francisella tularensis subsp. holarctica OSU18 | 2 | 2 | 2 |
| Francisella tularensis subsp. mediasiatica FSC147 | 7 | 6 | 7 |
| Francisella tularensis subsp. novicida U112 | 25 | 17 | 24 |
| Francisella tularensis subsp. tularensis FSC198 | 1 | 1 | 1 |
| Francisella tularensis subsp. tularensis SCHU S4 | 42 | 36 | 37 |
| Frankia casuarinae | 2 | 1 | 2 |
| Friend murine leukemia virus | 7 | 7 | 3 |
| Frog virus 3 | 2 | 2 | 2 |
| Fukomys damarensis (Damara mole-rat) | 1 | 1 | 1 |
| Fundulus heteroclitus (mummichog) | 3 | 3 | 3 |
| Fusarium fujikuroi IMI 58289 | 3 | 2 | 3 |
| Fusarium graminearum PH-1 | 19 | 18 | 19 |
| Fusarium oxysporum f. sp. lycopersici 4287 | 1 | 1 | 1 |
| Fusarium verticillioides 7600 | 2 | 2 | 2 |
| Fusobacterium nucleatum | 1 | 1 | 1 |
| Fusobacterium nucleatum subsp. nucleatum ATCC 25586 | 5 | 4 | 5 |
| GB virus C | 4 | 4 | 1 |
| Gadus morhua (Atlantic cod) | 1 | 1 | 1 |
| Galdieria sulphuraria | 1 | 1 | 1 |
| Galleria mellonella (greater wax moth) | 2 | 2 | 2 |
| Galleria mellonella densovirus | 1 | 1 | 1 |
| Gallid alphaherpesvirus 1 | 13 | 10 | 11 |
| Gallid alphaherpesvirus 2 (Marek disease virus type 1) | 37 | 30 | 20 |
| Gallid alphaherpesvirus 3 (Marek's disease virus type 2) | 4 | 3 | 4 |
| Gallionella capsiferriformans ES-2 | 1 | 1 | 1 |
| Gallus gallus (chicken) | 5308 | 3744 | 2254 |
| Gardnerella vaginalis ATCC 14019 | 1 | 1 | 1 |
| Garlic latent virus | 1 | 1 | 1 |
| Gasterosteus aculeatus (three-spined stickleback) | 2 | 2 | 2 |
| Gekko japonicus | 1 | 1 | 1 |
| Geobacillus kaustophilus HTA426 | 18 | 14 | 17 |
| Geobacillus stearothermophilus 10 | 1 | 1 | 1 |
| Geobacillus thermodenitrificans NG80-2 | 3 | 2 | 3 |
| Geobacillus thermoleovorans | 1 | 1 | 1 |
| Geobacillus virus E2 | 1 | 1 | 1 |
| Geobacter bemidjiensis Bem | 1 | 1 | 1 |
| Geobacter metallireducens GS-15 | 2 | 2 | 2 |
| Geobacter sulfurreducens KN400 | 3 | 2 | 3 |
| Geobacter sulfurreducens PCA | 18 | 13 | 16 |
| Geobacter uraniireducens Rf4 | 1 | 1 | 1 |
| Giardia lamblia ATCC 50803 | 52 | 46 | 45 |
| Gibbon ape leukemia virus (GALV) | 1 | 1 | 1 |
| Glaesserella parasuis | 1 | 1 | 1 |
| Glaesserella parasuis SH0165 | 5 | 4 | 5 |
| Glaesserella parasuis ZJ0906 | 1 | 1 | 1 |
| Gloeobacter violaceus PCC 7421 | 7 | 7 | 4 |
| Gluconacetobacter diazotrophicus PA1 5 | 1 | 1 | 1 |
| Gluconobacter oxydans 621H | 17 | 11 | 17 |
| Glycine max (soybean) | 536 | 424 | 420 |
| Glycine soja (wild soybean) | 1 | 1 | 1 |
| Goose parvovirus | 1 | 1 | 1 |
| Gorilla gorilla (western gorilla) | 3 | 3 | 3 |
| Gossypium arboreum (tree cotton) | 1 | 1 | 1 |
| Gossypium hirsutum (cotton) | 21 | 19 | 21 |
| Gossypium raimondii | 2 | 2 | 2 |
| Gottschalkia acidurici 9a | 1 | 1 | 1 |
| Granulibacter bethesdensis CGDNIH1 | 1 | 1 | 1 |
| Grapevine Algerian latent virus | 1 | 1 | 1 |
| Grapevine fanleaf virus | 2 | 2 | 2 |
| Grapevine virus A | 1 | 1 | 1 |
| Grapevine virus B | 1 | 1 | 1 |
| Groundnut bud necrosis virus | 1 | 1 | 1 |
| H-1 parvovirus | 1 | 1 | 1 |
| Habenaria mosaic virus | 1 | 1 | 1 |
| Haemophilus influenzae | 2 | 2 | 2 |
| Haemophilus influenzae 86-028NP | 30 | 30 | 25 |
| Haemophilus influenzae F3031 | 1 | 1 | 1 |
| Haemophilus influenzae PittEE | 1 | 1 | 1 |
| Haemophilus influenzae PittGG | 1 | 1 | 1 |
| Haemophilus influenzae Rd KW20 | 60 | 52 | 50 |
| Haloarcula hispanica ATCC 33960 | 1 | 1 | 1 |
| Haloarcula marismortui ATCC 43049 | 3 | 2 | 3 |
| Halobacterium salinarum | 1 | 1 | 1 |
| Halobacterium salinarum NRC-1 | 23 | 19 | 19 |
| Halobacterium salinarum R1 | 24 | 21 | 10 |
| Haloferax mediterranei ATCC 33500 | 7 | 3 | 7 |
| Haloferax volcanii DS2 | 29 | 22 | 25 |
| Halogeometricum borinquense | 2 | 1 | 2 |
| Halomonas elongata DSM 2581 | 1 | 1 | 1 |
| Haloquadratum walsbyi DSM 16790 | 2 | 2 | 2 |
| Halorubrum lacusprofundi ATCC 49239 | 1 | 1 | 1 |
| Halorubrum pleomorphic virus 1 | 2 | 1 | 2 |
| Halothermothrix orenii H 168 | 2 | 2 | 2 |
| Halothiobacillus neapolitanus c2 | 1 | 1 | 1 |
| Hammondia hammondi | 2 | 1 | 2 |
| Hantaan orthohantavirus | 13 | 12 | 2 |
| Hantavirus Z10 | 1 | 1 | 1 |
| Haplochromis burtoni (Burton's mouthbrooder) | 2 | 1 | 2 |
| Hazara virus | 1 | 1 | 1 |
| Heartland virus | 2 | 2 | 2 |
| Helianthus annuus (common sunflower) | 4 | 4 | 4 |
| Helicobacter acinonychis str. Sheeba | 2 | 1 | 2 |
| Helicobacter hepaticus ATCC 51449 | 7 | 7 | 7 |
| Helicobacter mustelae 12198 | 3 | 2 | 3 |
| Helicobacter pylori | 1 | 1 | 1 |
| Helicobacter pylori 2017 | 1 | 1 | 1 |
| Helicobacter pylori 26695 | 285 | 239 | 171 |
| Helicobacter pylori 51 | 2 | 2 | 2 |
| Helicobacter pylori 52 | 1 | 1 | 1 |
| Helicobacter pylori B38 | 9 | 8 | 7 |
| Helicobacter pylori B8 | 16 | 13 | 13 |
| Helicobacter pylori F32 | 1 | 1 | 1 |
| Helicobacter pylori G27 | 35 | 28 | 23 |
| Helicobacter pylori HPAG1 | 10 | 10 | 8 |
| Helicobacter pylori J99 | 163 | 138 | 41 |
| Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 | 2 | 2 | 2 |
| Helicobacter pylori OK113 | 1 | 1 | 1 |
| Helicobacter pylori P12 | 8 | 6 | 6 |
| Helicobacter pylori Shi470 | 1 | 1 | 1 |
| Helicobacter pylori v225d | 2 | 2 | 1 |
| Helicoverpa armigera (cotton bollworm) | 12 | 9 | 12 |
| Helicoverpa armigera NPV NNg1 | 1 | 1 | 1 |
| Helicoverpa armigera densovirus | 1 | 1 | 1 |
| Helicoverpa armigera nucleopolyhedrovirus | 4 | 3 | 4 |
| Helicoverpa armigera nucleopolyhedrovirus G4 | 5 | 5 | 5 |
| Hemileuca sp. nucleopolyhedrovirus | 1 | 1 | 1 |
| Hendra henipavirus | 17 | 16 | 4 |
| Hepatitis B virus | 694 | 675 | 4 |
| Hepatitis C virus genotype 1 | 562 | 560 | 2 |
| Hepatitis C virus genotype 2 | 10 | 10 | 1 |
| Hepatitis C virus genotype 3 | 4 | 4 | 1 |
| Hepatitis C virus genotype 4 | 2 | 2 | 1 |
| Hepatitis C virus genotype 5 | 1 | 1 | 1 |
| Hepatitis E virus | 43 | 42 | 4 |
| Hepatitis GB virus B | 4 | 4 | 1 |
| Hepatitis delta virus | 13 | 13 | 1 |
| Hepatovirus A | 8 | 8 | 2 |
| Herbaspirillum seropedicae | 1 | 1 | 1 |
| Herbaspirillum seropedicae SmR1 | 9 | 6 | 8 |
| Heterocephalus glaber (naked mole-rat) | 6 | 4 | 6 |
| Hevea brasiliensis (rubber tree) | 3 | 2 | 3 |
| Hibiscus chlorotic ringspot virus | 1 | 1 | 1 |
| Histoplasma capsulatum NAm1 | 1 | 1 | 1 |
| Homo sapiens (human) | 856204 | 535053 | 19105 |
| Homo sapiens neanderthalensis (Neandertal) | 330 | 223 | 30 |
| Hordeum vulgare (barley) | 83 | 78 | 64 |
| Hordeum vulgare subsp. vulgare (domesticated barley) | 1 | 1 | 1 |
| Human T-cell leukemia virus type I | 184 | 183 | 4 |
| Human T-lymphotropic virus 2 | 16 | 16 | 3 |
| Human adenovirus B1 | 3 | 2 | 2 |
| Human alphaherpesvirus 1 (Herpes simplex virus type 1) | 694 | 536 | 79 |
| Human alphaherpesvirus 2 (Herpes simplex virus type 2) | 60 | 49 | 25 |
| Human alphaherpesvirus 3 (Varicella-zoster virus) | 79 | 68 | 29 |
| Human betaherpesvirus 5 (Human cytomegalovirus) | 519 | 399 | 130 |
| Human betaherpesvirus 6A | 23 | 17 | 18 |
| Human betaherpesvirus 6B | 10 | 9 | 8 |
| Human betaherpesvirus 7 | 5 | 4 | 3 |
| Human coronavirus 229E | 7 | 7 | 4 |
| Human coronavirus HKU1 | 5 | 5 | 3 |
| Human coronavirus NL63 | 7 | 7 | 4 |
| Human coronavirus OC43 | 7 | 7 | 4 |
| Human endogenous retrovirus K113 | 1 | 1 | 1 |
| Human gammaherpesvirus 4 (Epstein-Barr virus) | 720 | 658 | 66 |
| Human gammaherpesvirus 8 (Kaposi's sarcoma-associated herpesvirus) | 317 | 284 | 53 |
| Human gyrovirus 1 | 1 | 1 | 1 |
| Human herpesvirus 4 type 2 (Epstein-Barr virus type 2) | 26 | 18 | 13 |
| Human herpesvirus 5 strain AD169 | 1 | 1 | 1 |
| Human herpesvirus 8 type M | 57 | 52 | 22 |
| Human immunodeficiency virus 1 (HIV-1) | 2136 | 2039 | 10 |
| Human immunodeficiency virus 2 | 62 | 57 | 8 |
| Human mastadenovirus A | 8 | 7 | 5 |
| Human mastadenovirus B | 4 | 4 | 3 |
| Human mastadenovirus C | 79 | 71 | 12 |
| Human mastadenovirus D | 5 | 5 | 4 |
| Human mastadenovirus E | 16 | 15 | 6 |
| Human metapneumovirus | 44 | 38 | 12 |
| Human orthopneumovirus | 63 | 53 | 10 |
| Human papillomavirus | 7 | 7 | 3 |
| Human papillomavirus 179 | 17 | 13 | 9 |
| Human papillomavirus 5 | 14 | 13 | 3 |
| Human papillomavirus type 10 | 2 | 2 | 1 |
| Human papillomavirus type 16 | 630 | 527 | 8 |
| Human papillomavirus type 26 | 1 | 1 | 1 |
| Human papillomavirus type 53 | 1 | 1 | 1 |
| Human papillomavirus type 6b | 2 | 2 | 2 |
| Human papillomavirus type 90 | 2 | 2 | 2 |
| Human parvovirus B19 | 25 | 23 | 5 |
| Human polyomavirus 1 | 1 | 1 | 1 |
| Human polyomavirus 6 | 1 | 1 | 1 |
| Human polyomavirus 7 | 1 | 1 | 1 |
| Human respirovirus 1 | 6 | 6 | 2 |
| Human respirovirus 3 | 33 | 27 | 6 |
| Human rotavirus B | 2 | 2 | 2 |
| Human rubulavirus 2 | 15 | 14 | 4 |
| Human spumaretrovirus | 2 | 2 | 2 |
| Hungateiclostridium thermocellum | 1 | 1 | 1 |
| Hungateiclostridium thermocellum ATCC 27405 | 23 | 14 | 17 |
| Hungateiclostridium thermocellum DSM 1313 | 1 | 1 | 1 |
| Hydra vulgaris | 10 | 7 | 9 |
| Hydrogenobacter thermophilus TK-6 | 4 | 3 | 3 |
| Hydrogenovibrio crunogenus XCL-2 | 2 | 2 | 2 |
| Hyperthermus butylicus DSM 5456 | 1 | 1 | 1 |
| Hyphantria cunea nucleopolyhedrovirus | 6 | 5 | 4 |
| Ictalurus punctatus (channel catfish) | 23 | 21 | 23 |
| Ictidomys tridecemlineatus (thirteen-lined ground squirrel) | 9 | 3 | 9 |
| Infectious bronchitis virus | 39 | 36 | 6 |
| Infectious bursal disease virus (Gumboro virus) | 38 | 35 | 3 |
| Infectious hematopoietic necrosis virus | 3 | 3 | 2 |
| Infectious pancreatic necrosis virus | 4 | 3 | 2 |
| Infectious spleen and kidney necrosis virus | 5 | 5 | 5 |
| Influenza A virus (A/California/07/2009(H1N1)) | 13 | 12 | 4 |
| Influenza A virus (A/Hong Kong/1073/99(H9N2)) | 34 | 31 | 8 |
| Influenza A virus (A/Korea/426/1968(H2N2)) | 10 | 10 | 5 |
| Influenza A virus (A/New York/392/2004(H3N2)) | 64 | 57 | 10 |
| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | 251 | 216 | 12 |
| Influenza A virus (A/Shanghai/02/2013(H7N9)) | 22 | 20 | 7 |
| Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) | 125 | 110 | 12 |
| Influenza B virus (B/Lee/1940) | 41 | 38 | 13 |
| Influenza C virus (C/Ann Arbor/1/50) | 11 | 11 | 6 |
| Invertebrate iridescent virus 6 | 3 | 2 | 3 |
| Ixodes scapularis (black-legged tick) | 12 | 10 | 12 |
| J-virus | 2 | 2 | 2 |
| JC polyomavirus | 39 | 37 | 6 |
| Jaagsiekte sheep retrovirus | 10 | 10 | 2 |
| Jannaschia sp. CCS1 | 1 | 1 | 1 |
| Japanese encephalitis virus | 42 | 42 | 1 |
| Jatropha curcas | 6 | 4 | 6 |
| Jembrana disease virus | 1 | 1 | 1 |
| Juglans regia (English walnut) | 2 | 2 | 2 |
| Junonia coenia densovirus | 1 | 1 | 1 |
| Kappapapillomavirus 2 | 2 | 2 | 2 |
| Ketogulonicigenium vulgare Y25 | 1 | 1 | 1 |
| Kingella kingae | 1 | 1 | 1 |
| Klebsiella aerogenes KCTC 2190 | 1 | 1 | 1 |
| Klebsiella michiganensis E718 | 1 | 1 | 1 |
| Klebsiella michiganensis KCTC 1686 | 2 | 1 | 2 |
| Klebsiella pneumoniae | 85 | 68 | 39 |
| Klebsiella pneumoniae 342 | 16 | 14 | 14 |
| Klebsiella pneumoniae CG43 | 6 | 6 | 3 |
| Klebsiella pneumoniae KCTC 2242 | 2 | 2 | 1 |
| Klebsiella pneumoniae subsp. pneumoniae HS11286 | 17 | 14 | 8 |
| Klebsiella pneumoniae subsp. pneumoniae MGH 78578 | 15 | 14 | 12 |
| Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 | 25 | 21 | 20 |
| Kluyveromyces lactis | 35 | 28 | 29 |
| Kluyveromyces marxianus DMKU3-1042 | 5 | 4 | 5 |
| Koala retrovirus | 1 | 1 | 1 |
| Komagataella phaffii GS115 | 7 | 6 | 7 |
| La Crosse virus | 2 | 2 | 1 |
| Labrenzia aggregata | 1 | 1 | 1 |
| Laccaria bicolor S238N-H82 | 3 | 3 | 3 |
| Lachancea thermotolerans CBS 6340 | 4 | 2 | 4 |
| Lachnoclostridium phytofermentans ISDg | 2 | 2 | 2 |
| Lactobacillus acidophilus NCFM | 11 | 10 | 9 |
| Lactobacillus brevis | 2 | 1 | 2 |
| Lactobacillus brevis ATCC 367 | 4 | 3 | 4 |
| Lactobacillus brevis KB290 | 1 | 1 | 1 |
| Lactobacillus casei BL23 | 10 | 9 | 10 |
| Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002 | 2 | 2 | 2 |
| Lactobacillus fermentum IFO 3956 | 1 | 1 | 1 |
| Lactobacillus gasseri | 2 | 2 | 2 |
| Lactobacillus gasseri ATCC 33323 = JCM 1131 | 3 | 3 | 3 |
| Lactobacillus johnsonii NCC 533 | 3 | 2 | 3 |
| Lactobacillus paracasei ATCC 334 | 1 | 1 | 1 |
| Lactobacillus phage A2 | 2 | 2 | 2 |
| Lactobacillus plantarum | 2 | 2 | 2 |
| Lactobacillus plantarum WCFS1 | 40 | 33 | 34 |
| Lactobacillus plantarum subsp. plantarum ST-III | 3 | 3 | 3 |
| Lactobacillus reuteri DSM 20016 | 5 | 4 | 5 |
| Lactobacillus reuteri JCM 1112 | 3 | 3 | 2 |
| Lactobacillus reuteri SD2112 | 3 | 2 | 3 |
| Lactobacillus rhamnosus ATCC 8530 | 2 | 1 | 2 |
| Lactobacillus rhamnosus GG | 11 | 7 | 8 |
| Lactobacillus salivarius UCC118 | 5 | 5 | 4 |
| Lactococcus lactis | 10 | 10 | 7 |
| Lactococcus lactis subsp. cremoris | 1 | 1 | 1 |
| Lactococcus lactis subsp. cremoris MG1363 | 22 | 19 | 17 |
| Lactococcus lactis subsp. cremoris NZ9000 | 3 | 3 | 2 |
| Lactococcus lactis subsp. lactis | 7 | 5 | 5 |
| Lactococcus lactis subsp. lactis CV56 | 1 | 1 | 1 |
| Lactococcus lactis subsp. lactis Il1403 | 64 | 49 | 47 |
| Lactococcus lactis subsp. lactis KF147 | 4 | 4 | 4 |
| Lactococcus lactis subsp. lactis bv. diacetylactis | 1 | 1 | 1 |
| Lactococcus phage TP901-1 | 1 | 1 | 1 |
| Lactococcus virus bIL170 | 1 | 1 | 1 |
| Lactuca sativa (cultivated lettuce) | 1 | 1 | 1 |
| Laribacter hongkongensis | 2 | 1 | 2 |
| Larimichthys crocea (large yellow croaker) | 49 | 35 | 47 |
| Lassa mammarenavirus | 15 | 15 | 4 |
| Lates calcarifer (barramundi perch) | 8 | 7 | 8 |
| Latimeria chalumnae (coelacanth) | 1 | 1 | 1 |
| Legionella longbeachae NSW150 | 1 | 1 | 1 |
| Legionella pneumophila 2300/99 Alcoy | 1 | 1 | 1 |
| Legionella pneumophila str. Corby | 6 | 5 | 6 |
| Legionella pneumophila str. Lens | 6 | 6 | 6 |
| Legionella pneumophila str. Paris | 8 | 5 | 8 |
| Legionella pneumophila subsp. pneumophila | 3 | 2 | 3 |
| Legionella pneumophila subsp. pneumophila LPE509 | 40 | 33 | 36 |
| Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 37 | 34 | 33 |
| Leishmania braziliensis MHOM/BR/75/M2904 | 15 | 13 | 14 |
| Leishmania donovani | 43 | 38 | 37 |
| Leishmania infantum JPCM5 | 27 | 25 | 23 |
| Leishmania major strain Friedlin | 62 | 54 | 55 |
| Leishmania mexicana MHOM/GT/2001/U1103 | 10 | 8 | 10 |
| Leptinotarsa decemlineata (Colorado potato beetle) | 3 | 3 | 2 |
| Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' | 3 | 3 | 3 |
| Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 | 29 | 23 | 22 |
| Leptospira interrogans serovar Lai str. 56601 | 21 | 20 | 17 |
| Leptospira santarosai serovar Shermani str. LT 821 | 1 | 1 | 1 |
| Leptospira santarosai str. 2000027870 | 1 | 1 | 1 |
| Lettuce mosaic virus | 2 | 2 | 1 |
| Lettuce necrotic yellows virus | 2 | 2 | 1 |
| Lily symptomless virus (LSV) | 1 | 1 | 1 |
| Limulus polyphemus (Atlantic horseshoe crab) | 1 | 1 | 1 |
| Listeria innocua Clip11262 | 5 | 4 | 4 |
| Listeria monocytogenes | 6 | 6 | 3 |
| Listeria monocytogenes 08-5578 | 1 | 1 | 1 |
| Listeria monocytogenes 10403S | 5 | 4 | 4 |
| Listeria monocytogenes EGD | 1 | 1 | 1 |
| Listeria monocytogenes EGD-e | 207 | 163 | 113 |
| Listeria monocytogenes L312 | 1 | 1 | 1 |
| Listeria monocytogenes M7 | 5 | 1 | 5 |
| Listeria monocytogenes serotype 4b str. CLIP 80459 | 4 | 3 | 4 |
| Listeria monocytogenes serotype 4b str. F2365 | 21 | 18 | 15 |
| Listeria monocytogenes serotype 4b str. LL195 | 1 | 1 | 1 |
| Listeria phage A118 | 2 | 1 | 2 |
| Listeria phage P35 | 1 | 1 | 1 |
| Lloviu cuevavirus | 2 | 1 | 2 |
| Loa loa (eye worm) | 1 | 1 | 1 |
| Lonchura striata domestica (Bengalese finch) | 3 | 2 | 3 |
| Lotus japonicus | 39 | 33 | 23 |
| Loxodonta africana (African savanna elephant) | 5 | 4 | 4 |
| Lujo mammarenavirus | 1 | 1 | 1 |
| Lumpy skin disease virus NI-2490 | 1 | 1 | 1 |
| Lupinus angustifolius (narrow-leaved blue lupine) | 2 | 2 | 2 |
| Lymantria dispar multiple nucleopolyhedrovirus | 3 | 2 | 3 |
| Lymphocystis disease virus - isolate China | 2 | 2 | 2 |
| Lymphocytic choriomeningitis mammarenavirus | 18 | 16 | 4 |
| Macaca fascicularis (crab-eating macaque) | 66 | 51 | 60 |
| Macaca mulatta (Rhesus monkey) | 616 | 468 | 365 |
| Macaca mulatta polyomavirus 1 | 4 | 4 | 2 |
| Macaca nemestrina (pig-tailed macaque) | 2 | 2 | 2 |
| Macacine alphaherpesvirus 1 (monkey B virus) | 3 | 2 | 3 |
| Macacine betaherpesvirus 3 (Rhesus cytomegalovirus) | 5 | 3 | 4 |
| Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus) | 2 | 2 | 2 |
| Macacine gammaherpesvirus 5 (Rhesus rhadinovirus) | 3 | 3 | 3 |
| Macaque simian foamy virus | 1 | 1 | 1 |
| Machupo mammarenavirus | 3 | 3 | 2 |
| Magnetococcus marinus MC-1 | 1 | 1 | 1 |
| Magnetospirillum gryphiswaldense MSR-1 | 2 | 2 | 2 |
| Magnetospirillum magneticum AMB-1 | 6 | 6 | 6 |
| Maize mosaic nucleorhabdovirus | 3 | 1 | 3 |
| Maize yellow dwarf virus RMV | 1 | 1 | 1 |
| Mal de Rio Cuarto virus | 1 | 1 | 1 |
| Malassezia globosa CBS 7966 | 3 | 3 | 3 |
| Malus domestica (apple) | 45 | 38 | 35 |
| Mamastrovirus 1 | 3 | 3 | 2 |
| Mamestra configurata nucleopolyhedrovirus A | 1 | 1 | 1 |
| Mammalian orthoreovirus 1 | 2 | 2 | 1 |
| Mammalian orthoreovirus 3 | 10 | 7 | 5 |
| Mammalian rubulavirus 5 | 25 | 24 | 4 |
| Manduca sexta (tobacco hornworm) | 2 | 2 | 2 |
| Manihot esculenta (cassava) | 1 | 1 | 1 |
| Mannheimia haemolytica M42548 | 1 | 1 | 1 |
| Mannheimia haemolytica PHL213 | 2 | 2 | 1 |
| Marburg marburgvirus | 25 | 23 | 7 |
| Marinithermus hydrothermalis DSM 14884 | 1 | 1 | 1 |
| Marinobacter hydrocarbonoclasticus ATCC 49840 | 4 | 2 | 4 |
| Marinobacter hydrocarbonoclasticus VT8 | 2 | 2 | 1 |
| Marinomonas mediterranea MMB-1 | 2 | 2 | 2 |
| Mason-Pfizer monkey virus | 11 | 10 | 3 |
| Measles morbillivirus | 107 | 90 | 6 |
| Medicago truncatula (barrel medic) | 53 | 45 | 48 |
| Megavirus chiliensis | 1 | 1 | 1 |
| Meiothermus ruber DSM 1279 | 1 | 1 | 1 |
| Meleagris gallopavo (turkey) | 49 | 36 | 28 |
| Melon necrotic spot virus | 11 | 6 | 5 |
| Melopsittacus undulatus (budgerigar) | 2 | 2 | 2 |
| Meriones unguiculatus (Mongolian gerbil) | 6 | 4 | 6 |
| Merkel cell polyomavirus | 17 | 17 | 4 |
| Mesocricetus auratus (golden hamster) | 65 | 50 | 57 |
| Mesorhizobium ciceri biovar biserrulae WSM1271 | 1 | 1 | 1 |
| Mesorhizobium japonicum MAFF 303099 | 16 | 14 | 16 |
| Metallosphaera cuprina Ar-4 | 2 | 1 | 2 |
| Metallosphaera sedula | 1 | 1 | 1 |
| Metallosphaera sedula DSM 5348 | 21 | 3 | 21 |
| Metarhizium acridum CQMa 102 | 2 | 2 | 2 |
| Metarhizium robertsii ARSEF 23 | 3 | 2 | 3 |
| Methanobrevibacter ruminantium M1 | 1 | 1 | 1 |
| Methanobrevibacter smithii ATCC 35061 | 1 | 1 | 1 |
| Methanocaldococcus fervens AG86 | 1 | 1 | 1 |
| Methanocaldococcus infernus ME | 1 | 1 | 1 |
| Methanocaldococcus jannaschii DSM 2661 | 70 | 67 | 64 |
| Methanocella paludicola SANAE | 1 | 1 | 1 |
| Methanococcoides burtonii DSM 6242 | 4 | 3 | 4 |
| Methanococcus aeolicus Nankai-3 | 1 | 1 | 1 |
| Methanococcus maripaludis C7 | 1 | 1 | 1 |
| Methanococcus maripaludis S2 | 25 | 18 | 21 |
| Methanococcus voltae A3 | 2 | 2 | 2 |
| Methanoculleus marisnigri JR1 | 1 | 1 | 1 |
| Methanopyrus kandleri AV19 | 2 | 2 | 2 |
| Methanosarcina acetivorans C2A | 29 | 25 | 27 |
| Methanosarcina barkeri str. Fusaro | 7 | 5 | 7 |
| Methanosarcina mazei Go1 | 22 | 21 | 19 |
| Methanothermobacter marburgensis str. Marburg | 5 | 3 | 5 |
| Methanothermobacter thermautotrophicus str. Delta H | 23 | 21 | 21 |
| Methanothrix thermoacetophila PT | 1 | 1 | 1 |
| Methylacidiphilum infernorum V4 | 1 | 1 | 1 |
| Methylobacterium radiotolerans JCM 2831 | 3 | 1 | 3 |
| Methylocella silvestris BL2 | 2 | 1 | 2 |
| Methylococcus capsulatus str. Bath | 8 | 6 | 8 |
| Methylomicrobium alcaliphilum 20Z | 1 | 1 | 1 |
| Methylorubrum extorquens AM1 | 4 | 3 | 3 |
| Methylorubrum extorquens PA1 | 1 | 1 | 1 |
| Microcebus murinus (gray mouse lemur) | 4 | 4 | 4 |
| Micrococcus luteus NCTC 2665 | 1 | 1 | 1 |
| Microcystis aeruginosa NIES-843 | 8 | 4 | 5 |
| Micromonas pusilla CCMP1545 | 4 | 4 | 1 |
| Micromonospora aurantiaca ATCC 27029 | 1 | 1 | 1 |
| Microplitis demolitor bracovirus | 3 | 3 | 2 |
| Microtus ochrogaster (prairie vole) | 9 | 9 | 6 |
| Middle East respiratory syndrome-related coronavirus | 34 | 33 | 7 |
| Minute virus of mice | 7 | 7 | 2 |
| Moesziomyces antarcticus | 1 | 1 | 1 |
| Mokola lyssavirus | 3 | 3 | 2 |
| Molluscum contagiosum virus subtype 1 | 4 | 3 | 2 |
| Moloney murine leukemia virus | 19 | 19 | 3 |
| Moniliophthora perniciosa | 2 | 1 | 2 |
| Monodelphis domestica (gray short-tailed opossum) | 32 | 16 | 28 |
| Monosiga brevicollis MX1 | 1 | 1 | 1 |
| Moorella thermoacetica ATCC 39073 | 1 | 1 | 1 |
| Mopeia virus AN20410 | 5 | 3 | 2 |
| Moraxella catarrhalis | 2 | 1 | 2 |
| Moraxella catarrhalis BBH18 | 7 | 5 | 7 |
| Morus notabilis | 1 | 1 | 1 |
| Mouse mammary tumor virus | 8 | 8 | 3 |
| Mumps rubulavirus | 29 | 23 | 7 |
| Mungbean yellow mosaic India virus | 7 | 6 | 4 |
| Mungbean yellow mosaic virus | 1 | 1 | 1 |
| Mupapillomavirus 1 | 4 | 4 | 2 |
| Murid betaherpesvirus 1 (Murine cytomegalovirus) | 7 | 6 | 6 |
| Murid betaherpesvirus 8 | 1 | 1 | 1 |
| Murid gammaherpesvirus 4 (Murine herpesvirus 68) | 69 | 56 | 28 |
| Murine adenovirus 2 | 1 | 1 | 1 |
| Murine hepatitis virus | 41 | 39 | 8 |
| Murine hepatitis virus strain JHM | 3 | 3 | 2 |
| Murine polyomavirus | 8 | 7 | 4 |
| Murine polyomavirus strain BG | 2 | 2 | 2 |
| Murine respirovirus | 32 | 29 | 8 |
| Murine type C retrovirus | 1 | 1 | 1 |
| Murray Valley encephalitis virus | 2 | 2 | 1 |
| Mus caroli (Ryukyu mouse) | 25 | 25 | 19 |
| Mus musculus (house mouse) | 271148 | 191100 | 13559 |
| Mus musculus domesticus (western European house mouse) | 3 | 3 | 3 |
| Mus musculus molossinus (Japanese wild mouse) | 2 | 2 | 2 |
| Mus musculus musculus (eastern European house mouse) | 113 | 107 | 5 |
| Mus musculus polyomavirus 2 | 1 | 1 | 1 |
| Mus pahari (shrew mouse) | 37 | 37 | 32 |
| Musa acuminata (dwarf banana) | 4 | 3 | 4 |
| Musca domestica (house fly) | 6 | 5 | 5 |
| Mustela putorius furo (domestic ferret) | 18 | 12 | 16 |
| Mycobacterium avium 104 | 9 | 7 | 9 |
| Mycobacterium avium subsp. paratuberculosis K-10 | 14 | 12 | 14 |
| Mycobacterium leprae TN | 22 | 21 | 14 |
| Mycobacterium marinum E11 | 3 | 3 | 1 |
| Mycobacterium marinum M | 10 | 10 | 10 |
| Mycobacterium phage SWU1 | 1 | 1 | 1 |
| Mycobacterium phage TM4 | 2 | 2 | 2 |
| Mycobacterium tuberculosis 7199-99 | 3 | 3 | 3 |
| Mycobacterium tuberculosis CCDC5079 | 1 | 1 | 1 |
| Mycobacterium tuberculosis CDC1551 | 21 | 20 | 17 |
| Mycobacterium tuberculosis EAI5 | 1 | 1 | 1 |
| Mycobacterium tuberculosis F11 | 3 | 3 | 3 |
| Mycobacterium tuberculosis H37Ra | 24 | 23 | 22 |
| Mycobacterium tuberculosis H37Rv | 2225 | 1819 | 923 |
| Mycobacterium tuberculosis KZN 1435 | 1 | 1 | 1 |
| Mycobacterium tuberculosis KZN 4207 | 1 | 1 | 1 |
| Mycobacterium tuberculosis str. Erdman = ATCC 35801 | 2 | 2 | 2 |
| Mycobacterium tuberculosis variant africanum GM041182 | 1 | 1 | 1 |
| Mycobacterium tuberculosis variant bovis AF2122/97 | 36 | 32 | 35 |
| Mycobacterium tuberculosis variant bovis BCG str. Mexico | 1 | 1 | 1 |
| Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 | 13 | 11 | 13 |
| Mycobacterium ulcerans Agy99 | 4 | 4 | 4 |
| Mycobacterium virus Bethlehem | 1 | 1 | 1 |
| Mycobacterium virus Bxb1 | 2 | 2 | 1 |
| Mycobacterium virus Fruitloop | 1 | 1 | 1 |
| Mycobacterium virus L5 | 5 | 2 | 5 |
| Mycobacteroides abscessus | 3 | 3 | 3 |
| Mycolicibacter sinensis | 1 | 1 | 1 |
| Mycolicibacterium smegmatis | 1 | 1 | 1 |
| Mycolicibacterium smegmatis MC2 155 | 196 | 166 | 164 |
| Mycoplasma agalactiae PG2 | 8 | 3 | 8 |
| Mycoplasma arthritidis 158L3-1 | 3 | 3 | 2 |
| Mycoplasma bovis Hubei-1 | 1 | 1 | 1 |
| Mycoplasma bovis PG45 | 3 | 3 | 3 |
| Mycoplasma capricolum subsp. capricolum ATCC 27343 | 1 | 1 | 1 |
| Mycoplasma gallisepticum str. F | 1 | 1 | 1 |
| Mycoplasma gallisepticum str. R(low) | 9 | 8 | 7 |
| Mycoplasma genitalium G37 | 26 | 22 | 19 |
| Mycoplasma hyopneumoniae 232 | 8 | 7 | 8 |
| Mycoplasma hyopneumoniae J | 3 | 3 | 3 |
| Mycoplasma hyorhinis DBS 1050 | 1 | 1 | 1 |
| Mycoplasma mobile 163K | 7 | 6 | 3 |
| Mycoplasma mycoides subsp. mycoides SC str. PG1 | 4 | 3 | 4 |
| Mycoplasma penetrans HF-2 | 1 | 1 | 1 |
| Mycoplasma pneumoniae M129 | 42 | 34 | 31 |
| Mycoplasma pneumoniae M129-B7 | 1 | 1 | 1 |
| Mycoplasma synoviae 53 | 3 | 3 | 2 |
| Myotis davidii | 3 | 3 | 3 |
| Mythimna loreyi densovirus | 1 | 1 | 1 |
| Mytilus galloprovincialis (Mediterranean mussel) | 1 | 1 | 1 |
| Myxococcus xanthus DK 1622 | 63 | 45 | 43 |
| Myxoma virus | 10 | 10 | 10 |
| Myzus persicae (green peach aphid) | 3 | 2 | 3 |
| Nanoarchaeum equitans Kin4-M | 1 | 1 | 1 |
| Nasonia vitripennis (jewel wasp) | 20 | 13 | 18 |
| Natrialba phage PhiCh1 | 1 | 1 | 1 |
| Natronomonas pharaonis DSM 2160 | 13 | 13 | 4 |
| Necator americanus | 2 | 2 | 2 |
| Neisseria gonorrhoeae | 1 | 1 | 1 |
| Neisseria gonorrhoeae FA 1090 | 80 | 55 | 62 |
| Neisseria gonorrhoeae MS11 | 2 | 1 | 2 |
| Neisseria gonorrhoeae NCCP11945 | 11 | 8 | 10 |
| Neisseria lactamica 020-06 | 1 | 1 | 1 |
| Neisseria meningitidis 053442 | 4 | 4 | 4 |
| Neisseria meningitidis 8013 | 3 | 3 | 2 |
| Neisseria meningitidis FAM18 | 10 | 6 | 6 |
| Neisseria meningitidis H44/76 | 2 | 2 | 2 |
| Neisseria meningitidis MC58 | 94 | 78 | 72 |
| Neisseria meningitidis NZ-05/33 | 5 | 5 | 3 |
| Neisseria meningitidis WUE 2594 | 2 | 2 | 2 |
| Neisseria meningitidis Z2491 | 15 | 13 | 12 |
| Neisseria meningitidis alpha14 | 1 | 1 | 1 |
| Nelumbo nucifera (sacred lotus) | 2 | 2 | 2 |
| Nematostella vectensis (starlet sea anemone) | 6 | 5 | 6 |
| Neospora caninum Liverpool | 4 | 3 | 4 |
| Neurospora crassa OR74A | 236 | 178 | 156 |
| Newcastle disease virus B1 | 59 | 50 | 6 |
| Nicotiana attenuata | 7 | 6 | 7 |
| Nicotiana sylvestris (wood tobacco) | 2 | 2 | 2 |
| Nicotiana tabacum (common tobacco) | 45 | 37 | 42 |
| Nicrophorus vespilloides | 2 | 2 | 2 |
| Nilaparvata lugens (brown planthopper) | 11 | 10 | 11 |
| Nipah henipavirus | 46 | 39 | 5 |
| Nitrobacter winogradskyi Nb-255 | 1 | 1 | 1 |
| Nitrosomonas europaea ATCC 19718 | 7 | 7 | 6 |
| Nitrosopumilus maritimus SCM1 | 2 | 1 | 2 |
| Nocardia farcinica | 1 | 1 | 1 |
| Nocardia farcinica IFM 10152 | 2 | 2 | 2 |
| Nodamura virus | 2 | 2 | 1 |
| Nomascus leucogenys (northern white-cheeked gibbon) | 2 | 2 | 2 |
| Nora virus | 1 | 1 | 1 |
| Norovirus GI | 6 | 6 | 2 |
| Norovirus GII | 3 | 3 | 2 |
| Norovirus GV | 7 | 7 | 2 |
| Nosema ceranae BRL01 | 1 | 1 | 1 |
| Nostoc punctiforme PCC 73102 | 9 | 9 | 8 |
| Nostoc sp. PCC 7120 = FACHB-418 | 86 | 66 | 61 |
| Nothobranchius furzeri (turquoise killifish) | 2 | 1 | 2 |
| Notothenia coriiceps (black rockcod) | 1 | 1 | 1 |
| Novosphingobium aromaticivorans | 1 | 1 | 1 |
| Novosphingobium aromaticivorans DSM 12444 | 3 | 3 | 3 |
| Novosphingobium sp. KA1 | 1 | 1 | 1 |
| Oat blue dwarf virus | 1 | 1 | 1 |
| Octodon degus (degu) | 1 | 1 | 1 |
| Octopus vulgaris (common octopus) | 1 | 1 | 1 |
| Odobenus rosmarus divergens (Pacific walrus) | 1 | 1 | 1 |
| Odocoileus virginianus texanus | 1 | 1 | 1 |
| Odontoglossum ringspot virus | 2 | 1 | 2 |
| Oenococcus oeni PSU-1 | 9 | 6 | 8 |
| Ogataea parapolymorpha DL-1 | 7 | 6 | 7 |
| Oligotropha carboxidovorans OM5 | 4 | 2 | 4 |
| Olive mild mosaic virus | 1 | 1 | 1 |
| Oncorhynchus kisutch (coho salmon) | 1 | 1 | 1 |
| Oncorhynchus mykiss (rainbow trout) | 204 | 145 | 150 |
| Onion yellows phytoplasma | 1 | 1 | 1 |
| Onion yellows phytoplasma OY-M | 1 | 1 | 1 |
| Orcinus orca (killer whale) | 1 | 1 | 1 |
| Oreochromis niloticus (Nile tilapia) | 77 | 57 | 71 |
| Orf virus | 11 | 11 | 8 |
| Orgyia pseudotsugata multiple nucleopolyhedrovirus | 2 | 2 | 2 |
| Orientia tsutsugamushi str. Boryong | 1 | 1 | 1 |
| Orientia tsutsugamushi str. Ikeda | 1 | 1 | 1 |
| Ornithorhynchus anatinus (platypus) | 5 | 5 | 5 |
| Oropouche virus | 1 | 1 | 1 |
| Oryctolagus cuniculus (rabbit) | 1205 | 914 | 548 |
| Oryza brachyantha (malo sina) | 3 | 3 | 3 |
| Oryza meridionalis (Australian wild rice) | 1 | 1 | 1 |
| Oryza sativa (rice) | 1 | 1 | 1 |
| Oryza sativa Indica Group (long-grained rice) | 3 | 3 | 1 |
| Oryza sativa Japonica Group (Japanese rice) | 751 | 632 | 581 |
| Oryzias latipes (Japanese medaka) | 155 | 120 | 125 |
| Oryzias melastigma (Indian medaka) | 2 | 2 | 2 |
| Ostreococcus lucimarinus CCE9901 | 1 | 1 | 1 |
| Ostreococcus tauri | 6 | 6 | 6 |
| Ostreococcus tauri virus 2 | 1 | 1 | 1 |
| Ostrinia furnacalis (Asian corn borer) | 1 | 1 | 1 |
| Otolemur garnettii (small-eared galago) | 3 | 2 | 3 |
| Ourmia melon virus | 1 | 1 | 1 |
| Ovine enzootic nasal tumor virus | 1 | 1 | 1 |
| Ovine gammaherpesvirus 2 | 3 | 3 | 3 |
| Ovis aries (sheep) | 1351 | 975 | 599 |
| Paenarthrobacter aurescens TC1 | 2 | 2 | 2 |
| Paenarthrobacter nicotinovorans | 1 | 1 | 1 |
| Paenibacillus larvae subsp. larvae | 1 | 1 | 1 |
| Paenibacillus polymyxa M1 | 1 | 1 | 1 |
| Paenibacillus polymyxa SC2 | 2 | 2 | 2 |
| Paenibacillus sp. Y412MC10 | 1 | 1 | 1 |
| Pan paniscus (pygmy chimpanzee) | 1 | 1 | 1 |
| Pan troglodytes (chimpanzee) | 76 | 66 | 64 |
| Panicum mosaic satellite virus | 2 | 2 | 1 |
| Panine betaherpesvirus 2 (Chimpanzee cytomegalovirus) | 1 | 1 | 1 |
| Pantoea agglomerans | 1 | 1 | 1 |
| Pantoea ananatis LMG 20103 | 1 | 1 | 1 |
| Papaver somniferum (opium poppy) | 1 | 1 | 1 |
| Papaya mosaic virus | 3 | 3 | 1 |
| Papaya ringspot virus | 5 | 5 | 1 |
| Papiine alphaherpesvirus 2 | 1 | 1 | 1 |
| Papilio xuthus (Asian swallowtail) | 2 | 2 | 2 |
| Papio anubis (olive baboon) | 31 | 20 | 29 |
| Paprika mild mottle virus | 2 | 1 | 2 |
| Parabacteroides distasonis ATCC 8503 | 11 | 2 | 11 |
| Paraburkholderia phymatum STM815 | 2 | 1 | 2 |
| Paraburkholderia xenovorans LB400 | 17 | 12 | 14 |
| Paracoccidioides brasiliensis Pb18 | 1 | 1 | 1 |
| Paracoccidioides lutzii Pb01 | 5 | 5 | 5 |
| Paracoccus aminophilus | 3 | 1 | 3 |
| Paracoccus denitrificans PD1222 | 19 | 16 | 13 |
| Parageobacillus thermoglucosidasius C56-YS93 | 1 | 1 | 1 |
| Paralichthys olivaceus (Japanese flounder) | 29 | 24 | 28 |
| Paramecium bursaria Chlorella virus 1 | 7 | 7 | 7 |
| Paramecium tetraurelia strain d4-2 | 9 | 5 | 9 |
| Parastagonospora nodorum SN15 | 2 | 2 | 2 |
| Parechovirus A | 1 | 1 | 1 |
| Pariacoto virus | 1 | 1 | 1 |
| Parus major (Great Tit) | 2 | 2 | 2 |
| Pasteurella multocida | 4 | 4 | 4 |
| Pasteurella multocida subsp. multocida str. HN06 | 2 | 2 | 1 |
| Pasteurella multocida subsp. multocida str. Pm70 | 8 | 7 | 7 |
| Pea seed-borne mosaic virus | 1 | 1 | 1 |
| Peanut bud necrosis virus | 2 | 2 | 2 |
| Peanut stunt virus | 2 | 2 | 1 |
| Pectobacterium atrosepticum SCRI1043 | 15 | 11 | 13 |
| Pectobacterium carotovorum subsp. carotovorum PC1 | 4 | 3 | 4 |
| Pediculus humanus corporis (human body louse) | 8 | 7 | 8 |
| Pedobacter heparinus DSM 2366 | 1 | 1 | 1 |
| Pelargonium flower break virus | 3 | 2 | 2 |
| Pelobacter carbinolicus DSM 2380 | 1 | 1 | 1 |
| Pelobacter propionicus DSM 2379 | 1 | 1 | 1 |
| Pelodiscus sinensis (Chinese soft-shelled turtle) | 4 | 2 | 4 |
| Penaeus vannamei (Pacific white shrimp) | 19 | 17 | 19 |
| Penicillium digitatum Pd1 | 3 | 3 | 3 |
| Penicillium rubens Wisconsin 54-1255 | 13 | 10 | 13 |
| Pepino mosaic virus | 2 | 2 | 2 |
| Periplaneta fuliginosa densovirus | 2 | 2 | 1 |
| Perkinsus marinus ATCC 50983 | 1 | 1 | 1 |
| Peromyscus maniculatus bairdii (prairie deer mouse) | 1 | 1 | 1 |
| Peste des petits ruminants virus | 7 | 6 | 6 |
| Phaeodactylum tricornutum CCAP 1055/1 | 10 | 6 | 10 |
| Phage Gifsy-1 | 1 | 1 | 1 |
| Phaseolus vulgaris (French bean) | 17 | 15 | 16 |
| Photobacterium damselae subsp. damselae | 1 | 1 | 1 |
| Photobacterium leiognathi subsp. mandapamensis svers.1.1. | 1 | 1 | 1 |
| Photobacterium profundum SS9 | 1 | 1 | 1 |
| Photorhabdus laumondii subsp. laumondii TTO1 | 5 | 5 | 5 |
| Physcomitrella patens | 49 | 37 | 47 |
| Physeter catodon (sperm whale) | 7 | 7 | 1 |
| Phytophthora infestans T30-4 | 13 | 10 | 11 |
| Phytophthora sojae | 3 | 3 | 3 |
| Picrophilus torridus DSM 9790 | 6 | 3 | 6 |
| Pieris rapae (cabbage white) | 3 | 2 | 3 |
| Pinus sylvestris (Scots pine) | 1 | 1 | 1 |
| Pipistrellus bat coronavirus HKU5 | 1 | 1 | 1 |
| Planktothrix phage PaV-LD | 1 | 1 | 1 |
| Plantago asiatica mosaic virus | 1 | 1 | 1 |
| Plasmodium berghei | 1 | 1 | 1 |
| Plasmodium berghei ANKA | 56 | 50 | 46 |
| Plasmodium chabaudi chabaudi | 2 | 2 | 2 |
| Plasmodium falciparum (malaria parasite P. falciparum) | 6 | 6 | 1 |
| Plasmodium falciparum 3D7 | 925 | 785 | 354 |
| Plasmodium knowlesi strain H | 8 | 8 | 7 |
| Plasmodium reichenowi | 1 | 1 | 1 |
| Plasmodium vivax (malaria parasite P. vivax) | 48 | 43 | 30 |
| Plasmodium yoelii | 12 | 10 | 10 |
| Plum pox virus | 5 | 5 | 1 |
| Plutella xylostella (diamondback moth) | 14 | 10 | 12 |
| Pneumonia virus of mice J3666 | 3 | 2 | 3 |
| Podospora anserina S mat+ | 2 | 2 | 2 |
| Poecilia reticulata (guppy) | 2 | 2 | 2 |
| Polyomavirus sp. | 1 | 1 | 1 |
| Pongo abelii (Sumatran orangutan) | 6 | 5 | 6 |
| Populus euphratica (Euphrates poplar) | 2 | 2 | 2 |
| Populus trichocarpa (black cottonwood) | 41 | 31 | 41 |
| Porcine circovirus 1 | 1 | 1 | 1 |
| Porcine circovirus 2 | 14 | 14 | 3 |
| Porcine circovirus type 1/2a | 1 | 1 | 1 |
| Porcine epidemic diarrhea virus | 34 | 33 | 5 |
| Porcine hemagglutinating encephalomyelitis virus | 2 | 2 | 1 |
| Porcine kobuvirus | 1 | 1 | 1 |
| Porcine parvovirus | 3 | 3 | 3 |
| Porcine reproductive and respiratory syndrome virus | 103 | 91 | 11 |
| Porcine rubulavirus | 1 | 1 | 1 |
| Porcine torovirus | 2 | 2 | 1 |
| Porphyromonas gingivalis ATCC 33277 | 55 | 44 | 30 |
| Porphyromonas gingivalis TDC60 | 2 | 2 | 2 |
| Porphyromonas gingivalis W83 | 61 | 51 | 45 |
| Potato leafroll virus | 3 | 3 | 3 |
| Potato mop-top virus | 2 | 2 | 2 |
| Potato virus A | 3 | 3 | 1 |
| Potato virus X | 7 | 7 | 4 |
| Potato virus Y | 10 | 10 | 2 |
| Primate bocaparvovirus 1 | 4 | 4 | 3 |
| Prochlorococcus marinus str. AS9601 | 1 | 1 | 1 |
| Prochlorococcus marinus str. MIT 9312 | 1 | 1 | 1 |
| Prochlorococcus marinus subsp. marinus str. CCMP1375 | 2 | 2 | 2 |
| Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1 | 3 | 2 | 3 |
| Proteus mirabilis BB2000 | 1 | 1 | 1 |
| Proteus mirabilis HI4320 | 17 | 11 | 17 |
| Proteus vulgaris | 8 | 6 | 5 |
| Providencia alcalifaciens Dmel2 | 1 | 1 | 1 |
| Providencia stuartii | 2 | 2 | 2 |
| Prunus avium (sweet cherry) | 2 | 1 | 2 |
| Prunus mume (Japanese apricot) | 1 | 1 | 1 |
| Prunus necrotic ringspot virus | 1 | 1 | 1 |
| Prunus persica (peach) | 12 | 8 | 12 |
| Pseudoalteromonas haloplanktis TAC125 | 9 | 8 | 8 |
| Pseudoalteromonas sp. SM9913 | 1 | 1 | 1 |
| Pseudoalteromonas virus PM2 | 1 | 1 | 1 |
| Pseudogymnoascus destructans 20631-21 | 1 | 1 | 1 |
| Pseudomonas aeruginosa | 25 | 20 | 17 |
| Pseudomonas aeruginosa B136-33 | 3 | 2 | 3 |
| Pseudomonas aeruginosa LESB58 | 5 | 5 | 4 |
| Pseudomonas aeruginosa M18 | 3 | 3 | 3 |
| Pseudomonas aeruginosa MTB-1 | 1 | 1 | 1 |
| Pseudomonas aeruginosa NCGM2.S1 | 1 | 1 | 1 |
| Pseudomonas aeruginosa PA7 | 11 | 9 | 11 |
| Pseudomonas aeruginosa PAO1 | 1264 | 925 | 605 |
| Pseudomonas aeruginosa PAO1-VE13 | 1 | 1 | 1 |
| Pseudomonas aeruginosa UCBPP-PA14 | 75 | 50 | 61 |
| Pseudomonas aeruginosa c7447m | 2 | 2 | 2 |
| Pseudomonas alkylphenolica | 1 | 1 | 1 |
| Pseudomonas brassicacearum subsp. brassicacearum NFM421 | 1 | 1 | 1 |
| Pseudomonas fluorescens | 3 | 3 | 3 |
| Pseudomonas fluorescens A506 | 1 | 1 | 1 |
| Pseudomonas fluorescens F113 | 4 | 4 | 4 |
| Pseudomonas fluorescens Pf0-1 | 3 | 3 | 3 |
| Pseudomonas fluorescens SBW25 | 2 | 2 | 2 |
| Pseudomonas phage AF | 1 | 1 | 1 |
| Pseudomonas phage phi8 | 1 | 1 | 1 |
| Pseudomonas protegens Pf-5 | 7 | 6 | 7 |
| Pseudomonas putida | 15 | 15 | 14 |
| Pseudomonas putida BIRD-1 | 1 | 1 | 1 |
| Pseudomonas putida DOT-T1E | 2 | 2 | 2 |
| Pseudomonas putida F1 | 6 | 6 | 6 |
| Pseudomonas putida GB-1 | 2 | 1 | 2 |
| Pseudomonas putida KT2440 | 117 | 89 | 83 |
| Pseudomonas putida NBRC 14164 | 1 | 1 | 1 |
| Pseudomonas putida S16 | 2 | 2 | 2 |
| Pseudomonas putida W619 | 1 | 1 | 1 |
| Pseudomonas savastanoi pv. phaseolicola 1448A | 12 | 8 | 12 |
| Pseudomonas sp. ADP | 2 | 2 | 2 |
| Pseudomonas sp. MC1 | 1 | 1 | 1 |
| Pseudomonas stutzeri A1501 | 4 | 4 | 4 |
| Pseudomonas stutzeri ATCC 17588 = LMG 11199 | 1 | 1 | 1 |
| Pseudomonas stutzeri CCUG 29243 | 1 | 1 | 1 |
| Pseudomonas syringae pv. maculicola str. M6 | 1 | 1 | 1 |
| Pseudomonas syringae pv. syringae | 2 | 1 | 2 |
| Pseudomonas syringae pv. syringae B728a | 13 | 13 | 12 |
| Pseudomonas syringae pv. tomato str. DC3000 | 79 | 65 | 48 |
| Pseudomonas virus DMS3 | 1 | 1 | 1 |
| Pseudomonas virus PaP3 | 1 | 1 | 1 |
| Pseudomonas virus Yua | 1 | 1 | 1 |
| Pseudomonas virus phi6 | 7 | 6 | 3 |
| Pseudoplusia includens SNPV IE | 1 | 1 | 1 |
| Pteropus vampyrus (large flying fox) | 2 | 2 | 2 |
| Puumala orthohantavirus | 2 | 2 | 1 |
| Pyricularia oryzae 70-15 | 59 | 39 | 58 |
| Pyrobaculum aerophilum str. IM2 | 11 | 9 | 11 |
| Pyrobaculum calidifontis JCM 11548 | 4 | 4 | 4 |
| Pyrobaculum ferrireducens | 1 | 1 | 1 |
| Pyrococcus abyssi GE5 | 13 | 12 | 11 |
| Pyrococcus furiosus COM1 | 4 | 3 | 4 |
| Pyrococcus furiosus DSM 3638 | 88 | 76 | 69 |
| Pyrococcus horikoshii OT3 | 91 | 80 | 70 |
| Pyrococcus sp. ST04 | 1 | 1 | 1 |
| Pyrus x bretschneideri (Chinese white pear) | 2 | 2 | 2 |
| Python bivittatus (Burmese python) | 1 | 1 | 1 |
| Rabbit fibroma virus | 1 | 1 | 1 |
| Rabbit hemorrhagic disease virus | 7 | 7 | 1 |
| Rabies lyssavirus | 32 | 31 | 5 |
| Rahnella aquatilis HX2 | 1 | 1 | 1 |
| Ralstonia solanacearum CFBP2957 | 1 | 1 | 1 |
| Ralstonia solanacearum GMI1000 | 14 | 11 | 12 |
| Ralstonia solanacearum MolK2 | 3 | 1 | 3 |
| Raptor adenovirus 1 | 1 | 1 | 1 |
| Raspberry bushy dwarf virus | 1 | 1 | 1 |
| Rat cytomegalovirus Maastricht | 1 | 1 | 1 |
| Rattus exulans (Polynesian rat) | 2 | 2 | 1 |
| Rattus norvegicus (Norway rat) | 85748 | 59327 | 7163 |
| Red clover necrotic mosaic virus | 5 | 5 | 4 |
| Redspotted grouper nervous necrosis virus | 1 | 1 | 1 |
| Respiratory syncytial virus | 63 | 59 | 9 |
| Reston ebolavirus | 9 | 8 | 4 |
| Reticuloendotheliosis virus | 3 | 2 | 2 |
| Rhinovirus A | 3 | 3 | 1 |
| Rhinovirus B14 | 2 | 2 | 1 |
| Rhinovirus C | 2 | 2 | 1 |
| Rhizobium etli CFN 42 | 30 | 21 | 26 |
| Rhizobium leguminosarum bv. trifolii CB782 | 1 | 1 | 1 |
| Rhizobium leguminosarum bv. viciae 3841 | 17 | 11 | 17 |
| Rhodobacter capsulatus SB 1003 | 35 | 21 | 29 |
| Rhodobacter sphaeroides 2.4.1 | 99 | 75 | 49 |
| Rhodobacter sphaeroides ATCC 17025 | 3 | 3 | 2 |
| Rhodobacter sphaeroides ATCC 17029 | 7 | 7 | 4 |
| Rhodobacter sphaeroides KD131 | 1 | 1 | 1 |
| Rhodococcus fascians D188 | 1 | 1 | 1 |
| Rhodococcus hoagii | 11 | 8 | 9 |
| Rhodococcus hoagii 103S | 2 | 2 | 2 |
| Rhodococcus jostii RHA1 | 19 | 12 | 19 |
| Rhodococcus opacus B4 | 1 | 1 | 1 |
| Rhodopseudomonas palustris CGA009 | 19 | 12 | 18 |
| Rhodopseudomonas palustris DX-1 | 1 | 1 | 1 |
| Rhodopseudomonas palustris TIE-1 | 4 | 3 | 4 |
| Rhodospirillum centenum SW | 1 | 1 | 1 |
| Rhodospirillum rubrum ATCC 11170 | 8 | 6 | 6 |
| Rhodothermus marinus DSM 4252 | 4 | 2 | 4 |
| Rice black streaked dwarf virus | 7 | 5 | 3 |
| Rice dwarf virus | 1 | 1 | 1 |
| Rice gall dwarf virus | 2 | 2 | 2 |
| Rice grassy stunt tenuivirus | 2 | 1 | 2 |
| Rice ragged stunt virus | 1 | 1 | 1 |
| Rice stripe tenuivirus | 6 | 6 | 2 |
| Rice yellow mottle virus | 3 | 3 | 1 |
| Ricinus communis (castor bean) | 6 | 6 | 6 |
| Rickettsia bellii RML369-C | 1 | 1 | 1 |
| Rickettsia conorii str. Malish 7 | 7 | 6 | 4 |
| Rickettsia prowazekii str. Madrid E | 9 | 7 | 9 |
| Rickettsia rickettsii str. 'Sheila Smith' | 1 | 1 | 1 |
| Rickettsia typhi str. Wilmington | 5 | 3 | 5 |
| Riemerella anatipestifer ATCC 11845 = DSM 15868 | 3 | 3 | 3 |
| Riemerella anatipestifer RA-CH-1 | 1 | 1 | 1 |
| Rift Valley fever virus | 22 | 21 | 5 |
| Rinderpest virus (strain Kabete O) | 4 | 4 | 2 |
| Rippkaea orientalis PCC 8801 | 1 | 1 | 1 |
| Rosa chinensis (China rose) | 1 | 1 | 1 |
| Roseobacter denitrificans OCh 114 | 2 | 2 | 2 |
| Ross River virus | 5 | 5 | 2 |
| Rotavirus A | 37 | 35 | 11 |
| Rotavirus C | 14 | 14 | 7 |
| Rotavirus D chicken/05V0049/DEU/2005 | 1 | 1 | 1 |
| Rotavirus G chicken/03V0567/DEU/2003 | 1 | 1 | 1 |
| Rotavirus G3 | 3 | 2 | 3 |
| Rotavirus I | 1 | 1 | 1 |
| Rous sarcoma virus | 25 | 25 | 3 |
| Rubella virus | 12 | 11 | 2 |
| Ruegeria pomeroyi DSS-3 | 4 | 4 | 3 |
| Ruminiclostridium cellulolyticum H10 | 3 | 1 | 3 |
| Ryegrass mottle virus | 1 | 1 | 1 |
| SARS coronavirus Rs_672/2006 | 5 | 5 | 4 |
| SFTS virus HB29 | 4 | 4 | 2 |
| Saccharolobus solfataricus | 12 | 9 | 10 |
| Saccharolobus solfataricus 98/2 | 1 | 1 | 1 |
| Saccharolobus solfataricus P2 | 133 | 113 | 84 |
| Saccharomyces cerevisiae (baker's yeast) | 6 | 6 | 5 |
| Saccharomyces cerevisiae S288C | 16533 | 10608 | 3422 |
| Saccharomyces eubayanus | 4 | 3 | 4 |
| Saccharophagus degradans 2-40 | 2 | 2 | 2 |
| Saccharopolyspora erythraea NRRL 2338 | 8 | 6 | 7 |
| Saccoglossus kowalevskii | 3 | 3 | 1 |
| Saffold virus | 2 | 2 | 1 |
| Saimiri boliviensis (Bolivian squirrel monkey) | 7 | 3 | 7 |
| Saimiriine betaherpesvirus 4 | 1 | 1 | 1 |
| Saimiriine gammaherpesvirus 2 (Herpesvirus saimiri) | 2 | 2 | 2 |
| Saint Louis encephalitis virus | 3 | 3 | 1 |
| Salinibacter ruber DSM 13855 | 1 | 1 | 1 |
| Salinispora arenicola CNS-205 | 1 | 1 | 1 |
| Salmo salar (Atlantic salmon) | 71 | 57 | 63 |
| Salmon isavirus | 4 | 4 | 3 |
| Salmonella enterica | 1 | 1 | 1 |
| Salmonella enterica subsp. arizonae serovar 62:z4,z23:- str. RSK2980 | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Bovismorbificans | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Choleraesuis | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 | 5 | 5 | 5 |
| Salmonella enterica subsp. enterica serovar Dublin | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Enteritidis | 2 | 2 | 2 |
| Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 | 7 | 6 | 7 |
| Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 | 3 | 3 | 2 |
| Salmonella enterica subsp. enterica serovar Heidelberg | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Newport str. SL254 | 2 | 2 | 1 |
| Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 | 6 | 6 | 5 |
| Salmonella enterica subsp. enterica serovar Typhi | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Typhi str. CT18 | 66 | 48 | 53 |
| Salmonella enterica subsp. enterica serovar Typhi str. Ty2 | 22 | 16 | 18 |
| Salmonella enterica subsp. enterica serovar Typhimurium | 11 | 11 | 9 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S | 28 | 17 | 26 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. DT2 | 1 | 1 | 1 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 974 | 697 | 473 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 | 20 | 13 | 20 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1 | 4 | 3 | 4 |
| Salmonella phage SPN1S | 1 | 1 | 1 |
| Salmonella phage SPN9CC | 1 | 1 | 1 |
| Salmonella virus P22 | 25 | 20 | 6 |
| Salmonella virus SP6 | 4 | 2 | 3 |
| Sandfly fever Naples virus | 1 | 1 | 1 |
| Sapovirus Mc10 | 3 | 3 | 1 |
| Sarcophilus harrisii (Tasmanian devil) | 1 | 1 | 1 |
| Satellite tobacco mosaic virus | 1 | 1 | 1 |
| Scheffersomyces stipitis CBS 6054 | 15 | 11 | 12 |
| Schistosoma haematobium | 1 | 1 | 1 |
| Schistosoma japonicum | 1 | 1 | 1 |
| Schistosoma mansoni | 44 | 36 | 40 |
| Schizophyllum commune H4-8 | 6 | 4 | 6 |
| Schizosaccharomyces japonicus yFS275 | 2 | 2 | 2 |
| Schizosaccharomyces pombe (fission yeast) | 2466 | 1621 | 986 |
| Sclerotinia sclerotiorum 1980 UF-70 | 9 | 7 | 9 |
| Selaginella moellendorffii | 3 | 2 | 3 |
| Semliki Forest virus | 31 | 31 | 2 |
| Senecavirus A | 3 | 3 | 1 |
| Sepik virus | 2 | 2 | 1 |
| Serinus canaria (Common canary) | 1 | 1 | 1 |
| Serratia marcescens | 1 | 1 | 1 |
| Serratia marcescens FGI94 | 1 | 1 | 1 |
| Serratia marcescens subsp. marcescens Db11 | 7 | 5 | 6 |
| Serratia proteamaculans 568 | 2 | 2 | 2 |
| Serratia sp. AS12 | 1 | 1 | 1 |
| Sesbania mosaic virus | 8 | 7 | 4 |
| Setaria italica (foxtail millet) | 3 | 2 | 3 |
| Severe acute respiratory syndrome coronavirus 2 | 16 | 16 | 2 |
| Severe acute respiratory syndrome-related coronavirus | 210 | 191 | 13 |
| Severe fever with thrombocytopenia virus | 1 | 1 | 1 |
| Shallot yellow stripe virus | 1 | 1 | 1 |
| Sheeppox virus | 2 | 2 | 2 |
| Sheldgoose hepatitis B virus | 1 | 1 | 1 |
| Shewanella amazonensis SB2B | 1 | 1 | 1 |
| Shewanella baltica OS155 | 1 | 1 | 1 |
| Shewanella baltica OS678 | 1 | 1 | 1 |
| Shewanella frigidimarina NCIMB 400 | 1 | 1 | 1 |
| Shewanella loihica PV-4 | 2 | 2 | 2 |
| Shewanella oneidensis MR-1 | 115 | 82 | 73 |
| Shewanella sp. ANA-3 | 10 | 4 | 10 |
| Shigella dysenteriae Sd197 | 4 | 4 | 4 |
| Shigella flexneri | 9 | 7 | 8 |
| Shigella flexneri 2a str. 2457T | 14 | 13 | 12 |
| Shigella flexneri 2a str. 301 | 39 | 33 | 32 |
| Shigella flexneri 5 str. 8401 | 5 | 4 | 5 |
| Shigella flexneri 5a str. M90T | 68 | 61 | 25 |
| Shigella sonnei | 1 | 1 | 1 |
| Shigella sonnei Ss046 | 4 | 3 | 4 |
| Shigella virus Sf6 | 2 | 2 | 2 |
| Shrimp white spot syndrome virus | 21 | 14 | 12 |
| Simian T-lymphotropic virus 1 | 1 | 1 | 1 |
| Simian adenovirus 1 | 1 | 1 | 1 |
| Simian adenovirus 3 | 1 | 1 | 1 |
| Simian foamy virus | 5 | 5 | 3 |
| Simian immunodeficiency virus | 75 | 74 | 7 |
| Simian immunodeficiency virus SIV-mnd 2 | 10 | 9 | 5 |
| Simian mastadenovirus C | 1 | 1 | 1 |
| Simian virus 40 | 59 | 56 | 6 |
| Simian-Human immunodeficiency virus | 6 | 6 | 5 |
| Sin Nombre orthohantavirus | 6 | 5 | 3 |
| Sindbis virus | 24 | 24 | 4 |
| Singapore grouper iridovirus | 6 | 6 | 5 |
| Sinorhizobium fredii NGR234 | 10 | 8 | 8 |
| Sinorhizobium meliloti | 1 | 1 | 1 |
| Sinorhizobium meliloti 1021 | 138 | 98 | 108 |
| Sinorhizobium meliloti 2011 | 2 | 1 | 2 |
| Sinorhizobium meliloti RU11/001 | 2 | 2 | 2 |
| Sinorhizobium meliloti Rm41 | 1 | 1 | 1 |
| Sitophilus zeamais (maize weevil) | 1 | 1 | 1 |
| Snow goose hepatitis B virus | 2 | 1 | 2 |
| Solanum lycopersicum (tomato) | 883 | 705 | 592 |
| Solanum pennellii | 2 | 2 | 2 |
| Solanum tuberosum (potato) | 83 | 67 | 73 |
| Sonchus yellow net nucleorhabdovirus | 1 | 1 | 1 |
| Sorangium cellulosum So ce56 | 2 | 2 | 2 |
| Sordaria macrospora k-hell | 4 | 3 | 4 |
| Sorghum bicolor (sorghum) | 19 | 16 | 18 |
| Sosuga virus | 1 | 1 | 1 |
| Southern bean mosaic virus | 1 | 1 | 1 |
| Southern rice black-streaked dwarf virus | 8 | 7 | 5 |
| Soybean mosaic virus | 4 | 4 | 1 |
| Sparus aurata (gilthead seabream) | 1 | 1 | 1 |
| Sphingobium japonicum UT26S | 1 | 1 | 1 |
| Sphingobium sp. SYK-6 | 5 | 3 | 5 |
| Sphingomonas sp. Leaf34 | 1 | 1 | 1 |
| Sphingomonas wittichii RW1 | 1 | 1 | 1 |
| Sphingopyxis alaskensis RB2256 | 2 | 1 | 2 |
| Spinacia oleracea (spinach) | 6 | 5 | 6 |
| Spiroplasma citri | 2 | 2 | 2 |
| Spodoptera frugiperda ascovirus 1a | 1 | 1 | 1 |
| Spodoptera frugiperda multiple nucleopolyhedrovirus | 1 | 1 | 1 |
| Spodoptera litura | 2 | 2 | 2 |
| Spodoptera litura nucleopolyhedrovirus | 5 | 5 | 2 |
| Spodoptera litura nucleopolyhedrovirus II | 1 | 1 | 1 |
| Staphylococcus arlettae | 1 | 1 | 1 |
| Staphylococcus aureus | 80 | 71 | 57 |
| Staphylococcus aureus 04-02981 | 5 | 5 | 5 |
| Staphylococcus aureus 1801-1 2010 | 1 | 1 | 1 |
| Staphylococcus aureus Bmb9393 | 3 | 2 | 3 |
| Staphylococcus aureus RF122 | 19 | 16 | 9 |
| Staphylococcus aureus subsp. aureus 11819-97 | 3 | 3 | 3 |
| Staphylococcus aureus subsp. aureus 6850 | 3 | 2 | 3 |
| Staphylococcus aureus subsp. aureus CN1 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus COL | 53 | 42 | 35 |
| Staphylococcus aureus subsp. aureus DSM 20231 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus ED98 | 7 | 7 | 5 |
| Staphylococcus aureus subsp. aureus JH1 | 2 | 2 | 2 |
| Staphylococcus aureus subsp. aureus JKD6159 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus M013 | 2 | 2 | 2 |
| Staphylococcus aureus subsp. aureus MRSA252 | 65 | 63 | 42 |
| Staphylococcus aureus subsp. aureus MSSA476 | 6 | 6 | 6 |
| Staphylococcus aureus subsp. aureus MW2 | 29 | 23 | 23 |
| Staphylococcus aureus subsp. aureus Mu3 | 9 | 6 | 5 |
| Staphylococcus aureus subsp. aureus Mu50 | 38 | 30 | 28 |
| Staphylococcus aureus subsp. aureus N315 | 55 | 50 | 44 |
| Staphylococcus aureus subsp. aureus NCTC 8325 | 147 | 122 | 101 |
| Staphylococcus aureus subsp. aureus ST228 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus ST398 | 3 | 3 | 2 |
| Staphylococcus aureus subsp. aureus T0131 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus USA300_FPR3757 | 30 | 28 | 13 |
| Staphylococcus aureus subsp. aureus USA300_TCH1516 | 35 | 28 | 24 |
| Staphylococcus aureus subsp. aureus VC40 | 1 | 1 | 1 |
| Staphylococcus aureus subsp. aureus str. Newman | 91 | 64 | 45 |
| Staphylococcus carnosus subsp. carnosus TM300 | 3 | 2 | 2 |
| Staphylococcus epidermidis | 1 | 1 | 1 |
| Staphylococcus epidermidis ATCC 12228 | 5 | 4 | 5 |
| Staphylococcus epidermidis RP62A | 27 | 24 | 18 |
| Staphylococcus haemolyticus JCSC1435 | 2 | 1 | 2 |
| Staphylococcus lugdunensis HKU09-01 | 1 | 1 | 1 |
| Staphylococcus lugdunensis N920143 | 4 | 2 | 4 |
| Staphylococcus pseudintermedius ED99 | 2 | 1 | 2 |
| Staphylococcus saprophyticus subsp. saprophyticus | 1 | 1 | 1 |
| Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292 | 2 | 2 | 2 |
| Staphylococcus saprophyticus subsp. saprophyticus MS1146 | 1 | 1 | 1 |
| Staphylococcus sciuri | 1 | 1 | 1 |
| Staphylococcus simulans | 2 | 2 | 2 |
| Staphylococcus simulans bv. staphylolyticus | 2 | 2 | 1 |
| Staphylococcus virus 11 | 2 | 2 | 1 |
| Staphylococcus virus IPLA35 | 1 | 1 | 1 |
| Staphylococcus warneri | 1 | 1 | 1 |
| Staphylococcus warneri SG1 | 1 | 1 | 1 |
| Stenotrophomonas maltophilia D457 | 1 | 1 | 1 |
| Stenotrophomonas maltophilia K279a | 21 | 13 | 18 |
| Stigmatella aurantiaca DW4/3-1 | 2 | 1 | 2 |
| Streptobacillus moniliformis DSM 12112 | 2 | 2 | 1 |
| Streptococcus agalactiae | 2 | 2 | 2 |
| Streptococcus agalactiae 2603V/R | 19 | 13 | 15 |
| Streptococcus agalactiae A909 | 8 | 7 | 6 |
| Streptococcus agalactiae NEM316 | 15 | 10 | 13 |
| Streptococcus agalactiae SA20-06 | 1 | 1 | 1 |
| Streptococcus cristatus ATCC 51100 | 1 | 1 | 1 |
| Streptococcus dysgalactiae subsp. equisimilis | 1 | 1 | 1 |
| Streptococcus equi subsp. equi 4047 | 2 | 2 | 2 |
| Streptococcus equi subsp. zooepidemicus | 2 | 2 | 2 |
| Streptococcus equi subsp. zooepidemicus MGCS10565 | 2 | 2 | 2 |
| Streptococcus gordonii str. Challis substr. CH1 | 24 | 17 | 22 |
| Streptococcus infantis | 1 | 1 | 1 |
| Streptococcus mutans | 3 | 3 | 3 |
| Streptococcus mutans GS-5 | 1 | 1 | 1 |
| Streptococcus mutans NN2025 | 2 | 2 | 2 |
| Streptococcus mutans UA159 | 191 | 144 | 121 |
| Streptococcus oralis subsp. tigurinus AZ_3a | 2 | 1 | 2 |
| Streptococcus parasanguinis ATCC 15912 | 2 | 2 | 1 |
| Streptococcus parasanguinis FW213 | 7 | 2 | 4 |
| Streptococcus phage Cp1 | 1 | 1 | 1 |
| Streptococcus phage TP-J34 | 1 | 1 | 1 |
| Streptococcus pneumoniae | 2 | 2 | 2 |
| Streptococcus pneumoniae ATCC 700669 | 8 | 7 | 6 |
| Streptococcus pneumoniae CGSP14 | 3 | 1 | 3 |
| Streptococcus pneumoniae D39 | 104 | 89 | 64 |
| Streptococcus pneumoniae G54 | 6 | 5 | 5 |
| Streptococcus pneumoniae Hungary19A-6 | 1 | 1 | 1 |
| Streptococcus pneumoniae INV104 | 1 | 1 | 1 |
| Streptococcus pneumoniae R6 | 157 | 130 | 100 |
| Streptococcus pneumoniae TCH8431/19A | 2 | 2 | 2 |
| Streptococcus pneumoniae TIGR4 | 26 | 26 | 19 |
| Streptococcus pyogenes | 5 | 5 | 4 |
| Streptococcus pyogenes A20 | 1 | 1 | 1 |
| Streptococcus pyogenes Alab49 | 1 | 1 | 1 |
| Streptococcus pyogenes M1 GAS | 85 | 72 | 36 |
| Streptococcus pyogenes MGAS10270 | 1 | 1 | 1 |
| Streptococcus pyogenes MGAS10394 | 6 | 6 | 6 |
| Streptococcus pyogenes MGAS10750 | 1 | 1 | 1 |
| Streptococcus pyogenes MGAS15252 | 1 | 1 | 1 |
| Streptococcus pyogenes MGAS1882 | 2 | 2 | 2 |
| Streptococcus pyogenes MGAS2096 | 1 | 1 | 1 |
| Streptococcus pyogenes MGAS315 | 9 | 8 | 9 |
| Streptococcus pyogenes MGAS5005 | 23 | 17 | 16 |
| Streptococcus pyogenes MGAS6180 | 1 | 1 | 1 |
| Streptococcus pyogenes MGAS8232 | 10 | 9 | 8 |
| Streptococcus pyogenes MGAS9429 | 4 | 4 | 4 |
| Streptococcus pyogenes NZ131 | 13 | 10 | 11 |
| Streptococcus pyogenes SSI-1 | 1 | 1 | 1 |
| Streptococcus pyogenes str. Manfredo | 3 | 3 | 3 |
| Streptococcus sanguinis SK36 | 16 | 9 | 13 |
| Streptococcus suis 05ZYH33 | 9 | 9 | 8 |
| Streptococcus suis 98HAH33 | 2 | 2 | 2 |
| Streptococcus suis BM407 | 12 | 12 | 12 |
| Streptococcus suis P1/7 | 4 | 4 | 4 |
| Streptococcus suis SC84 | 1 | 1 | 1 |
| Streptococcus suis YB51 | 1 | 1 | 1 |
| Streptococcus thermophilus | 3 | 2 | 3 |
| Streptococcus thermophilus CNRZ1066 | 3 | 2 | 3 |
| Streptococcus thermophilus JIM 8232 | 3 | 2 | 3 |
| Streptococcus thermophilus LMD-9 | 4 | 3 | 3 |
| Streptococcus thermophilus LMG 18311 | 12 | 11 | 9 |
| Streptococcus uberis 0140J | 1 | 1 | 1 |
| Streptomyces avermitilis MA-4680 = NBRC 14893 | 7 | 5 | 7 |
| Streptomyces azureus | 1 | 1 | 1 |
| Streptomyces bingchenggensis BCW-1 | 1 | 1 | 1 |
| Streptomyces cattleya NRRL 8057 = DSM 46488 | 1 | 1 | 1 |
| Streptomyces clavuligerus | 3 | 3 | 3 |
| Streptomyces coelicolor A3(2) | 269 | 207 | 204 |
| Streptomyces griseus subsp. griseus NBRC 13350 | 10 | 10 | 9 |
| Streptomyces lividans TK24 | 1 | 1 | 1 |
| Streptomyces rochei | 1 | 1 | 1 |
| Streptomyces roseochromogenus subsp. oscitans DS 12.976 | 1 | 1 | 1 |
| Streptomyces scabiei 87.22 | 1 | 1 | 1 |
| Streptomyces sp. SirexAA-E | 2 | 2 | 2 |
| Streptomyces venezuelae | 3 | 3 | 3 |
| Streptomyces venezuelae ATCC 10712 | 3 | 3 | 3 |
| Streptomyces viridosporus ATCC 14672 | 1 | 1 | 1 |
| Streptomyces virus phiBT1 | 1 | 1 | 1 |
| Streptomyces virus phiC31 | 6 | 4 | 2 |
| Strongylocentrotus purpuratus (purple sea urchin) | 93 | 72 | 75 |
| Struthio camelus australis | 2 | 2 | 2 |
| Sturnus vulgaris (Common starling) | 2 | 2 | 2 |
| Sudan ebolavirus | 1 | 1 | 1 |
| Sugarcane mosaic virus | 2 | 2 | 1 |
| Suid alphaherpesvirus 1 (Pseudorabies virus) | 86 | 72 | 35 |
| Sulfolobus acidocaldarius DSM 639 | 15 | 12 | 13 |
| Sulfolobus acidocaldarius Ron12/I | 1 | 1 | 1 |
| Sulfolobus islandicus | 5 | 3 | 3 |
| Sulfolobus islandicus HVE10/4 | 1 | 1 | 1 |
| Sulfolobus islandicus REY15A | 4 | 3 | 4 |
| Sulfolobus islandicus filamentous virus | 1 | 1 | 1 |
| Sulfolobus islandicus rod-shaped virus 2 | 3 | 2 | 3 |
| Sulfolobus turreted icosahedral virus 1 | 1 | 1 | 1 |
| Sulfolobus turreted icosahedral virus 2 | 2 | 2 | 1 |
| Sulfolobus virus Ragged Hills | 1 | 1 | 1 |
| Sulfurisphaera tokodaii str. 7 | 29 | 27 | 28 |
| Sus scrofa (pig) | 4716 | 3429 | 1911 |
| Sus scrofa domesticus (domestic pig) | 2 | 1 | 2 |
| Sweet potato chlorotic stunt virus | 1 | 1 | 1 |
| Sweet potato feathery mottle virus | 2 | 2 | 1 |
| Symbiobacterium thermophilum IAM 14863 | 4 | 2 | 4 |
| Synechococcus elongatus PCC 6301 | 26 | 22 | 15 |
| Synechococcus elongatus PCC 7942 = FACHB-805 | 28 | 22 | 21 |
| Synechococcus sp. CC9311 | 1 | 1 | 1 |
| Synechococcus sp. CC9902 | 1 | 1 | 1 |
| Synechococcus sp. PCC 7002 | 5 | 5 | 5 |
| Synechococcus sp. RCC307 | 1 | 1 | 1 |
| Synechococcus sp. WH 8102 | 10 | 8 | 6 |
| Synechococcus virus Syn5 | 1 | 1 | 1 |
| Synechocystis sp. PCC 6803 | 262 | 209 | 189 |
| Synechocystis sp. PCC 6803 substr. PCC-N | 1 | 1 | 1 |
| Synechocystis sp. PCC 6803 substr. PCC-P | 2 | 2 | 2 |
| Tacaribe mammarenavirus | 5 | 4 | 3 |
| Tachysurus fulvidraco (yellow catfish) | 2 | 2 | 2 |
| Taenia solium (pork tapeworm) | 1 | 1 | 1 |
| Taeniopygia guttata (zebra finch) | 65 | 51 | 46 |
| Takifugu rubripes (torafugu) | 35 | 30 | 33 |
| Talaromyces marneffei ATCC 18224 | 3 | 2 | 3 |
| Talaromyces stipitatus ATCC 10500 | 4 | 1 | 4 |
| Tanapox virus | 2 | 2 | 2 |
| Tannerella forsythia 92A2 | 1 | 1 | 1 |
| Tembusu virus | 3 | 3 | 1 |
| Tetrahymena thermophila SB210 | 35 | 31 | 31 |
| Tetrapisispora phaffii CBS 4417 | 1 | 1 | 1 |
| Thalassiosira pseudonana CCMP1335 | 3 | 3 | 3 |
| Theileria annulata | 8 | 6 | 7 |
| Theilovirus | 6 | 6 | 1 |
| Theobroma cacao (cacao) | 2 | 2 | 2 |
| Thermoanaerobacter pseudethanolicus ATCC 33223 | 1 | 1 | 1 |
| Thermobifida fusca YX | 9 | 7 | 9 |
| Thermococcus kodakarensis KOD1 | 53 | 43 | 43 |
| Thermococcus litoralis DSM 5473 | 3 | 3 | 2 |
| Thermococcus onnurineus NA1 | 12 | 9 | 11 |
| Thermococcus sibiricus MM 739 | 6 | 6 | 4 |
| Thermoplasma acidophilum DSM 1728 | 27 | 25 | 25 |
| Thermoplasma volcanium GSS1 | 5 | 5 | 5 |
| Thermoproteus tenax Kra 1 | 1 | 1 | 1 |
| Thermosynechococcus elongatus BP-1 | 45 | 38 | 29 |
| Thermosynechococcus sp. NK55a | 1 | 1 | 1 |
| Thermothelomyces thermophilus ATCC 42464 | 2 | 2 | 2 |
| Thermothielavioides terrestris NRRL 8126 | 1 | 1 | 1 |
| Thermotoga maritima MSB8 | 161 | 140 | 128 |
| Thermotoga neapolitana DSM 4359 | 4 | 4 | 3 |
| Thermotoga petrophila RKU-1 | 4 | 4 | 3 |
| Thermus thermophilus HB27 | 60 | 53 | 49 |
| Thermus thermophilus HB8 | 214 | 194 | 159 |
| Thermus thermophilus JL-18 | 1 | 1 | 1 |
| Thermus thermophilus SG0.5JP17-16 | 1 | 1 | 1 |
| Thermus virus P23-77 | 1 | 1 | 1 |
| Thioalkalivibrio nitratireducens DSM 14787 | 1 | 1 | 1 |
| Thogoto thogotovirus | 2 | 2 | 1 |
| Tick-borne encephalitis virus | 11 | 11 | 1 |
| Tobacco etch virus | 3 | 3 | 1 |
| Tobacco mosaic virus | 20 | 20 | 4 |
| Tobacco rattle virus | 3 | 3 | 2 |
| Tobacco vein banding mosaic virus | 1 | 1 | 1 |
| Tomato aspermy virus | 2 | 2 | 1 |
| Tomato bushy stunt virus | 26 | 21 | 4 |
| Tomato chlorosis virus | 4 | 4 | 1 |
| Tomato golden mosaic virus | 4 | 3 | 3 |
| Tomato leaf curl Gujarat virus | 2 | 2 | 2 |
| Tomato leaf curl Kerala virus | 1 | 1 | 1 |
| Tomato leaf curl New Delhi virus | 1 | 1 | 1 |
| Tomato leaf curl Palampur virus | 1 | 1 | 1 |
| Tomato leaf curl virus | 1 | 1 | 1 |
| Tomato mosaic virus | 3 | 3 | 2 |
| Tomato spotted wilt tospovirus | 14 | 13 | 3 |
| Tomato torrado virus | 2 | 2 | 1 |
| Tomato yellow leaf curl Sardinia virus | 2 | 2 | 1 |
| Tomato yellow leaf curl Vietnam betasatellite | 1 | 1 | 1 |
| Tomato yellow leaf curl virus | 4 | 4 | 1 |
| Toxoplasma gondii ME49 | 120 | 102 | 87 |
| Trametes versicolor FP-101664 SS1 | 5 | 4 | 5 |
| Treponema denticola ATCC 35405 | 26 | 20 | 17 |
| Treponema pallidum subsp. pallidum SS14 | 2 | 2 | 2 |
| Treponema pallidum subsp. pallidum str. Nichols | 20 | 17 | 16 |
| Tribolium castaneum (red flour beetle) | 103 | 68 | 93 |
| Trichinella spiralis | 6 | 6 | 4 |
| Trichoderma atroviride IMI 206040 | 6 | 5 | 5 |
| Trichoderma reesei QM6a | 25 | 21 | 16 |
| Trichoderma virens Gv29-8 | 1 | 1 | 1 |
| Trichodesmium erythraeum IMS101 | 3 | 2 | 3 |
| Trichodysplasia spinulosa-associated polyomavirus | 2 | 2 | 1 |
| Trichomonas vaginalis G3 | 28 | 20 | 27 |
| Trichophyton benhamiae CBS 112371 | 2 | 2 | 2 |
| Trichophyton rubrum CBS 118892 | 2 | 2 | 2 |
| Trichoplax adhaerens | 1 | 1 | 1 |
| Trichoplusia ni single nucleopolyhedrovirus | 1 | 1 | 1 |
| Trichormus variabilis ATCC 29413 | 3 | 3 | 3 |
| Triticum aestivum (bread wheat) | 304 | 265 | 205 |
| Trypanosoma brucei brucei TREU927 | 230 | 196 | 186 |
| Trypanosoma brucei gambiense DAL972 | 2 | 2 | 1 |
| Trypanosoma cruzi strain CL Brener | 101 | 92 | 80 |
| Trypanosoma grayi | 2 | 2 | 2 |
| Tula orthohantavirus | 3 | 3 | 2 |
| Tupaia chinensis (Chinese tree shrew) | 1 | 1 | 1 |
| Turkey adenovirus 3 | 1 | 1 | 1 |
| Turkey astrovirus 2 | 1 | 1 | 1 |
| Turkey coronavirus | 2 | 2 | 2 |
| Turnip crinkle virus | 8 | 8 | 3 |
| Turnip mosaic virus | 10 | 10 | 1 |
| Turnip vein-clearing virus | 1 | 1 | 1 |
| Turnip yellow mosaic virus | 1 | 1 | 1 |
| Turnip yellows virus | 1 | 1 | 1 |
| Tursiops truncatus (common bottlenose dolphin) | 4 | 4 | 4 |
| UR2 sarcoma virus | 1 | 1 | 1 |
| Ureaplasma parvum serovar 3 str. ATCC 700970 | 2 | 2 | 2 |
| Ureaplasma urealyticum serovar 10 str. ATCC 33699 | 1 | 1 | 1 |
| Ursus maritimus (polar bear) | 2 | 2 | 2 |
| Ustilago maydis 521 | 26 | 25 | 23 |
| Uukuniemi virus | 2 | 2 | 1 |
| Vaccinia virus | 197 | 164 | 83 |
| Variegated squirrel bornavirus 1 | 15 | 15 | 6 |
| Variola virus (smallpox virus) | 4 | 4 | 2 |
| Veillonella parvula DSM 2008 | 1 | 1 | 1 |
| Venezuelan equine encephalitis virus | 7 | 7 | 2 |
| Verticillium dahliae VdLs.17 | 5 | 4 | 5 |
| Vesicular stomatitis Alagoas virus | 1 | 1 | 1 |
| Vesicular stomatitis Indiana virus | 45 | 40 | 5 |
| Vibrio alginolyticus | 7 | 7 | 7 |
| Vibrio alginolyticus NBRC 15630 = ATCC 17749 | 2 | 2 | 2 |
| Vibrio anguillarum 775 | 5 | 5 | 4 |
| Vibrio campbellii ATCC BAA-1116 | 4 | 3 | 3 |
| Vibrio cholerae AM-19226 | 5 | 2 | 5 |
| Vibrio cholerae M66-2 | 4 | 3 | 4 |
| Vibrio cholerae MJ-1236 | 10 | 10 | 6 |
| Vibrio cholerae MO10 | 1 | 1 | 1 |
| Vibrio cholerae O1 biovar El Tor str. N16961 | 126 | 101 | 103 |
| Vibrio cholerae O1 str. 2010EL-1786 | 10 | 9 | 9 |
| Vibrio cholerae O395 | 72 | 57 | 55 |
| Vibrio coralliilyticus | 1 | 1 | 1 |
| Vibrio parahaemolyticus | 3 | 3 | 2 |
| Vibrio parahaemolyticus O1:Kuk str. FDA_R31 | 1 | 1 | 1 |
| Vibrio parahaemolyticus RIMD 2210633 | 67 | 47 | 42 |
| Vibrio tasmaniensis LGP32 | 1 | 1 | 1 |
| Vibrio virus CTXphi | 1 | 1 | 1 |
| Vibrio virus Kappa | 1 | 1 | 1 |
| Vibrio vulnificus | 8 | 7 | 8 |
| Vibrio vulnificus CMCP6 | 17 | 12 | 11 |
| Vibrio vulnificus MO6-24/O | 15 | 11 | 13 |
| Vibrio vulnificus YJ016 | 15 | 12 | 15 |
| Vicugna pacos (alpaca) | 7 | 6 | 7 |
| Vigna radiata (mung bean) | 2 | 2 | 2 |
| Viral hemorrhagic septicemia virus Fil3 | 4 | 4 | 3 |
| Visna-maedi virus | 2 | 2 | 2 |
| Vitis vinifera (wine grape) | 88 | 63 | 76 |
| Vollenhovia emeryi | 1 | 1 | 1 |
| Volvox carteri f. nagariensis | 1 | 1 | 1 |
| Vulpes vulpes (red fox) | 1 | 1 | 1 |
| Weissella cibaria | 2 | 2 | 2 |
| West Nile virus | 62 | 61 | 3 |
| Wheat dwarf virus | 1 | 1 | 1 |
| Wheat streak mosaic virus | 5 | 5 | 1 |
| Wheat yellow mosaic virus | 2 | 2 | 1 |
| White spot syndrome virus | 4 | 4 | 2 |
| Wolbachia endosymbiont of Drosophila melanogaster | 2 | 2 | 2 |
| Wolinella succinogenes DSM 1740 | 7 | 3 | 5 |
| Wongabel hapavirus | 1 | 1 | 1 |
| Xanthobacter autotrophicus Py2 | 1 | 1 | 1 |
| Xanthomonas albilineans GPE PC73 | 1 | 1 | 1 |
| Xanthomonas axonopodis Xac29-1 | 1 | 1 | 1 |
| Xanthomonas campestris pv. campestris str. 8004 | 31 | 20 | 25 |
| Xanthomonas campestris pv. campestris str. ATCC 33913 | 47 | 34 | 39 |
| Xanthomonas campestris pv. campestris str. B100 | 3 | 3 | 3 |
| Xanthomonas campestris pv. vesicatoria str. 85-10 | 23 | 19 | 17 |
| Xanthomonas citri | 2 | 1 | 2 |
| Xanthomonas citri pv. citri str. 306 | 22 | 18 | 20 |
| Xanthomonas citri pv. fuscans | 1 | 1 | 1 |
| Xanthomonas citri pv. vignicola | 1 | 1 | 1 |
| Xanthomonas citri subsp. citri Aw12879 | 1 | 1 | 1 |
| Xanthomonas oryzae pv. oryzae | 1 | 1 | 1 |
| Xanthomonas oryzae pv. oryzae KACC 10331 | 18 | 17 | 16 |
| Xanthomonas oryzae pv. oryzae MAFF 311018 | 6 | 2 | 6 |
| Xanthomonas oryzae pv. oryzae PXO99A | 15 | 11 | 15 |
| Xanthomonas oryzae pv. oryzicola BLS256 | 6 | 5 | 6 |
| Xenopus laevis (African clawed frog) | 2984 | 2095 | 1577 |
| Xenopus tropicalis (tropical clawed frog) | 339 | 280 | 286 |
| Xenorhabdus bovienii SS-2004 | 2 | 2 | 2 |
| Xenorhabdus nematophila ATCC 19061 | 2 | 2 | 2 |
| Xylella fastidiosa | 2 | 1 | 2 |
| Xylella fastidiosa 9a5c | 9 | 9 | 7 |
| Xylella fastidiosa Temecula1 | 11 | 8 | 11 |
| Yaba monkey tumor virus | 1 | 1 | 1 |
| Yaba-like disease virus | 1 | 1 | 1 |
| Yarrowia lipolytica CLIB122 | 19 | 14 | 18 |
| Yellow fever virus | 14 | 14 | 1 |
| Yersinia enterocolitica | 37 | 28 | 22 |
| Yersinia enterocolitica W22703 | 7 | 4 | 7 |
| Yersinia enterocolitica subsp. enterocolitica 8081 | 42 | 30 | 31 |
| Yersinia pestis | 35 | 32 | 17 |
| Yersinia pestis Angola | 2 | 2 | 2 |
| Yersinia pestis CO92 | 60 | 47 | 40 |
| Yersinia pestis Java 9 | 2 | 1 | 2 |
| Yersinia pestis KIM10+ | 40 | 30 | 30 |
| Yersinia pestis biovar Medievalis str. Harbin 35 | 2 | 1 | 2 |
| Yersinia pestis biovar Microtus str. 91001 | 6 | 6 | 6 |
| Yersinia phage PY54 | 1 | 1 | 1 |
| Yersinia pseudotuberculosis | 2 | 2 | 2 |
| Yersinia pseudotuberculosis IP 31758 | 2 | 2 | 2 |
| Yersinia pseudotuberculosis IP 32953 | 35 | 27 | 29 |
| Yersinia pseudotuberculosis PB1/+ | 8 | 6 | 4 |
| Yersinia pseudotuberculosis YPIII | 17 | 9 | 14 |
| Zaire ebolavirus | 92 | 85 | 7 |
| Zanthoxylum piperitum (Japanese-pepper) | 1 | 1 | 1 |
| Zanthoxylum schinifolium (Sichuan-pepper) | 1 | 1 | 1 |
| Zea mays (maize) | 665 | 543 | 461 |
| Zea mays subsp. mays (maize) | 7 | 6 | 6 |
| Zika virus | 35 | 34 | 2 |
| Zobellia galactanivorans | 1 | 1 | 1 |
| Zonotrichia albicollis (white-throated sparrow) | 2 | 1 | 2 |
| Zucchini yellow mosaic virus | 4 | 4 | 1 |
| Zygosaccharomyces rouxii | 5 | 3 | 3 |
| Zymomonas mobilis subsp. mobilis ATCC 10988 | 1 | 1 | 1 |
| Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 | 13 | 10 | 12 |
| Zymoseptoria tritici IPO323 | 3 | 2 | 3 |
| [Bacillus thuringiensis] serovar konkukian str. 97-27 | 15 | 11 | 15 |
| [Bacillus] selenitireducens MLS10 | 1 | 1 | 1 |
| [Candida] auris | 4 | 4 | 3 |
| [Candida] glabrata | 45 | 32 | 40 |
| [Clostridium] bolteae 90A9 | 1 | 1 | 1 |
| [Enterobacter] lignolyticus SCF1 | 4 | 3 | 4 |
| [Haemophilus] ducreyi 35000HP | 41 | 25 | 25 |
| [Mannheimia] succiniciproducens MBEL55E | 1 | 1 | 1 |
| [Nectria] haematococca mpVI 77-13-4 | 1 | 1 | 1 |
| uncultured bacterium | 2 | 2 | 2 |