Proteomics

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Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.


ABSTRACT: Environmental meta-omics is rapidly expanding as sequencing capabilities improve, computing technologies become more accessible, and associated costs are reduced. The in situ snapshots of marine microbial life afforded by these data provide a growing knowledge of the functional roles of communities in ecosystem processes. Metaproteomics allows for the characterization of the dynamic proteome of a complex microbial community. It has the potential to reveal impacts of microbial metabolism on biogeochemical transport, storage and cycling (for example, Hawley et al., 2014), while additionally clarifying which taxonomic groups perform these roles. Previous work illuminated many of the important functions and interactions within marine microbial communities (for example, Morris et al., 2010), but a review of ocean metaproteomics literature revealed little standardization in bioinformatics pipelines for detecting peptides and inferring and annotating proteins. As prevalence of these data sets grows, there is a critical need to develop standardized approaches for mass spectrometry (MS) proteomic spectrum identification and annotation to maximize the scientific value of the data obtained. Here, we demonstrate that bioinformatics decisions made throughout the peptide identification process are as important for data interpretation as choices of sampling protocol and bacterial community manipulation experimental design. Our analysis offers a best practices guide for environmental metaproteomics.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Chelodina longicollis   Trichoderma reesei RUT C-30   Pongo abelii   Ursus americanus   Cleome angustifolia   Nicotiana bonariensis   Fasciola hepatica   environmental samples   Corynebacterium glutamicum K051   Thelohanellus kitauei   Pseudomonas sp.   Brassica napus   Cyanistes caeruleus   Pomacea canaliculata   Anneissia japonica   Bacillus thuringiensis   Bothrops asper   Bovine leukemia virus   Nostoc punctiforme PCC 73102   Equus asinus africanus   Myodes glareolus   Eubacterium limosum   Ralstonia solanacearum GMI1000   albimanus section   Solidesulfovibrio magneticus RS-1   unidentified chimeric sequence   Lathyrus sativus   prokaryotic environmental samples   Alligator sinensis   Prunus avium   Tuber melanosporum Mel28   Actinoplanes sp. SE50/110   Hepatitis B virus   artificial sequences   Agaricus bisporus   Microcystis aeruginosa NIES-843   Cryptococcus neoformans var. grubii H99W   Noccaea caerulescens   Macaca fascicularis fascicularis   Mylodon darwinii   Mycobacterium tuberculosis M24   Ganoderma lingzhi   Luteibacter   Oryza sativa Indica Group   Leishmania mexicana   Syntrophus aciditrophicus   Rhodococcus jostii RHA1   Eriocheir sinensis   Taraxacum sp.   Mammalia   Neosciurus carolinensis   Acetivibrio thermocellus   Roseibaca calidilacus   Strawberry leafy fruit phytoplasma   Chaetoceros sp.   Clostridioides difficile   Ecrobia maritima   Colon   Allexis   Sphingobium sp. AM   Arachis hypogaea   Daktulosphaira vitifoliae   Nitrospira marina Nb-295   Caryophyllales   Neisseria gonorrhoeae   Mollivirus sibericum   Francisella tularensis   Aquilaria sinensis   Lactobacillus crispatus   Pseudoalteromonas sp. D41   Pyrococcus abyssi   Populus tremula   Beta vulgaris   Clostridium autoethanogenum   Pectobacterium carotovorum   environmental samples   Mycobacterium tuberculosis SP13   Argulus foliaceus   Citrobacter freundii   Anisakis simplex complex   Ictidomys tridecemlineatus arenicola   Nitrososphaera viennensis   Phaeodactylum tricornutum   Zymomonas mobilis   Diaphorina citri   Riptortus pedestris   Phaseolus vulgaris   Mycoplasmopsis bovis HB0801   Schistosoma japonicum   unclassified Bacillarnavirus   Pichia fermentans   Rhizorhabdus wittichii   Roseburia   Dioscorea alata   Parhyale hawaiensis   Saccharomyces cerevisiae EC1118   Toxoplasma gondii type III   Neisseria meningitidis   Tilletia indica   Enhydra lutris nereis   Streptomyces sp. EF-93   Orthopoxvirus   Mytilus edulis   Candida dubliniensis CD36   Azospirillum brasilense FP2   Shigella flexneri 2a str. 2457T   Prevotella bryantii B14   Fraxinus nigra   sediment metagenome   Salmonella enterica subsp. enterica serovar Typhimurium str. SDT1291   Bradyrhizobium diazoefficiens USDA 110   Inquilinus limosus   Halorubrum lacusprofundi ATCC 49239   Staphylococcus pseudintermedius   Aspergillus brasiliensis   Wolbachia endosymbiont of Onchocerca volvulus str. Cameroon   Candida albicans SC5314   Burkholderia cenocepacia H111   Bos taurus   Novosphingobium nitrogenifigens   Phoenix dactylifera   Salmonella enterica subsp. enterica serovar Typhimurium str. ST1489   Human immunodeficiency virus   Trichomonas vaginalis   Deinococcus radiodurans ATCC 13939   Cryptococcus neoformans var. grubii VNI   Breviolum minutum   Serratia phage JS26   Amphimedon   Cryptococcus neoformans var. grubii H99   Taiwanofungus camphoratus   Garcinia mangostana   Zymoseptoria tritici IPO323   Streptococcus thermophilus LMD-9   Synechococcus sp. WH 7803   Pseudomonas sp. UK4   Pseudomonas ogarae   Oryctolagus cuniculus algirus   Orbicella faveolata   Quercus   Trichoderma sp. 1 YW-2011   Burkholderia thailandensis   Thermodesulfobium acidiphilum   Secale cereale x Triticum turgidum subsp. durum   Archaea   Anser cygnoides   Agkistrodon contortrix   Chaetodon lunulatus   Ruegeria pomeroyi   Santalum album   Campylobacter fetus subsp. fetus 82-40   Dokdonia sp. MED134   Acidipropionibacterium acidipropionici   uncultured marine microorganism   Saccharopolyspora erythraea   Tepidimicrobium xylanilyticum   Sparus aurata   Giardia intestinalis   Bombus terrestris audax   Drosophila simulans   Ruminiclostridium cellulolyticum H10   Solanum peruvianum   Citrullus lanatus   Nostoc sp. PCC 7120 = FACHB-418   Sphingobium chlorophenolicum   Marchantia polymorpha   Mycobacteroides abscessus ATCC 19977   Fraxinus mandshurica   Plasmodium berghei   Sepioloidea lineolata   Vibrio parahaemolyticus   Ustilago maydis virus P4   Trametes versicolor   Synechococcus phage syn9   Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10   Nicotiana paniculata   Gadus morhua   Sus scrofa   Meles meles   Lolium multiflorum   Globicatella sanguinis   Pinus nigra   Ecrobia ventrosa   Solanum lycopersicum x Solanum tuberosum   Apis mellifera pomonella   Bithynia siamensis goniomphalos   Mycoplasmopsis agalactiae   Bacillus subtilis   Bordetella pertussis Tohama I   Papio hamadryas   Synechocystis sp. PCC 6803   metagenomes   Bicyclus anynana   Lichtheimia corymbifera JMRC:FSU:9682   Salmonella enterica subsp. enterica serovar Typhimurium   Podospora anserina S mat+   Frankliniella sp. BIOUG14947-G11   Skeletonema dohrnii   Influenza A virus (A/Aichi/68/2007(H3N2))   Xylocopa violacea   Cupriavidus necator N-1   Populus trichocarpa   Mycobacterium marinum   Emiliania huxleyi   Staphylococcus aureus subsp. aureus USA300_FPR3757   Agaricus bisporus var. bisporus   Mrakia psychrophila   Streptomyces sp. MBT42   Streptococcus pneumoniae   Nepenthes ventricosa x Nepenthes alata   Corynebacterium diphtheriae NCTC 13129   Varroa destructor   Cajanus cajan   Tannerella forsythia 92A2   Culex pipiens pipiens   Musa acuminata subsp. acuminata   Meandrina meandrites   Mycobacterium tuberculosis   Helicobacter pylori H13-1   Euterpe oleracea   Desulforamulus reducens MI-1   Paenibacillus amylolyticus   Bacillus sp. 142311   Chlorocebus sabaeus   Daphnia pulex   Dorea longicatena DSM 13814   Onchocerca volvulus   Apis mellifera   Shigella sonnei 53G   Nicotiana maritima   Escherichia coli str. K-12 substr. W3110   Euphorbia characias   Methanothermococcus thermolithotrophicus DSM 2095   Montastraea cavernosa   Dendrobium sp. XMW-2002-13   Cedrela fissilis   Dichomitus squalens   Pseudomonas fluorescens   Plasmodium yoelii yoelii 17XNL   Trypanosoma cruzi strain Esmeraldo   Glycine max x Glycine soja   Brassica oleracea var. alboglabra   Mycoplasma pneumoniae   Acidiphilium cryptum JF-5   Mycoplasma pneumoniae M29   Geobacillus kaustophilus   Xanthomonas translucens   Bothrops alcatraz   Amphibalanus amphitrite   unidentified marine bacterioplankton   Cassiopea xamachana   Acromyrmex echinatior   Xanthomonas citri pv. glycines str. 8ra   Dentex dentex   Synechocystis sp. PCC 6803 substr. GT-S   Clavibacter michiganensis subsp. nebraskensis NCPPB 2581   Plutella xylostella   Listeria phage A118   Saccharomyces cf. cerevisiae   Verticillium dahliae JR2   Exidia glandulosa HHB12029   Solanum tuberosum   Haemaphysalis longicornis   (Vitis vinifera x Vitis berlandieri) x Vitis berlandieri   Aedes aegypti aegypti   Morganella   Dioscorea oppositifolia   Methermicoccus shengliensis DSM 18856   Paramecium tetraurelia   Sorangium cellulosum So ce56   Naja ashei   Brassica oleracea var. capitata   Spodoptera frugiperda   Acesta excavata   Ophrys sphegodes   Loxodonta africana   Bordetella bronchiseptica RB50   Nicotiana x sanderae   Mycobacterium tuberculosis H37Ra   Anopheles gambiae   Tetrahymena thermophila CU428   Lecanicillium fungicola var. fungicola   Panax ginseng   Camellia sinensis   Nothobranchius furzeri   Saccharum hybrid cultivar x Sorghum bicolor   Schistosoma mansoni   Schizosaccharomyces pombe DM3650   Influenza A virus (A/New Caledonia/20-JY2/1999(H1N1))   Sulfuritalea   Neisseria meningitidis FAM18   Acinetobacter baumannii 1656-2   Leptospira interrogans   Phormidium sp. OSCR   Steinernema carpocapsae   Oenococcus oeni   Pichia kudriavzevii   Mycobacterium tuberculosis SP22   Bivalvia   Nevskia ramosa   HIV-1 M:B_HXB2R   Nicotiana africana   Cyanobacterium stanieri   Cereibacter sphaeroides 2.4.1   Desulfovibrio sp. G11   Pseudomonas pseudoalcaligenes   Fusarium graminearum PH-1   Pseudoalteromonas flavipulchra NCIMB 2033 = ATCC BAA-314   Campylobacter concisus 13826   Staphylococcus lugdunensis N920143   Boehmeria nivea   Architeuthis dux   Helicobacter pylori 26695   Bos indicus   Ehrlichia ruminantium str. Gardel   'Phaseolus vulgaris' phytoplasma   Quercus suber   Vulpes lagopus   Biomphalaria glabrata   Chroococcidiopsis thermalis PCC 7203   Bacillus subtilis subsp. subtilis   Rhizobium leguminosarum bv. viciae 3841   Candida albicans 24C   Homo sapiens subsp. 'Denisova'   Lotus japonicus   Brucella abortus 2308   Listeria phage A500   Oryza sativa   Carica papaya   Helicobacter pylori 26695-1   Synechococcus sp. PCC 7002   Halomonas sp.   Human herpesvirus 5 strain Merlin   Streptococcus suis SC84   Deinococcus deserti VCD115   Botrytis cinerea B05.10   Mycobacterium tuberculosis KZN 1435   Ovis canadensis mexicana   Scheffersomyces stipitis   Streptomyces sp. MBT84   Hermarchus sp. HER2   Sorghum bicolor x Saccharum hybrid cultivar   Triaenophorus crassus   Bacillus cytotoxicus NVH 391-98   Spongospora subterranea   Leishmania infantum JPCM5   Pongo pygmaeus   Staphylococcus aureus subsp. aureus USA300   Candidatus Protochlamydia amoebophila UWE25   Taeniopygia guttata   Dialister   Toxoplasma gondii GT1   Paracoccus denitrificans PD1222   Ipomoea batatas   Pachysolen tannophilus   Secale cereale   Wolbachia endosymbiont of Diaphorina citri   Acinetobacter baumannii ATCC 17978   Rhodothermus marinus DSM 4252   Pachycladon exile   Hyalella azteca   Pogonomyrmex rugosus   Cicer arietinum   Phikzvirus phiKZ   Echinococcus granulosus   Tetraponera aethiops   Pogona vitticeps   Asterias rubens   Ursus arctos arctos   Oreochromis mossambicus   Pyrococcus furiosus   Aspergillus fumigatus   Taenia solium   Tetrahymena thermophila SB210   Yersinia pestis   Vertebrata   Daphnia magna   Onchocerca ochengi   Lactococcus lactis subsp. cremoris MG1363   Streptococcus pneumoniae TIGR4   Blastococcus saxobsidens   Acipenser baerii x Acipenser schrenckii   Aspergillus aculeatus ATCC 16872   Nicotiana alata   Mycobacterium avium subsp. paratuberculosis K-10   Desulforapulum autotrophicum HRM2   Pyrenochaeta sp.   Bordetella parapertussis   Bacteroides thetaiotaomicron VPI-5482   Plasmodium falciparum FcB1/Columbia   Viola tricolor   Laxus oneistus   Ustilaginoidea virens   Amphistegina lobifera   Roseobacter sp. MED193   Thermococcus gammatolerans EJ3   Sarcophilus harrisii   Acidovorax citrulli   Thermus thermophilus   Sophora alopecuroides   Mycoplasma gallisepticum   Botrytis cinerea T4   Litoricola marina   Cupriavidus metallidurans   Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2   fungal sp. 5OL6-6PL1   Bombyx mori   Staphylococcus sp. 1   Nicotiana longiflora   Legionella pneumophila   Cylindrospermopsis raciborskii CS-509   Geobacter sulfurreducens   synthetic construct   Clostridium tetani E88   Micrococcus luteus   Clostridium saccharoperbutylacetonicum   Yarrowia lipolytica   Leishmania chagasi   Selenomonas sputigena ATCC 35185   Capsicum annuum var. annuum   Olavius algarvensis Gamma 1 endosymbiont   Naja mossambica   Enterobacter cloacae   Tropilaelaps mercedesae   Pseudomonas fluorescens PF5   Calvadosia cruxmelitensis   Acidithiobacillus ferrooxidans ATCC 53993   Anacardium occidentale   Cyclopes didactylus   Spondylus gaederopus   Thalassiosira cf. oceanica   Streptomyces coelicolor   Lagomorpha   Granulicatella adiacens ATCC 49175   Bacillus weihenstephanensis   Malaclemys terrapin   Vibrio cholerae   Bemisia tabaci   unidentified   Bacillus subtilis subsp. subtilis str. 168   Allochromatium vinosum DSM 180   Colpophyllia natans   Myxococcus xanthus DZ2   Bacteroides fragilis 638R   Tequatrovirus T4   Malus domestica   Tamias striatus   Mycoplasma feriruminatoris   Euprymna scolopes   Blumeria graminis f. sp. tritici   Faecalibacterium prausnitzii   Rhodobacter capsulatus SB 1003   Francisella tularensis subsp. holarctica   Klebsiella aerogenes   Pseudo-nitzschia delicatissima   Equus sp.   Staphylococcus aureus subsp. aureus USA300_TCH1516   Paracoccidioides lutzii Pb01   Physcomitrella   Clostridium phage c-st   Caretta caretta x Chelonia mydas   Acanthamoeba polyphaga mimivirus   Plasmodium falciparum D10   Neisseria gonorrhoeae FA 1090   Paramoeba perurans   Salmo salar   Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ   Haloferax volcanii DS2   Clostridioides difficile 050-P50-2011   Eremothecium gossypii   Murine leukemia virus isolates   Pygoscelis adeliae   Giardia lamblia ATCC 50803   Plasmodium falciparum 58.1   Viola   Mycobacterium tuberculosis CAS   Cryptosporidium andersoni   Stigmatella aurantiaca DW4/3-1   Chromatiales bacterium OalgGamma1   Rhizobium leguminosarum bv. phaseoli CCGM1   Formosa sp. Hel3_A1_48   Dendroaspis angusticeps   Meyerozyma guilliermondii ATCC 6260   Peterozyma xylosa   Chitinophaga pinensis   Dolichospermum circinale AWQC131C   Populus tremula x Populus alba   Mus musculus   Pteropus rodricensis   Microcystis aeruginosa   Naja pallida   Odontotaenius disjunctus   Lonicera japonica   Borreliella burgdorferi B31   Francisella tularensis subsp. tularensis   Fusobacterium nucleatum subsp. nucleatum ATCC 25586   Cyanidioschyzon merolae   Nicotiana rustica   Volvariella volvacea V23   Methanothermobacter thermautotrophicus   Plasmodium knowlesi strain H   Saturnispora dispora   Sepiadarium austrinum   Deltaproteobacteria bacterium RIFCSPLOWO2_12_FULL_50_11   Burkholderia ubonensis MSMB22   Helianthus tuberosus   Salmonella enterica subsp. enterica serovar Typhimurium str. LT2   Lacticaseibacillus rhamnosus GG   Rickettsia conorii subsp. raoultii   Streptococcus agalactiae   Euzebya tangerina   Bacteroides caccae   Spinacia oleracea   Flavobacterium columnare   Mytilus edulis/galloprovincialis MCLGV-2007   Mycobacterium tuberculosis SP1   Mammuthus primigenius   Chloromonas nivalis   Sarcoptes scabiei   Salmonella enterica subsp. enterica serovar Cerro   Nitrospinae   Pseudomonas pseudoalcaligenes CECT 5344   Escherichia coli Nissle 1917   Pseudomonas stutzeri   Leishmania braziliensis   Ovis   Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150   Bacillus amyloliquefaciens   Escherichia coli str. K-12 substr. MG1655   Cryptochiton stelleri   Staphylococcus aureus   Nicotiana glutinosa   Chlorella sp. SAG 211-18   Cowpox virus (Brighton Red)   Clostridioides difficile ATCC 43255   Pinus radiata   Malassezia globosa   phytoplankton environmental sample   Ophrys garganica   Trichinella pseudospiralis   Labeo rohita   Rhizobium sp. Leaf68   Morchella importuna   Herbaspirillum seropedicae   West Nile virus   Coprococcus comes ATCC 27758   Aspergillus fumigatus Af293   Streptococcus uberis   Olavius algarvensis Delta 1 endosymbiont   Lipomyces starkeyi   Serendipita vermifera MAFF 305830   Loxosceles intermedia   Foeniculum vulgare   Schistocephalus solidus   Trypanosoma brucei brucei TREU927   Minona ileanae   Sinopodophyllum hexandrum   Conus striatus   Laodelphax striatellus   Toxoplasma gondii   Lolium perenne subsp. perenne   Anaerostipes caccae L1-92   Brochothrix thermosphacta   Coprothermobacter   Tuber indicum   Human alphaherpesvirus 1 strain KOS   Heloderma suspectum suspectum   Agkistrodon piscivorus   Lingulodinium polyedra   Mucilaginibacter   Oenothera elata   Leishmania tropica   Phytophthora capsici LT1534   Hendra virus horse/Australia/Hendra/1994   Naja naja   Glycine soja   Manduca sexta   Ambystoma mexicanum   Botrytis cinerea   Piscirickettsia salmonis AUSTRAL-005   Pachycladon enysii   Mustela sp.   Tapirus terrestris   Neurospora crassa   Martes martes   Vibrio vulnificus VV   Phytophthora capsici   Rheum palmatum   Lachancea kluyveri   Marthasterias glacialis   Malassezia sympodialis   Leishmania sp. MHOM/IN/80/DD8   Saccharum hybrid cultivar SP80-3280   marine plankton environmental sample   Synechocystis sp. PCC 6803 substr. PCC-P   Felis catus   Myotis ricketti   HIV-1 M:G_PT919   Naja mandalayensis   Enterococcus mundtii CRL35   Glossina morsitans   Brassica oleracea   Corucia zebrata   Catenibacterium   Ictidomys tridecemlineatus   Conus betulinus   Aeropyrum pernix K1   unclassified Candidatus Omnitrophica   Paracentrotus lividus   Pituophis melanoleucus   Corynebacterium diphtheriae   Yersinia pseudotuberculosis   Zoanthus sp.   Tetronarce californica   Solenopsis invicta   Pseudomonas jessenii   Rhodospirillum rubrum ATCC 11170   Deinococcus radiodurans   Mycobacterium tuberculosis variant bovis   Saccostrea glomerata   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu   Pasteurella multocida subsp. multocida str. Pm70   Ectocarpus siliculosus   Pedobacter sp.   Rhizobium leguminosarum bv. viciae Vc2   Saccharolobus solfataricus   Pseudomonas aeruginosa LESlike1   Musa acuminata AAA Group   Aiptasia   Sistrurus miliarius barbouri   Nicotiana tabacum   Roseobacter denitrificans OCh 114   Pyricularia oryzae B157   Aedes aegypti densovirus   marine metagenome   Peromyscus leucopus   Myxococcus xanthus DK 1622   H1N1 subtype   Buddenbrockia plumatellae   Tropheryma whipplei TW08/27   Dinoroseobacter shibae DFL 12 = DSM 16493   Aspergillus niger   Brevibacterium casei   Citrus maxima   Phytophthora pisi   Candidatus Profftella armatura   Brachylophosaurus canadensis   Moraxella catarrhalis   Paulownia fortunei   Serendipita vermifera 'subsp. bescii'   Mycobacterium avium subsp. paratuberculosis   Crustacea   Canis lupus familiaris   Human immunodeficiency virus 1   Actinomycetia   Sulfurihydrogenibium   Sturnus vulgaris   Galloanserae   Sphingomonas sp. Leaf257   Polytomella parva   Clostridioides difficile str. A-027   Synechocystis sp.   Mycoplasma pneumoniae M129-B7   Vibrio harveyi   Pinctada maxima   Equus caballus   Ambrosiozyma philentoma   Leishmania braziliensis MHOM/BR/75/M2904   Nilaparvata lugens   Xenopus laevis   Saccharomyces cerevisiae   Clostridium botulinum F str. Langeland   Phytophthora sojae   Chlamydomonas reinhardtii CC3269   Fusarium sp.   Hypsizygus marmoreus   Coelodonta antiquitatis   Leucoraja erinacea   Castor canadensis   Enterococcus faecium   Polyporus umbellatus GSX09   Lactiplantibacillus plantarum WCFS1   Acholeplasma laidlawii PG-8A   Haberlea rhodopensis   Alligator mississippiensis   Lactococcus phage   Chlorella sp. FC2 IITG   Leishmania tarentolae   Carnobacterium divergens   Rangifer tarandus   Hymenolepis microstoma   Legionella pneumophila str. Paris   Clostridioides difficile R20291   Rhynchocyon petersi   Hepatitis E virus type 1   Chlamydia trachomatis D/UW-3/CX   Persicaria minor   Cricetulus barabensis   Polaribacter marinivivus   Colinus virginianus   Bubalus bubalis   Acinetobacter baumannii AB307-0294   Carya cathayensis   Avicennia officinalis   Lachancea waltii NCYC 2644   Caulobacter vibrioides NA1000   Vibrio anguillarum   Porphyromonas gingivalis   Acanthoscurria geniculata   Cowpox virus   Tenebrio molitor   Cavia porcellus   Treponema   Sulfobacillus thermosulfidooxidans   Nicotiana repanda   Lutra lutra   Anaerococcus hydrogenalis DSM 7454   Nostoc sp.   Agrobacterium fabrum str. C58   Streptococcus mutans UA159   Ictalurus punctatus   Oenothera glazioviana   uncultured bacterium   Larimichthys crocea   Sulfolobus islandicus LAL14/1   Oryctolagus cuniculus cuniculus   Cylindrospermopsis raciborskii CS-506   Candida tropicalis   Mentha spicata   Qipengyuania flava   Legionella   Acetomicrobium mobile   Cytomegalovirus   Pisolithus tinctorius Marx 270   Arvicola   Bacillus mycoides DSM 2048   Cyprinus carpio   Acinetobacter baylyi ADP1   Clostridium cellulovorans 743B   Dictyostelium discoideum AX4   Thermococcus kodakarensis KOD1   Apis mellifera ligustica   [Candida] boidinii   Human immunodeficiency virus type 1 3916-CRO   Micrurus fulvius   Nephila clavipes   Populus cathayana   Craterostigma plantagineum   Callinectes sapidus   Bos grunniens   Paracoccidioides brasiliensis Pb18   Trypanosoma cruzi   Lens culinaris   Lobaria pulmonaria   Aspergillus terreus   Synechococcus sp.   Candidatus Glomeribacter   Alces alces   Olavius algarvensis spirochete endosymbiont   Aspergillus flavus partitivirus 1   Synechocystis sp. PCC 6803 substr. GT-I   Bothrops moojeni   Toxoplasma gondii RH   Quercus robur   Picea abies   Listeria monocytogenes EGD   [Ruminococcus] gnavus ATCC 29149   Staphylococcus aureus subsp. aureus MRSA252   Acinetobacter baumannii D1279779   Rhipicephalus sanguineus complex sp. ME-2011   Granulicella sp.   Clostridium butyricum E4 str. BoNT E BL5262   Haemophilus influenzae   Escherichia coli BL21(DE3)   Viridiplantae   Lactococcus lactis   Plasmodium berghei ANKA   Tubastraea coccinea   Cuon alpinus   Pseudomonas syringae pv. syringae   Bacillus pumilus   Methylorubrum extorquens DM4   Enchytraeus crypticus   Aspergillus niger ATCC 13496   Klebsiella pneumoniae 342   Aspergillus niger NRRL3   Staphylococcus aureus subsp. aureus COL   Capsicum annuum   Bradyrhizobium   Leptopilina   Lactococcus lactis subsp. lactis Il1403   Myzus persicae   Zalophus californianus   Entamoeba histolytica   Thermococcus eurythermalis   Salmonella enterica subsp. enterica serovar Enteritidis   Geobacillus stearothermophilus   Oryza barthii   Schizophyllum commune H4-8   Ebolavirus   Coprococcus eutactus   Bacillus thuringiensis Bt407   rhizosphere soil bacteria ensemble   Panicum virgatum   Fusarium graminearum   Aliivibrio fischeri   Xanthomonas retroflexus   Armoracia rusticana   Venturia inaequalis   Synechococcus phage S-SSM7   Calicophoron daubneyi   Stegodyphus mimosarum   Rattus norvegicus   Sinorhizobium meliloti   Latilactobacillus curvatus   Gardnerella vaginalis   Fomitopsis pinicola   Bemisia cf. tabaci Middle East-Asia Minor 1   Triticum aestivum   Valsa mali   Bothrops jararaca   [Ruminococcus] gnavus   Bacillus mycoides NBRC 101238 = DSM 11821   Thermoanaerobacter pseudethanolicus   Arachis hypogaea var. vulgaris   Amblyomma americanum   Chlorella vulgaris   Saccharomyces cerevisiae S288C   Streptomyces coelicolor A3(2)   Anopheles culicifacies B   Eimeria tenella   Trichoderma harzianum CBS 226.95   Corallium rubrum   Acyrthosiphon pisum   Megaloceros giganteus   Lithobius forficatus   Rhizobium cf. leguminosarum   Formosa sp. Hel1_33_131   Gyrodactylus kobayashii   Leptospirillum   Toxoplasma   Camponotus floridanus   Blattella germanica   Pomacea maculata   Phascolarctos cinereus   Piaractus mesopotamicus   Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044   Strongylocentrotus purpuratus   Rhizobium leguminosarum bv. viciae   Nakazawaea wickerhamii   Acinetobacter sp.   Nicotiana forgetiana   Danio rerio   Acaryochloris marina MBIC11017   Lentimonas   Pseudovibrio sp. FO-BEG1   Rapana venosa   Bacillus pseudomycoides DSM 12442   Rhodopseudomonas palustris CGA009   Enterococcus faecium DO   Cairina moschata   Macaca fascicularis   Staphylococcus lugdunensis   Conus geographus   Prochlorococcus marinus subsp. marinus str. CCMP1375   Streptococcus pyogenes   Komagataella phaffii   Zygaena filipendulae   Olavius algarvensis   Cancer irroratus   Mycobacterium tuberculosis K   Hippophae rhamnoides   Leishmania infantum   Drosophila pseudoobscura   Citeromyces matritensis   Gorilla gorilla gorilla   Macadamia   Aedes aegypti   Apostichopus japonicus   Mastigamoeba balamuthi ATTC 30984   Melopsittacus undulatus   Ixodes ricinus   Influenza A virus (A/California/07/2009(H1N1))   Bison   Vitis riparia   Micrurus tener   Cuniculiplasma divulgatum   Capreolus capreolus   Olavius algarvensis Delta 4 endosymbiont   Candidatus Paraburkholderia kirkii   Lingulodinium   Apteronotus leptorhynchus   Helicobacter hepaticus   Trypanosoma brucei brucei   Paenibacillus polymyxa ATCC 842   Eucalyptus spp. mixed library   Saccharomyces cerevisiae BY4741   Caprinae   Acidithiobacillus ferrooxidans   Plasmodium falciparum   soil metagenome   Nostoc sp. FB71   Pseudodiploria clivosa   Castor fiber   Cenchrus americanus   Bacillus cereus F837/76   Stappia stellulata DSM 5886   Thermothelomyces heterothallicus   Gossypium robinsonii   Clostridioides difficile 630   Cervus nippon nippon   Escherichia coli O26:H11   Lactiplantibacillus plantarum JDM1   Alteromonas macleodii ATCC 27126   Burkholderia cenocepacia J2315   bioreactor sludge metagenome   Spiroplasma melliferum   Corynebacterium glutamicum   mixed culture metagenome   Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456   Candidatus Methylomirabilis oxyfera   Salmonella enterica subsp. enterica serovar Typhimurium str. 5579   Dendroaspis polylepis polylepis   Azumapecten farreri   Toxoplasma gondii ME49   Cucumis sativus   wastewater metagenome   Aggregatibacter actinomycetemcomitans D7S-1   Crassostrea hongkongensis   Staphylococcus cohnii   Platichthys flesus   Mayaro virus (strain Brazil)   Nicotiana langsdorffii   Vibrio fluvialis   Nicotiana gossei   Cellulomonas gilvus ATCC 13127   Myxobilatus gasterostei   Echis carinatus   Heliocidaris erythrogramma   Thermochaetoides thermophila DSM 1495   Bacillus anthracis str. Sterne   Thermus thermophilus HB8   Tritrichomonas foetus   Burkholderia pseudomallei K96243   Stagonospora   Equidae   Vulpes vulpes   Lolium arundinaceum   Prorocentrum donghaiense   Xanthomonas campestris pv. vesicatoria str. 85-10   Leishmania major strain Friedlin   Theobroma cacao   Salmonella enterica subsp. enterica serovar Muenchen   Eukaryota   Pseudomonas composti   human gut metagenome   Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841   Prevotella intermedia ATCC 25611 = DSM 20706   Nitrospira moscoviensis   Human herpesvirus 4 type 1   Butyrivibrio proteoclasticus B316   Aspergillus giganteus   Pseudomonas aeruginosa PA14   Rickettsia slovaca 13-B   Cecropia peltata   Renibacterium salmoninarum ATCC 33209   Axis axis   Microbiota   Brucella   Aspergillus tubingensis   Pinus taeda   Listeria monocytogenes   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580   Panopea generosa   Naja annulifera   Dasypogon diadema   Melioribacter roseus P3M-2   Siphoviridae   Firmicutes   Peniophora incarnata   Manica rubida   Dickeya solani   Nosema ceranae   Rhizobium sp. CIAT652   Bartonella quintana JK 31   Saimiri boliviensis boliviensis   Vaccinia virus   Klebsiella pneumoniae   Scophthalmus maximus   Crotalus horridus   Passer domesticus domesticus   Vairimorpha necatrix   Staphylococcus aureus subsp. aureus str. Newman   Crunoecia irrorata   Rhizobium favelukesii   Schizosaccharomyces pombe OY26   Ornithodoros moubata   Thermoclostridium stercorarium   Dreissena polymorpha   Anopheles culicifacies A   Alcaligenes faecalis   Brucella abortus S19   Mycobacterium marinum ATCC BAA-535   Betainfluenzavirus   Camelus dromedarius   Clostridium cellulovorans   Escherichia coli O157:NM   Hippopotamus amphibius   Bothrops leucurus   Leishmania donovani   Panine betaherpesvirus 2   Vitis labrusca x Vitis riparia   Ralstonia pickettii   Limnobacter thiooxidans   Cladocopium goreaui   Candida parapsilosis CDC317   Aspergillus fumigatus var. fumigatus   Triticum turgidum subsp. durum   Coxiella burnetii   Lingula anatina   unclassified Marseilleviridae   Cellulophaga baltica NN016038   Medicago truncatula var. truncatula   HIV-1 vector pNL4-3   freshwater sediment metagenome   Candidatus Nitrospira inopinata   Syntrophomonas wolfei   Neospora caninum   Pteropus alecto   Scorpaena plumieri   Wolbachia pipientis wMelCS   Brucella abortus   Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940   Olea europaea   Syntrophobacter fumaroxidans MPOB   Lactobacillus johnsonii N6.2   Stylophora pistillata   Capra ibex   Pseudomonas aeruginosa PAK   Haemophilus haemolyticus   Spheniscus demersus   Cryptococcus neoformans var. grubii H99S   environmental samples   Penaeus vannamei   Boiga irregularis   Malassezia pachydermatis   Hydra vulgaris   Paucilactobacillus suebicus   Pachycladon novaezelandiae   Spiroplasma melliferum KC3   Avian infectious bronchitis virus (strain Beaudette CK)   Aspergillus versicolor   Myrmica rubra   Pseudomonas aeruginosa LESB58   Zea mays   SARS bat coronavirus   Tachaea chinensis   Legionella pneumophila subsp. pneumophila   Nosema apis   Vibrio alginolyticus   Human alphaherpesvirus 1   Brassica oleracea var. italica   Helicobacter pylori A45   Coxsackievirus B3   Anopheles stephensi   Mytilus galloprovincialis   Crotalus durissus terrificus   Synechococcus sp. BL107   Bothrops jararacussu   Thermochaetoides thermophila   Listeria monocytogenes serotype 4b   Salmonella enterica subsp. enterica serovar Typhi str. CT18   Stenotrophomonas rhizophila   Pseudomonas aeruginosa PAO1   Nannochloropsis oceanica strain IMET1   Human herpesvirus 2 strain 186   Ictalurid herpesvirus 1   Palaemonetes sp. common grass shrimp associated circular virus   Moorella thermoacetica ATCC 39073   Plasmodium vivax   Nannospalax galili   [Candida] glabrata CBS 138   Chlamydia trachomatis 434/Bu   Streptomyces sp. MC1   Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120200   Paenibacillus polymyxa   Nematostella vectensis   Candida parapsilosis   Leishmania donovani BPK282A1   Bacillus thuringiensis serovar berliner ATCC 10792   Methanobacterium   Sulfurospirillum multivorans DSM 12446   Ceratopteris richardii   Sorghum bicolor   Ciona intestinalis   Medicago truncatula   Eimeria acervulina   Serpentes sp. WLS21042014   Pseudomonas sp. 'Pseudom. M1'   Osphranter rufus   Haloferax volcanii   Mengo virus   soil bacterium TS1114R   Acanthochromis polyacanthus   Triatoma dimidiata   Gallus   Tuber aestivum   Eggerthella phage P3   Dictyostelium discoideum   Ctenopharyngodon idella   Malassezia furfur   Alteromonadales   Gallus gallus   Ursus maritimus   Sciuridae   Aspergillus carbonarius ITEM 5010   Bifidobacterium longum NCC2705   Naja oxiana   biofilm metagenome   Mus musculus wagneri   Klebsiella pneumoniae BIDMC 40   Sedum plumbizincicola   Halomonas sp. TD01   Pachycladon fastigiatum   Mycobacterium tuberculosis SP7   Roseburia inulinivorans DSM 16841   Bombus terrestris   Tortispora caseinolytica   Pseudomonas aeruginosa   Influenza A virus (H1N1)   Schizosaccharomyces pombe   Neoporphyra haitanensis   Octopus vulgaris   Phaeocystis antarctica   Dehalococcoides mccartyi   Alternaria tomato   Aspergillus niger CBS 513.88   Glycine max   Cutibacterium acnes SK137   Hippoglossus hippoglossus   Andrias davidianus   Phytophthora infestans T30-4   Aeropyrum pernix   Trichomonas gallinae   Burkholderia sp. Bk   Physcomitrium patens   Caballeronia mineralivorans   Nelumbo nucifera subsp. nucifera   Bartonella quintana   Ficus carica   Nicotiana clevelandii   Crithidia fasciculata   Brucella abortus 104M   other sequences   Ursus arctos   Babjeviella inositovora   Streptomyces venezuelae   Neospora caninum Liverpool   Candidatus Thioglobus autotrophicus   Human papillomavirus type 16   Trypanosoma   Streptococcus mutans 19   Rathayibacter toxicus   Trichomonas vaginalis G3   Mariprofundus ferrooxydans   Pseudomonas aeruginosa str. E2UoS   Klebsiella variicola At-22   Trichodesmium erythraeum IMS101   Sporocytophaga myxococcoides   Acipenser   Influenza A virus   mixed sample   Schistosoma haematobium   Venturia pyrina   Plasmodium sp. pBT9   Rhizoctonia solani AG-8 WAC10335   Hebomoia glaucippe   Lactiplantibacillus plantarum subsp. plantarum   Piper nigrum   Afipia carboxidovorans   Bacillus amyloliquefaciens DSM 7 = ATCC 23350   Mycobacterium tuberculosis H37Rv_2009   soil bacterium 10G-05   Cellulophaga baltica 18   Simulium damnosum s.l. Me1   Synechococcus elongatus   Myzus persicae persicae   Candidatus Thiosymbion oneisti   Vibrio cholerae O1 str. VC91   Equisetum arvense   Trypanosoma cruzi strain CL Brener   Legionella pneumophila subsp. pneumophila str. Philadelphia 1   Desulfofundulus kuznetsovii DSM 6115   Scylla paramamosain   Willaertia magna   Amphora coffeiformis   Dictyostelia   Thermosynechococcus vestitus BP-1   Methanothrix   Acinetobacter calcoaceticus/baumannii complex   Onchocerca lupi   Xanthomonas campestris   Campylobacter jejuni   Nicotiana noctiflora   Selaginella moellendorffii   Pseudomonas putida KT2440   Cervus elaphus   Paenibacillus sp.   Papaver somniferum   Arabidopsis   Nerodia clarkii   Vitis riparia x Vitis rupestris   Clostridium perfringens   Vitis vinifera   Muvirus mu   Anguilla anguilla   Geodermatophilus obscurus DSM 43160   Tetranychus urticae   Liberibacter endosymbiont of Diaphorina citri   Wolbachia sp. wMelPop   Thalassiosira oceanica CCMP1005   Gammarus pulex   Trichoplax sp. H2   Meleagris gallopavo   Bacillus cereus ATCC 10987   Porphyromonas gingivalis W83   Coffea canephora   Aspergillus flavus FRR 342   Mahonia   Ovis aries musimon   Equus hydruntinus   Pseudomonas aeruginosa PAO1H2O   Aspergillus flavus   Cyprinodon variegatus   Python bivittatus   Sitobion avenae   Caenorhabditis elegans   Acinetobacter baumannii   Herpes simplex virus unknown type   Mycobacterium tuberculosis variant bovis AN5   Cytophaga hutchinsonii   Microplitis mediator   Colobus guereza   Leishmania donovani Ld 2001   Coprothermobacter proteolyticus   Mycolicibacterium smegmatis   Pseudodiploria strigosa   Eucalyptus   Syntrophus aciditrophicus SB   Streptococcus equi subsp. equi   Pyrus x bretschneideri   Camelidae   Toxoplasma gondii GAB3-2007-GAL-DOM9   Escherichia coli   Myrmica ruginodis   Ferroplasma   Amblyrhynchus cristatus   Campylobacter concisus UNSWCD   Chlorocebus aethiops aethiops   Prochlorococcus marinus str. MIT 9312   Telmatactis   Kluyveromyces marxianus   Natronomonas pharaonis DSM 2160   Corynebacterium glutamicum ATCC 13032   Exiguobacterium sp. SH31   Galleria mellonella   Rousettus aegyptiacus   Magnetospirillum gryphiswaldense   Eryx colubrinus loveridgei   Nicotiana quadrivalvis   Fusarium graminearum GZ3639   Klebsiella pneumoniae UHKPC27   Streptococcus pyogenes M1 GAS   Streptococcus suis   Panthera leo   Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821   Akkermansia muciniphila ATCC BAA-835   Fagus grandifolia   Pseudomonas syringae   Pseudomonas phage EL   Neisseria meningitidis MC58   Populus yunnanensis   Nepenthes rafflesiana   Salmonella enterica subsp. enterica serovar Newport   Bacillus velezensis   Palaemon carinicauda   mouse gut metagenome   Ogataea polymorpha   Butyrivibrio fibrisolvens   Leishmania mexicana MHOM/GT/2001/U1103   Datura stramonium   Bothrops insularis   Pachycladon cheesemanii   Fusarium cf. oxysporum   Dichocoenia stokesii   Candidatus Margulisbacteria   Angiostrongylus cantonensis   Propionibacterium freudenreichii   Thymallus thymallus   Cucurbita maxima   Heterosigma akashiwo   Entamoeba histolytica HM-1:IMSS-A   Mycoplasma suis KI3806   Mus musculus x Rattus norvegicus   Orbicella annularis   Pseudomonas putida BIRD-1   Staphylococcus aureus subsp. aureus NN50   Candida tropicalis MYA-3404   Sulfolobus islandicus REY15A   Aspergillus terreus NIH2624   Acanthaster planci   Escherichia coli K-12   Bacillus cereus ATCC 14579   Dinosauria   Marchantia polymorpha subsp. ruderalis   Mucidula mucida   Heligmosomoides polygyrus bakeri   Thermothelomyces thermophilus ATCC 42464   Klebsiella pneumoniae LCT-KP289   Burkholderia dolosa AU0158   Erysipelothrix rhusiopathiae   Human coronavirus NL63   Rhizopus delemar   Candidatus Accumulibacter   Streptococcus equi subsp. equi 4047   Dengue virus   Gammarus fossarum   Aedes albopictus   Gnathostoma spinigerum   Ostreococcus tauri   Nanger dama mhorr   Pyricularia oryzae   Tetropium castaneum   Pseudomonas putida   Bacillus licheniformis   Arion vulgaris   Hydrolagus colliei   Mus musculus musculus x Mus musculus castaneus   Oscillatoriaceae cyanobacterium   Staphylococcus sp. KDM4   Bactrocera dorsalis   Plasmodium falciparum 3D7   Acanthamoeba polyphaga   Paenibacillus pabuli   Mycobacterium tuberculosis SP10   Dryopteris affinis subsp. affinis   Candidatus Pelagibacter ubique   Shewanella oneidensis MR-1   Camponotus fellah   Vipera berus berus   Vaccinia virus WR   environmental samples   Sinorhizobium meliloti BL225C   Merluccius bilinearis   Tremarctos ornatus   Synechococcus sp. YX04-3   Amycolatopsis   Bodo saltans   Pan troglodytes   Sepia officinalis   Komagataella pastoris DSMZ 70382   Candidatus Kuenenia stuttgartiensis   Giardia sp.   Severe acute respiratory syndrome coronavirus 2   Nepenthes ampullaria   Orycteropus afer   Capsaspora owczarzaki   Prochlorococcus marinus subsp. pastoris str. CCMP1986   Leuconostoc gelidum subsp. gasicomitatum   Fusarium oxysporum f. sp. lycopersici   Klebsiella pneumoniae JH1   Momordica cochinchinensis   Python molurus   Sistrurus catenatus   Saccharum hybrid cultivar   Saccharomyces cerevisiae W303   environmental samples   Durusdinium trenchii   Plasmodium yoelii yoelii   Faustovirus   Paulownia   cf. Chlorella sp.   Microbacterium sp.   Mus   Buchnera aphidicola (Acyrthosiphon pisum)   Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759   Methylorubrum extorquens PA1   Listeria monocytogenes EGD-e   Mammut americanum   Komagataeibacter europaeus   Aspergillus fumigatus CEA10   Tribolium castaneum   Fusarium fujikuroi IMI 58289   Crocosphaera subtropica ATCC 51142   Filifactor alocis   Halomonas sp. HL-48   Bradyrhizobium diazoefficiens   Colobanthus quitensis   Serratia inhibens PRI-2C   Ornithodoros erraticus   Panagrolaimus   Trypanosoma cruzi Dm28c   Linnemannia elongata AG-77   Stylosanthes guianensis   Haemonchus contortus   Plasmodium vivax Sal-1   Capra pyrenaica   Catalpa fargesii   Mycoplasma hominis ATCC 23114   Liquorilactobacillus nagelii   Mycobacterium tuberculosis C StG4006   Fibrobacter succinogenes subsp. succinogenes S85   Ophiophagus hannah   Oryza sativa Japonica Group   Scolopendra morsitans   Tuber albidum   Vibrio cholerae O1 biovar El Tor str. N16961   Millerozyma acaciae   Macaca mulatta   Kalanchoe fedtschenkoi   Gasterosteus aculeatus   Clostridium butyricum DSM 10702   Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130   Bacteria   Clavispora lusitaniae ATCC 42720   Saccharomycopsis capsularis   Tyrannosaurus rex   Salmonella bongori   Paracatenula sp. 'standrea' Elba   Conus zonatus   Tradescantia spathacea   Malassezia sympodialis ATCC 42132   Mammuthus sp.   Desmodesmus subspicatus   Toxoplasma gondii PRU   Saccharina japonica   Petunia   Rattus rattus   Halobacterium   Beauveria bassiana ARSEF 2860   Listeria monocytogenes serotype 4b str. F2365   Mycolicibacterium smegmatis MC2 155   Staphylococcus epidermidis   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344   Bothrops cotiara   Influenza A virus (A/WSN/1933(H1N1))   Hyphomicrobium sp. MC8b   Klebsiella pneumoniae ATCC 43816   Paracoccus denitrificans   Mytilus sp. CHGF4   Panthera tigris   Mycobacterium tuberculosis variant bovis str. Ravenel   rat gut metagenome   Bacillus cereus   Anopheles gambiae str. PEST   [Candida] auris   Arcobacter   Opsanus beta   Perkinsus marinus   Schmidtea mediterranea   microbial mat metagenome   Stichodactyla haddoni   Fragaria x ananassa   Breviatea   Mycobacteroides abscessus   Oryza longistaminata   Halobacterium salinarum R1   Solanum lycopersicum   Coronavirus PREDICT CoV-2   Dimocarpus longan   Magnaporthe sp. MG05   Influenza A virus (A/Viet Nam/1203/2004(H5N1))   Laurasiatheria   Coffea eugenioides   uncultured soil microorganism   Francisella tularensis subsp. holarctica FSC200   Vitis   Carnobacterium maltaromaticum   Coccinia grandis   Oomycota   Escherichia phage vB_EcoP_SU10   Knufia petricola   Ferrimicrobium acidiphilum DSM 19497   Xenopsylla cheopis   Coprococcus sp. ART55/1   Channa striata   Photinus pyralis   Toxoplasma gondii CtCo5   Viruses   Cyclotella cryptica   Serratia plymuthica   Dirofilaria immitis   Aspergillus oryzae var. oryzae   Klebsiella variicola   Enterococcus faecalis   Lactuca sativa   Brassica carinata   Microbacterium oxydans   Bothrops atrox   Brassica oleracea var. botrytis   Cricetulus griseus   Coffea arabica   Conus caracteristicus   Emiliania   uncultured microorganism   Pseudomonas putida F1   Penicilliopsis zonata   Equus asinus   Ursus deningeri   Plasmodium falciparum Dd2   Tospovirus kiwifruit/YXW/2014   Bacteria incertae sedis   Entamoeba histolytica HM-1:IMSS   Tilletia controversa   Algoriphagus marincola HL-49   Leishmania major   Didelphis aurita   Chlamydia trachomatis L2/434/Bu(i)   Flavivirus   Oreochromis niloticus niloticus   Nephotettix cincticeps   Histomonas meleagridis   Euglena gracilis   Arabidopsis thaliana   Strigomonas culicis   Aspergillus sydowii   Chenopodium quinoa   Musa ABB Group   Picea likiangensis var. rubescens   Shigella dysenteriae   Aspergillus   Mycobacterium tuberculosis TKK-01-0032   Gynandropsis gynandra   Gorilla   Dunaliella salina   Pseudomonas taiwanensis   Mycobacterium avium 100   Bungarus   Naegleria fowleri   Hevea brasiliensis   Brachyspiraceae   Tursiops truncatus   Thermoplasma acidophilum DSM 1728   Brassica rapa   Rosa chinensis   Penicillium sp. B12   Bacillus thuringiensis serovar kurstaki str. HD73   Pythium sp. PV So7   Clostridium botulinum A str. Hall   Nicotiana benavidesii   Limosilactobacillus mucosae LM1   Notamacropus eugenii   Cervus elaphus elaphus   Norovirus   Photobacterium profundum SS9   Planctopirus limnophila DSM 3776   Lilium   environmental samples   Artemisia annua   Rhinocerotidae   [Candida] glabrata   Modestobacter marinus BC501   Lineus longissimus   Acinetobacter baumannii ACICU   Deinococcus radiodurans R1   Escherichia phage T7   Fusarium oxysporum f. sp. cucumerinum   Teleogryllus oceanicus   Prototheca zopfii   Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088   Takifugu fasciatus   Corynebacterium diphtheriae bv. mitis str. ISS 3319   Afrohybanthus enneaspermus   Saccharomyces mikatae IFO 1815   Pongo sp.   Aspergillus aff. niger A2   Clavibacter michiganensis subsp. michiganensis NCPPB 382   Methanoculleus sp. 10   Rupicapra rupicapra   Haemophilus influenzae Rd KW20   Mycobacterium tuberculosis LAM7   Pogostemon cablin   Methanosarcina mazei Go1   Paraconiothyrium   Angiostrongylus vasorum   Soa   Klebsiella pneumoniae ATCC BAA-2146   Mycoplasma pneumoniae 19294   Brugia malayi   Trichinella britovi   Corynebacterium ulcerans bv. belfanti   Candidatus Midichloriaceae   Ensifer adhaerens   Japanese encephalitis virus   Leishmania guyanensis species complex   Oryctolagus cuniculus   Bacillus cereus AH187   Cucumber mosaic virus   Candidatus Riegeria   Helicobacter pylori J99   Staphylococcus aureus subsp. aureus   Plum pox virus   Cryptosporidium parvum   Harmonia axyridis   Spirometra erinaceieuropaei   Nymphicus hollandicus   Saiga tatarica   uncultured Phormidium sp.   Betacoronavirus sp.   Alicycliphilus denitrificans BC   Trypanosoma vivax Y486   Metopolophium dirhodum   Betaproteobacteria bacterium RIFCSPLOWO2_02_64_14   Agrostis stolonifera   Petunia x hybrida   Nicotiana plumbaginifolia   Geobacter sulfurreducens PCA   Sulfolobus acidocaldarius   gut metagenome   Cellvibrio japonicus Ueda107   Citrus wilsonii   Ophrys x arachnitiformis subsp. archipelagi   Mycoplasma gallisepticum S6   Crocuta   Xanthomonas campestris pv. campestris str. B100   Francisella tularensis subsp. novicida U112   Desulfoluna spongiiphila   Bordetella pertussis   Listeria monocytogenes HCC23   Amblyomma sculptum   Bartonella henselae str. Houston-1   Kluyveromyces lactis NRRL Y-1140   Vicia faba   Diplonema papillatum   Agrobacterium tumefaciens   Beauveria bassiana CGMCC 7.34   Ciona robusta   Candidatus Endoriftia persephone   Hordeum vulgare   Vitis hybrid cultivar   Coxiella-like endosymbiont of Rhipicephalus sanguineus complex   Acanthoscurria rondoniae   Human herpesvirus 5 strain AD169   Actinomycetospora chiangmaiensis DSM 45062   Stenotrophomonas maltophilia   Methanospirillum hungatei JF-1   Influenza A virus (A/California/07-00002/2009(H1N1))   Sinorhizobium americanum CCGM7   Klebsiella pneumoniae MGH 78578   Geobacillus kaustophilus HTA426   Epichloe festucae E2368   Anas platyrhynchos   Pseudoliparis swirei   Castor   Leuconostoc gelidum subsp. gelidum   Erythrobacter sp. HL-111   Phaeodactylum tricornutum CCAP 1055/1   Ianthella basta   Rhodopseudomonas palustris   Stephanorhinus   Pachysolen tannophilus NRRL Y-2460   Mycoplasma hyopneumoniae 232   Dehalococcoides mccartyi CG1   Chlorocebus aethiops   Cupiennius salei   Escherichia coli O157:H7 str. EDL933   Elymus sibiricus   Synechocystis sp. PCC 6803 substr. Kazusa   Eucalyptus globulus   Candida dubliniensis   Roseburia hominis A2-183   Chlamydia trachomatis L2/434/Bu(f)   Antidorcas marsupialis   Homo sapiens   Macaca nemestrina   Microcystis aeruginosa PCC 7806   Musa AAB Group   Mycobacterium tuberculosis variant bovis BCG   Ovis aries   Tuber magnatum   Clematis chinensis   Nicotiana benthamiana   Aeromonas sp. enrichment culture clone AM2   Brucella anthropi ATCC 49188   Komagataella pastoris   Helicobacter pylori E48   Escherichia coli HT115   Bifidobacterium kashiwanohense PV20-2   Trifolium pratense subsp. pratense   Staphylococcus aureus subsp. aureus NCTC 8325   Yersinia ruckeri   Riftia pachyptila   Modiolus kurilensis   Teseptimavirus T7   Olavius algarvensis Gamma 3 endosymbiont   Giardia intestinalis assemblage A   Ixodes scapularis   Rhodotorula toruloides   Ricinus communis   Halobacterium salinarum   Latrodectus hesperus   Acinetobacter sp. PM-14   Litoditis marina   Streptococcus agalactiae FSL S3-026   Philodryas patagoniensis   Sordaria macrospora   Cyberlindnera jadinii   Ailuropoda melanoleuca   Myotis lucifugus   Schizosaccharomyces pombe 927   Shigella sonnei   Planococcus halocryophilus Or1   Podospora   Passer hispaniolensis   Moringa oleifera   Elizabethkingia anophelis   Dendrobium huoshanense   Cynodon dactylon   Anisakis simplex   Acanthoscurria gomesiana   Aspergillus flavus NRRL3357   Lactobacillus   Andreprevotia sp. IGB-42   Lactobacillus johnsonii   Hadronyche infensa   Helicoverpa armigera armigera   Botryococcus braunii   Acinetobacter baumannii AB5075   Jatropha curcas   Gammarus roeselii   Francisella tularensis subsp. holarctica LVS   Limosilactobacillus fermentum CECT 5716   Saccharomyces cerevisiae YJM789   Human coronavirus HKU1   Bradyrhizobium japonicum   Salmonella enterica subsp. enterica serovar Typhimurium str. A130   Chlamydia trachomatis   Bacillus altitudinis   Acheta domesticus   Streptomyces avidinii   Leptospermum scoparium   Taenia hydatigena   Kryptolebias marmoratus   Moneuplotes crassus   Trichechus manatus   Salmonella enterica subsp. enterica serovar Enteritidis str. P125109   Quercus petraea   Salmo sp.   Tupavirus   Pinus pinaster   Medicago sativa   Anastrepha ludens   Cricetidae   Frankia alni   Lactococcus lactis subsp. cremoris UC509.9   Acipenser transmontanus   Liquorilactobacillus hordei   Delftia acidovorans SPH-1   Murine hepatitis virus strain A59   Neomegalonema perideroedes   Crassostrea gigas   Colwellia psychrerythraea 34H   Streptomyces lincolnensis   Cyanophora paradoxa   Lactobacillus iners   glacier metagenome   Nelumbo nucifera   Amaranthus tricolor   Brucella melitensis   Flavobacterium sp. 316   Streptococcus dysgalactiae subsp. equisimilis SK1249   Daboia russelii   Methanosarcina acetivorans   Human herpesvirus 4 strain B95-8   Human betaherpesvirus 5   Burkholderia cenocepacia K56-2Valvano   Ascoidea rubescens   Elaeis guineensis   Puccinellia tenuiflora   Avena sativa   Strigamia maritima   Citrus hybrid cultivar   Schizosaccharomyces pombe 972h-   Tomato yellow leaf curl virus   Crocuta crocuta   Delonix regia   Trichodesmium   Streptococcus pyogenes MGAS5005   Fusarium oxysporum f. sp. conglutinans Fo5176   Eulimnogammarus cyaneus   Myxobolus honghuensis   Veillonella parvula DSM 2008   Cloning vector pEGFP-C1   Staphylococcus xylosus   Helianthus annuus   Craterostigmus tasmanianus   Yersinia pestis KIM D27   Candidatus Carsonella ruddii DC   Prevotella ruminicola 23   Gorilla gorilla   Anoplocephala perfoliata   Sordaria macrospora k-hell   Oncorhynchus tshawytscha   Spironucleus salmonicida   Methanohalophilus   Thalassiosira pseudonana   Sulfolobus islandicus   Nicotiana glauca   Drosophila mauritiana   Yersinia enterocolitica   Hepatitis C virus genotype 1   Yersinia pestis CO92   Blumeria hordei DH14   Chinchilla lanigera   Gigantopelta aegis   Beta vulgaris subsp. vulgaris   Beauveria bassiana   Thalassiosira pseudonana CCMP1335   Canis lupus x Canis lupus familiaris   Populus tomentosa   Chara australis   Pseudomonas aeruginosa UCBPP-PA14   Dolichospermum circinale AWQC310F   Francisella orientalis FNO12   Prochlorococcus marinus str. MIT 9313   Megoura viciae   Aggregatibacter actinomycetemcomitans   Synechococcus elongatus PCC 7942 = FACHB-805   Homo   Nepenthes x hookeriana   Shewanella baltica   Pseudotsuga menziesii var. menziesii   Gossypium   Epstein-barr virus strain p3hr-1   Trichoderma reesei QM6a   Pandanus amaryllifolius   Fungi   Heterorhabditis megidis   Porphyromonas gingivalis ATCC 33277   Dickeya dadantii subsp. dadantii   Burkholderia pseudomallei 1026b   Cancer   Ascaris suum   Thermococcus gammatolerans   Influenza A virus (A/Wilson-Smith/1933(H1N1))   Brachionus plicatilis   Tarenaya hassleriana   Diplazium maximum   Frankia coriariae   Cervus nippon hortulorum   Acanthamoeba castellanii mimivirus   Capra hircus   Streptococcus pyogenes ABC020006030   Aspergillus nidulans   Diploria labyrinthiformis   Rosaceae   Ruminiclostridium papyrosolvens DSM 2782   Ecrobia   Desulfovibrio ferrophilus   Staphylococcus haemolyticus   Aspergillus nidulans TN02A3   Bothrops brazili   Aves   Austrolebias   Alphainfluenzavirus   Influenza B virus (B/Memphis/13/2003)   Aplysia californica   Tetrahymena thermophila   Broussonetia papyrifera   Rhipicephalus microplus   Morganella   Candidatus Brocadia sapporoensis   Amycolatopsis mediterranei S699   Ceuthophilus sp. Ceu_104_TX_San_Rattlesnake   Metarhizium robertsii   Mustela putorius furo   Mycobacterium tuberculosis str. Beijing/W BT1   Tremella   Bienertia sinuspersici   Gulo gulo   Chryseobacterium indologenes   Trichoderma reesei QM9414   Tilletia caries   Sanghuangporus   anaerobic digester metagenome   Kuraishia capsulata   Quercus ilex   Burkholderia cenocepacia   Bacteroides sp. 1_1_11   Mycobacterium tuberculosis H37Rv   Brassica oleracea var. gemmifera   Opisthorchis viverrini   Desmodus rotundus   Xanthomonas oryzae pv. oryzae PXO99A   Potentilla saundersiana   Streptococcus pneumoniae R6   environmental samples   Lentinula edodes   Escherichia coli O157:H7 str. TW14359   Tetratrichomonas gallinarum   Aerococcus urinae NBRC 15544 = CCUG 36881   Madurella mycetomatis   Amblyomma cajennense   Acinetobacter nosocomialis   Acanthamoeba castellanii str. Neff   Daphnia   Arbacia punctulata   Acanthamoeba castellanii   Plasmodium falciparum 365.1   Pisum sativum   Citrus sinensis   Viola odorata   Phlebotomus papatasi   Burkholderia sp. 2332   Dugesia japonica   Populus tremula x Populus tremuloides   Physalis angulata   Nicotiana sylvestris   Bacillus toyonensis BCT-7112   Fusarium oxysporum f. sp. lycopersici 4287   Aspergillus wentii   Haptophyta   Brachypodium distachyon   Rhizophagus irregularis   Strongyloides venezuelensis   Lentibacter algarum   Human alphaherpesvirus 1 strain 17   Frankia alni ACN14a   Dactylorhiza   Crotalus adamanteus   Neptuniibacter caesariensis   Gossypium hirsutum   Aeromonas salmonicida subsp. salmonicida   Mycobacterium tuberculosis H37RvAE   Pseudomonas sp. Lz4W   Blautia producta ATCC 27340 = DSM 2950   Glia   Lentilactobacillus kefiri   Tepidanaerobacter acetatoxydans   Plasmodium yoelii   Thalassiosira oceanica   Polypodium hydriforme   Lynx lynx   Pseudomonas fluorescens SBW25   Parasteatoda tepidariorum   Octopodiformes   Echinococcus ortleppi   Haliotis discus hannai   Cupriavidus pinatubonensis JMP134   Homo sapiens/Mus musculus xenograft   Doryteuthis pealeii   Paradendryphiella salina   Tilletia laevis   Strix varia   uncultured Desulfobacterium sp.   Russula atropurpurea   Rickettsia conorii str. Malish 7   Lentinus crinitus   Parasynechococcus marenigrum WH 8102   human metagenome   Saccharum officinarum   Candidatus Accumulibacter phosphatis   Streptococcus pyogenes STAB901   Oryzias latipes   Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499   Periplaneta americana   Lagenaria siceraria   Neisseria meningitidis serogroup B   Rahnella aquatilis   Rickettsia massiliae MTU5   Rickettsia rickettsii   Synechococcus cyanophage syn   Pleuromamma xiphias   Aepyceros melampus   Meyerozyma guilliermondii   Nostoc flagelliforme   Naja nigricincta nigricincta   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S   Chlorobaculum tepidum   Serpentes   Pristhesancus sp. 00004635   Lymnaea stagnalis   Triatoma sordida   Clostridia   Avena strigosa   Myxobolus wulii   Faecalibacterium prausnitzii SL3/3   Musa   Oryctolagus sp. 'Rabbit_OD'   Vigna mungo   Lasius niger   Dehalobacter restrictus   Priestia megaterium DSM 319   Rickettsia akari   Shigella flexneri   Rupicapra pyrenaica   Ustilago maydis   Vespula vulgaris   Tomato spotted wilt orthotospovirus   Methylocystis sp. SC2   Oleidesulfovibrio alaskensis G20   Sus scrofa domesticus   Olavius algarvensis sulfate-reducing endosymbiont   Sinorhizobium americanum   Tetrastichus   uncultured Clostridium sp.   Fusarium oxysporum Fo47   unclassified Bacteria   Bursaphelenchus xylophilus   Escherichia coli O157:H7   Naja sagittifera   Struthio camelus   Trypanosoma brucei   Wheat dwarf virus - [Taiyuan]   Helicoverpa armigera   Hypsiglena jani   Saccharum sp.   Manihot esculenta   Heterocephalus glaber   Oryza australiensis   Lysiphlebus fabarum   Penicillium verrucosum   Caldanaerobacter subterraneus subsp. tengcongensis MB4   Actinidia chinensis var. chinensis   Streptomyces lividans TK24   Dehalococcoides mccartyi CBDB1   Bothrops neuwiedi   Levilactobacillus brevis   Cupriavidus basilensis   Streptococcus thermophilus   Roseburia intestinalis L1-82   Hominidae   Entamoeba histolytica HM-1:IMSS-B   Triticum monococcum subsp. monococcum   Oncorhynchus mykiss   Viola tricolor subsp. tricolor   Brenneria nigrifluens   Scutigera coleoptrata   Pseudotsuga menziesii   Trypanosoma cruzi cruzi   Streptomyces sp.   Candida albicans   Murine leukemia virus   Dionaea muscipula   Coxiella burnetii RSA 493   Drosophila melanogaster   Erysipelatoclostridium ramosum DSM 1402   Juglans regia   Rhodnius prolixus   Chlamydomonas reinhardtii   Acinetobacter baumannii AB_TG2631   Sterolibacterium denitrificans   Lacticaseibacillus rhamnosus   Nitrospirillum amazonense CBAmc   Orthomyxoviridae   Streptomyces griseorubens   Passiflora edulis   hybrid   Mesocricetus auratus   Phaeobacter sp. MED193   Bifidobacterium pseudolongum   Spirochaeta sp. ELBA   Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819   Pyricularia oryzae P131   unclassified Thermococcus   Drosophila   Marseillevirus   Cercopithecidae   Phytophthora infestans   Streptococcus pneumoniae SP14-BS69   Mycoplasma pneumoniae M129   Streptococcus pneumoniae D39   Proteus mirabilis HI4320   Bacillariophyta   Citrobacter rodentium   Staphylococcus saprophyticus   Tannerella forsythia   Aspergillus nidulans FGSC A4  

SUBMITTER: Brook Nunn  

LAB HEAD: Brook L. Nunn

PROVIDER: PXD006688 | Pride | 2019-01-25

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
2014_Sept_08_BeringSea08.pep.xml Pepxml
2014_Sept_08_BeringSea08.raw Raw
Items per page:
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Publications

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Timmins-Schiffman Emma E   May Damon H DH   Mikan Molly M   Riffle Michael M   Frazar Chris C   Harvey H R HR   Noble William S WS   Nunn Brook L BL  

The ISME journal 20161108 2


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