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(v1.7.1.9056) unit tests

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dr. M.S. (Matthijs) Berends
2021-11-29 11:55:18 +01:00
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commit 5375f75829
21 changed files with 42 additions and 74 deletions
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data-raw/microorganisms.txt
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@ -2526,9 +2526,7 @@
"B_AEQRV" "Aequorivita" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "" "" "genus" "" 515048 "LPSN" 3 "427000006"
"B_AEQRV_AEST" "Aequorivita aestuarii" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "aestuarii" "" "species" "Hahnke et al., 2017" 795331 "LPSN" 3 "character(0)"
"B_AEQRV_ANTR" "Aequorivita antarctica" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "antarctica" "" "species" "Bowman et al., 2002" 772870 "LPSN" 3 "425986000"
"B_AEQRV_AQMR" "Aequorivita aquimaris" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "aquimaris" "" "species" "Garcia-Lopez et al., 2020" 7810 "LPSN" 3 "character(0)"
"B_AEQRV_AQMR" "Aequorivita aquimaris" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "aquimaris" "" "species" "Garcia-Lopez et al., 2020" 240 "LPSN" 3 "character(0)"
"B_AEQRV_AQMR" "Aequorivita aquimaris" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "aquimaris" "" "species" "Garcia-Lopez et al., 2020" 10522 "LPSN" 3 "character(0)"
"B_AEQRV_CPSS" "Aequorivita capsosiphonis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "capsosiphonis" "" "species" "Park et al., 2009" 787769 "LPSN" 3 "character(0)"
"B_AEQRV_CROC" "Aequorivita crocea" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "crocea" "" "species" "Bowman et al., 2002" 772871 "LPSN" 3 "427267004"
"B_AEQRV_ECHN" "Aequorivita echinoideorum" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "echinoideorum" "" "species" "Hahnke et al., 2017" 795332 "LPSN" 3 "character(0)"
@ -2539,7 +2537,6 @@
"B_AEQRV_SSKK" "Aequorivita soesokkakensis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "soesokkakensis" "" "species" "Hahnke et al., 2017" 795334 "LPSN" 3 "character(0)"
"B_AEQRV_SBLT" "Aequorivita sublithincola" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "sublithincola" "" "species" "Bowman et al., 2002" 772873 "LPSN" 3 "426358009"
"B_AEQRV_TDRD" "Aequorivita todarodis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "todarodis" "" "species" "Zhang et al., 2020" 1653 "LPSN" 3 "character(0)"
"B_AEQRV_TDRD" "Aequorivita todarodis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "todarodis" "" "species" "Zhang et al., 2020" 7480 "LPSN" 3 "character(0)"
"B_AEQRV_VSCS" "Aequorivita viscosa" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "viscosa" "" "species" "Liu et al., 2013" 791065 "LPSN" 3 "character(0)"
"B_AEQRV_VLDV" "Aequorivita vladivostokensis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aequorivita" "vladivostokensis" "" "species" "Hahnke et al., 2017" 795335 "LPSN" 3 "character(0)"
"B_AERBC" "Aeribacillus" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Aeribacillus" "" "" "genus" "" 517994 "LPSN" 2 "771465008"
@ -10655,9 +10652,7 @@
"C_BCHNR_WRGH_CLRN" "Buchnerina wrightiana clarioniana" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Ellipsolagenidae" "Buchnerina" "wrightiana" "clarioniana" "infraspecies" "McCulloch, 1977" "CoL" 3 "character(0)"
"C_BCHNR_YKYM" "Buchnerina yokoyamae" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Ellipsolagenidae" "Buchnerina" "yokoyamae" "" "species" "Millett, 1895" "CoL" 3 "character(0)"
"B_BUDVC" "Budvicia" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "Budvicia" "" "" "genus" "" 4094 "LPSN" 1 "55851000"
"B_BUDVC" "Budvicia" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "Budvicia" "" "" "genus" "" 515277 "LPSN" 1 "55851000"
"B_BUDVC_AQTC" "Budvicia aquatica" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "Budvicia" "aquatica" "" "species" "Bouvet et al., 1985" 7142 "LPSN" 1 "75464008"
"B_BUDVC_AQTC" "Budvicia aquatica" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "Budvicia" "aquatica" "" "species" "Bouvet et al., 1985" 774260 "LPSN" 1 "75464008"
"B_BUDVC_DPLP" "Budvicia diplopodorum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "Budvicia" "diplopodorum" "" "species" "Lang et al., 2013" 790413 "LPSN" 1 "character(0)"
"B_[FAM]_BUDVICIC" "Budviciaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Budviciaceae" "" "" "" "family" "Adeolu et al., 2016" "manually added" 1 "character(0)"
"C_BHRNG" "Buehringa" "Chromista" "Ciliophora" "Oligotrichea" "Strombidiida" "Strombidiidae" "Buehringa" "" "" "genus" "" "CoL" 3 "character(0)"
@ -10870,7 +10865,6 @@
"B_BRKHL_VRNS" "Burkholderia pseudomultivorans" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "pseudomultivorans" "" "species" "Peeters et al., 2014" 791434 "LPSN" 2 "character(0)"
"B_BRKHL_PURQ" "Burkholderia puraquae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "puraquae" "" "species" "Martina et al., 2018" 796421 "LPSN" 2 "character(0)"
"B_BRKHL_PYRR" "Burkholderia pyrrocinia" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "pyrrocinia" "" "species" "Vandamme et al., 2004" 7158 "LPSN" 2 "113677007"
"B_BRKHL_PYRR" "Burkholderia pyrrocinia" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "pyrrocinia" "" "species" "Vandamme et al., 2004" 774298 "LPSN" 2 "113677007"
"B_BRKHL_SMNL" "Burkholderia seminalis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "seminalis" "" "species" "Vanlaere et al., 2008" 787432 "LPSN" 2 "3441000146100"
"B_BRKHL_SNGL" "Burkholderia singularis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "singularis" "" "species" "Vandamme et al., 2017" 796265 "LPSN" 2 "character(0)"
"B_BRKHL_STBL" "Burkholderia stabilis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Burkholderia" "stabilis" "" "species" "Vandamme et al., 2000" 774304 "LPSN" 2 "416616001"
@ -14884,7 +14878,6 @@
"F_CLVTS_TNTC" "Clavatospora tentacula" "Fungi" "Ascomycota" "Sordariomycetes" "Microascales" "Halosphaeriaceae" "Clavatospora" "tentacula" "" "species" "Sv Nilsson, 1964" "CoL" 3 "character(0)"
"B_CLVBC" "Clavibacter" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "" "" "genus" "" 515381 "LPSN" 2 "432467001"
"B_CLVBC_CPSC" "Clavibacter capsici" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "capsici" "" "species" "Li et al., 2018" 7145 "LPSN" 2 "character(0)"
"B_CLVBC_CPSC" "Clavibacter capsici" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "capsici" "" "species" "Li et al., 2018" 798782 "LPSN" 2 "character(0)"
"B_CLVBC_INSD" "Clavibacter insidiosus" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "insidiosus" "" "species" "Li et al., 2018" 798137 "LPSN" 2 "character(0)"
"B_CLVBC_MCHG" "Clavibacter michiganensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "michiganensis" "" "species" "Davis et al., 1984" 783651 "LPSN" 2 "434065004"
"B_CLVBC_MCHG_CLFR" "Clavibacter michiganensis californiensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "michiganensis" "californiensis" "species" "Yasuhara-Bell et al., 2015" 792619 "LPSN" 2 "character(0)"
@ -14892,9 +14885,7 @@
"B_CLVBC_MCHG_MCHG" "Clavibacter michiganensis michiganensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "michiganensis" "michiganensis" "subsp." "Davis et al., 1984" 774773 "LPSN" 2 "434699002"
"B_CLVBC_MCHG_PHSL" "Clavibacter michiganensis phaseoli" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "michiganensis" "phaseoli" "species" "Gonzalez et al., 2014" 791833 "LPSN" 2 "character(0)"
"B_CLVBC_NBRS" "Clavibacter nebraskensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "nebraskensis" "" "species" "Li et al., 2018" 7143 "LPSN" 2 "character(0)"
"B_CLVBC_NBRS" "Clavibacter nebraskensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "nebraskensis" "" "species" "Li et al., 2018" 798139 "LPSN" 2 "character(0)"
"B_CLVBC_SPDN" "Clavibacter sepedonicus" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "sepedonicus" "" "species" "Li et al., 2018" 7144 "LPSN" 2 "character(0)"
"B_CLVBC_SPDN" "Clavibacter sepedonicus" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "sepedonicus" "" "species" "Li et al., 2018" 798141 "LPSN" 2 "character(0)"
"B_CLVBC_TSSL" "Clavibacter tessellarius" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "tessellarius" "" "species" "Li et al., 2018" 798142 "LPSN" 2 "character(0)"
"B_CLVBC_ZHNG" "Clavibacter zhangzhiyongii" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Clavibacter" "zhangzhiyongii" "" "species" "Tian et al., 2021" 19559 "LPSN" 2 "character(0)"
"F_CLVSP" "Clavispora" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Metschnikowiaceae" "Clavispora" "" "" "genus" "" "CoL" 3 "28615005"
@ -15725,7 +15716,6 @@
"B_CMPNL_PABL" "Companilactobacillus pabuli" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "pabuli" "" "species" "Jung et al., 2021" 17745 "LPSN" 2 "character(0)"
"B_CMPNL_PRLM" "Companilactobacillus paralimentarius" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "paralimentarius" "" "species" "Zheng et al., 2020" 10797 "LPSN" 2 "character(0)"
"B_CMPNL_SLSC" "Companilactobacillus salsicarnum" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "salsicarnum" "" "species" "Zheng et al., 2020" 10719 "LPSN" 2 "character(0)"
"B_CMPNL_SNTS" "Companilactobacillus suantsaicola" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "suantsaicola" "" "species" "Zheng et al., 2020" 18766 "LPSN" 2 "character(0)"
"B_CMPNL_SNTS" "Companilactobacillus suantsaicola" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "suantsaicola" "" "species" "Zheng et al., 2020" 12970 "LPSN" 2 "character(0)"
"B_CMPNL_TCCT" "Companilactobacillus tucceti" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "tucceti" "" "species" "Zheng et al., 2020" 10821 "LPSN" 2 "character(0)"
"B_CMPNL_VRSM" "Companilactobacillus versmoldensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Companilactobacillus" "versmoldensis" "" "species" "Zheng et al., 2020" 10825 "LPSN" 2 "character(0)"
@ -20814,10 +20804,8 @@
"C_ELLDS_MEDS" "Eggerelloides medius" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Prolixoplectidae" "Eggerelloides" "medius" "" "species" "Hoglund, 1947" "CoL" 3 "character(0)"
"C_ELLDS_SCBR" "Eggerelloides scaber" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Prolixoplectidae" "Eggerelloides" "scaber" "" "species" "Williamson, 1858" "CoL" 3 "character(0)"
"C_ELLDS_SCBR_INRN" "Eggerelloides scaber inornata" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Prolixoplectidae" "Eggerelloides" "scaber" "inornata" "infraspecies" "Rhumbler, 1936" "CoL" 3 "character(0)"
"B_EGGRT" "Eggerthella" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "" "" "genus" "" 521510 "LPSN" 2 "c(\"414079001\", \"414080003\", \"414075007\")"
"B_EGGRT" "Eggerthella" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "" "" "genus" "" 515567 "LPSN" 2 "c(\"414079001\", \"414080003\", \"414075007\")"
"B_EGGRT_GDYN" "Eggerthella guodeyinii" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "guodeyinii" "" "species" "Ge et al., 2021" 20102 "LPSN" 2 "character(0)"
"B_EGGRT_LENT" "Eggerthella lenta" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "lenta" "" "species" "Wade et al., 2008" 775884 "LPSN" 2 "414077004"
"B_EGGRT_LENT" "Eggerthella lenta" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "lenta" "" "species" "Wade et al., 2008" 7150 "LPSN" 2 "414077004"
"B_EGGRT_SNNS" "Eggerthella sinensis" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "Eggerthella" "sinensis" "" "species" "Lau et al., 2008" 785467 "LPSN" 2 "414078009"
"B_[FAM]_EGGRTHLL" "Eggerthellaceae" "Bacteria" "Actinobacteria" "Coriobacteriia" "Eggerthellales" "Eggerthellaceae" "" "" "" "family" "CoL" 2 "770382002"
@ -26256,7 +26244,6 @@
"B_GORDN_ACHN" "Gordonia aichiensis" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "aichiensis" "" "species" "Klatte et al., 1994" 776577 "LPSN" 2 "416711002"
"B_GORDN_ALKL" "Gordonia alkaliphila" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "alkaliphila" "" "species" "Cha et al., 2013" 790425 "LPSN" 2 "character(0)"
"B_GORDN_ALKN" "Gordonia alkanivorans" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "alkanivorans" "" "species" "Kummer et al., 1999" 776578 "LPSN" 2 "432009007"
"B_GORDN_AMAR" "Gordonia amarae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "amarae" "" "species" "Klatte et al., 1994" 776579 "LPSN" 2 "432969007"
"B_GORDN_AMAR" "Gordonia amarae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "amarae" "" "species" "Klatte et al., 1994" 7149 "LPSN" 2 "432969007"
"B_GORDN_AMCL" "Gordonia amicalis" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "amicalis" "" "species" "Kim et al., 2000" 776580 "LPSN" 2 "432010002"
"B_GORDN_ARAI" "Gordonia araii" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Gordoniaceae" "Gordonia" "araii" "" "species" "Kageyama et al., 2006" 785295 "LPSN" 2 "character(0)"
@ -28978,13 +28965,10 @@
"C_HHRYA_VRDS" "Holophrya viridis" "Chromista" "Ciliophora" "Prostomatea" "Prostomatida" "Holophryidae" "Holophrya" "viridis" "" "species" "" "CoL" 3 "character(0)"
"C_HHRYA_VORX" "Holophrya vorax" "Chromista" "Ciliophora" "Prostomatea" "Prostomatida" "Holophryidae" "Holophrya" "vorax" "" "species" "Dragesco, 1960" "CoL" 3 "character(0)"
"C_[FAM]_HOLPHRYD" "Holophryidae" "Chromista" "Ciliophora" "Prostomatea" "Prostomatida" "Holophryidae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_HLSPR" "Holospora" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "" "" "genus" "" 521511 "LPSN" 2 "432450008"
"B_HLSPR" "Holospora" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "" "" "genus" "" 517251 "LPSN" 2 "432450008"
"B_HLSPR_CRYP" "Holospora caryophila" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "caryophila" "" "species" "Preer et al., 1982" 784018 "LPSN" 2 "433982009"
"B_HLSPR_ELGN" "Holospora elegans" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "elegans" "" "species" "Preer et al., 1982" 784019 "LPSN" 2 "434171007"
"B_HLSPR_OBTS" "Holospora obtusa" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "obtusa" "" "species" "Gromov et al., 1981" 784020 "LPSN" 2 "434038006"
"B_HLSPR_OBTS" "Holospora obtusa" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "obtusa" "" "species" "Gromov et al., 1981" 7154 "LPSN" 2 "434038006"
"B_HLSPR_UNDL" "Holospora undulata" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "undulata" "" "species" "Gromov et al., 1981" 784021 "LPSN" 2 "433983004"
"B_HLSPR_UNDL" "Holospora undulata" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "Holosporaceae" "Holospora" "undulata" "" "species" "Gromov et al., 1981" 7155 "LPSN" 2 "433983004"
"B_[FAM]_HOLOSPRC" "Holosporaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rickettsiales" "Holosporaceae" "" "" "" "family" "" "CoL" 2 "414206002"
"B_[ORD]_HOLSPRLS" "Holosporales" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Holosporales" "" "" "" "" "order" "CoL" 2 "character(0)"
@ -31349,7 +31333,6 @@
"B_LCTPL_DWNS" "Lactiplantibacillus daowaiensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "daowaiensis" "" "species" "Zheng et al., 2020" 10693 "LPSN" 2 "character(0)"
"B_LCTPL_DNGL" "Lactiplantibacillus dongliensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "dongliensis" "" "species" "Zheng et al., 2020" 10692 "LPSN" 2 "character(0)"
"B_LCTPL_FBFR" "Lactiplantibacillus fabifermentans" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "fabifermentans" "" "species" "Zheng et al., 2020" 10753 "LPSN" 2 "character(0)"
"B_LCTPL_GARI" "Lactiplantibacillus garii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "garii" "" "species" "Zheng et al., 2020" 18769 "LPSN" 2 "character(0)"
"B_LCTPL_GARI" "Lactiplantibacillus garii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "garii" "" "species" "Zheng et al., 2020" 12997 "LPSN" 2 "character(0)"
"B_LCTPL_HRBR" "Lactiplantibacillus herbarum" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "herbarum" "" "species" "Zheng et al., 2020" 10861 "LPSN" 2 "character(0)"
"B_LCTPL_MDST" "Lactiplantibacillus modestisalitolerans" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactiplantibacillus" "modestisalitolerans" "" "species" "Zheng et al., 2020" 10859 "LPSN" 2 "character(0)"
@ -33843,7 +33826,6 @@
"B_LVLCT_SPCH" "Levilactobacillus spicheri" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "spicheri" "" "species" "Zheng et al., 2020" 10816 "LPSN" 2 "character(0)"
"B_LVLCT_SNTS" "Levilactobacillus suantsaii" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "suantsaii" "" "species" "Zheng et al., 2020" 10661 "LPSN" 2 "character(0)"
"B_LVLCT_SNTS1" "Levilactobacillus suantsaiihabitans" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "suantsaiihabitans" "" "species" "Zheng et al., 2020" 12998 "LPSN" 2 "character(0)"
"B_LVLCT_SNTS1" "Levilactobacillus suantsaiihabitans" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "suantsaiihabitans" "" "species" "Zheng et al., 2020" 18767 "LPSN" 2 "character(0)"
"B_LVLCT_TNGY" "Levilactobacillus tangyuanensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "tangyuanensis" "" "species" "Zheng et al., 2020" 10669 "LPSN" 2 "character(0)"
"B_LVLCT_TNGJ" "Levilactobacillus tongjiangensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "tongjiangensis" "" "species" "Zheng et al., 2020" 10667 "LPSN" 2 "character(0)"
"B_LVLCT_WNGK" "Levilactobacillus wangkuiensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Levilactobacillus" "wangkuiensis" "" "species" "Liu et al., 2021" 20124 "LPSN" 2 "character(0)"
@ -38985,7 +38967,6 @@
"B_MRCMS" "Muricomes" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Lachnospiraceae" "Muricomes" "" "" "genus" 518843 "LPSN" 2 "character(0)"
"B_MRCMS_INTS" "Muricomes intestini" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Lachnospiraceae" "Muricomes" "intestini" "" "species" "Lagkouvardos et al., 2016" 793540 "LPSN" 2 "character(0)"
"B_MURCL" "Muriicola" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Muriicola" "" "" "genus" "" 7206 "LPSN" 3 "character(0)"
"B_MURCL" "Muriicola" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Muriicola" "" "" "genus" "" 518000 "LPSN" 3 "character(0)"
"B_MURCL_JJNS" "Muriicola jejuensis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Muriicola" "jejuensis" "" "species" "Kahng et al., 2010" 788644 "LPSN" 3 "character(0)"
"B_MURCL_MRNN" "Muriicola marianensis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Muriicola" "marianensis" "" "species" "Hu et al., 2015" 792561 "LPSN" 3 "character(0)"
"B_MURCL_SOLI" "Muriicola soli" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Muriicola" "soli" "" "species" "Kang et al., 2021" 20129 "LPSN" 3 "character(0)"
@ -39077,12 +39058,10 @@
"B_MYCBC_CLRF" "Mycobacterium celeriflavum" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "celeriflavum" "" "species" "Shahraki et al., 2018" 792559 "LPSN" 2 "character(0)"
"B_MYCBC_CHLN" "Mycobacterium chelonae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chelonae" "" "species" "Kubica et al., 1972" 778416 "LPSN" 2 "752713421000087040"
"B_MYCBC_CHLN_BOVS" "Mycobacterium chelonae bovis" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chelonae" "bovis" "species" "Kim et al., 2017" 796016 "LPSN" 2 "1079401000112105"
"B_MYCBC_CHLN_CHLN" "Mycobacterium chelonae chelonae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chelonae" "chelonae" "subsp." "Kubica et al., 1972" 786944 "LPSN" 2 "character(0)"
"B_MYCBC_CHLN_CHLN" "Mycobacterium chelonae chelonae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chelonae" "chelonae" "subsp." "Kubica et al., 1972" 9034 "LPSN" 2 "character(0)"
"B_MYCBC_CHLN_GWNK" "Mycobacterium chelonae gwanakae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chelonae" "gwanakae" "species" "Kim et al., 2018" 797993 "LPSN" 2 "character(0)"
"B_MYCBC_CHIT" "Mycobacterium chitae" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chitae" "" "species" "Tsukamura, 1967" 778423 "LPSN" 2 "89896008"
"B_MYCBC_CHLR" "Mycobacterium chlorophenolicum" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chlorophenolicum" "" "species" "Haggblom et al., 1994" 16956 "LPSN" 2 "713611009"
"B_MYCBC_CHLR" "Mycobacterium chlorophenolicum" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chlorophenolicum" "" "species" "Haggblom et al., 1994" 778424 "LPSN" 2 "713611009"
"B_MYCBC_CHBN" "Mycobacterium chubuense" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "chubuense" "" "species" "Tsukamura, 1981" 778425 "LPSN" 2 "20498000"
"B_MYCBC_CLMB" "Mycobacterium colombiense" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "colombiense" "" "species" "Murcia et al., 2006" 785392 "LPSN" 2 "5381000146104"
"B_MYCBC_CNCP" "Mycobacterium conceptionense" "Bacteria" "Actinobacteria" "Actinobacteria" "Mycobacteriales" "Mycobacteriaceae" "Mycobacterium" "conceptionense" "" "species" "Adekambi et al., 2006" 785474 "LPSN" 2 "450471003"
@ -41367,7 +41346,6 @@
"B_NESSR_SBFL" "Neisseria subflava" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "subflava" "" "species" "Trevisan, 1889" 778639 "LPSN" 2 "77700001"
"B_NESSR_WDSW" "Neisseria wadsworthii" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "wadsworthii" "" "species" "Wolfgang et al., 2011" 789000 "LPSN" 2 "450421001"
"B_NESSR_WEVR" "Neisseria weaveri" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "weaveri" "" "species" "Holmes et al., 1993" 778640 "LPSN" 2 "113894007"
"B_NESSR_WEVR" "Neisseria weaveri" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "weaveri" "" "species" "Holmes et al., 1993" 789964 "LPSN" 2 "113894007"
"B_NESSR_WEIX" "Neisseria weixii" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "weixii" "" "species" "Zhang et al., 2019" 5270 "LPSN" 2 "character(0)"
"B_NESSR_ZLPH" "Neisseria zalophi" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "zalophi" "" "species" "Volokhov et al., 2018" 797869 "LPSN" 2 "character(0)"
"B_NESSR_ZDGM" "Neisseria zoodegmatis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Neisseriales" "Neisseriaceae" "Neisseria" "zoodegmatis" "" "species" "Vandamme et al., 2006" 785315 "LPSN" 2 "449121005"
@ -43144,7 +43122,6 @@
"B_NVHRB_HUMI" "Noviherbaspirillum humi" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "humi" "" "species" "Sundararaman et al., 2017" 795132 "LPSN" 2 "character(0)"
"B_NVHRB_MLTH" "Noviherbaspirillum malthae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "malthae" "" "species" "Lin et al., 2013" 791255 "LPSN" 2 "character(0)"
"B_NVHRB_MSSL" "Noviherbaspirillum massiliense" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "massiliense" "" "species" "Chaudhary et al., 2017" 7160 "LPSN" 2 "character(0)"
"B_NVHRB_MSSL" "Noviherbaspirillum massiliense" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "massiliense" "" "species" "Chaudhary et al., 2017" 795435 "LPSN" 2 "character(0)"
"B_NVHRB_PSYC" "Noviherbaspirillum psychrotolerans" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "psychrotolerans" "" "species" "Lin et al., 2013" 791259 "LPSN" 2 "character(0)"
"B_NVHRB_SOLI" "Noviherbaspirillum soli" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "soli" "" "species" "Lin et al., 2013" 791256 "LPSN" 2 "character(0)"
"B_NVHRB_SWNN" "Noviherbaspirillum suwonense" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Oxalobacteraceae" "Noviherbaspirillum" "suwonense" "" "species" "Kim et al., 2014" 791816 "LPSN" 2 "character(0)"
@ -46086,7 +46063,6 @@
"C_PRKRN_WTZL" "Parakeronopsis wetzeli" "Chromista" "Ciliophora" "Hypotrichea" "Stichotrichida" "Keronidae" "Parakeronopsis" "wetzeli" "" "species" "Shi, 1999" "CoL" 3 "character(0)"
"B_PRLCT" "Paralactobacillus" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Paralactobacillus" "" "" "genus" "Leisner et al., 2020" 516258 "LPSN" 2 "431579000"
"B_PRLCT_SLNG" "Paralactobacillus selangorensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Paralactobacillus" "selangorensis" "" "species" "Leisner et al., 2000" 9452 "LPSN" 2 "433290004"
"B_PRLCT_SLNG" "Paralactobacillus selangorensis" "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Paralactobacillus" "selangorensis" "" "species" "Leisner et al., 2000" 779168 "LPSN" 2 "433290004"
"C_PRLGN" "Paralagenidium" "Chromista" "Oomycota" "Peronosporea" "Peronosporales" "Pythiaceae" "Paralagenidium" "" "" "genus" "" "CoL" 3 "character(0)"
"C_PRLGN_KRLN" "Paralagenidium karlingii" "Chromista" "Oomycota" "Peronosporea" "Peronosporales" "Pythiaceae" "Paralagenidium" "karlingii" "" "species" "Grooters et al., 2013" "CoL" 3 "character(0)"
"B_PRLCL" "Paralcaligenes" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Alcaligenaceae" "Paralcaligenes" "" "" "genus" "" 518111 "LPSN" 2 "character(0)"
@ -49657,7 +49633,6 @@
"B_PHTBC_HLTL" "Photobacterium halotolerans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "halotolerans" "" "species" "Rivas et al., 2006" 779531 "LPSN" 1 "character(0)"
"B_PHTBC_ILPS" "Photobacterium iliopiscarium" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "iliopiscarium" "" "species" "Urakawa et al., 1999" 779532 "LPSN" 1 "427632007"
"B_PHTBC_INDC" "Photobacterium indicum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "indicum" "" "species" "Ivanova et al., 2004" 7152 "LPSN" 1 "432889009"
"B_PHTBC_INDC" "Photobacterium indicum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "indicum" "" "species" "Ivanova et al., 2004" 779533 "LPSN" 1 "432889009"
"B_PHTBC_JEAN" "Photobacterium jeanii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "jeanii" "" "species" "Chimetto et al., 2010" 788966 "LPSN" 1 "character(0)"
"B_PHTBC_KSHT" "Photobacterium kishitanii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "kishitanii" "" "species" "Ast et al., 2007" 786711 "LPSN" 1 "character(0)"
"B_PHTBC_LGNT" "Photobacterium leiognathi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Photobacterium" "leiognathi" "" "species" "Boisvert et al., 1967" 784624 "LPSN" 1 "115052008"
@ -49703,7 +49678,6 @@
"B_PHTRH_LMND_LMND" "Photorhabdus laumondii laumondii" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "laumondii" "laumondii" "subsp." "Machado et al., 2018" 798517 "LPSN" 1 "character(0)"
"B_PHTRH_LMNS" "Photorhabdus luminescens" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "luminescens" "" "species" "Boemare et al., 1999" 779539 "LPSN" 1 "115023005"
"B_PHTRH_LMNS_LMNS" "Photorhabdus luminescens luminescens" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "luminescens" "luminescens" "subsp." "Fischer-Le Saux et al., 1999" 13667 "LPSN" 1 "432228005"
"B_PHTRH_LMNS_LMNS" "Photorhabdus luminescens luminescens" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "luminescens" "luminescens" "subsp." "Fischer-Le Saux et al., 1999" 779543 "LPSN" 1 "432228005"
"B_PHTRH_LMNS_MXCN" "Photorhabdus luminescens mexicana" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "luminescens" "mexicana" "species" "Machado et al., 2019" 800147 "LPSN" 1 "character(0)"
"B_PHTRH_NMNN" "Photorhabdus namnaonensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "namnaonensis" "" "species" "Machado et al., 2018" 798789 "LPSN" 1 "character(0)"
"B_PHTRH_NNPT" "Photorhabdus noenieputensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Enterobacterales" "Morganellaceae" "Photorhabdus" "noenieputensis" "" "species" "Machado et al., 2018" 798693 "LPSN" 1 "character(0)"
@ -53778,7 +53752,6 @@
"C_PPHNA_TRTS" "Pseudopolymorphina tortuosa" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Polymorphinidae" "Pseudopolymorphina" "tortuosa" "" "species" "Vella, 1957" "CoL" 3 "character(0)"
"C_PPHNA_VART" "Pseudopolymorphina variata" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Polymorphinidae" "Pseudopolymorphina" "variata" "" "species" "Jones et al., 1866" "CoL" 3 "character(0)"
"C_PPHNA_VNKL" "Pseudopolymorphina vonkleinsmidi" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Polymorphinidae" "Pseudopolymorphina" "vonkleinsmidi" "" "species" "McCulloch, 1977" "CoL" 3 "character(0)"
"B_PSDPN" "Pseudopontixanthobacter" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Erythrobacteraceae" "Pseudopontixanthobacter" "" "" "genus" "Sun et al., 2020" 14527 "LPSN" 2 "character(0)"
"B_PSDPN" "Pseudopontixanthobacter" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Erythrobacteraceae" "Pseudopontixanthobacter" "" "" "genus" "Sun et al., 2020" 2893 "LPSN" 2 "character(0)"
"B_PSDPN_CNFL" "Pseudopontixanthobacter confluentis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Erythrobacteraceae" "Pseudopontixanthobacter" "confluentis" "" "species" "Liu et al., 2021" 3158 "LPSN" 2 "character(0)"
"B_PSDPN_SDMN" "Pseudopontixanthobacter sediminis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Erythrobacteraceae" "Pseudopontixanthobacter" "sediminis" "" "species" "Liu et al., 2021" 3209 "LPSN" 2 "character(0)"
@ -54331,7 +54304,6 @@
"B_[ORD]_PNCCCCLS" "Puniceicoccales" "Bacteria" "Verrucomicrobia" "Opitutae" "Puniceicoccales" "(unknown family)" "" "" "" "order" "" "CoL" 2 "character(0)"
"B_PNCCC" "Puniceicoccus" "Bacteria" "Verrucomicrobia" "Opitutae" "Puniceicoccales" "Puniceicoccaceae" "Puniceicoccus" "" "" "genus" "" 517529 "LPSN" 3 "character(0)"
"B_PNCCC_VRMC" "Puniceicoccus vermicola" "Bacteria" "Verrucomicrobia" "Opitutae" "Puniceicoccales" "Puniceicoccaceae" "Puniceicoccus" "vermicola" "" "species" "Choo et al., 2007" 786065 "LPSN" 3 "character(0)"
"B_PSLLM" "Pusillimonas" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Alcaligenaceae" "Pusillimonas" "" "" "genus" "" 516438 "LPSN" 2 "character(0)"
"B_PSLLM" "Pusillimonas" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Alcaligenaceae" "Pusillimonas" "" "" "genus" "" 3599 "LPSN" 2 "character(0)"
"B_PSLLM_CAEN" "Pusillimonas caeni" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Alcaligenaceae" "Pusillimonas" "caeni" "" "species" "Jin et al., 2017" 795134 "LPSN" 2 "character(0)"
"B_PSLLM_GNSN" "Pusillimonas ginsengisoli" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Alcaligenaceae" "Pusillimonas" "ginsengisoli" "" "species" "Srinivasan et al., 2010" 788686 "LPSN" 2 "character(0)"
@ -57962,7 +57934,6 @@
"B_SLNVB_SMNS" "Salinivibrio siamensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Salinivibrio" "siamensis" "" "species" "Chamroensaksri et al., 2009" 787805 "LPSN" 1 "character(0)"
"B_SLNVB_SCMP" "Salinivibrio socompensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "Vibrionaceae" "Salinivibrio" "socompensis" "" "species" "Galisteo et al., 2020" 5551 "LPSN" 1 "character(0)"
"B_SLNVR" "Salinivirga" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Salinivirgaceae" "Salinivirga" "" "" "genus" 89 "LPSN" 3 "character(0)"
"B_SLNVR" "Salinivirga" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Salinivirgaceae" "Salinivirga" "" "" "genus" 519128 "LPSN" 3 "character(0)"
"B_SLNVR_CYNB" "Salinivirga cyanobacteriivorans" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Salinivirgaceae" "Salinivirga" "cyanobacteriivorans" "" "species" "Ben Hania et al., 2017" 795083 "LPSN" 3 "character(0)"
"B_[FAM]_SALNVRGC" "Salinivirgaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Salinivirgaceae" "" "" "" "family" "CoL" 2 "character(0)"
"B_SLNVM" "Salinovum" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Salinovum" "" "" "genus" 519197 "LPSN" 2 "character(0)"
@ -60163,7 +60134,6 @@
"B_SPHNGB_CIBI" "Sphingobacterium cibi" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "cibi" "" "species" "Lai et al., 2016" 794899 "LPSN" 3 "character(0)"
"B_SPHNGB_CLDN" "Sphingobacterium cladoniae" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "cladoniae" "" "species" "Lee et al., 2013" 790546 "LPSN" 3 "705164003"
"B_SPHNGB_CMPS" "Sphingobacterium composti" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "composti" "" "species" "Ten et al., 2007" 785810 "LPSN" 3 "character(0)"
"B_SPHNGB_CMPS" "Sphingobacterium composti" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "composti" "" "species" "Ten et al., 2007" 786529 "LPSN" 3 "character(0)"
"B_SPHNGB_CRTC" "Sphingobacterium corticibacter" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "corticibacter" "" "species" "Li et al., 2019" 5212 "LPSN" 3 "character(0)"
"B_SPHNGB_CTRM" "Sphingobacterium corticibacterium" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "corticibacterium" "" "species" "Li et al., 2020" 14684 "LPSN" 3 "character(0)"
"B_SPHNGB_CRTC1" "Sphingobacterium corticis" "Bacteria" "Bacteroidetes" "Sphingobacteriia" "Sphingobacteriales" "Sphingobacteriaceae" "Sphingobacterium" "corticis" "" "species" "Li et al., 2017" 796053 "LPSN" 3 "character(0)"
@ -70355,7 +70325,6 @@
"B_XNTHM_PRFR" "Xanthomonas perforans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "perforans" "" "species" "Jones et al., 2006" 785205 "LPSN" 1 "6131000146108"
"B_XNTHM_PHSL" "Xanthomonas phaseoli" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "phaseoli" "" "species" "Gabriel et al., 1989" 785206 "LPSN" 1 "440323006"
"B_XNTHM_PISI" "Xanthomonas pisi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "pisi" "" "species" "Vauterin et al., 1995" 785207 "LPSN" 1 "439621006"
"B_XNTHM_POPL" "Xanthomonas populi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "populi" "" "species" "Ride et al., 1992" 785208 "LPSN" 1 "439622004"
"B_XNTHM_POPL" "Xanthomonas populi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "populi" "" "species" "Ride et al., 1992" 7159 "LPSN" 1 "439622004"
"B_XNTHM_PRNC" "Xanthomonas prunicola" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "prunicola" "" "species" "Lopez et al., 2018" 797769 "LPSN" 1 "character(0)"
"B_XNTHM_SCCH" "Xanthomonas sacchari" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xanthomonas" "sacchari" "" "species" "Vauterin et al., 1995" 786750 "LPSN" 1 "character(0)"

2
data-raw/mo.md5
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@ -1 +1 @@
dbe572abad4a2dc85db8cb146b74beb9
638a06636d8b547c2cb9d1ec243ecb7e

4
data-raw/reproduction_of_microorganisms_update.R
View File

@ -365,7 +365,9 @@ MOs <- MOs %>%
records_ids <- taxonomy %>%
mutate(across(1:3, function(x) { x[is.na(x)] <- ""; x}),
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))) %>%
transmute(fullname, species_id = as.numeric(record_no))
transmute(fullname, species_id = as.numeric(record_no)) %>%
arrange(fullname, species_id) %>%
distinct(fullname, .keep_all = TRUE)
message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
MOs <- MOs %>%
select(-species_id) %>%