| escherichia coli | 524 | species | bacteria | bacteria | 562 |
| human immunodeficiency virus 1 | 410 | species | viruses | viruses | 11676 |
| human immunodeficiency virus 2 | 399 | species | viruses | viruses | 11709 |
| nicotiana tabacum | 304 | species | plants | | 4097 |
| hepatitis c virus | 289 | species | viruses | viruses | 11103 |
| staphylococcus aureus | 271 | species | bacteria | bacteria | 1280 |
| human herpesvirus 4 | 257 | species | viruses | viruses | 10376 |
| hepatitis b virus | 246 | species | viruses | viruses | 10407 |
| pseudomonas aeruginosa | 243 | species | bacteria | bacteria | 287 |
| unidentified influenza virus | 240 | species | viruses | viruses | 11309 |
| human papillomavirus | 235 | species | viruses | viruses | 10566 |
| bacillus subtilis | 219 | species | bacteria | bacteria | 1423 |
| plasmodium falciparum | 209 | species | invertebrates | protozoa | 5833 |
| listeria monocytogenes | 207 | species | bacteria | bacteria | 1639 |
| streptococcus pneumoniae | 199 | species | bacteria | bacteria | 1313 |
| vaccinia virus | 197 | species | viruses | viruses | 10245 |
| candida albicans | 181 | species | plants | fungi | 5476 |
| vesicular stomatitis virus | 177 | species | viruses | viruses | 11276 |
| human herpesvirus 1 | 171 | species | viruses | viruses | 10298 |
| human herpesvirus 5 | 159 | species | viruses | viruses | 10359 |
| agrobacterium tumefaciens | 155 | species | bacteria | bacteria | 358 |
| haemophilus influenzae | 148 | species | bacteria | bacteria | 727 |
| toxoplasma gondii | 148 | species | invertebrates | protozoa | 5811 |
| lymphocytic choriomeningitis mammarenavirus | 148 | species | viruses | viruses | 11623 |
| klebsiella pneumoniae | 146 | species | bacteria | bacteria | 573 |
| vibrio cholerae | 145 | species | bacteria | bacteria | 666 |
| borreliella burgdorferi | 144 | species | bacteria | bacteria | 139 |
| chlamydia pneumoniae | 143 | species | bacteria | bacteria | 83558 |
| shigella flexneri | 142 | species | bacteria | bacteria | 623 |
| human t-lymphotropic virus 1 | 137 | no rank | viruses | viruses | 11908 |
| neisseria gonorrhoeae | 136 | species | bacteria | bacteria | 485 |
| influenza a virus | 135 | species | viruses | viruses | 11320 |
| pseudomonas putida | 133 | species | bacteria | bacteria | 303 |
| legionella pneumophila | 133 | species | bacteria | bacteria | 446 |
| enterococcus faecalis | 132 | species | bacteria | bacteria | 1351 |
| mycobacterium bovis | 132 | species | bacteria | bacteria | 1765 |
| neisseria meningitidis | 130 | species | bacteria | bacteria | 487 |
| trypanosoma cruzi | 130 | species | invertebrates | protozoa | 5693 |
| chlamydia trachomatis | 129 | species | bacteria | bacteria | 813 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| yersinia enterocolitica | 126 | species | bacteria | bacteria | 630 |
| mycobacterium avium | 125 | species | bacteria | bacteria | 1764 |
| pseudomonas fluorescens | 122 | species | bacteria | bacteria | 294 |
| bordetella pertussis | 122 | species | bacteria | bacteria | 520 |
| bacillus anthracis | 122 | species | bacteria | bacteria | 1392 |
| measles virus | 119 | species | viruses | viruses | 11234 |
| rice stripe virus | 118 | species | viruses | viruses | 12331 |
| enterovirus c | 118 | species | viruses | viruses | 138950 |
| enterococcus faecium | 116 | species | bacteria | bacteria | 1352 |
| staphylococcus epidermidis | 114 | species | bacteria | bacteria | 1282 |
| streptococcus pyogenes | 113 | species | bacteria | bacteria | 1314 |
| human herpesvirus 3 | 113 | species | viruses | viruses | 10335 |
| bacillus cereus | 111 | species | bacteria | bacteria | 1396 |
| aspergillus niger | 110 | species | plants | fungi | 5061 |
| aspergillus fumigatus | 109 | species | plants | fungi | 746128 |
| burkholderia cepacia | 107 | species | bacteria | bacteria | 292 |
| sindbis virus | 107 | species | viruses | viruses | 11034 |
| salmonella enterica | 107 | species | bacteria | bacteria | 28901 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| yersinia pestis | 105 | species | bacteria | bacteria | 632 |
| ricinus communis | 104 | species | plants | | 3988 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| serratia marcescens | 100 | species | bacteria | bacteria | 615 |
| yersinia pseudotuberculosis | 99 | species | bacteria | bacteria | 633 |
| leishmania donovani | 98 | species | invertebrates | protozoa | 5661 |
| entamoeba histolytica | 98 | species | invertebrates | protozoa | 5759 |
| bacteroides fragilis | 97 | species | bacteria | bacteria | 817 |
| west nile virus | 97 | species | viruses | viruses | 11082 |
| human herpesvirus 2 | 96 | species | viruses | viruses | 10310 |
| rabies virus | 96 | species | viruses | viruses | 11292 |
| mycobacterium leprae | 95 | species | bacteria | bacteria | 1769 |
| human herpesvirus 6 | 94 | species | viruses | viruses | 10368 |
| mycoplasma pneumoniae | 93 | species | bacteria | bacteria | 2104 |
| fusarium oxysporum | 93 | species | plants | fungi | 5507 |
| newcastle disease virus | 93 | species | viruses | viruses | 11176 |
| cryptosporidium parvum | 92 | species | invertebrates | protozoa | 5807 |
| enterobacter cloacae | 90 | species | bacteria | bacteria | 550 |
| jc polyomavirus | 89 | species | viruses | viruses | 10632 |
| foot-and-mouth disease virus | 89 | species | viruses | viruses | 12110 |
| acinetobacter baumannii | 88 | species | bacteria | bacteria | 470 |
| treponema pallidum | 87 | species | bacteria | bacteria | 160 |
| moraxella catarrhalis | 87 | species | bacteria | bacteria | 480 |
| salmonella enterica subsp. enterica serovar enteritidis | 87 | no rank | bacteria | bacteria | 149539 |
| rhizopus oryzae | 86 | species | plants | fungi | 64495 |
| salmonella enterica subsp. enterica serovar typhi | 85 | no rank | bacteria | bacteria | 90370 |
| classical swine fever virus | 84 | species | viruses | viruses | 11096 |
| japanese encephalitis virus | 83 | species | viruses | viruses | 11072 |
| yellow fever virus | 83 | species | viruses | viruses | 11089 |
| aspergillus flavus | 81 | species | plants | fungi | 5059 |
| human parvovirus b19 | 81 | species | viruses | viruses | 10798 |
| proteus mirabilis | 80 | species | bacteria | bacteria | 584 |
| shigella dysenteriae | 80 | species | bacteria | bacteria | 622 |
| plasmodium vivax | 80 | species | invertebrates | protozoa | 5855 |
| variola virus | 80 | species | viruses | viruses | 10255 |
| stenotrophomonas maltophilia | 80 | species | bacteria | bacteria | 40324 |
| ralstonia solanacearum | 79 | species | bacteria | bacteria | 305 |
| adeno-associated virus - 2 | 79 | species | viruses | viruses | 10804 |
| acanthamoeba castellanii | 78 | species | invertebrates | protozoa | 5755 |
| trichinella spiralis | 78 | species | invertebrates | helminths | 6334 |
| acinetobacter calcoaceticus | 77 | species | bacteria | bacteria | 471 |