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Table 5 Module based identification of potential biomass-degrading cow rumen draft genomes

From: Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Draft genome Taxonomic affiliation M1 M2 M3 M4 M5
AJa,b Bacteroidales + + + +  
AGaa,b Bacteroidales +     
AC2aa,b Bacteroidales   +    
AIaa,b Clostridiales +    +  
APbb,c Clostridiales +    +  
AHb Bacteroidales +    +  
AFa Spirochaetales     +  
AN Clostridiales     +  
AWa Clostridiales     +  
ATa Clostridiales      +
ADa Myxococcales      
AMa Spirochaetales      
AQ Bacteroidales      
AS1a Clostridiales      
BOa Clostridiales      
  1. aAJ, AGa, AC2a and AIa are supported by evidence for lignocellulolytic activity according to carbohydrolytic activity tests [19].
  2. bThe draft genomes AJ, AGa, AC2a, AIa, APb and AH were also predicted by an SVM-based method for predicting lignocellulose degraders (counting only the unambiguous predictions of the SVM classifier) [28].
  3. cAPb was mapped using 16S rRNA marker genes to the known lignocellulose-degrading organism B. fibrisolvens[19].
  4. We used the weights of the consensus plant biomass degradation modules (PDMs) in the 15 draft genomes of the cow rumen metagenome to predict the draft genomes with lignocellulolytic activities (indicated by + signs), using the weight thresholds reported in Table 4.