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We processed the genomes included in Metaref with PhyloPhlAn, a pipeline developed for confidently detecting inconsistencies between the microbial taxonomy and phylogeny that can be explained only assuming taxonomic mislabeling. Using the pipeline we were able to detect these inconsistencies and provide more plausible assignments when this was possible at high confidence. The pipeline also refines the assignments by providing species-level placements for taxa previously assigned at genus-level only

Taxonomy Correction

GenomeOriginal and Corrected Lineage
Acidiphilium sp. PM, DSM 24941 f__Acetobacteraceae.g__Acidiphilium.s__?.t__t651324003
f__Acetobacteraceae.g__Acidiphilium.s__multivorum.t__651324003
Acidovorax ebreus TPSY f__Comamonadaceae.g__Acidovorax.s__?.t__t643348541
f__Comamonadaceae.g__Alicycliphilus.s__denitrificans.t__643348541
Acidovorax sp. JS42 f__Comamonadaceae.g__Acidovorax.s__?.t__t639633003
f__Comamonadaceae.g__Alicycliphilus.s__denitrificans.t__639633003
Acinetobacter baumannii 6013113 f__Moraxellaceae.g__Acinetobacter.s__?.t__t647000203
f__Moraxellaceae.g__Acinetobacter.s__baumannii.t__647000203
Acinetobacter baumannii 6013150 f__Moraxellaceae.g__Acinetobacter.s__?.t__t647000204
f__Moraxellaceae.g__Acinetobacter.s__baumannii.t__647000204
Acinetobacter baumannii 6014059 f__Moraxellaceae.g__Acinetobacter.s__?.t__t647000205
f__Moraxellaceae.g__Acinetobacter.s__baumannii.t__647000205
Acinetobacter sp. DR1 f__Moraxellaceae.g__Acinetobacter.s__?.t__t648028004
f__Moraxellaceae.g__Acinetobacter.s__calcoaceticus.t__648028004
Acinetobacter sp. RUH2624 f__Moraxellaceae.g__Acinetobacter.s__?.t__t647533107
f__Moraxellaceae.g__Acinetobacter.s__baumannii.t__647533107
Acinetobacter sp. SH024 f__Moraxellaceae.g__Acinetobacter.s__?.t__t647533108
f__Moraxellaceae.g__Acinetobacter.s__calcoaceticus.t__647533108
Actinomyces sp. oral taxon 178 F0338 f__Actinomycetaceae.g__Actinomyces.s__?.t__t649989903
f__Actinomycetaceae.g__Actinomyces.s__odontolyticus.t__649989903
Actinomyces sp. oral taxon 180 F0310 f__Actinomycetaceae.g__Actinomyces.s__?.t__t649989904
f__Actinomycetaceae.g__Actinomyces.s__odontolyticus.t__649989904
Afipia sp. 1NLS2 f__Bradyrhizobiaceae.g__Afipia.s__?.t__t648276616
f__Bradyrhizobiaceae.g__Oligotropha.s__carboxidovorans.t__648276616
Agreia sp. PHSC20C1 f__Microbacteriaceae.g__Agreia.s__?.t__t638341246
f__Microbacteriaceae.g__Clavibacter.s__michiganensis.t__638341246
Agrobacterium sp. ATCC 31749 f__Rhizobiaceae.g__Agrobacterium.s__?.t__t651324008
f__Rhizobiaceae.g__Agrobacterium.s__umefaciens.t__651324008
Agrobacterium sp. H13-3 f__Rhizobiaceae.g__Agrobacterium.s__?.t__t650716007
f__Rhizobiaceae.g__Agrobacterium.s__umefaciens.t__650716007
Anaeromyxobacter sp K f__Myxococcaceae.g__Anaeromyxobacter.s__?.t__t642555106
f__Myxococcaceae.g__Anaeromyxobacter.s__dehalogenans.t__642555106
Anaeromyxobacter sp. Fw109-5 f__Myxococcaceae.g__Anaeromyxobacter.s__?.t__t640753003
f__Myxococcaceae.g__Anaeromyxobacter.s__dehalogenans.t__640753003
Arthrospira sp. PCC 8005 f__Phormidiaceae.g__Arthrospira.s__?.t__t648276619
f__Phormidiaceae.g__Arthrospira.s__maxima.t__648276619
Bacillus sp. BT1B_CT2 f__Bacillaceae.g__Bacillus.s__?.t__t649989910
f__Bacillaceae.g__Bacillus.s__licheniformis.t__649989910
Bacteroides dorei 5_1_36/D4 f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206258
f__Bacteroidaceae.g__Bacteroides.s__dorei.t__646206258
Bacteroides sp. 1_1_6 f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206272
f__Bacteroidaceae.g__Bacteroides.s__hetaiotaomicron.t__646206272
Bacteroides sp. 2_1_16 f__Bacteroidaceae.g__Bacteroides.s__?.t__t647533110
f__Bacteroidaceae.g__Bacteroides.s__fragilis.t__647533110
Bacteroides sp. 2_1_22 f__Bacteroidaceae.g__Bacteroides.s__?.t__t647533111
f__Bacteroidaceae.g__Bacteroides.s__ovatus.t__647533111
Bacteroides sp. 2_1_56FAA f__Bacteroidaceae.g__Bacteroides.s__?.t__t651324014
f__Bacteroidaceae.g__Bacteroides.s__fragilis.t__651324014
Bacteroides sp. 2_1_7 f__Bacteroidaceae.g__Bacteroides.s__?.t__t645058782
f__Porphyromonadaceae.g__Parabacteroides.s__distasonis.t__645058782
Bacteroides sp. 2_2_4 f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206266
f__Bacteroidaceae.g__Bacteroides.s__ovatus.t__646206266
Bacteroides sp. 3_1_23 f__Bacteroidaceae.g__Bacteroides.s__?.t__t648861003
f__Bacteroidaceae.g__Bacteroides.s__ovatus.t__648861003
Bacteroides sp. 3_1_33FAA f__Bacteroidaceae.g__Bacteroides.s__?.t__t647533113
f__Bacteroidaceae.g__Bacteroides.s__dorei.t__647533113
Bacteroides sp. 3_1_40A f__Bacteroidaceae.g__Bacteroides.s__?.t__t649989913
f__Bacteroidaceae.g__Bacteroides.s__vulgatus.t__649989913
Bacteroides sp. 3_2_5 f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206273
f__Bacteroidaceae.g__Bacteroides.s__fragilis.t__646206273
Bacteroides sp. 4_1_36 f__Bacteroidaceae.g__Bacteroides.s__?.t__t649989914
f__Bacteroidaceae.g__Bacteroides.s__uniformis.t__649989914
Bacteroides sp. 4_3_47FAA f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206274
f__Bacteroidaceae.g__Bacteroides.s__vulgatus.t__646206274
Bacteroides sp. 9_1_42FAA f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206263
f__Bacteroidaceae.g__Bacteroides.s__dorei.t__646206263
Bacteroides sp. D1 f__Bacteroidaceae.g__Bacteroides.s__?.t__t646206264
f__Bacteroidaceae.g__Bacteroides.s__ovatus.t__646206264
Bacteroides sp. D2 f__Bacteroidaceae.g__Bacteroides.s__?.t__t645951811
f__Bacteroidaceae.g__Bacteroides.s__ovatus.t__645951811
Bacteroides sp. D20 f__Bacteroidaceae.g__Bacteroides.s__?.t__t647533114
f__Bacteroidaceae.g__Bacteroides.s__uniformis.t__647533114
Bifidobacterium sp. 12_1_47BFAA f__Bifidobacteriaceae.g__Bifidobacterium.s__?.t__t649989916
f__Bifidobacteriaceae.g__Bifidobacterium.s__longum.t__649989916
Borrelia burgdorferi SV1 f__Borreliaceae.g__Borrelia.s__?.t__t642791624
f__Borreliaceae.g__Borrelia.s__burgdorferi.t__642791624
Bradyrhizobiaceae bacterium SG-6C f__Bradyrhizobiaceae.g__?.s__?.t__t651324015
f__Bradyrhizobiaceae.g__Oligotropha.s__carboxidovorans.t__651324015
Brucella sp. F5/99 f__Brucellaceae.g__Brucella.s__?.t__t645951812
f__Brucellaceae.g__Brucella.s__ceti.t__645951812
Burkholderia cepacia 383 f__Burkholderiaceae.g__Burkholderia.s__?.t__t637000051
f__Burkholderiaceae.g__Burkholderia.s__cenocepacia.t__637000051
Burkholderiales bacterium 1_1_47 f__Sutterellaceae.g__Parasutterella.s__?.t__t648861006
f__Sutterellaceae.g__Parasutterella.s__excrementihominis.t__648861006
Chloroflexus sp. Y-400-fl f__Chloroflexaceae.g__Chloroflexus.s__?.t__t643692015
f__Chloroflexaceae.g__Chloroflexus.s__aurantiacus.t__643692015
Clostridiales sp. SM4/1 f__?.g__?.s__?.t__t650377988
f__Clostridiaceae.g__Clostridium.s__symbiosum.t__650377988
Clostridiales sp. SS3/4 f__?.g__?.s__?.t__t650377989
f__Clostridiaceae.g__Clostridium.s__symbiosum.t__650377989
Clostridium cf. saccharolyticum K10 f__Clostridiaceae.g__Clostridium.s__?.t__t650377923
f__Clostridiaceae.g__Clostridium.s__symbiosum.t__650377923
Clostridium sp M62/1 f__Clostridiaceae.g__Clostridium.s__?.t__t643886005
f__Clostridiaceae.g__Clostridium.s__symbiosum.t__643886005
Enterococcus faecalis PC4.1 f__Enterococcaceae.g__Enterococcus.s__faecalis.t__t647000238
f__Enterococcaceae.g__Enterococcus.s__faecium.t__647000238
Erwinia sp. Ejp617 f__Enterobacteriaceae.g__Erwinia.s__?.t__t650377931
f__Enterobacteriaceae.g__Erwinia.s__pyrifoliae.t__650377931
Escherichia sp. 3_2_53FAA f__Enterobacteriaceae.g__Escherichia.s__?.t__t646206259
f__Enterobacteriaceae.g__Escherichia.s__coli.t__646206259
Escherichia sp. 4_1_40B f__Enterobacteriaceae.g__Escherichia.s__?.t__t645058836
f__Enterobacteriaceae.g__Escherichia.s__coli.t__645058836
Faecalibacterium cf. prausnitzii KLE1255 f__Ruminococcaceae.g__Faecalibacterium.s__?.t__t649989951
f__Ruminococcaceae.g__Faecalibacterium.s__prausnitzii.t__649989951
Francisella sp. TX077308 f__Francisellaceae.g__Francisella.s__?.t__t650716037
f__Francisellaceae.g__Francisella.s__philomiragia.t__650716037
Fusobacterium sp. 11_3_2 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t651324032
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__651324032
Fusobacterium sp. 21_1A f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t651324033
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__651324033
Fusobacterium sp. 3_1_27 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t647533169
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__647533169
Fusobacterium sp. 3_1_33 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t647533170
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__647533170
Fusobacterium sp. 3_1_36A2 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t647533171
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__647533171
Fusobacterium sp. 4_1_13 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t646206253
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__646206253
Fusobacterium sp. 7_1 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t646206252
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__646206252
Fusobacterium sp. D11 f__Fusobacteriaceae.g__Fusobacterium.s__?.t__t645058833
f__Fusobacteriaceae.g__Fusobacterium.s__nucleatum.t__645058833
Geobacillus sp. G11MC16 f__Bacillaceae.g__Geobacillus.s__?.t__t642791603
f__Bacillaceae.g__Geobacillus.s__hermodenitrificans.t__642791603
Geobacillus sp. Y4.1MC1 f__Bacillaceae.g__Geobacillus.s__?.t__t649633047
f__Bacillaceae.g__Geobacillus.s__hermoglucosidasius.t__649633047
Glaciecola sp. HTCC 2999 f__Alteromonadaceae.g__Glaciecola.s__?.t__t643886097
f__Alteromonadaceae.g__Alteromonas.s__macleodii.t__643886097
Haemophilus aegyptius ATCC 11116 f__Pasteurellaceae.g__Haemophilus.s__aegyptius.t__t651324038
f__Pasteurellaceae.g__Haemophilus.s__influenzae.t__651324038
Halobacterium sp. NRC-1 f__Halobacteriaceae.g__Halobacterium.s__?.t__t638154504
f__Halobacteriaceae.g__Halobacterium.s__salinarum.t__638154504
Klebsiella sp. 1_1_55 f__Enterobacteriaceae.g__Klebsiella.s__?.t__t647533174
f__Enterobacteriaceae.g__Klebsiella.s__pneumoniae.t__647533174
Klebsiella sp. MS 92-3 f__Enterobacteriaceae.g__Klebsiella.s__?.t__t651324045
f__Enterobacteriaceae.g__Klebsiella.s__pneumoniae.t__651324045
Megasphaera genomosp. UPII 199-6 f__Veillonellaceae.g__Megasphaera.s__?.t__t651324070
f__Veillonellaceae.g__Megasphaera.s__genomosp_.t__651324070
Mycobacterium gilvum Spyr1 f__Mycobacteriaceae.g__Mycobacterium.s__?.t__t649633070
f__Mycobacteriaceae.g__Mycobacterium.s__gilvum.t__649633070
Paenibacillus sp. D14 f__Paenibacillaceae.g__Paenibacillus.s__?.t__t647533191
f__Paenibacillaceae.g__Paenibacillus.s__polymyxa.t__647533191
Paenibacillus sp. HGF7 f__Paenibacillaceae.g__Paenibacillus.s__?.t__t651324081
f__Paenibacillaceae.g__Paenibacillus.s__larvae.t__651324081
Propionibacterium acidifaciens F0233 f__Porphyromonadaceae.g__Porphyromonas.s__?.t__t645058700
f__Porphyromonadaceae.g__Porphyromonas.s__endodontalis.t__645058700
Propionibacterium sp. 409-HC1 f__Propionibacteriaceae.g__Propionibacterium.s__?.t__t651324091
f__Propionibacteriaceae.g__Propionibacterium.s__acnes.t__651324091
Propionibacterium sp. 434-HC2 f__Propionibacteriaceae.g__Propionibacterium.s__?.t__t651324092
f__Propionibacteriaceae.g__Propionibacterium.s__acnes.t__651324092
Pseudoalteromonas atlantica T6c f__Pseudoalteromonadaceae.g__Pseudoalteromonas.s__atlantica.t__t637000216
f__Alteromonadaceae.g__Alteromonas.s__macleodii.t__637000216
Pseudoalteromonas sp. SM9913 f__Pseudoalteromonadaceae.g__Pseudoalteromonas.s__?.t__t649633085
f__Pseudoalteromonadaceae.g__Pseudoalteromonas.s__haloplanktis.t__649633085
Pseudoalteromonas sp. TW-7 f__Pseudoalteromonadaceae.g__Pseudoalteromonas.s__?.t__t639857033
f__Pseudoalteromonadaceae.g__Pseudoalteromonas.s__haloplanktis.t__639857033
Ralstonia sp. 5_7_47FAA f__Burkholderiaceae.g__Ralstonia.s__?.t__t649989994
f__Burkholderiaceae.g__Ralstonia.s__pickettii.t__649989994
Rhizobium leguminosarum bv. trifolii WSM2304 f__Rhizobiaceae.g__Rhizobium.s__leguminosarum.t__t643348569
f__Rhizobiaceae.g__Rhizobium.s__etli.t__643348569
Rhodobacter sp. SW2 f__Rhodobacteraceae.g__Rhodobacter.s__?.t__t647000304
f__Rhodobacteraceae.g__Rhodobacter.s__sphaeroides.t__647000304
Rhodobacterales sp.HTCC2255 f__Rhodobacteraceae.g__?.s__?.t__t639857003
f__Alteromonadaceae.g__Alteromonas.s__macleodii.t__639857003
Ruminococcus sp. 5_1_39BFAA f__Ruminococcaceae.g__Ruminococcus.s__?.t__t646206280
f__Ruminococcaceae.g__Ruminococcus.s__obeum.t__646206280
Ruminococcus sp. SR1/5 f__Ruminococcaceae.g__Ruminococcus.s__?.t__t650377968
f__Ruminococcaceae.g__Ruminococcus.s__obeum.t__650377968
Salmonella enterica enterica sv Typhimurium LT2 LT2 f__Enterobacteriaceae.g__Salmonella.s__typhimurium.t__t637000255
f__Enterobacteriaceae.g__Salmonella.s__enterica.t__637000255
Shigella sp. D9 f__Enterobacteriaceae.g__Shigella.s__?.t__t645058835
f__Enterobacteriaceae.g__Escherichia.s__coli.t__645058835
Stenotrophomonas sp. SKA14 f__Xanthomonadaceae.g__Stenotrophomonas.s__?.t__t647533230
f__Xanthomonadaceae.g__Stenotrophomonas.s__maltophilia.t__647533230
Streptomyces griseus XyelbKG-1 1 f__Streptomycetaceae.g__Streptomyces.s__?.t__t647000328
f__Streptomycetaceae.g__Streptomyces.s__griseus.t__647000328
Synechococcus sp. RS9916 f__Synechococcaceae.g__Synechococcus.s__?.t__t639857007
f__Synechococcaceae.g__Prochlorococcus.s__marinus.t__639857007
Synechococcus sp. RS9917 f__Synechococcaceae.g__Synechococcus.s__?.t__t638341213
f__Synechococcaceae.g__Prochlorococcus.s__marinus.t__638341213
Veillonella sp. 3_1_44 f__Veillonellaceae.g__Veillonella.s__?.t__t647533241
f__Veillonellaceae.g__Veillonella.s__parvula.t__647533241
Veillonella sp. 6_1_27 f__Veillonellaceae.g__Veillonella.s__?.t__t647533242
f__Veillonellaceae.g__Veillonella.s__parvula.t__647533242
Veillonella sp. oral taxon 158 F0412 f__Veillonellaceae.g__Veillonella.s__?.t__t649990027
f__Veillonellaceae.g__Veillonella.s__parvula.t__649990027
Vibrio cholerae CIRS 101 f__Vibrionaceae.g__Vibrio.s__cholera.t__t645058746
f__Vibrionaceae.g__Vibrio.s__cholerae.t__645058746
Vibrio sp. Ex25 f__Vibrionaceae.g__Vibrio.s__?.t__t646311966
f__Vibrionaceae.g__Vibrio.s__alginolyticus.t__646311966
Vibrio sp. Ex25 f__Vibrionaceae.g__Vibrio.s__?.t__t638341229
f__Vibrionaceae.g__Vibrio.s__alginolyticus.t__638341229
Vibrio sp. MED222 f__Vibrionaceae.g__Vibrio.s__?.t__t638341230
f__Vibrionaceae.g__Vibrio.s__splendidus.t__638341230
Vibrio sp. RC341 f__Vibrionaceae.g__Vibrio.s__?.t__t647000343
f__Vibrionaceae.g__Vibrio.s__mimicus.t__647000343
Vibrio sp. RC586 f__Vibrionaceae.g__Vibrio.s__?.t__t647000344
f__Vibrionaceae.g__Vibrio.s__mimicus.t__647000344
Vibrionales sp. SWAT-3 f__Vibrionaceae.g__?.s__?.t__t640963044
f__Vibrionaceae.g__Vibrio.s__splendidus.t__640963044
Wolbachia sp. wRi f__Anaplasmataceae.g__Wolbachia.s__?.t__t643692055
f__Anaplasmataceae.g__Wolbachia.s__endosymbiont.t__643692055