GTDB-ground all remaining records: +515 blocks across 207 records (24 -> 231/295) (#185)

Ran `gtdb_ground.py --community <file> --apply` (rank-aware: species -> GTDB:s__
via id/name; genus/family -> g__/f__ by genome-majority; ambiguous/eukaryote
skipped) over the 271 records that lacked GTDB grounding. Add-only text edits
(no reflow); GTDB CURIEs are pattern-checked strings, not OAK-bound, so no
id-label drift. The 64 records still ungrounded have only genus-ambiguous,
eukaryotic, or unmapped taxa.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: realmarcin

kb/communities/AMD_Acidophile_Heterotroph_Network.yaml

@@ -42,6 +42,14 @@ taxonomy:
     term:
       id: NCBITaxon:62140
       label: Acidiphilium multivorum
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acidiphilium_multivorum
+      gtdb_taxon: Acidiphilium multivorum
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium;s__Acidiphilium multivorum
+      ncbi_source_id: NCBITaxon:62140
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Facultative anaerobic acidophilic heterotroph isolated from pyritic acid mine drainage. This
       α-proteobacterium couples Fe(III) reduction to organic carbon oxidation under anaerobic conditions
       and performs aerobic heterotrophy when oxygen is available. It completely oxidizes sugars (glucose,
@@ -78,6 +86,14 @@ taxonomy:
     term:
       id: NCBITaxon:121039
       label: Ferrimicrobium acidiphilum
+    gtdb_classification:
+      gtdb_id: GTDB:s__Ferrimicrobium_acidiphilum
+      gtdb_taxon: Ferrimicrobium acidiphilum
+      gtdb_lineage: d__Bacteria;p__Actinomycetota;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__Ferrimicrobium;s__Ferrimicrobium acidiphilum
+      ncbi_source_id: NCBITaxon:121039
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [mapped via NCBI species name — no species-level NCBI id in table]
     notes: 'Obligately heterotrophic iron-oxidizing actinobacterium from the subclass Acidimicrobidae.
       Unlike most heterotrophs, F. acidiphilum catalyzes both dissimilatory oxidation and reduction of
       soluble iron while requiring organic carbon for growth. This dual capability makes it unique among
@@ -113,6 +129,14 @@ taxonomy:
     term:
       id: NCBITaxon:524
       label: Acidiphilium cryptum
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acidiphilium_multivorum
+      gtdb_taxon: Acidiphilium multivorum
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium;s__Acidiphilium multivorum
+      ncbi_source_id: NCBITaxon:524
+      majority_fraction: 1.0
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Facultative anaerobic acidophile capable of coupling complete oxidation of organic substrates
       to Fe(III) reduction at pH 3-5. This organism demonstrates metabolic versatility by performing aerobic
       respiration with oxygen, anaerobic respiration with ferric iron, or fermentation. It oxidizes a
@@ -147,6 +171,14 @@ taxonomy:
     term:
       id: NCBITaxon:525
       label: Acidocella facilis
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acidocella_facilis
+      gtdb_taxon: Acidocella facilis
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella;s__Acidocella facilis
+      ncbi_source_id: NCBITaxon:525
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Obligately aerobic heterotrophic α-proteobacterium with strict respiratory metabolism. Unlike
       facultative anaerobes in the genus Acidiphilium, A. facilis requires oxygen as terminal electron
       acceptor and cannot perform Fe(III) reduction. It degrades organic compounds using dissolved oxygen
@@ -178,6 +210,14 @@ taxonomy:
     term:
       id: NCBITaxon:50715
       label: Acidisphaera rubrifaciens
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acidisphaera_rubrifaciens
+      gtdb_taxon: Acidisphaera rubrifaciens
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera;s__Acidisphaera rubrifaciens
+      ncbi_source_id: NCBITaxon:50715
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Aerobic photoheterotrophic α-proteobacterium that produces bacteriochlorophyll a and carotenoids
       under aerobic conditions. This unique organism combines heterotrophic carbon metabolism with light-harvesting
       capability, allowing it to supplement energy from organic carbon oxidation with photosynthetic light

kb/communities/AMD_Nitrososphaerota_Archaeal.yaml

@@ -45,6 +45,14 @@ taxonomy:
     term:
       id: NCBITaxon:1078905
       label: Nitrosotalea devaniterrae
+    gtdb_classification:
+      gtdb_id: GTDB:s__Nitrosotalea_devanaterra
+      gtdb_taxon: Nitrosotalea devanaterra
+      gtdb_lineage: d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosotalea;s__Nitrosotalea devanaterra
+      ncbi_source_id: NCBITaxon:1078905
+      majority_fraction: 1.0
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Obligately acidophilic ammonia-oxidizing archaeon from the phylum Nitrososphaerota, class
       Nitrososphaeria. This chemolithoautotrophic organism represents the first cultivated acidophilic
       AOA, isolated from acidic agricultural soil (pH 4.5). Grows optimally at pH 4.0-5.5 with extraordinary
@@ -94,6 +102,14 @@ taxonomy:
     term:
       id: NCBITaxon:497726
       label: Nitrososphaera
+    gtdb_classification:
+      gtdb_id: GTDB:g__Nitrososphaera
+      gtdb_taxon: Nitrososphaera
+      gtdb_lineage: d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Nitrososphaera
+      ncbi_source_id: NCBITaxon:497726
+      majority_fraction: 0.833
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]
     notes: 'Mesophilic ammonia-oxidizing archaea related to Nitrososphaera viennensis but adapted to acidic
       conditions (pH 3.5-5.0). Detected in AMD-impacted sediments through 16S rRNA and amoA gene sequencing,
       with OTUs clustering with acidic soil- associated Nitrososphaera lineages. These archaea possess
@@ -131,6 +147,14 @@ taxonomy:
     term:
       id: NCBITaxon:74969
       label: Ferroplasma acidiphilum
+    gtdb_classification:
+      gtdb_id: GTDB:s__Ferroplasma_acidarmanus
+      gtdb_taxon: Ferroplasma acidarmanus
+      gtdb_lineage: d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma;s__Ferroplasma acidarmanus
+      ncbi_source_id: NCBITaxon:74969
+      majority_fraction: 0.91
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: 'Cell wall-lacking archaeon (Thermoplasmatales, Thermoplasmata) found in acid mine drainage
       alongside Nitrososphaerota AOA. Grows chemomixotrophically, oxidizing ferrous iron for energy while
       consuming organic matter. In the context of the archaeal nitrifying community, Ferroplasma plays

kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml

@@ -42,6 +42,14 @@ taxonomy:
     term:
       id: NCBITaxon:213118
       label: Desulfobacterales
+    gtdb_classification:
+      gtdb_id: GTDB:o__Desulfobacterales
+      gtdb_taxon: Desulfobacterales
+      gtdb_lineage: d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales
+      ncbi_source_id: NCBITaxon:213118
+      majority_fraction: 0.81
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at o__ rank; 5 GTDB taxa under the NCBI taxon]
     notes: Desulfobacterales is used as a conservative NCBI-grounded representation for common marine
       sulfate-reducing bacterial partners of ANME aggregates.
   functional_role:

kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml

@@ -39,6 +39,14 @@ taxonomy:
     term:
       id: NCBITaxon:28216
       label: Betaproteobacteria
+    gtdb_classification:
+      gtdb_id: GTDB:c__Gammaproteobacteria
+      gtdb_taxon: Gammaproteobacteria
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria
+      ncbi_source_id: NCBITaxon:28216
+      majority_fraction: 1.0
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at c__ rank; 3 GTDB taxa under the NCBI taxon]
     notes: Accumulibacter is represented with the validated Betaproteobacteria class term because the record
       captures the full-scale community and clade-level microdiversity rather than a cultured isolate.
   functional_role:
@@ -66,6 +74,14 @@ taxonomy:
     term:
       id: NCBITaxon:201174
       label: Actinomycetota
+    gtdb_classification:
+      gtdb_id: GTDB:p__Actinomycetota
+      gtdb_taxon: Actinomycetota
+      gtdb_lineage: d__Bacteria;p__Actinomycetota
+      ncbi_source_id: NCBITaxon:201174
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at p__ rank; 6 GTDB taxa under the NCBI taxon]
     notes: Tetrasphaera-related Actinobacteria were abundant by qFISH but underrepresented in the metagenome,
       likely because of DNA extraction bias against gram-positive bacteria.
   functional_role:
@@ -92,6 +108,14 @@ taxonomy:
     term:
       id: NCBITaxon:976
       label: Bacteroidota
+    gtdb_classification:
+      gtdb_id: GTDB:p__Bacteroidota
+      gtdb_taxon: Bacteroidota
+      gtdb_lineage: d__Bacteria;p__Bacteroidota
+      ncbi_source_id: NCBITaxon:976
+      majority_fraction: 0.999
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at p__ rank; 8 GTDB taxa under the NCBI taxon]
     notes: Bacteroidetes-related Saprospiraceae and other flanking bacteria contribute to biomass processing
       and were prominent in metagenomic assignments.
   functional_role:

kb/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.yaml

@@ -48,6 +48,14 @@ taxonomy:
     term:
       id: NCBITaxon:33952
       label: Acetobacterium woodii
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acetobacterium_woodii
+      gtdb_taxon: Acetobacterium woodii
+      gtdb_lineage: d__Bacteria;p__Bacillota_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium;s__Acetobacterium woodii
+      ncbi_source_id: NCBITaxon:33952
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [mapped via NCBI species name — no species-level NCBI id in table]
     notes: Recombinant lactate-producing A. woodii mutant used as the acetogenic CO2/H2-converting
       partner.
   abundance_level: ABUNDANT
@@ -70,6 +78,14 @@ taxonomy:
     term:
       id: NCBITaxon:332101
       label: Clostridium drakei
+    gtdb_classification:
+      gtdb_id: GTDB:s__Clostridium_AM_drakei
+      gtdb_taxon: Clostridium_AM drakei
+      gtdb_lineage: d__Bacteria;p__Bacillota_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM;s__Clostridium_AM drakei
+      ncbi_source_id: NCBITaxon:332101
+      majority_fraction: 1.0
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
     notes: Wild-type chain-elongating partner that converts lactate-derived intermediates toward
       caproic acid.
   abundance_level: ABUNDANT

kb/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.yaml

@@ -48,6 +48,14 @@ taxonomy:
     term:
       id: NCBITaxon:201174
       label: Actinomycetota
+    gtdb_classification:
+      gtdb_id: GTDB:p__Actinomycetota
+      gtdb_taxon: Actinomycetota
+      gtdb_lineage: d__Bacteria;p__Actinomycetota
+      ncbi_source_id: NCBITaxon:201174
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at p__ rank; 6 GTDB taxa under the NCBI taxon]
     notes: A novel anaerobic acetylenotroph in the phylum Actinobacteria was
       identified by metagenomic analysis of the stable enrichment.
   functional_role:

kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml

@@ -37,6 +37,14 @@ taxonomy:
     term:
       id: NCBITaxon:287
       label: Pseudomonas aeruginosa
+    gtdb_classification:
+      gtdb_id: GTDB:s__Pseudomonas_aeruginosa
+      gtdb_taxon: Pseudomonas aeruginosa
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa
+      ncbi_source_id: NCBITaxon:287
+      majority_fraction: 0.99
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:
@@ -46,6 +54,14 @@ taxonomy:
     term:
       id: NCBITaxon:470
       label: Acinetobacter baumannii
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acinetobacter_baumannii
+      gtdb_taxon: Acinetobacter baumannii
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter baumannii
+      ncbi_source_id: NCBITaxon:470
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:
@@ -55,6 +71,14 @@ taxonomy:
     term:
       id: NCBITaxon:644
       label: Aeromonas hydrophila
+    gtdb_classification:
+      gtdb_id: GTDB:s__Aeromonas_hydrophila
+      gtdb_taxon: Aeromonas hydrophila
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas;s__Aeromonas hydrophila
+      ncbi_source_id: NCBITaxon:644
+      majority_fraction: 0.96
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:

kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml

@@ -36,6 +36,14 @@ taxonomy:
     term:
       id: NCBITaxon:470
       label: Acinetobacter baumannii
+    gtdb_classification:
+      gtdb_id: GTDB:s__Acinetobacter_baumannii
+      gtdb_taxon: Acinetobacter baumannii
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter baumannii
+      ncbi_source_id: NCBITaxon:470
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:
@@ -45,6 +53,14 @@ taxonomy:
     term:
       id: NCBITaxon:287
       label: Pseudomonas aeruginosa
+    gtdb_classification:
+      gtdb_id: GTDB:s__Pseudomonas_aeruginosa
+      gtdb_taxon: Pseudomonas aeruginosa
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa
+      ncbi_source_id: NCBITaxon:287
+      majority_fraction: 0.99
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:
@@ -54,6 +70,14 @@ taxonomy:
     term:
       id: NCBITaxon:644
       label: Aeromonas hydrophila
+    gtdb_classification:
+      gtdb_id: GTDB:s__Aeromonas_hydrophila
+      gtdb_taxon: Aeromonas hydrophila
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas;s__Aeromonas hydrophila
+      ncbi_source_id: NCBITaxon:644
+      majority_fraction: 0.96
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19)
   functional_role:
   - CROSS_FEEDER
   evidence:

kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml

@@ -31,6 +31,14 @@ taxonomy:
     term:
       id: NCBITaxon:28065
       label: Rhodoferax
+    gtdb_classification:
+      gtdb_id: GTDB:g__Rhodoferax
+      gtdb_taxon: Rhodoferax
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax
+      ncbi_source_id: NCBITaxon:28065
+      majority_fraction: 0.718
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at g__ rank; 4 GTDB taxa under the NCBI taxon]
     notes: Iron-cycling Gammaproteobacteria-lineage Rhodoferax sp. that
       becomes numerically dominant in transition-zone and permafrost
       microbiomes following extended anaerobic thaw.
@@ -53,6 +61,14 @@ taxonomy:
     term:
       id: NCBITaxon:96
       label: Gallionella
+    gtdb_classification:
+      gtdb_id: GTDB:g__Gallionella
+      gtdb_taxon: Gallionella
+      gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella
+      ncbi_source_id: NCBITaxon:96
+      majority_fraction: 1.0
+      is_reclassified: false
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at g__ rank; 1 GTDB taxa under the NCBI taxon]
     notes: Iron-cycling Gammaproteobacteria-lineage Gallionella sp. that, with
       Rhodoferax sp., accounts for 65% of community abundance in the
       transition-zone and permafrost depths after extended thaw.
@@ -73,6 +89,14 @@ taxonomy:
     term:
       id: NCBITaxon:224756
       label: Methanomicrobia
+    gtdb_classification:
+      gtdb_id: GTDB:c__Methanosarcinia
+      gtdb_taxon: Methanosarcinia
+      gtdb_lineage: d__Archaea;p__Halobacteriota;c__Methanosarcinia
+      ncbi_source_id: NCBITaxon:224756
+      majority_fraction: 0.617
+      is_reclassified: true
+      mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-06-19) [grounded at c__ rank; 9 GTDB taxa under the NCBI taxon]
     notes: Co-resident acetoclastic methanogenic archaea whose CH4-metabolism
       gene abundance decreased during extended thaw, consistent with competitive
       suppression by Fe(III) reduction. Methanomicrobia is used as the closest