Skip to main content

Advertisement

Table 3 Prediction of the plant biomass degradation capabilities for 15 draft genomes

From: De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

  AC2a AGa AIa-2 AJ APb AFa AH AWa ADa AMa AN AQ AS1 ATa BOa
eSVMCAZY_B ++ ++ ++ + ++ ++ 0 - - - - - - - - - - - - - - - -
eSVMbPFAM ++ ++ ++ ++ ++ - ++ + - - - - - - - - - - - -
CMC GH5 (TW-33) GH5 (TW-40) GH10 (TW-34) GH5 (TW-39)            
GH26 (TW-10)
GH10 (TW-8)
GH5 (MH-2)
XYL   GH10 (TW-25) GH10 (TW-30) GH10 (TW-8)            
GH10 (TW-31)
GH10 (TW-37)
SWG   GH5 (TW-40)              
GH5 (MH-2)
MIS GH9 (TW-64) GH5 (TW-40)   GH5 (TW-39)            
GH5 (MH-2)
GH9 (TW-50)
AVI GH9 (TW-64) GH5 (TW-40)   GH5 (TW-39)            
GH5 (MH-2)
GH9 (TW-50)
LIC   GH5 (TW-40)   GH5 (TW-39)            
GH5 (MH-2)
GH9 (TW-50)
  1. Genome reconstructions from the metagenome of a microbial community adherent to switchgrass in the cow rumen were obtained by taxonomic binning of assembled sequences in the original study. Symbols depict the prediction outcome of a voting committee of the 5 eSVMCAZY_B and the eSVMbPFAM classifiers with the best macro-accuracy (see text for the description of the classifiers). ++: genome classified as plant biomass degrader by all classifiers; +: genome classified as plant biomass degrader by 4 out of 5 classifiers; 0: ambiguous prediction; -: genome classified as not plant biomass degrader by 4 out of 5 classifiers; --: genome classified as not plant biomass degrader by all classifiers. For every draft genome, the presence of genes encoding glycoside hydrolases with verified enzymatic activity for different substrates in this study [14] is indicated. The genome and substrate names correspond to those of Figure 3 and Table S6 of the study.
  2. Hydrolytic activity detected on:
  3. (CMC) 1% (w/v) carboxymethyl cellulose agar.
  4. (XYL) 1% (w/v) Xylan.
  5. (SWG) 1% (w/v) IL-Switchgrass.
  6. (MIS) 1% (w/v) IL-Miscanthus.
  7. (AVI) 1% (w/v) IL-Avicel.