Table 1 Choline TMA lyase gene occurrence in rumen microbial datasets
From: Occurrence and expression of genes encoding methyl-compound production in rumen bacteria
Rumen bacteria | Phylum | Strain | IMG gene ID | Locus Tag | aa | Origin |
|---|---|---|---|---|---|---|
Hungate1000 [28] | ||||||
 Rumen bacteria | ||||||
  Olsenella umbonata | Actinobacteria | A2 (DSM 22619) | 2608576534 | Ga0059087_11836 | 847 | sheep |
  Olsenella umbonata | Actinobacteria | KHGC19 | 2663665377 | Ga0104367_1620 | 847 | cow |
   [Eubacterium] sp. | Firmicutes | AB3007 | 2561437736 | P156DRAFT_0760 | 847 | cow |
  Enterococcus sp. | Firmicutes | KPPR-6 | 2608578278 | Ga0059091_105198 | 857 | cow |
  Lachnoclostridium aerotolerans | Firmicutes | X8A62 (DSM 5434) | 2558962511 | T546DRAFT_01546 | 848 | sheep |
  Clostridium sartagoforme | Firmicutes | AAU1 | 2543441078 | A500_11264 | 846 | buffalo |
  Desulfotomaculum ruminis | Firmicutes | DL (DSM 2154) | 650891141 | Desru_2090 | 847 | sheep |
  Desulfovibrio legallii | Proteobacteria | KHC7 | 2654384186 | Ga0104380_103103 | 848 | cow |
  Desulfovibrio desulfuricans | Proteobacteria | G11 (DSM 7057) | 2595153453 | IE73DRAFT_02008 | 848 | cow |
  Desulfovibrio desulfuricans subsp. desulfuricans | Proteobacteria | Mb (ATCC 27774) | 643582164 | Ddes_1357 | 848 | sheep |
 Faecal bacteria | ||||||
  Clostridium algidicarnis | Firmicutes | B3 | 2562235685 | BV55DRAFT_1892 | 847 | cow |
  Clostridium paraputrificum | Firmicutes | AGR2156 | 2525457652 | G594DRAFT_02041 | 846 | calf |
  Lachnoclostridium citroniae | Firmicutes | NLAE-zl-G70 | 2624603054 | Ga0070263_11089 | 855 | goat |
  Lachnoclostridium clostridioforme | Firmicutes | AGR2157 | 2525451452 | G614DRAFT_00825 | 853 | calf |
  Lachnoclostridium lavalense | Firmicutes | NLAE-zl-G277 | 2624766256 | Ga0070262_11929 | 846 | goat |
  Lachnoclostridium celerecrescens | Firmicutes | 18A (DSM 5628) | 2596304492 | H171DRAFT_4337 | 847 | cow |
  Proteus mirabilis | Proteobacteria | NLAE-zl-G534 | 2624727893 | Ga0066901_10954 | 1142 | goat |
  Proteus mirabilis | Proteobacteria | NLAE-zl-C285 | 2656994829 | Ga0104388_10857 | 1142 | cow |
 Rumen metagenome assembled genomes (MAGs [27]) | ||||||
  hRUG882 | Firmicutes | N/A | N/A | NODE_2309_length_24057 _cov_25.2708_2 | 857 | cow |
  RUG067 | Firmicutes | N/A | N/A | k87_66874274_20 | 872 | cow |
  RUG514 | Proteobacteria | N/A | N/A | k87_1124619_4 | 811 | cow |
  RUG618 | Firmicutes | N/A | N/A | k87_25912225_4 | 855 | cow |
  RUG706 | Firmicutes | N/A | N/A | scaffold_2105_5 | 857 | cow |
  RUG708 | Firmicutes | N/A | N/A | k87_13261599_27 | 860 | cow |
  RUG778 | Actinobacteria | N/A | N/A | scaffold_14892_2 | 848 | cow |
 High/Low microbiome [26] | ||||||
  NZ sheep rumen microbiome combined assembly | Actinobacteria | N/A | 37167 | loc_1053724451 | 799 | sheep |
  NZ sheep rumen microbiome combined assembly | Actinobacteria | N/A | 37167 | loc_1077539681 | 398 | sheep |
  NZ sheep rumen microbiome combined assembly | Firmicutes | N/A | 37167 | loc_1014482251 | 394 | sheep |