(v1.5.0.9030) as.ab() speed improvement

v1.8.2
parent 0e0e3c4ffa
commit 0d29bde693
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.5.0.9029
Version: 1.5.0.9030
Date: 2021-03-05
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

@ -1,4 +1,4 @@
# AMR 1.5.0.9029
# AMR 1.5.0.9030
## <small>Last updated: 5 March 2021</small>
### New
@ -45,8 +45,8 @@
```
### Changed
* Microbial taxonomy updated to 3 March 2021 (according to the [LSPN](https://lpsn.dsmz.de))
* Added 3,372 new names and 1,523 existing names became synomyms
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
* Added 3,372 new species and 1,523 existing species became synomyms
* The URL of a bacterial species (`mo_url()`) will now lead to https://lpsn.dsmz.de
* Big update for plotting classes `rsi`, `<mic>`, and `<disk>`:
* Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
@ -71,6 +71,7 @@
* `random_disk()` and `random_mic()` now have an expanded range in their randomisation
* Support for GISA (glycopeptide-intermediate *S. aureus*), so e.g. `mo_genus("GISA")` will return `"Staphylococcus"`
* Added translations of German and Spanish for more than 200 antimicrobial drugs
* Speed improvement for `as.ab()` when the input is an official name or ATC code
### Other
* Big documentation updates
@ -677,7 +678,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Based on the Compound ID, almost 5,000 official brand names have been added from many different countries
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
* All `atc_*` functions are superseded by `ab_*` functions
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New argument `colours` to set the bar colours

@ -105,14 +105,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
already_regex <- isTRUE(list(...)$already_regex)
fast_mode <- isTRUE(list(...)$fast_mode)
if (all(toupper(x) %in% antibiotics$ab)) {
# valid AB code, but not yet right class
return(set_clean_class(toupper(x),
new_class = c("ab", "character")))
}
x_bak <- x
x <- toupper(x)
x_nonNA <- x[!is.na(x)]
if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
# all valid AB codes, but not yet right class
return(set_clean_class(x,
new_class = c("ab", "character")))
}
if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
# all valid AB names
out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
out[is.na(x)] <- NA_character_
return(out)
}
if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
# all valid ATC codes
out <- antibiotics$ab[match(x, antibiotics$atc)]
out[is.na(x)] <- NA_character_
return(out)
}
# remove diacritics
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
x <- gsub('"', "", x, fixed = TRUE)

@ -131,16 +131,15 @@ catalogue_of_life_version <- function() {
#' @export
#' @noRd
print.catalogue_of_life_version <- function(x, ...) {
lst <- x
cat(paste0(font_bold("Included in this AMR package (v", utils::packageDescription("AMR")$Version, ") are:\n\n", collapse = ""),
font_underline(lst$CoL$version), "\n",
" Available at: ", lst$CoL$url, "\n",
" Number of included species: ", format(lst$CoL$n, big.mark = ","), "\n",
font_underline(paste0(lst$LPSN$version, " (",
lst$LPSN$yearmonth, ")")), "\n",
" Available at: ", lst$LPSN$url, "\n",
" Number of included species: ", format(lst$LPSN$n, big.mark = ","), "\n\n",
"=> Total number of species included: ", format(lst$total_included$n_total_species, big.mark = ","), "\n",
"=> Total number of synonyms included: ", format(lst$total_included$n_total_synonyms, big.mark = ","), "\n\n",
font_underline(x$CoL$version), "\n",
" Available at: ", font_blue(x$CoL$url), "\n",
" Number of included microbial species: ", format(x$CoL$n, big.mark = ","), "\n",
font_underline(paste0(x$LPSN$version, " (",
x$LPSN$yearmonth, ")")), "\n",
" Available at: ", font_blue(x$LPSN$url), "\n",
" Number of included bacterial species: ", format(x$LPSN$n, big.mark = ","), "\n\n",
"=> Total number of species included: ", format(x$total_included$n_total_species, big.mark = ","), "\n",
"=> Total number of synonyms included: ", format(x$total_included$n_total_synonyms, big.mark = ","), "\n\n",
"See for more info ?microorganisms and ?catalogue_of_life.\n"))
}

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@ -43,21 +43,23 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {
MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae",
"auricularis", "caeli", "capitis", "caprae",
"carnosus", "chromogenes", "cohnii", "condimenti",
"auricularis", "borealis", "caeli", "capitis", "caprae",
"carnosus", "casei", "chromogenes", "cohnii", "condimenti",
"croceilyticus",
"debuckii", "devriesei", "edaphicus", "epidermidis",
"equorum", "felis", "fleurettii", "gallinarum",
"haemolyticus", "hominis", "jettensis", "kloosii",
"lentus", "lugdunensis", "massiliensis", "microti",
"muscae", "nepalensis", "pasteuri", "petrasii",
"pettenkoferi", "piscifermentans", "pseudoxylosus",
"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
"sciuri", "simulans", "stepanovicii", "succinus",
"ureilyticus",
"vitulinus", "vitulus", "warneri", "xylosus")
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
"mo", drop = TRUE]
} else if (type == "CoPS") {
MO_staph[which(MO_staph$species %in% c("coagulase-positive",
MO_staph[which(MO_staph$species %in% c("coagulase-positive", "coagulans",
"agnetis", "argenteus",
"cornubiensis",
"delphini", "lutrae",

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@ -63572,7 +63572,7 @@
"B_TNNRL" "Tannerella" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tannerellaceae" "Tannerella" "" "" "genus" "" "e8627ab2a13d9f950d8d76c21e5752dd" "CoL" 3
"B_TNNRL_FRSY" "Tannerella forsythia" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tannerellaceae" "Tannerella" "forsythia" "" "species" "Sakamoto et al., 2002" "8b7a3936af4c4b28e091c5bd99a5dc1f" "CoL" 3
"B_TNNRL_SRPN" "Tannerella serpentiformis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tannerellaceae" "Tannerella" "serpentiformis" "" "species" "Ansbro et al., 2020" "8243" "LPSN" 3 "character(0)"
"B_[FAM]_TANNRLLC" "Tannerellaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tannerellaceae" "" "" "" "family" "" "CoL" 3 "NULL"
"B_[FAM]_TANNRLLC" "Tannerellaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tannerellaceae" "" "" "" "family" "" "CoL" 3 "character(0)"
"B_TNTCH" "Tanticharoenia" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Acetobacteraceae" "Tanticharoenia" "" "" "genus" "" "a0bd95198fb0ce2982593ba8245446dc" "CoL" 2
"B_TNTCH_AIDA" "Tanticharoenia aidae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Acetobacteraceae" "Tanticharoenia" "aidae" "" "species" "Vu et al., 2016" "794099" "LPSN" 2
"B_TNTCH_SKRT" "Tanticharoenia sakaeratensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Acetobacteraceae" "Tanticharoenia" "sakaeratensis" "" "species" "Yukphan et al., 2008" "b368080d2456ee85beb933826d5fa9fe" "CoL" 2
@ -63682,7 +63682,7 @@
"C_TLTRC_NATH" "Telotrochidium nathei" "Chromista" "Ciliophora" "Oligohymenophorea" "Peritrichida" "Opisthonectidae" "Telotrochidium" "nathei" "" "species" "Gulati, 1926" "c3729e25193dbda10ba96aac9eb9c084" "CoL" 3
"B_TMPRT" "Temperatibacter" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Kordiimonadales" "Temperatibacteraceae" "Temperatibacter" "" "" "genus" "" "LPSN" 2
"B_TMPRT_MRNS" "Temperatibacter marinus" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Kordiimonadales" "Temperatibacteraceae" "Temperatibacter" "marinus" "" "species" "Teramoto et al., 2014" "792170" "LPSN" 2
"B_[FAM]_TMPRTBCT" "Temperatibacteraceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Kordiimonadales" "Temperatibacteraceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_TMPRTBCT" "Temperatibacteraceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Kordiimonadales" "Temperatibacteraceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_TNCBC" "Tenacibaculum" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Tenacibaculum" "" "" "genus" "" "1758b554c15e725956f920b9d4a9719a" "CoL" 3 "440478001"
"B_TNCBC_ADRT" "Tenacibaculum adriaticum" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Tenacibaculum" "adriaticum" "" "species" "Heindl et al., 2008" "b2ef07f238a79f8303134577cd95b974" "CoL" 3
"B_TNCBC_AEST" "Tenacibaculum aestuarii" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Tenacibaculum" "aestuarii" "" "species" "Jung et al., 2006" "c726308f8b025db377208907cd804f5d" "CoL" 3
@ -63725,7 +63725,7 @@
"B_TNGNB_TSMG" "Tengunoibacter tsumagoiensis" "Bacteria" "Chloroflexi" "Ktedonobacteria" "Ktedonobacterales" "Dictyobacteraceae" "Tengunoibacter" "tsumagoiensis" "" "species" "Wang et al., 2019" "801287" "LPSN" 3
"B_TNBCL" "Tenuibacillus" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Tenuibacillus" "" "" "genus" "" "5f89b52b106309a524f4ef715620da27" "CoL" 2
"B_TNBCL_MLTV" "Tenuibacillus multivorans" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Tenuibacillus" "multivorans" "" "species" "Ren et al., 2005" "fe2bb49c0017f25e909bfabc8a4d6387" "CoL" 2
"B_[FAM]_TENUIFLC" "Tenuifilaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tenuifilaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_TENUIFLC" "Tenuifilaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tenuifilaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_TNFLM" "Tenuifilum" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tenuifilaceae" "Tenuifilum" "" "" "genus" "Podosokorskaya et al., 2021" "17605" "LPSN" 3 "character(0)"
"B_TNFLM_THLS" "Tenuifilum thalassicum" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Tenuifilaceae" "Tenuifilum" "thalassicum" "" "species" "Podosokorskaya et al., 2021" "17639" "LPSN" 3 "character(0)"
"C_TNTLL" "Tenuitella" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Globigerinitidae" "Tenuitella" "" "" "genus" "" "86287c465f89d25c1f1176d2b9b91c14" "CoL" 3
@ -63733,12 +63733,12 @@
"C_TNTLL_FLSH" "Tenuitella fleisheri" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Globigerinitidae" "Tenuitella" "fleisheri" "" "species" "Li, 1987" "dbd4cd0241c4d4a9463dde984dacffb7" "CoL" 3
"C_TNTLL_IOTA" "Tenuitella iota" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Globigerinitidae" "Tenuitella" "iota" "" "species" "Parker, 1962" "3a71e5c87fe9b43b381d627509eee67f" "CoL" 3
"C_TNTLL_PRKR" "Tenuitella parkerae" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Globigerinitidae" "Tenuitella" "parkerae" "" "species" "Bronnimann et al., 1971" "e08dad8b87fa7945077c91346ea8aa3f" "CoL" 3
"B_[FAM]_TPDMRPHC" "Tepidamorphaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Tepidamorphaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_TPDMRPHC" "Tepidamorphaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Tepidamorphaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_TPDMR" "Tepidamorphus" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Tepidamorphaceae" "Tepidamorphus" "" "" "genus" "" "cb22ac3935c34510e44022cd8370ae63" "CoL" 2
"B_TPDMR_GMMT" "Tepidamorphus gemmatus" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Tepidamorphaceae" "Tepidamorphus" "gemmatus" "" "species" "Albuquerque et al., 2010" "bc115e44e121e2ab1dcda272d41c6ca3" "CoL" 2
"B_TPDNR" "Tepidanaerobacter" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Tepidanaerobacteraceae" "Tepidanaerobacter" "" "" "genus" "" "b7f6313a14e39f70260d80976a773ff2" "CoL" 2
"B_TPDNR_SYNT" "Tepidanaerobacter syntrophicus" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Tepidanaerobacteraceae" "Tepidanaerobacter" "syntrophicus" "" "species" "Sekiguchi et al., 2006" "485d0cc18b9daea8fa6438db49f2ea68" "CoL" 2
"B_[FAM]_TPDNRBCT" "Tepidanaerobacteraceae" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Tepidanaerobacteraceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_TPDNRBCT" "Tepidanaerobacteraceae" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Tepidanaerobacteraceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_TPDBC" "Tepidibacillus" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Tepidibacillus" "" "" "genus" "" "LPSN" 2
"B_TPDBC_DCTR" "Tepidibacillus decaturensis" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Tepidibacillus" "decaturensis" "" "species" "Dong et al., 2016" "794662" "LPSN" 2
"B_TPDBC_FRMN" "Tepidibacillus fermentans" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Tepidibacillus" "fermentans" "" "species" "Slobodkina et al., 2014" "791029" "LPSN" 2
@ -63755,8 +63755,8 @@
"B_TCLLA_XAVR" "Tepidicella xavieri" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Comamonadaceae" "Tepidicella" "xavieri" "" "species" "Franca et al., 2006" "01dc9e80e24908d21d76cd64964bb865" "CoL" 2
"B_TPDFR" "Tepidiforma" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "Tepidiformaceae" "Tepidiforma" "" "" "genus" "Kochetkova et al., 2020" "4933" "LPSN" 3 "character(0)"
"B_TPDFR_BNCH" "Tepidiforma bonchosmolovskayae" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "Tepidiformaceae" "Tepidiforma" "bonchosmolovskayae" "" "species" "Kochetkova et al., 2020" "5702" "LPSN" 3 "character(0)"
"B_[FAM]_TEPDFRMC" "Tepidiformaceae" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "Tepidiformaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_TPDFRMLS" "Tepidiformales" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_TEPDFRMC" "Tepidiformaceae" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "Tepidiformaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_TPDFRMLS" "Tepidiformales" "Bacteria" "Chloroflexi" "Tepidiformia" "Tepidiformales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TPDMC" "Tepidimicrobium" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tepidimicrobium" "" "" "genus" "" "28ab86a22e261a7221404255817e9695" "CoL" 2
"B_TPDMC_FRRP" "Tepidimicrobium ferriphilum" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tepidimicrobium" "ferriphilum" "" "species" "Slobodkin et al., 2006" "cd5da17ff17585fc761f1d9c4278dc3d" "CoL" 2
"B_TPDMC_XYLN" "Tepidimicrobium xylanilyticum" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tepidimicrobium" "xylanilyticum" "" "species" "Niu et al., 2009" "eee1d6ec46689fef81685d4c979318bf" "CoL" 2
@ -63776,15 +63776,15 @@
"B_TPDPH_THRM" "Tepidiphilus thermophilus" "Bacteria" "Proteobacteria" "Hydrogenophilalia" "Hydrogenophilales" "Hydrogenophilaceae" "Tepidiphilus" "thermophilus" "" "species" "Poddar et al., 2014" "791469" "LPSN" 2
"B_TPDSP" "Tepidisphaera" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "Tepidisphaeraceae" "Tepidisphaera" "" "" "genus" "" "LPSN" 3
"B_TPDSP_MUCS" "Tepidisphaera mucosa" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "Tepidisphaeraceae" "Tepidisphaera" "mucosa" "" "species" "Kovaleva et al., 2015" "792542" "LPSN" 3
"B_[FAM]_TPDSPHRC" "Tepidisphaeraceae" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "Tepidisphaeraceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_TPDSPHRL" "Tepidisphaerales" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_TPDSPHRC" "Tepidisphaeraceae" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "Tepidisphaeraceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_TPDSPHRL" "Tepidisphaerales" "Bacteria" "Planctomycetes" "Phycisphaerae" "Tepidisphaerales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TPDTG" "Tepiditoga" "Bacteria" "Thermotogae" "Thermotogae" "Petrotogales" "Petrotogaceae" "Tepiditoga" "" "" "genus" "Mori et al., 2021" "17602" "LPSN" 3 "character(0)"
"B_TPDTG_SPRL" "Tepiditoga spiralis" "Bacteria" "Thermotogae" "Thermotogae" "Petrotogales" "Petrotogaceae" "Tepiditoga" "spiralis" "" "species" "Mori et al., 2021" "17621" "LPSN" 3 "character(0)"
"B_TRSKL" "Terasakiella" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "Terasakiella" "" "" "genus" "" "3b5efb047b84daf75c6b3ad275e7cbe4" "CoL" 2
"B_TRSKL_BRSS" "Terasakiella brassicae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "Terasakiella" "brassicae" "" "species" "Han et al., 2016" "794045" "LPSN" 2
"B_TRSKL_PSLL" "Terasakiella pusilla" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "Terasakiella" "pusilla" "" "species" "Satomi et al., 2002" "acacf1d511e2e893a13d07239f37e7fc" "CoL" 2
"B_TRSKL_SLNC" "Terasakiella salincola" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "Terasakiella" "salincola" "" "species" "Yoon et al., 2018" "797788" "LPSN" 2
"B_[FAM]_TERSKLLC" "Terasakiellaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_TERSKLLC" "Terasakiellaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Terasakiellaceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_TRSKS" "Terasakiispira" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Halomonadaceae" "Terasakiispira" "" "" "genus" "" "LPSN" 1
"B_TRSKS_PPHN" "Terasakiispira papahanaumokuakeensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Halomonadaceae" "Terasakiispira" "papahanaumokuakeensis" "" "species" "Zepeda et al., 2015" "793295" "LPSN" 1
"C_TRBRS" "Terebrospira" "Chromista" "Ciliophora" "Kinetofragminophora" "Apostomatida" "Foettingeriidae" "Terebrospira" "" "" "genus" "" "6acd0bef7bc242cbd706846af3f3b63e" "CoL" 3
@ -63836,8 +63836,8 @@
"B_TRRLC" "Terrilactibacillus" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Terrilactibacillus" "" "" "genus" "Prasirtsak et al., 2016" "518916" "LPSN" 2 "character(0)"
"B_TRRLC_LVLC" "Terrilactibacillus laevilacticus" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Terrilactibacillus" "laevilacticus" "" "species" "Prasirtsak et al., 2016" "793949" "LPSN" 2 "character(0)"
"B_TRRLC_TMRN" "Terrilactibacillus tamarindi" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Terrilactibacillus" "tamarindi" "" "species" "Kingkaew et al., 2020" "8246" "LPSN" 2 "character(0)"
"B_[FAM]_TRRMCRBC" "Terrimicrobiaceae" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "Terrimicrobiaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_TRRMCRBL" "Terrimicrobiales" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_TRRMCRBC" "Terrimicrobiaceae" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "Terrimicrobiaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_TRRMCRBL" "Terrimicrobiales" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TRRMC" "Terrimicrobium" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "Terrimicrobiaceae" "Terrimicrobium" "" "" "genus" "" "LPSN" 3
"B_TRRMC_SCCH" "Terrimicrobium sacchariphilum" "Bacteria" "Verrucomicrobia" "Terrimicrobia" "Terrimicrobiales" "Terrimicrobiaceae" "Terrimicrobium" "sacchariphilum" "" "species" "Qiu et al., 2016" "791764" "LPSN" 3
"B_TRRMN" "Terrimonas" "Bacteria" "Bacteroidetes" "Chitinophagia" "Chitinophagales" "Chitinophagaceae" "Terrimonas" "" "" "genus" "" "75a69e5acba6294f2a88486b954cad12" "CoL" 3 "433880000"
@ -64268,7 +64268,7 @@
"B_THLSSB_DVRN" "Thalassobacillus devorans" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Thalassobacillus" "devorans" "" "species" "Garcia et al., 2005" "c15693715610ae23154d60267ecfcf50" "CoL" 2
"B_THLSSB_HWNG" "Thalassobacillus hwangdonensis" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Thalassobacillus" "hwangdonensis" "" "species" "Lee et al., 2010" "da869f8ab011f9b909096c2e37a46615" "CoL" 2
"B_THLSSB_PLLS" "Thalassobacillus pellis" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Bacillaceae" "Thalassobacillus" "pellis" "" "species" "Sanchez-Porro et al., 2011" "f542a263ae2f3d8fd5a5cb6d3f8d5a2c" "CoL" 2
"B_[FAM]_THLSSBCL" "Thalassobaculaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassobaculaceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_THLSSBCL" "Thalassobaculaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassobaculaceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_TSBCLM" "Thalassobaculum" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassobaculaceae" "Thalassobaculum" "" "" "genus" "" "435ec7e5be3a056afa6fba0b00c5080b" "CoL" 2
"B_TSBCLM_FLVM" "Thalassobaculum fulvum" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassobaculaceae" "Thalassobaculum" "fulvum" "" "species" "Su et al., 2016" "794197" "LPSN" 2 "character(0)"
"B_TSBCLM_LTRM" "Thalassobaculum litoreum" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassobaculaceae" "Thalassobaculum" "litoreum" "" "species" "Zhang et al., 2008" "c790c17e43278cfc223b4d8f05ee1b35" "CoL" 2
@ -64318,7 +64318,7 @@
"B_THLSSS_TPDP" "Thalassospira tepidiphila" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassospiraceae" "Thalassospira" "tepidiphila" "" "species" "Kodama et al., 2008" "f51f4394a3d1114260172708c64a8016" "CoL" 2
"B_THLSSS_XMNN" "Thalassospira xiamenensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassospiraceae" "Thalassospira" "xiamenensis" "" "species" "Liu et al., 2007" "60ec13e103c9d3460af6e3f0f0591d64" "CoL" 2
"B_THLSSS_XNHN" "Thalassospira xianhensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassospiraceae" "Thalassospira" "xianhensis" "" "species" "Zhao et al., 2010" "9ebd0b03f2596b2ca4dfddb098db4cc8" "CoL" 2
"B_[FAM]_THLSSSPR" "Thalassospiraceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassospiraceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_THLSSSPR" "Thalassospiraceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Thalassospiraceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_TSTLA" "Thalassotalea" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Alteromonadales" "Colwelliaceae" "Thalassotalea" "" "" "genus" "" "LPSN" 1
"B_TSTLA_AGRP" "Thalassotalea agariperforans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Alteromonadales" "Colwelliaceae" "Thalassotalea" "agariperforans" "" "species" "Zhang et al., 2014" "791723" "LPSN" 1
"B_TSTLA_AGRV" "Thalassotalea agarivorans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Alteromonadales" "Colwelliaceae" "Thalassotalea" "agarivorans" "" "species" "Zhang et al., 2014" "791722" "LPSN" 1
@ -64581,8 +64581,8 @@
"B_THRMNRB_RCRS" "Thermoanaerobacterium thermostercoris" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Thermoanaerobacteraceae" "Thermoanaerobacterium" "thermostercoris" "" "species" "Romano et al., 2011" "023d3069afe1efc3898cdf27dcdd29ec" "CoL" 2
"B_THRMNRB_RGNS" "Thermoanaerobacterium thermosulfurigenes" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Thermoanaerobacteraceae" "Thermoanaerobacterium" "thermosulfurigenes" "" "species" "Lee et al., 1993" "e34aa4f8356a2ecedef7cfb6bef4b5ff" "CoL" 2
"B_THRMNRB_XYLN" "Thermoanaerobacterium xylanolyticum" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Thermoanaerobacteraceae" "Thermoanaerobacterium" "xylanolyticum" "" "species" "Lee et al., 1993" "2cf4018360d7e9e98215a9d6adbb10af" "CoL" 2
"B_[FAM]_THRMNRBC1" "Thermoanaerobaculaceae" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "Thermoanaerobaculaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_THRMNRBC1" "Thermoanaerobaculales" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_THRMNRBC1" "Thermoanaerobaculaceae" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "Thermoanaerobaculaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_THRMNRBC1" "Thermoanaerobaculales" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TRBCLM" "Thermoanaerobaculum" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "Thermoanaerobaculaceae" "Thermoanaerobaculum" "" "" "genus" "" "LPSN" 3
"B_TRBCLM_AQTC" "Thermoanaerobaculum aquaticum" "Bacteria" "Acidobacteria" "Thermoanaerobaculia" "Thermoanaerobaculales" "Thermoanaerobaculaceae" "Thermoanaerobaculum" "aquaticum" "" "species" "Losey et al., 2013" "791289" "LPSN" 3
"F_THRMS" "Thermoascus" "Fungi" "Ascomycota" "Eurotiomycetes" "Eurotiales" "Trichocomaceae" "Thermoascus" "" "" "genus" "" "d87c999a98b9cf16d0fcc3dbe03d6796" "CoL" 3
@ -64700,11 +64700,11 @@
"B_THRMF" "Thermoflavimicrobium" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Thermoactinomycetaceae" "Thermoflavimicrobium" "" "" "genus" "" "a2650aac7ac63a811b74b99bac81a8d8" "CoL" 2
"B_THRMF_DAQU" "Thermoflavimicrobium daqui" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Thermoactinomycetaceae" "Thermoflavimicrobium" "daqui" "" "species" "Li et al., 2019" "5341" "LPSN" 2 "character(0)"
"B_THRMF_DCHT" "Thermoflavimicrobium dichotomicum" "Bacteria" "Firmicutes" "Bacilli" "Caryophanales" "Thermoactinomycetaceae" "Thermoflavimicrobium" "dichotomicum" "" "species" "Yoon et al., 2005" "e3c1ac7d9f321e528bcfdd35f1ec9b24" "CoL" 2
"B_[FAM]_THRMFLXC" "Thermoflexaceae" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "Thermoflexaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_THRMFLXL" "Thermoflexales" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_THRMFLXC" "Thermoflexaceae" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "Thermoflexaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_THRMFLXL" "Thermoflexales" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TBCTR" "Thermoflexibacter" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermoflexibacteraceae" "Thermoflexibacter" "" "" "genus" "Hahnke et al., 2017" "519190" "LPSN" 3 "character(0)"
"B_TBCTR_RUBR" "Thermoflexibacter ruber" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermoflexibacteraceae" "Thermoflexibacter" "ruber" "" "species" "Hahnke et al., 2019" "795356" "LPSN" 3 "character(0)"
"B_[FAM]_THRMFLXB" "Thermoflexibacteraceae" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermoflexibacteraceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_THRMFLXB" "Thermoflexibacteraceae" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermoflexibacteraceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_TFLXS" "Thermoflexus" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "Thermoflexaceae" "Thermoflexus" "" "" "genus" "" "LPSN" 3
"B_TFLXS_HGNH" "Thermoflexus hugenholtzii" "Bacteria" "Chloroflexi" "Thermoflexia" "Thermoflexales" "Thermoflexaceae" "Thermoflexus" "hugenholtzii" "" "species" "Dodsworth et al., 2018" "791860" "LPSN" 3
"B_THRMG" "Thermogemmatispora" "Bacteria" "Chloroflexi" "Ktedonobacteria" "Thermogemmatisporales" "Thermogemmatisporaceae" "Thermogemmatispora" "" "" "genus" "" "7d5babf6d2efdc2d417955539b3d80a6" "CoL" 3
@ -64720,7 +64720,7 @@
"B_TGTTA" "Thermogutta" "Bacteria" "Planctomycetes" "Planctomycetia" "Pirellulales" "Thermoguttaceae" "Thermogutta" "" "" "genus" "" "LPSN" 3
"B_TGTTA_HYPG" "Thermogutta hypogea" "Bacteria" "Planctomycetes" "Planctomycetia" "Pirellulales" "Thermoguttaceae" "Thermogutta" "hypogea" "" "species" "Slobodkina et al., 2015" "792617" "LPSN" 3
"B_TGTTA_TRRF" "Thermogutta terrifontis" "Bacteria" "Planctomycetes" "Planctomycetia" "Pirellulales" "Thermoguttaceae" "Thermogutta" "terrifontis" "" "species" "Slobodkina et al., 2015" "792616" "LPSN" 3
"B_[FAM]_THRMGTTC" "Thermoguttaceae" "Bacteria" "Planctomycetes" "Planctomycetia" "Pirellulales" "Thermoguttaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_THRMGTTC" "Thermoguttaceae" "Bacteria" "Planctomycetes" "Planctomycetia" "Pirellulales" "Thermoguttaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"A_THRMG" "Thermogymnomonas" "Archaea" "Euryarchaeota" "Thermoplasmata" "Thermoplasmatales" "" "Thermogymnomonas" "" "" "genus" "" "d505e1592fbb20f1705dff182d9a488a" "CoL" 3
"A_THRMG_ACDC" "Thermogymnomonas acidicola" "Archaea" "Euryarchaeota" "Thermoplasmata" "Thermoplasmatales" "" "Thermogymnomonas" "acidicola" "" "species" "Itoh et al., 2007" "5417e5ba3dcbbdb9966534125e7d9828" "CoL" 3
"B_THRMH" "Thermohalobacter" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Clostridiaceae" "Thermohalobacter" "" "" "genus" "" "36364d20bb7e79966816692259bede9f" "CoL" 2
@ -64778,7 +64778,7 @@
"B_TMNMA" "Thermonema" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermonemataceae" "Thermonema" "" "" "genus" "" "35662bf41ed5c7ebb63b0a58382862dc" "CoL" 3
"B_TMNMA_LPSM" "Thermonema lapsum" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermonemataceae" "Thermonema" "lapsum" "" "species" "Hudson et al., 1989" "62264849c0755543edd22b69218382ac" "CoL" 3
"B_TMNMA_RSSN" "Thermonema rossianum" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermonemataceae" "Thermonema" "rossianum" "" "species" "Nobre et al., 1997" "68492fadf21bf1ad95248ffe65a4b414" "CoL" 3
"B_[FAM]_THRMNMTC" "Thermonemataceae" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermonemataceae" "" "" "" "family" "" "CoL" 3 "NULL"
"B_[FAM]_THRMNMTC" "Thermonemataceae" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Thermonemataceae" "" "" "" "family" "" "CoL" 3 "character(0)"
"B_TPHGS" "Thermophagus" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Marinilabiliaceae" "Thermophagus" "" "" "genus" "" "LPSN" 3
"B_TPHGS_XMNN" "Thermophagus xiamenensis" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Marinilabiliaceae" "Thermophagus" "xiamenensis" "" "species" "Gao et al., 2013" "790360" "LPSN" 3
"A_THRMP" "Thermoplasma" "Archaea" "Euryarchaeota" "Thermoplasmata" "Thermoplasmatales" "Thermoplasmataceae" "Thermoplasma" "" "" "genus" "" "635808ad22b439effff2b7ed61a892b5" "CoL" 3
@ -64802,8 +64802,8 @@
"B_THRMSD" "Thermosediminibacter" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Thermosediminibacteraceae" "Thermosediminibacter" "" "" "genus" "" "ae4befc3daa9752894c819ef16b62047" "CoL" 2
"B_THRMSD_LTRP" "Thermosediminibacter litoriperuensis" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Thermosediminibacteraceae" "Thermosediminibacter" "litoriperuensis" "" "species" "Lee et al., 2006" "596eb6981de28c09f261b7c0236b4406" "CoL" 2
"B_THRMSD_OCEN" "Thermosediminibacter oceani" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Thermosediminibacteraceae" "Thermosediminibacter" "oceani" "" "species" "Lee et al., 2006" "6597aed6d8c639cf593eb4347269fc95" "CoL" 2
"B_[FAM]_THRMSDMN" "Thermosediminibacteraceae" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Thermosediminibacteraceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[ORD]_THRMSDMN" "Thermosediminibacterales" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "" "" "" "" "order" "" "LPSN" 2 "NULL"
"B_[FAM]_THRMSDMN" "Thermosediminibacteraceae" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "Thermosediminibacteraceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_[ORD]_THRMSDMN" "Thermosediminibacterales" "Bacteria" "Firmicutes" "Clostridia" "Thermosediminibacterales" "" "" "" "" "order" "" "LPSN" 2 "character(0)"
"B_TMSNS" "Thermosinus" "Bacteria" "Firmicutes" "Negativicutes" "Selenomonadales" "Sporomusaceae" "Thermosinus" "" "" "genus" "" "c222b2d119b9b218621adcadd893b087" "CoL" 2
"B_TMSNS_CRBX" "Thermosinus carboxydivorans" "Bacteria" "Firmicutes" "Negativicutes" "Selenomonadales" "Sporomusaceae" "Thermosinus" "carboxydivorans" "" "species" "Sokolova et al., 2004" "cbd7eb342e4a2dc4a2fc68536b0fb561" "CoL" 2
"B_TSPHO" "Thermosipho" "Bacteria" "Thermotogae" "Thermotogae" "Thermotogales" "Fervidobacteriaceae" "Thermosipho" "" "" "genus" "" "19bf50f5100db5c757c95ed2fd08e9c5" "CoL" 3
@ -64851,8 +64851,8 @@
"B_[FAM]_THERMTGC" "Thermotogaceae" "Bacteria" "Thermotogae" "Thermotogae" "Thermotogales" "Thermotogaceae" "" "" "" "family" "" "20853ed096a9f26ae5446f6472f8455e" "CoL" 2
"B_[PHL]_THERMOTG" "Thermotogae" "Bacteria" "Thermotogae" "(unknown class)" "(unknown order)" "(unknown family)" "" "" "" "phylum" "" "6d2581bf62879d6a64b229d06dd83349" "CoL" 2
"B_[ORD]_THRMTGLS" "Thermotogales" "Bacteria" "Thermotogae" "Thermotogae" "Thermotogales" "(unknown family)" "" "" "" "order" "" "b34f697382f0d3b0147c4adc0f2cc41e" "CoL" 2
"B_[FAM]_THRMTMCL" "Thermotomaculaceae" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "Thermotomaculaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_THRMTMCL" "Thermotomaculales" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_THRMTMCL" "Thermotomaculaceae" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "Thermotomaculaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_THRMTMCL" "Thermotomaculales" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_TMCLM" "Thermotomaculum" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "Thermotomaculaceae" "Thermotomaculum" "" "" "genus" "" "LPSN" 3
"B_TMCLM_HYDR" "Thermotomaculum hydrothermale" "Bacteria" "Acidobacteria" "Holophagae" "Thermotomaculales" "Thermotomaculaceae" "Thermotomaculum" "hydrothermale" "" "species" "Izumi et al., 2017" "789712" "LPSN" 3
"B_TTNCA" "Thermotunica" "Bacteria" "Actinobacteria" "Actinobacteria" "Pseudonocardiales" "Pseudonocardiaceae" "Thermotunica" "" "" "genus" "" "LPSN" 2
@ -64921,7 +64921,7 @@
"B_THLBS_DNTR" "Thioalbus denitrificans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Ectothiorhodospiraceae" "Thioalbus" "denitrificans" "" "species" "Park et al., 2011" "dee0471696331ba6aa3dffeb6b68ffb0" "CoL" 1
"B_THLKL" "Thioalkalibacter" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioalkalibacteraceae" "Thioalkalibacter" "" "" "genus" "" "aeb9b992db99dda446a4ab141c5288b2" "CoL" 1
"B_THLKL_HLPH" "Thioalkalibacter halophilus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioalkalibacteraceae" "Thioalkalibacter" "halophilus" "" "species" "Banciu et al., 2009" "691990a5a8c59dc5c357e4773e9a883d" "CoL" 1
"B_[FAM]_THLKLBCT" "Thioalkalibacteraceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioalkalibacteraceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_THLKLBCT" "Thioalkalibacteraceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioalkalibacteraceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_THLKLC" "Thioalkalicoccus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thioalkalicoccus" "" "" "genus" "" "903ba05df1a77fbf713abf0a890ae156" "CoL" 1
"B_THLKLC_LMNS" "Thioalkalicoccus limnaeus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thioalkalicoccus" "limnaeus" "" "species" "Bryantseva et al., 2000" "59641d21d8cc47ff22b45a70f8a3842f" "CoL" 1
"B_THLKLS" "Thioalkalispira" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioalkalispiraceae" "Thioalkalispira" "" "" "genus" "" "41632710ea5012ebf2c58adbd3d8d149" "CoL" 1
@ -64940,7 +64940,7 @@
"B_THLKLV_VRST" "Thioalkalivibrio versutus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Ectothiorhodospiraceae" "Thioalkalivibrio" "versutus" "" "species" "Sorokin et al., 2001" "c94100d3ffd9bd0b2607a59a26de0d39" "CoL" 1
"B_THIBC" "Thiobaca" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thiobaca" "" "" "genus" "" "b997cf181d25553904e8e2994fd2a937" "CoL" 1
"B_THIBC_TRPR" "Thiobaca trueperi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thiobaca" "trueperi" "" "species" "Rees et al., 2002" "2ded61c4f11c57003d03ba3ed1c3128c" "CoL" 1
"B_[FAM]_THIBCLLC" "Thiobacillaceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Thiobacillaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_THIBCLLC" "Thiobacillaceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Thiobacillaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_THBCL" "Thiobacillus" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Thiobacillaceae" "Thiobacillus" "" "" "genus" "" "624755bbb39c9d54bdc1244c8c54c7fa" "CoL" 2
"B_THBCL_DNTR" "Thiobacillus denitrificans" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Thiobacillaceae" "Thiobacillus" "denitrificans" "" "species" "Kelly et al., 1989" "d591d26556a7e1123ca8fbc9e51d4cfe" "CoL" 2
"B_THBCL_THPR" "Thiobacillus thioparus" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Thiobacillaceae" "Thiobacillus" "thioparus" "" "species" "Beijerinck, 1904" "a031f46f2df132f5679191c0ba25ff64" "CoL" 2
@ -64977,7 +64977,7 @@
"B_THDCT_ELGN" "Thiodictyon elegans" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thiodictyon" "elegans" "" "species" "Winogradsky, 1888" "62c34ee73e5048cc182883754517f697" "CoL" 1
"B_THIFB" "Thiofaba" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Halothiobacillaceae" "Thiofaba" "" "" "genus" "" "bd8ce3c9a021ec5497bd92fb674c415f" "CoL" 1
"B_THIFB_TPDP" "Thiofaba tepidiphila" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Halothiobacillaceae" "Thiofaba" "tepidiphila" "" "species" "Mori et al., 2008" "7ca4438f84833f1b9bb0ccc1d7f01f53" "CoL" 1
"B_[FAM]_THIOFILC" "Thiofilaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiofilaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_THIOFILC" "Thiofilaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiofilaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_THFLM" "Thiofilum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiofilaceae" "Thiofilum" "" "" "genus" "" "LPSN" 1
"B_THFLM_FLXL" "Thiofilum flexile" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiofilaceae" "Thiofilum" "flexile" "" "species" "Boden et al., 2018" "798540" "LPSN" 1
"B_THFLV" "Thioflavicoccus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Chromatiaceae" "Thioflavicoccus" "" "" "genus" "" "a4aeb30960a98bc3fecc6605ab987c12" "CoL" 1
@ -65007,7 +65007,7 @@
"B_THLPL_BRND" "Thiolapillus brandeum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "" "Thiolapillus" "brandeum" "" "species" "Nunoura et al., 2015" "792488" "LPSN" 1
"B_THILN" "Thiolinea" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiolineaceae" "Thiolinea" "" "" "genus" "" "LPSN" 1
"B_THILN_DSCF" "Thiolinea disciformis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiolineaceae" "Thiolinea" "disciformis" "" "species" "Boden et al., 2018" "798539" "LPSN" 1
"B_[FAM]_THIOLINC" "Thiolineaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiolineaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_THIOLINC" "Thiolineaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiolineaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_THMRG" "Thiomargarita" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiotrichaceae" "Thiomargarita" "" "" "genus" "" "5a26b6a1835379acb3cffdcbcfd99c91" "CoL" 1
"B_THMRG_NMBN" "Thiomargarita namibiensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiotrichaceae" "Thiomargarita" "namibiensis" "" "species" "Schulz et al., 1999" "a9ba2a3cb363d5eb3786a719d5d9ca15" "CoL" 1
"B_THMCR" "Thiomicrorhabdus" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Piscirickettsiaceae" "Thiomicrorhabdus" "" "" "genus" "" "LPSN" 1
@ -65045,7 +65045,7 @@
"B_THPLC_CHIL" "Thioploca chileae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiotrichaceae" "Thioploca" "chileae" "" "species" "Maier et al., 1984" "5675fcc93a6bef560ccaf461f4ec1f2f" "CoL" 1
"B_THPLC_INGR" "Thioploca ingrica" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiotrichaceae" "Thioploca" "ingrica" "" "species" "Maier, 1984" "a0d6071d70f82ad80844f0b5f93cb0cb" "CoL" 1
"B_THPLC_SCHM" "Thioploca schmidlei" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Thiotrichales" "Thiotrichaceae" "Thioploca" "schmidlei" "" "species" "Lauterborn, 1907" "cee845beb085c6a5a48c7c3d34001620" "CoL" 1
"B_[FAM]_THPRFNDC" "Thioprofundaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioprofundaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_THPRFNDC" "Thioprofundaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioprofundaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_THPRF" "Thioprofundum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioprofundaceae" "Thioprofundum" "" "" "genus" "" "36ab6a8df22fdda37ae6229ed5556ff3" "CoL" 1
"B_THPRF_HSPD" "Thioprofundum hispidum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioprofundaceae" "Thioprofundum" "hispidum" "" "species" "Mori et al., 2011" "b7c4756df55d7499019f904c544fdb8e" "CoL" 1
"B_THPRF_LTHT" "Thioprofundum lithotrophicum" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Thioprofundaceae" "Thioprofundum" "lithotrophicum" "" "species" "Takai et al., 2010" "712bbe6a127d6f7d836ed00e7cfd04a8" "CoL" 1
@ -65127,7 +65127,7 @@
"B_THRSL_ANPH" "Thorsellia anophelis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "Thorselliaceae" "Thorsellia" "anophelis" "" "species" "Kampfer et al., 2006" "d8548ca4e379fc5c08a87bcda653c954" "CoL" 1
"B_THRSL_KNDN" "Thorsellia kandunguensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "Thorselliaceae" "Thorsellia" "kandunguensis" "" "species" "Kampfer et al., 2015" "792574" "LPSN" 1
"B_THRSL_KNYN" "Thorsellia kenyensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "Thorselliaceae" "Thorsellia" "kenyensis" "" "species" "Kampfer et al., 2015" "792573" "LPSN" 1
"B_[FAM]_THORSLLC" "Thorselliaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "Thorselliaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_THORSLLC" "Thorselliaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "Thorselliaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"C_[ORD]_THRSTCHY" "Thraustochytrida" "Chromista" "Bigyra" "Labyrinthulea" "Thraustochytrida" "(unknown family)" "" "" "" "order" "" "8c6e22dfdb3f799dd63584e0697fa6a9" "CoL" 2
"C_[FAM]_THRSTCHY" "Thraustochytriidae" "Chromista" "Bigyra" "Labyrinthulea" "Thraustochytrida" "Thraustochytriidae" "" "" "" "family" "" "acf6bc5c6092778b8eb6e69c8f399b83" "CoL" 2
"C_THRST" "Thraustochytrium" "Chromista" "Bigyra" "Labyrinthulea" "Thraustochytrida" "Thraustochytriidae" "Thraustochytrium" "" "" "genus" "" "a93abb76fe265aaa87f80c795386323b" "CoL" 3
@ -65218,8 +65218,8 @@
"C_TBRLL_MGND" "Tiborella magnidentata" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Multiarcusellidae" "Tiborella" "magnidentata" "" "species" "Dumitrica et al., 1980" "15d9e83e673be5ba1d0a5be62a7530b3" "CoL" 3
"B_TCHWT" "Tichowtungia" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "Tichowtungiaceae" "Tichowtungia" "" "" "genus" "Mu et al., 2020" "13715" "LPSN" 3 "character(0)"
"B_TCHWT_AERT" "Tichowtungia aerotolerans" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "Tichowtungiaceae" "Tichowtungia" "aerotolerans" "" "species" "Mu et al., 2020" "13781" "LPSN" 3 "character(0)"
"B_[FAM]_TCHWTNGC" "Tichowtungiaceae" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "Tichowtungiaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_TCHWTNGL" "Tichowtungiales" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_TCHWTNGC" "Tichowtungiaceae" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "Tichowtungiaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_TCHWTNGL" "Tichowtungiales" "Bacteria" "Kiritimatiellaeota" "Tichowtungiia" "Tichowtungiales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"C_TDWLL" "Tidwellella" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Cibicididae" "Tidwellella" "" "" "genus" "" "f1e3427d9703a5a5062f7a84e12abb33" "CoL" 3
"C_TDWLL_EXRN" "Tidwellella exorna" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Cibicididae" "Tidwellella" "exorna" "" "species" "Phleger et al., 1951" "7d82e6962a3bcc4929f9dc5eda14f86b" "CoL" 3
"P_TGHMS" "Tieghemostelium" "Protozoa" "Mycetozoa" "Dictyosteliomycetes" "Dictyosteliales" "Raperosteliaceae" "Tieghemostelium" "" "" "genus" "" "ee8ec0d7032a9883693f57cc4d8f1208" "CoL" 3
@ -65502,8 +65502,8 @@
"B_TSSRL_CRTN" "Tissierella creatinini" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tissierella" "creatinini" "" "species" "Farrow et al., 1995" "339e983cdb60aa4d553db8c523faede4" "CoL" 2
"B_TSSRL_PHLA" "Tissierella creatinophila" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tissierella" "creatinophila" "" "species" "Harms et al., 1998" "ae681fb2b570c0ecb4c6c61da21d5d23" "CoL" 2
"B_TSSRL_PRCT" "Tissierella praeacuta" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "Tissierella" "praeacuta" "" "species" "Collins et al., 1986" "a4aaf5c45e3fde1acdc287846b97891d" "CoL" 2 "19185007"
"B_[FAM]_TISSRLLC" "Tissierellaceae" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[ORD]_TSSRLLLS" "Tissierellales" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "" "" "" "" "order" "" "LPSN" 2 "NULL"
"B_[FAM]_TISSRLLC" "Tissierellaceae" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "Tissierellaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_[ORD]_TSSRLLLS" "Tissierellales" "Bacteria" "Firmicutes" "Tissierellia" "Tissierellales" "" "" "" "" "order" "" "LPSN" 2 "character(0)"
"B_TISTL" "Tistlia" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Rhodovibrionaceae" "Tistlia" "" "" "genus" "" "27acbbd33e143aae286567990060bc71" "CoL" 2
"B_TISTL_CNST" "Tistlia consotensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Rhodovibrionaceae" "Tistlia" "consotensis" "" "species" "Diaz-Cardenas et al., 2010" "c7808e874c69792c3c2d51a096b0cf8e" "CoL" 2
"B_TSTRL" "Tistrella" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Geminicoccaceae" "Tistrella" "" "" "genus" "" "1ad3208e462b05da631dcbd38e5274a3" "CoL" 2
@ -65572,7 +65572,7 @@
"C_TLYPM_HRRD" "Tolypammina horrida" "Chromista" "Foraminifera" "Tubothalamea" "Spirillinida" "Ammodiscidae" "Tolypammina" "horrida" "" "species" "Cushman, 1919" "9c92cc92b10be496a405647025dc31ef" "CoL" 3
"C_TLYPM_SCHD" "Tolypammina schaudinni" "Chromista" "Foraminifera" "Tubothalamea" "Spirillinida" "Ammodiscidae" "Tolypammina" "schaudinni" "" "species" "Rhumbler, 1904" "ac66dbd10f4fab2f9e6b3b4eb245f53e" "CoL" 3
"C_TLYPM_VGNS" "Tolypammina vagans" "Chromista" "Foraminifera" "Tubothalamea" "Spirillinida" "Ammodiscidae" "Tolypammina" "vagans" "" "species" "Brady, 1879" "f7cee4a293e2d960fe205a3de0b05d02" "CoL" 3
"B_[FAM]_TLYPTHRC" "Tolypothrichaceae" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Nostocales" "Tolypothrichaceae" "" "" "" "family" "" "CoL" 3 "NULL"
"B_[FAM]_TLYPTHRC" "Tolypothrichaceae" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Nostocales" "Tolypothrichaceae" "" "" "" "family" "" "CoL" 3 "character(0)"
"B_TLYPT" "Tolypothrix" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Nostocales" "Tolypothrichaceae" "Tolypothrix" "" "" "genus" "" "c6db1336406fd831ef614976762fff76" "CoL" 3
"B_TLYPT_BYSS" "Tolypothrix byssoidea" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Nostocales" "Tolypothrichaceae" "Tolypothrix" "byssoidea" "" "species" "Kirchm" "f5bd0f1063b20493d88a81ec33110031" "CoL" 3
"B_TLYPT_BYSS_BYSS" "Tolypothrix byssoidea byssoidea" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Nostocales" "Tolypothrichaceae" "Tolypothrix" "byssoidea" "byssoidea" "infraspecies" "Krichm" "fbcd001c1ce5f90bf11dc33cd0ba3e86" "CoL" 3
@ -65861,7 +65861,7 @@
"C_TRNSH_HSKY" "Transhsuum hisuikyoense" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Hsuidae" "Transhsuum" "hisuikyoense" "" "species" "Isozaki et al., 1985" "6b9cd436533f27dbf98dc571821778b3" "CoL" 3
"B_TREBN" "Trebonia" "Bacteria" "Actinobacteria" "Actinobacteria" "Streptosporangiales" "Treboniaceae" "Trebonia" "" "" "genus" "Rapoport et al., 2020" "13046" "LPSN" 2 "character(0)"
"B_TREBN_KVET" "Trebonia kvetii" "Bacteria" "Actinobacteria" "Actinobacteria" "Streptosporangiales" "Treboniaceae" "Trebonia" "kvetii" "" "species" "Rapoport et al., 2020" "13061" "LPSN" 2 "character(0)"
"B_[FAM]_TREBONIC" "Treboniaceae" "Bacteria" "Actinobacteria" "Actinobacteria" "Streptosporangiales" "Treboniaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_TREBONIC" "Treboniaceae" "Bacteria" "Actinobacteria" "Actinobacteria" "Streptosporangiales" "Treboniaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"AN_[CLS]_TREMATOD" "Trematoda" "Animalia" "Platyhelminthes" "Trematoda" "(unknown order)" "(unknown family)" "" "" "" "class" "" "d42c1a9f3fd079134f6e4010e8309ac8" "CoL" 3
"C_TRMTP" "Trematophragmoides" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Haplophragmoididae" "Trematophragmoides" "" "" "genus" "" "d7a5afa9fb8021e22a896df5c159338b" "CoL" 3
"C_TRMTP_BRNN" "Trematophragmoides bruneiensis" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Haplophragmoididae" "Trematophragmoides" "bruneiensis" "" "species" "Bronnimann et al., 1986" "dd67a7255a6a65b03054231b54f7e1d1" "CoL" 3
@ -66058,7 +66058,7 @@
"B_TRPNM_STNS" "Treponema stenostreptum" "Bacteria" "Spirochaetes" "Spirochaetia" "Spirochaetales" "Treponemataceae" "Treponema" "stenostreptum" "" "species" "Abt et al., 2013" "791062" "LPSN" 2
"B_TRPNM_SCCN" "Treponema succinifaciens" "Bacteria" "Spirochaetes" "Spirochaetia" "Spirochaetales" "Treponemataceae" "Treponema" "succinifaciens" "" "species" "Cwyk et al., 1981" "7c0f43367b767cfc23b3db7d85b303af" "CoL" 2
"B_TRPNM_ZLZR" "Treponema zuelzerae" "Bacteria" "Spirochaetes" "Spirochaetia" "Spirochaetales" "Treponemataceae" "Treponema" "zuelzerae" "" "species" "Abt et al., 2013" "791063" "LPSN" 2
"B_[FAM]_TREPNMTC" "Treponemataceae" "Bacteria" "Spirochaetes" "Spirochaetia" "Spirochaetales" "Treponemataceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_TREPNMTC" "Treponemataceae" "Bacteria" "Spirochaetes" "Spirochaetia" "Spirochaetales" "Treponemataceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"C_TRTMP" "Tretomphaloides" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Rosalinidae" "Tretomphaloides" "" "" "genus" "" "522e7ee98dbbb7540cdcbc1d52f26882" "CoL" 3
"C_TRTMP_CLAR" "Tretomphaloides clara" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Rosalinidae" "Tretomphaloides" "clara" "" "species" "Cushman, 1934" "afdba4f69b4fbf3a2d2b12e2178dc1ff" "CoL" 3
"C_TRTMP_CNCN" "Tretomphaloides concinna" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Rosalinidae" "Tretomphaloides" "concinna" "" "species" "Brady, 1884" "95a8259697e6b4803c5f37ced0ac2fbd" "CoL" 3
@ -67435,7 +67435,7 @@
"AN_[FAM]_TROMBCLD" "Trombiculidae" "Animalia" "Arthropoda" "Arachnida" "Prostigmata" "Trombiculidae" "" "" "" "family" "" "96af7f160f5f0a0d9fed2425dcd88ffd" "CoL" 3
"B_TRPHR" "Tropheryma" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Tropherymataceae" "Tropheryma" "" "" "genus" "" "34de7993c421ace90f185b3cdcd7e040" "CoL" 2 "417733009"
"B_TRPHR_WHPP" "Tropheryma whipplei" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Tropherymataceae" "Tropheryma" "whipplei" "" "species" "La Scola et al., 2001" "69cba7f90b9c2d900e9e0c99d9f6dbec" "CoL" 2 "417060007"
"B_[FAM]_TRPHRYMT" "Tropherymataceae" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Tropherymataceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_TRPHRYMT" "Tropherymataceae" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Tropherymataceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_TRPCB" "Tropicibacter" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Tropicibacter" "" "" "genus" "" "12211ec712e348277288bfa06bf8c89b" "CoL" 2
"B_TRPCB_NPHT" "Tropicibacter naphthalenivorans" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodobacterales" "Rhodobacteraceae" "Tropicibacter" "naphthalenivorans" "" "species" "Harwati et al., 2009" "6fe2f1b7000cb48109fc3cf018abc6b4" "CoL" 2
"B_TRPCH" "Tropicihabitans" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Promicromonosporaceae" "Tropicihabitans" "" "" "genus" "" "LPSN" 2
@ -67455,7 +67455,7 @@
"B_TRUPR" "Truepera" "Bacteria" "DeinococcusThermus" "Deinococci" "Trueperales" "Trueperaceae" "Truepera" "" "" "genus" "" "3bad23d8ebf56b65989c93ce6ce4f1c3" "CoL" 3
"B_TRUPR_RDVC" "Truepera radiovictrix" "Bacteria" "DeinococcusThermus" "Deinococci" "Trueperales" "Trueperaceae" "Truepera" "radiovictrix" "" "species" "Albuquerque et al., 2005" "abf540bd9d925277c3d626c65b0aa594" "CoL" 3
"B_[FAM]_TRUEPERC" "Trueperaceae" "Bacteria" "Deinococcus-thermus" "Deinococci" "Deinococcales" "Trueperaceae" "" "" "" "family" "" "d002cc1d3b596ba4b741e98395726307" "CoL" 2
"B_[ORD]_TRUEPRLS" "Trueperales" "Bacteria" "DeinococcusThermus" "Deinococci" "Trueperales" "" "" "" "" "order" "" "CoL" 3 "NULL"
"B_[ORD]_TRUEPRLS" "Trueperales" "Bacteria" "DeinococcusThermus" "Deinococci" "Trueperales" "" "" "" "" "order" "" "CoL" 3 "character(0)"
"B_TRPRL" "Trueperella" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Actinomycetaceae" "Trueperella" "" "" "genus" "" "a373f5b224d2b70057ce6ebcb6c84e96" "CoL" 2 "704974007"
"B_TRPRL_ABRT" "Trueperella abortisuis" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Actinomycetaceae" "Trueperella" "abortisuis" "" "species" "Yassin et al., 2011" "ac2c02a1933d05a9c44fd0187d502bbf" "CoL" 2
"B_TRPRL_BRNR" "Trueperella bernardiae" "Bacteria" "Actinobacteria" "Actinobacteria" "Actinomycetales" "Actinomycetaceae" "Trueperella" "bernardiae" "" "species" "Yassin et al., 2011" "c7accb03b8e3d01546d847aacd696309" "CoL" 2 "704975008"
@ -67595,7 +67595,7 @@
"C_TRBRT_QNQL_EGLD" "Turborotalita quinqueloba egelida" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Globigerinidae" "Turborotalita" "quinqueloba" "egelida" "infraspecies" "Cifelli et al., 1970" "f72d08c8d3c733576d129f5e788bf3c1" "CoL" 3
"B_TRCBC" "Turicibacter" "Bacteria" "Firmicutes" "Erysipelotrichia" "Erysipelotrichales" "Turicibacteraceae" "Turicibacter" "" "" "genus" "" "8703c153e322e6afeba3ea4cf3a13b00" "CoL" 2
"B_TRCBC_SNGN" "Turicibacter sanguinis" "Bacteria" "Firmicutes" "Erysipelotrichia" "Erysipelotrichales" "Turicibacteraceae" "Turicibacter" "sanguinis" "" "species" "Bosshard et al., 2002" "e1a9359b6b6acbc7c50aa53e61a225d3" "CoL" 2 "440839009"
"B_[FAM]_TRCBCTRC" "Turicibacteraceae" "Bacteria" "Firmicutes" "Erysipelotrichia" "Erysipelotrichales" "Turicibacteraceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_TRCBCTRC" "Turicibacteraceae" "Bacteria" "Firmicutes" "Erysipelotrichia" "Erysipelotrichales" "Turicibacteraceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_TRCMN" "Turicimonas" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Sutterellaceae" "Turicimonas" "" "" "genus" "" "LPSN" 2
"B_TRCMN_MURS" "Turicimonas muris" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Sutterellaceae" "Turicimonas" "muris" "" "species" "Lagkouvardos et al., 2017" "793529" "LPSN" 2
"B_TRNRL" "Turneriella" "Bacteria" "Spirochaetes" "Spirochaetia" "Leptospirales" "Leptospiraceae" "Turneriella" "" "" "genus" "" "a94e392be1982a84b341aa5efdb70df9" "CoL" 3
@ -68048,7 +68048,7 @@
"B_USTTB" "Usitatibacter" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Usitatibacteraceae" "Usitatibacter" "" "" "genus" "Vieira et al., 2021" "17564" "LPSN" 2 "character(0)"
"B_USTTB_PLST" "Usitatibacter palustris" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Usitatibacteraceae" "Usitatibacter" "palustris" "" "species" "Vieira et al., 2021" "17571" "LPSN" 2 "character(0)"
"B_USTTB_RGSS" "Usitatibacter rugosus" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Usitatibacteraceae" "Usitatibacter" "rugosus" "" "species" "Vieira et al., 2021" "17572" "LPSN" 2 "character(0)"
"B_[FAM]_USTTBCTR" "Usitatibacteraceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Usitatibacteraceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_USTTBCTR" "Usitatibacteraceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Nitrosomonadales" "Usitatibacteraceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"F_UTHRM" "Utharomyces" "Fungi" "Zygomycota" "Mucoromycetes" "Mucorales" "Pilobolaceae" "Utharomyces" "" "" "genus" "" "ff5dc90bd5674f0677a9a19fa4566f5b" "CoL" 3
"F_UTHRM_EPLL" "Utharomyces epallocaulus" "Fungi" "Zygomycota" "Mucoromycetes" "Mucorales" "Pilobolaceae" "Utharomyces" "epallocaulus" "" "species" "Boedijn et al., 1980" "7ce527049ed49472ea68e45bf38e001b" "CoL" 3
"C_UVGRN" "Uvigerina" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Uvigerinidae" "Uvigerina" "" "" "genus" "" "3c39d33a30e5ebbed3091424bd1ae809" "CoL" 3
@ -68310,7 +68310,7 @@
"B_VLLTL_GYMS" "Vallitalea guaymasensis" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Vallitaleaceae" "Vallitalea" "guaymasensis" "" "species" "Lakhal et al., 2013" "790983" "LPSN" 2
"B_VLLTL_OKNW" "Vallitalea okinawensis" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Vallitaleaceae" "Vallitalea" "okinawensis" "" "species" "Sun et al., 2019" "799891" "LPSN" 2
"B_VLLTL_PRNY" "Vallitalea pronyensis" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Vallitaleaceae" "Vallitalea" "pronyensis" "" "species" "Ben Aissa et al., 2014" "791667" "LPSN" 2
"B_[FAM]_VALLITLC" "Vallitaleaceae" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Vallitaleaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_VALLITLC" "Vallitaleaceae" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Vallitaleaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"C_VLLPS" "Vallupus" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Pantanelliidae" "Vallupus" "" "" "genus" "" "8f85ff37118a029792f9a62d07db1026" "CoL" 3
"C_VLLPS_HPSN" "Vallupus hopsoni" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Pantanelliidae" "Vallupus" "hopsoni" "" "species" "Pessagno et al., 1984" "7b60983d03dc211e5bac148d01f2ee9c" "CoL" 3
"C_VLLPS_JPNC" "Vallupus japonicus" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Pantanelliidae" "Vallupus" "japonicus" "" "species" "Kawabata, 1988" "f43ca97f7e02521c9276a2c9364a0ed8" "CoL" 3
@ -68457,7 +68457,7 @@
"B_VLLNL_SMNL" "Veillonella seminalis" "Bacteria" "Firmicutes" "Negativicutes" "Veillonellales" "Veillonellaceae" "Veillonella" "seminalis" "" "species" "Aujoulat et al., 2014" "792209" "LPSN" 2
"B_VLLNL_TBTS" "Veillonella tobetsuensis" "Bacteria" "Firmicutes" "Negativicutes" "Veillonellales" "Veillonellaceae" "Veillonella" "tobetsuensis" "" "species" "Mashima et al., 2013" "790631" "LPSN" 2
"B_[FAM]_VELLNLLC" "Veillonellaceae" "Bacteria" "Firmicutes" "Negativicutes" "Selenomonadales" "Veillonellaceae" "" "" "" "family" "" "7d44edd71347e3bc307a13c9df11e82d" "CoL" 2
"B_[ORD]_VLLNLLLS" "Veillonellales" "Bacteria" "Firmicutes" "Negativicutes" "Veillonellales" "" "" "" "" "order" "" "CoL" 2 "NULL"
"B_[ORD]_VLLNLLLS" "Veillonellales" "Bacteria" "Firmicutes" "Negativicutes" "Veillonellales" "" "" "" "" "order" "" "CoL" 2 "character(0)"
"C_VLPTN" "Veleptingium" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Eptingiidae" "Veleptingium" "" "" "genus" "" "80a2f18d4b0f5bc8a7583198a83b3bb2" "CoL" 3
"C_VLPTN_ODGH" "Veleptingium odoghertyi" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Eptingiidae" "Veleptingium" "odoghertyi" "" "species" "Dumitrica et al., 2010" "d57e09a7e5a9e8ea941dbdeec5246b5e" "CoL" 3
"C_VLRNN" "Veleroninoides" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Haplophragmoididae" "Veleroninoides" "" "" "genus" "" "b977c58a9bf4c26618cec0fca294d834" "CoL" 3
@ -68470,7 +68470,7 @@
"C_VELLR_ZCCH" "Vellaria zucchellii" "Chromista" "Foraminifera" "Monothalamea" "Allogromiida" "Allogromiidae" "Vellaria" "zucchellii" "" "species" "Sabbatini et al., 2004" "46f5ed1b2aa94f7a2f5219792a0fb52f" "CoL" 3
"B_VNNVB" "Venenivibrio" "Bacteria" "Aquificae" "Aquificae" "Aquificales" "Hydrogenothermaceae" "Venenivibrio" "" "" "genus" "" "7b8e5e139ba024116fffef21ba79f6ec" "CoL" 3
"B_VNNVB_STGN" "Venenivibrio stagnispumantis" "Bacteria" "Aquificae" "Aquificae" "Aquificales" "Hydrogenothermaceae" "Venenivibrio" "stagnispumantis" "" "species" "Hetzer et al., 2008" "6d70c85ce355f1107601e055200755e0" "CoL" 3
"B_[FAM]_VNTSMNDC" "Ventosimonadaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Ventosimonadaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_VNTSMNDC" "Ventosimonadaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Ventosimonadaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_VNTSM" "Ventosimonas" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Ventosimonadaceae" "Ventosimonas" "" "" "genus" "" "LPSN" 1
"B_VNTSM_GRCL" "Ventosimonas gracilis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Ventosimonadaceae" "Ventosimonas" "gracilis" "" "species" "Lin et al., 2016" "794403" "LPSN" 1
"C_VNTRS" "Ventrostoma" "Chromista" "Foraminifera" "(unknown class)" "Lagenida" "Ellipsolagenidae" "Ventrostoma" "" "" "genus" "" "dc34bd0dbd0806dc4ed2132acdd4ea02" "CoL" 3
@ -68510,7 +68510,7 @@
"B_[ORD]_VRRCMCRB" "Verrucomicrobiales" "Bacteria" "Verrucomicrobia" "Verrucomicrobiae" "Verrucomicrobiales" "(unknown family)" "" "" "" "order" "" "3901448f99a0351c014d486b2aa0d0c5" "CoL" 2
"B_VRRCM" "Verrucomicrobium" "Bacteria" "Verrucomicrobia" "Verrucomicrobiae" "Verrucomicrobiales" "Verrucomicrobiaceae" "Verrucomicrobium" "" "" "genus" "" "66063b6260b74a2316a8c4db791c3bae" "CoL" 3
"B_VRRCM_SPNS" "Verrucomicrobium spinosum" "Bacteria" "Verrucomicrobia" "Verrucomicrobiae" "Verrucomicrobiales" "Verrucomicrobiaceae" "Verrucomicrobium" "spinosum" "" "species" "Schlesner, 1988" "fbcffaac4cf4d4176063d78b4fbff0ee" "CoL" 3
"B_VRRCS" "Verrucosispora" "Bacteria" "Actinobacteria" "Actinobacteria" "Micromonosporales" "Micromonosporaceae" "Verrucosispora" "" "" "genus" "" "LPSN" 2 "NULL"
"B_VRRCS" "Verrucosispora" "Bacteria" "Actinobacteria" "Actinobacteria" "Micromonosporales" "Micromonosporaceae" "Verrucosispora" "" "" "genus" "" "LPSN" 2 "character(0)"
"B_VRRCS_ENDP" "Verrucosispora endophytica" "Bacteria" "Actinobacteria" "Actinobacteria" "Micromonosporales" "Micromonosporaceae" "Verrucosispora" "endophytica" "" "species" "Ngaemthao et al., 2017" "796282" "LPSN" 2
"B_VRRCS_SNCH" "Verrucosispora sonchi" "Bacteria" "Actinobacteria" "Actinobacteria" "Micromonosporales" "Micromonosporaceae" "Verrucosispora" "sonchi" "" "species" "Ma et al., 2016" "794886" "LPSN" 2
"C_VRTBR" "Vertebralina" "Chromista" "Foraminifera" "Tubothalamea" "Miliolida" "Fischerinidae" "Vertebralina" "" "" "genus" "" "9b647f573d893fa8b20957a9754b25f2" "CoL" 3
@ -68682,8 +68682,8 @@
"B_[ORD]_VIBRINLS" "Vibrionales" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Vibrionales" "(unknown family)" "" "" "" "order" "" "dbfe8574a6bc99111ea7ab00e4d12127" "CoL" 1
"B_VCNMB" "Vicinamibacter" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "Vicinamibacteraceae" "Vicinamibacter" "" "" "genus" "" "LPSN" 3
"B_VCNMB_SLVS" "Vicinamibacter silvestris" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "Vicinamibacteraceae" "Vicinamibacter" "silvestris" "" "species" "Huber et al., 2016" "794351" "LPSN" 3
"B_[FAM]_VCNMBCTR" "Vicinamibacteraceae" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "Vicinamibacteraceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[ORD]_VCNMBCTR" "Vicinamibacterales" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "" "" "" "" "order" "" "LPSN" 3 "NULL"
"B_[FAM]_VCNMBCTR" "Vicinamibacteraceae" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "Vicinamibacteraceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_[ORD]_VCNMBCTR" "Vicinamibacterales" "Bacteria" "Acidobacteria" "Vicinamibacteria" "Vicinamibacterales" "" "" "" "" "order" "" "LPSN" 3 "character(0)"
"B_VCNGS" "Vicingus" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Cryomorphaceae" "Vicingus" "" "" "genus" "" "LPSN" 3
"B_VCNGS_SRPN" "Vicingus serpentipes" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Cryomorphaceae" "Vicingus" "serpentipes" "" "species" "Wiese et al., 2018" "797484" "LPSN" 3
"B_[FAM]_VICTVLLC" "Victivallaceae" "Bacteria" "Lentisphaerae" "Lentisphaeria" "Victivallales" "Victivallaceae" "" "" "" "family" "" "ac2947cd3db402cab04ced533e37672a" "CoL" 2
@ -69132,7 +69132,7 @@
"B_VLCNT_MDTL" "Vulcanithermus mediatlanticus" "Bacteria" "DeinococcusThermus" "Deinococci" "Thermales" "Thermaceae" "Vulcanithermus" "mediatlanticus" "" "species" "Miroshnichenko et al., 2003" "6525211d3cc270a7cf42164076a2fde3" "CoL" 3
"B_VLGTB" "Vulgatibacter" "Bacteria" "Proteobacteria" "Deltaproteobacteria" "Myxococcales" "Vulgatibacteraceae" "Vulgatibacter" "" "" "genus" "" "LPSN" 2
"B_VLGTB_INCM" "Vulgatibacter incomptus" "Bacteria" "Proteobacteria" "Deltaproteobacteria" "Myxococcales" "Vulgatibacteraceae" "Vulgatibacter" "incomptus" "" "species" "Yamamoto et al., 2014" "792215" "LPSN" 2
"B_[FAM]_VLGTBCTR" "Vulgatibacteraceae" "Bacteria" "Proteobacteria" "Deltaproteobacteria" "Myxococcales" "Vulgatibacteraceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_VLGTBCTR" "Vulgatibacteraceae" "Bacteria" "Proteobacteria" "Deltaproteobacteria" "Myxococcales" "Vulgatibacteraceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"C_VVLNA" "Vulvulina" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Spiroplectamminidae" "Vulvulina" "" "" "genus" "" "6d58e9733bf224e5910dca0a1d577fc7" "CoL" 3
"C_VVLNA_ARNC" "Vulvulina arenacea" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Spiroplectamminidae" "Vulvulina" "arenacea" "" "species" "Bagg, 1908" "a94334ee953037434c22d298ffaaba0a" "CoL" 3
"C_VVLNA_COLE" "Vulvulina colei" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Spiroplectamminidae" "Vulvulina" "colei" "" "species" "Cushman, 1932" "5fb533bd9fcb7ef284044632ef3be469" "CoL" 3
@ -69179,8 +69179,8 @@
"C_WRRNT" "Warrenita" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Hormosinidae" "Warrenita" "" "" "genus" "" "cf86c79938b945536aebfa8a4d232e87" "CoL" 3
"C_WRRNT_PLST" "Warrenita palustris" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Hormosinidae" "Warrenita" "palustris" "" "species" "Warren, 1957" "8b59afcf26c36a303fc0e071f82706c2" "CoL" 3
"C_[FAM]_WATZNARC" "Watznaueriaceae" "Chromista" "Haptophyta" "Coccolithophyceae" "Watznaueriales" "Watznaueriaceae" "" "" "" "family" "" "CoL" 2
"C_[ORD]_WATZNRLS" "Watznaueriales" "Chromista" "Haptophyta" "Coccolithophyceae" "Watznaueriales" "" "" "" "" "order" "" "CoL" 3 "NULL"
"B_WATRS" "Wautersia" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Wautersia" "" "" "genus" "" "LPSN" 2 "NULL"
"C_[ORD]_WATZNRLS" "Watznaueriales" "Chromista" "Haptophyta" "Coccolithophyceae" "Watznaueriales" "" "" "" "" "order" "" "CoL" 3 "character(0)"
"B_WATRS" "Wautersia" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Wautersia" "" "" "genus" "" "LPSN" 2 "character(0)"
"B_WATRS_NMZN" "Wautersia numazuensis" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Burkholderiales" "Burkholderiaceae" "Wautersia" "numazuensis" "" "species" "Kageyama et al., 2005" "783083" "LPSN" 2 "character(0)"
"B_WTRSL" "Wautersiella" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "Wautersiella" "" "" "genus" "" "b02f9cd342750409a6202b3433eb2054" "CoL" 3 "450449008"
"B_WTRSL_FLSN" "Wautersiella falsenii" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "Wautersiella" "falsenii" "" "species" "Kampfer et al., 2006" "9451ec288e9b10a9250d92a736a78f35" "CoL" 3 "450452000"
@ -69199,7 +69199,7 @@
"B_WKSLL" "Weeksella" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "Weeksella" "" "" "genus" "" "e9bdb4874ffed96bc180f56d0bb1b655" "CoL" 3 "28853003"
"B_WKSLL_MSSL" "Weeksella massiliensis" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "Weeksella" "massiliensis" "" "species" "Sankar et al., 2017" "795593" "LPSN" 3
"B_WKSLL_VIRS" "Weeksella virosa" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "Weeksella" "virosa" "" "species" "Holmes et al., 1987" "48559ca26a4647b08d86efee24b835d0" "CoL" 3 "83326004"
"B_[FAM]_WEEKSLLC" "Weeksellaceae" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_WEEKSLLC" "Weeksellaceae" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Weeksellaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"P_WEISR" "Weiseria" "Protozoa" "Microsporidia" "Microsporea" "Dissociodihaplophasida" "Caudosporidae" "Weiseria" "" "" "genus" "" "a4b226f834db6b6663564efb1845e2da" "CoL" 3
"P_WEISR_LRNT" "Weiseria laurentii" "Protozoa" "Microsporidia" "Microsporea" "Dissociodihaplophasida" "Caudosporidae" "Weiseria" "laurentii" "" "species" "Doby et al., 1964" "d6ef9be60b943c199797977491e87221" "CoL" 3
"P_WEISR_PLST" "Weiseria palustris" "Protozoa" "Microsporidia" "Microsporea" "Dissociodihaplophasida" "Caudosporidae" "Weiseria" "palustris" "" "species" "Anon ined" "4582799afc38b51ecee864c2e9dc06af" "CoL" 3
@ -69249,7 +69249,7 @@
"B_WNZHX_LIMI" "Wenzhouxiangella limi" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Wenzhouxiangellaceae" "Wenzhouxiangella" "limi" "" "species" "Zhang et al., 2020" "8904" "LPSN" 1 "character(0)"
"B_WNZHX_MARN" "Wenzhouxiangella marina" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Wenzhouxiangellaceae" "Wenzhouxiangella" "marina" "" "species" "Wang et al., 2015" "793226" "LPSN" 1
"B_WNZHX_SDMN" "Wenzhouxiangella sediminis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Wenzhouxiangellaceae" "Wenzhouxiangella" "sediminis" "" "species" "Guo et al., 2016" "794861" "LPSN" 1
"B_[FAM]_WNZHXNGL" "Wenzhouxiangellaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Wenzhouxiangellaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_WNZHXNGL" "Wenzhouxiangellaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Wenzhouxiangellaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"C_WVRLL" "Weverella" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Capnuchosphaeridae" "Weverella" "" "" "genus" "" "a08767d81529ce6960f1694f5ce66a9c" "CoL" 3
"C_WVRLL_GRCL" "Weverella gracilispinosa" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Capnuchosphaeridae" "Weverella" "gracilispinosa" "" "species" "Kozur et al., 2009" "2e1934915a86ac1c08ceb8c6f06f1df8" "CoL" 3
"C_WVRLL_LNGS" "Weverella longispinosa" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Capnuchosphaeridae" "Weverella" "longispinosa" "" "species" "Kozur et al., 2009" "31699d6952896dde359303d7ed4439cc" "CoL" 3
@ -69338,7 +69338,7 @@
"B_WLLMSN_SMNL" "Williamsoniiplasma somnilux" "Bacteria" "Tenericutes" "Mollicutes" "Mycoplasmatales" "Mycoplasmataceae" "Williamsoniiplasma" "somnilux" "" "species" "Gupta et al., 2019" "801383" "LPSN" 3 "character(0)"
"B_WLLMW" "Williamwhitmania" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Williamwhitmaniaceae" "Williamwhitmania" "" "" "genus" "" "LPSN" 3
"B_WLLMW_TRXC" "Williamwhitmania taraxaci" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Williamwhitmaniaceae" "Williamwhitmania" "taraxaci" "" "species" "Pikuta et al., 2017" "796067" "LPSN" 3
"B_[FAM]_WLLMWHTM" "Williamwhitmaniaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Williamwhitmaniaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_WLLMWHTM" "Williamwhitmaniaceae" "Bacteria" "Bacteroidetes" "Bacteroidia" "Bacteroidales" "Williamwhitmaniaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"F_WLLPS" "Williopsis" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Saccharomycetaceae" "Williopsis" "" "" "genus" "" "9cff5d4b014569fb3ff6bfb01ef76001" "CoL" 3
"F_WLLPS_BLGR" "Williopsis bulgarica" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Saccharomycetaceae" "Williopsis" "bulgarica" "" "species" "Garab et al., 1970" "962bebf9e46fc7022d4c488eb2964dcb" "CoL" 3
"C_[FAM]_WLLRDLLD" "Williriedellidae" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Williriedellidae" "" "" "" "family" "" "a0f4b942b466a3c2f4a449d56e5132e2" "CoL" 2
@ -69417,7 +69417,7 @@
"B_WOCAN_INDC" "Wocania indica" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Wocania" "indica" "" "species" "He et al., 2020" "12796" "LPSN" 3 "character(0)"
"B_WOESE" "Woeseia" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Woeseiaceae" "Woeseia" "" "" "genus" "" "LPSN" 1
"B_WOESE_OCEN" "Woeseia oceani" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Woeseiaceae" "Woeseia" "oceani" "" "species" "Du et al., 2016" "793768" "LPSN" 1
"B_[FAM]_WOESEIAC" "Woeseiaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Woeseiaceae" "" "" "" "family" "" "LPSN" 1 "NULL"
"B_[FAM]_WOESEIAC" "Woeseiaceae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Chromatiales" "Woeseiaceae" "" "" "" "family" "" "LPSN" 1 "character(0)"
"B_WHLFH" "Wohlfahrtiimonas" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "" "Wohlfahrtiimonas" "" "" "genus" "" "6f3108c95b28d654ae98e28e661a6afd" "CoL" 1 "709032002"
"B_WHLFH_CHTN" "Wohlfahrtiimonas chitiniclastica" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "" "Wohlfahrtiimonas" "chitiniclastica" "" "species" "Toth et al., 2008" "c8d928223dd674382ba94dfb28137456" "CoL" 1 "709033007"
"B_WHLFH_LARV" "Wohlfahrtiimonas larvae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "" "" "Wohlfahrtiimonas" "larvae" "" "species" "Lee et al., 2014" "791770" "LPSN" 1
@ -69517,7 +69517,7 @@
"F_XNTHT_PRVN" "Xanthothecium peruvianum" "Fungi" "Ascomycota" "Eurotiomycetes" "Onygenales" "Onygenaceae" "Xanthothecium" "peruvianum" "" "species" "Arx et al., 1973" "ec9a22380f2f3be13e03c15d91de42f5" "CoL" 3
"B_XNTHV" "Xanthovirga" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Flammeovirgaceae" "Xanthovirga" "" "" "genus" "Goldberg et al., 2020" "7250" "LPSN" 3 "character(0)"
"B_XNTHV_APLY" "Xanthovirga aplysinae" "Bacteria" "Bacteroidetes" "Cytophagia" "Cytophagales" "Flammeovirgaceae" "Xanthovirga" "aplysinae" "" "species" "Goldberg et al., 2020" "7330" "LPSN" 3 "character(0)"
"B_[FAM]_XENOCCCC" "Xenococcaceae" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Pleurocapsales" "Xenococcaceae" "" "" "" "family" "" "LPSN" 3 "NULL"
"B_[FAM]_XENOCCCC" "Xenococcaceae" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Pleurocapsales" "Xenococcaceae" "" "" "" "family" "" "LPSN" 3 "character(0)"
"B_XNCCC" "Xenococcus" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Pleurocapsales" "Xenococcaceae" "Xenococcus" "" "" "genus" "" "07f7637b90a16d3a43321c87e5fbd232" "CoL" 3
"B_XNCCC_KRNR" "Xenococcus kerneri" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Pleurocapsales" "Xenococcaceae" "Xenococcus" "kerneri" "" "species" "" "5dda49b62f447585e2efc3f962e2f663" "CoL" 3
"B_XNCCC_LMNR" "Xenococcus laminariae" "Bacteria" "Cyanobacteria" "Cyanophyceae" "Pleurocapsales" "Xenococcaceae" "Xenococcus" "laminariae" "" "species" "" "cc26b9d017917a398b8d3b3ed12ea326" "CoL" 3
@ -69627,7 +69627,7 @@
"B_XNMNS_ULMI" "Xylanimonas ulmi" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Promicromonosporaceae" "Xylanimonas" "ulmi" "" "species" "Heo et al., 2020" "5930" "LPSN" 2 "character(0)"
"B_XYLNV" "Xylanivirga" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Xylanivirgaceae" "Xylanivirga" "" "" "genus" "Liu et al., 2020" "8891" "LPSN" 2 "character(0)"
"B_XYLNV_THRM" "Xylanivirga thermophila" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Xylanivirgaceae" "Xylanivirga" "thermophila" "" "species" "Liu et al., 2020" "15256" "LPSN" 2 "character(0)"
"B_[FAM]_XYLNVRGC" "Xylanivirgaceae" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Xylanivirgaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_XYLNVRGC" "Xylanivirgaceae" "Bacteria" "Firmicutes" "Clostridia" "Eubacteriales" "Xylanivirgaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_XYLLL" "Xylella" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xylella" "" "" "genus" "" "e4bda0fe0740a9f4b8efd32ffb43a750" "CoL" 1
"B_XYLLL_FSTD" "Xylella fastidiosa" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xylella" "fastidiosa" "" "species" "Wells et al., 1987" "a117ebd7b714db0fe51d7aedd0abfebf" "CoL" 1
"B_XYLLL_FSTD_FSTD" "Xylella fastidiosa fastidiosa" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Lysobacterales" "Lysobacteraceae" "Xylella" "fastidiosa" "fastidiosa" "subsp." "Schaad et al., 2009" "787835" "LPSN" 1 "character(0)"
@ -69757,7 +69757,7 @@
"B_ZVRZN" "Zavarzinia" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Zavarziniaceae" "Zavarzinia" "" "" "genus" "" "5b67c3612144e487780a986c167f31b3" "CoL" 2
"B_ZVRZN_AQTL" "Zavarzinia aquatilis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Zavarziniaceae" "Zavarzinia" "aquatilis" "" "species" "Lee et al., 2019" "800146" "LPSN" 2
"B_ZVRZN_CMPR" "Zavarzinia compransoris" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Zavarziniaceae" "Zavarzinia" "compransoris" "" "species" "Meyer et al., 1994" "22706dd78f01cc6550f4d8adae35c7a8" "CoL" 2
"B_[FAM]_ZAVARZNC" "Zavarziniaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Zavarziniaceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_ZAVARZNC" "Zavarziniaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Rhodospirillales" "Zavarziniaceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"C_ZVDVS" "Zavodovskina" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Trochamminidae" "Zavodovskina" "" "" "genus" "" "a2f21b35d2a1cfbfabbeb941b7e9c5f0" "CoL" 3
"C_ZVDVS_CARY" "Zavodovskina careyi" "Chromista" "Foraminifera" "Globothalamea" "Lituolida" "Trochamminidae" "Zavodovskina" "careyi" "" "species" "Bronnimann et al., 1988" "832bf44e4050cc291526594a69e9d993" "CoL" 3
"C_ZFLRL" "Zeaflorilus" "Chromista" "Foraminifera" "Globothalamea" "Rotaliida" "Nonionidae" "Zeaflorilus" "" "" "genus" "" "88ccb9d7e23a27d26797862aa02136b4" "CoL" 3
@ -69785,7 +69785,7 @@
"C_ZHMJD_PRCR" "Zhamojdasphaera proceruspinosa" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Stylosphaeridae" "Zhamojdasphaera" "proceruspinosa" "" "species" "Lahm, 1984" "39a47d23c803535745f5935ddf2625b0" "CoL" 3
"B_ZHNLL" "Zhaonella" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Zhaonellaceae" "Zhaonella" "" "" "genus" "Lv et al., 2020" "7454" "LPSN" 2 "character(0)"
"B_ZHNLL_FRMC" "Zhaonella formicivorans" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Zhaonellaceae" "Zhaonella" "formicivorans" "" "species" "Lv et al., 2020" "7567" "LPSN" 2 "character(0)"
"B_[FAM]_ZHAONLLC" "Zhaonellaceae" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Zhaonellaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_ZHAONLLC" "Zhaonellaceae" "Bacteria" "Firmicutes" "Clostridia" "Thermoanaerobacterales" "Zhaonellaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"B_ZHNGL" "Zhengella" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Zhengella" "" "" "genus" "" "LPSN" 2
"B_ZHNGL_MNGR" "Zhengella mangrovi" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Hyphomicrobiales" "Notoacmeibacteraceae" "Zhengella" "mangrovi" "" "species" "Liao et al., 2018" "797832" "LPSN" 2
"B_ZHHNG" "Zhihengliuella" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Micrococcaceae" "Zhihengliuella" "" "" "genus" "" "ac547ae1868c6a70b3d06b1d5cdd0c05" "CoL" 2
@ -69807,7 +69807,7 @@
"B_ZHOUI_SPNG" "Zhouia spongiae" "Bacteria" "Bacteroidetes" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Zhouia" "spongiae" "" "species" "Zhuang et al., 2018" "797795" "LPSN" 3
"C_ZFNDM" "Zifondium" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Archaeodictyomitridae" "Zifondium" "" "" "genus" "" "cd70fd2f51a6e377d2802e66086a8c9a" "CoL" 3
"C_ZFNDM_LSSN" "Zifondium lassenensis" "Chromista" "Radiozoa" "Polycystina" "Paleo_radiozoa" "Archaeodictyomitridae" "Zifondium" "lassenensis" "" "species" "Pessagno, 1977" "cadf0ccfad07d735be2d2595cd468428" "CoL" 3
"B_ZMMRM" "Zimmermannella" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Zimmermannella" "" "" "genus" "" "CoL" 2 "NULL"
"B_ZMMRM" "Zimmermannella" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Zimmermannella" "" "" "genus" "" "CoL" 2 "character(0)"
"B_ZMMRM_ALBA" "Zimmermannella alba" "Bacteria" "Actinobacteria" "Actinobacteria" "Micrococcales" "Microbacteriaceae" "Zimmermannella" "alba" "" "species" "Lin et al., 2004" "ca5b7bfcc56c8aa9e6ca205d8b66bc71" "CoL" 2
"B_ZBLLL" "Zobellella" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Aeromonadales" "Aeromonadaceae" "Zobellella" "" "" "genus" "" "51c3fcfe669790d25fd97f47567fec75" "CoL" 1
"B_ZBLLL_AERP" "Zobellella aerophila" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Aeromonadales" "Aeromonadaceae" "Zobellella" "aerophila" "" "species" "Yi et al., 2011" "50912d446eed8233b233892052089ca0" "CoL" 1
@ -69828,7 +69828,7 @@
"B_ZOOGL_ORYZ" "Zoogloea oryzae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Rhodocyclales" "Zoogloeaceae" "Zoogloea" "oryzae" "" "species" "Xie et al., 2006" "8d3e70429ca7e98ea8377e6162a56e58" "CoL" 2
"B_ZOOGL_RMGR" "Zoogloea ramigera" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Rhodocyclales" "Zoogloeaceae" "Zoogloea" "ramigera" "" "species" "Itzigsohn, 1868" "c3b17c89881aa1f6935a5cc1c393e894" "CoL" 2
"B_ZOOGL_RSNP" "Zoogloea resiniphila" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Rhodocyclales" "Zoogloeaceae" "Zoogloea" "resiniphila" "" "species" "Mohn et al., 1999" "ec05679ed98314a8b2da69e012f7008b" "CoL" 2
"B_[FAM]_ZOOGLOEC" "Zoogloeaceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Rhodocyclales" "Zoogloeaceae" "" "" "" "family" "" "LPSN" 2 "NULL"
"B_[FAM]_ZOOGLOEC" "Zoogloeaceae" "Bacteria" "Proteobacteria" "Betaproteobacteria" "Rhodocyclales" "Zoogloeaceae" "" "" "" "family" "" "LPSN" 2 "character(0)"
"P_[CLS]_ZMSTGPHR" "Zoomastigophora" "Protozoa" "Sarcomastigophora" "Zoomastigophora" "(unknown order)" "(unknown family)" "" "" "" "class" "" "39ebe84ee9d1011bde2ce21b896afee7" "CoL" 3
"B_ZSHKL" "Zooshikella" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Hahellaceae" "Zooshikella" "" "" "genus" "" "172da1620442028c7bbd9106020269cc" "CoL" 1
"B_ZSHKL_GNGH" "Zooshikella ganghwensis" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Hahellaceae" "Zooshikella" "ganghwensis" "" "species" "Yi et al., 2003" "5cab7b61bed109e32e3a763ee0eb8764" "CoL" 1
@ -70019,7 +70019,7 @@
"F_ZYGTR_MRAK" "Zygotorulaspora mrakii" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "Saccharomycetaceae" "Zygotorulaspora" "mrakii" "" "species" "Kurtzman, 2003" "38dc88e91d1894b6b375569398abff63" "CoL" 3
"B_ZYMBC" "Zymobacter" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Halomonadaceae" "Zymobacter" "" "" "genus" "" "8b17264b62ae9d1496177f4050b6bda2" "CoL" 1
"B_ZYMBC_PALM" "Zymobacter palmae" "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Oceanospirillales" "Halomonadaceae" "Zymobacter" "palmae" "" "species" "Okamoto et al., 1995" "43198dad22d51bd21db3f82cd7114d23" "CoL" 1
"B_[FAM]_ZYMOMNDC" "Zymomonadaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Zymomonadaceae" "" "" "" "family" "" "CoL" 2 "NULL"
"B_[FAM]_ZYMOMNDC" "Zymomonadaceae" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Zymomonadaceae" "" "" "" "family" "" "CoL" 2 "character(0)"
"B_ZYMMN" "Zymomonas" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Zymomonadaceae" "Zymomonas" "" "" "genus" "" "25b3abf7a32fcaf405119a0ea113c754" "CoL" 2
"B_ZYMMN_MBLS" "Zymomonas mobilis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Zymomonadaceae" "Zymomonas" "mobilis" "" "species" "Kluyver et al., 1936" "a5ea7d5a6c283d01c62585fa78f10e94" "CoL" 2
"B_ZYMMN_MBLS_FRNC" "Zymomonas mobilis francensis" "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Sphingomonadales" "Zymomonadaceae" "Zymomonas" "mobilis" "francensis" "infraspecies" "Coton et al., 2006" "36b67004b5e483305be11aa516aea2f4" "CoL" 2

Binary file not shown.

@ -1 +1 @@
9b7ed0125f6b59c4bf111b5770e5d619
8c6d0e8e487d19d9a429abd64fce9290

@ -292,9 +292,7 @@ MOs <- MOs %>%
| rank %in% c("kingdom", "phylum", "class", "order", "family"))
~ 2,
TRUE ~ 3
)) %>%
# clean up
df_remove_nonASCII()
))
# add all mssing genera, families and orders
MOs <- MOs %>%
@ -359,14 +357,9 @@ MOs <- MOs %>%
) %>%
arrange(fullname)
# clean snomed
for (i in 1:nrow(MOs)) {
sno <- as.character(sort(unique(tolower(MOs[i, "snomed"][[1]]))))
if (length(sno) > 0) {
MOs[i, "snomed"][[1]] <- ifelse(length(sno[!sno == ""]) == 0, list(""), list(sno))
}
}
# clean up
MOs <- MOs %>%
df_remove_nonASCII()
# Merge synonyms ----------------------------------------------------------

Binary file not shown.

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>
@ -211,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>class</em>, <em>family</em>, <em>fullname</em>, <em>genus</em>, <em>kingdom</em>, <em>mo</em>, <em>order</em>, <em>phylum</em>, <em>prevalence</em>, <em>rank</em>, <em>ref</em>, <em>snomed</em>, <em>source</em>, <em>species</em>, <em>species_id</em> and <em>subspecies</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 5 March 2021 01:01:21 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 5 March 2021 09:32:45 CET. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
@ -234,7 +234,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: )</li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
</ul>
</div>
<div id="example-content" class="section level3">
@ -453,7 +453,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: )</li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
</ul>
</div>
<div id="example-content-1" class="section level3">

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509029" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9029">
<a href="#amr-1509029" class="anchor"></a>AMR 1.5.0.9029<small> Unreleased </small>
<div id="amr-1509030" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9030">
<a href="#amr-1509030" class="anchor"></a>AMR 1.5.0.9030<small> Unreleased </small>
</h1>
<div id="last-updated-5-march-2021" class="section level2">
<h2 class="hasAnchor">
@ -308,9 +308,9 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Microbial taxonomy updated to 3 March 2021 (according to the <a href="https://lpsn.dsmz.de">LSPN</a>)
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LSPN</a>)
<ul>
<li>Added 3,372 new names and 1,523 existing names became synomyms</li>
<li>Added 3,372 new species and 1,523 existing species became synomyms</li>
<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
</li>
</ul>
@ -349,6 +349,7 @@
<li>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code>
</li>
<li>Added translations of German and Spanish for more than 200 antimicrobial drugs</li>
<li>Speed improvement for <code><a href="../reference/as.ab.html">as.ab()</a></code> when the input is an official name or ATC code</li>
</ul>
</div>
<div id="other" class="section level3">
@ -1263,7 +1264,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Based on the Compound ID, almost 5,000 official brand names have been added from many different countries</li>
<li>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</li>
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</li>
<li>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</li>
<li>All <code>atc_*</code> functions are superseded by <code>ab_*</code> functions</li>
<li>All output will be translated by using an included translation file which <a href="https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a>
</li>
</ul>

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-03-05T00:31Z
last_built: 2021-03-05T09:15Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9030</span>
</span>
</div>

@ -88,13 +88,11 @@ test_that("CoL version info works", {
})
test_that("CoNS/CoPS are up to date", {
skip_on_cran()
uncategorised <- subset(microorganisms,
genus == "Staphylococcus" &
!species %in% c("", "aureus") &
!mo %in% c(MO_CONS, MO_COPS))
if (NROW(uncategorised) > 0) {
warning(paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")\n"))
}
expect(NROW(uncategorised) == 0,
failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")"))
})

@ -109,7 +109,7 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
Our full taxonomy of microorganisms is based on the authoritative and comprehensive:
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, included version: `r AMR:::catalogue_of_life$yearmonth_DSMZ`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::catalogue_of_life$yearmonth_LPSN`)
### Example content
@ -148,7 +148,7 @@ This data set is in R available as `microorganisms.old`, after you load the `AMR
This data set contains old, previously accepted taxonomic names. The data sources are the same as the `microorganisms` data set:
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, included version: `r AMR:::catalogue_of_life$yearmonth_DSMZ`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, last updated: `r AMR:::catalogue_of_life$yearmonth_LPSN`)
### Example content

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