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Table 2 Most actively transcribed genes for enzymes involved in carbohydrate or protein utilization of selected HR biofilm MAGs

From: Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Metagenome assembled genome (MAG)1 Assumed taxonomic affiliation Analyzed HR2 biofilm sample Gene transcripts involved in carbohydrate or protein utilization Predicted functional role in AD4
GenID Gene length Putative gene product Gene EC number Transcripts mapped Normalized number of transcripts [TPM]3
17 Bacteroidales (Prevotella sp.) T1OLR1500 Bin_17_01477 366 Deoxyguanosinetriphosphate triphosphohydrolase dgt 3.1.5.1 141 3.9 n/s
   Bin_17_01805 171 Hypothetical protein n/s n/s 28 3.4  
   Bin_17_00602 177 50S ribosomal protein rpmD n/s 10 1.5  
   Bin_17_00172 651     75 0.8  
   Bin_17_00603 519 50S ribosomal protein rpsE n/s 53 0.8  
   Bin_17_00862 1041 L-3,5-diaminohexanoate dehydrogenase kdd 1.4.1.11 92 0.6  
   Bin_17_00014 579 N-acetylhexosamine 1-kinase nahK 2.7.1.162 38 0.5  
18 Clostridiales (Acetivibrio sp.) M1OLR1500 Bin_18_02374 207 Small; acid-soluble spore protein C2 sspC   4876 619 Hydrolysis
   Bin_18_01750 144 Hypothetical protein n/s n/s 462 145  
   Bin_18_01164 192 Hypothetical protein n/s n/s 384 58  
   Bin_18_00189 786 Sulfurtransferase tusA 2.8.1.- 3938 53  
   Bin_18_01827 108 Hypothetical protein n/s n/s 74 46  
   Bin_18_02918 711 Glycerol uptake facilitator protein glpF n/s 573 9  
   Bin_18_01829 912 Lactose transport system permease protein lacF n/s 760 9  
   Bin_18_01831 1377 Beta-glucosidase A bglA 3.2.1.21 798 6  
   Bin_18_01301 1272 Peptidoglycan binding domain protein   n/s 678 5  
   Bin_18_01830 858 L-arabinose transport system permease protein araQ n/s 413 5  
   Bin_18_01016 1119 D-galactose-binding periplasmic protein precursor mglB n/s 309 3  
40 Lachnospirales (Herbinix sp.) M1OLR1500 Bin_40_01523 225 Acid-soluble spore protein C2 sspC_1 n/s 42,076 2942 Hydrolysis
   Bin_40_01017 114 Manganese containing catalase n/s n/s 5156 1711  
   Bin_40_00454 147 Hypothetical protein n/s n/s 5508 1017  
   Bin_40_00073 246 Hypothetical protein n/s n/s 17,299 1006  
   Bin_40_01138 228 Acid-soluble spore protein C2 sspC_2 n/s 14,627 994  
   Bin_40_00033 1770 Oligopeptide-binding protein oppA n/s 14,445 50  
   Bin_40_00081 819 Maritimacin n/s n/s 4915 42  
   Bin_40_00131 681 Thiamine transporter thiT n/s 3522 38  
   Bin_40_00519 1116 Trehalose import ATP-binding protein sugC n/s 6385 37  
   Bin_40_00505 1008 Glyceraldehyde-3-phosphate dehydrogenase gapN 1.2.1.12 4163 27  
   Bin_40_01590 1329 Maltose/maltodextrin-binding protein precursor malX n/s 5638 27  
107 Clostridiales (Clostridium sp.) T2OLR1500 Bin_107_01262 183 Small; acid-soluble spore protein C1 sspC1_1 n/s 29,669 3262 Hydrolysis
   Bin_107_01261 180 Small; acid-soluble spore protein C2 sspC2_2 n/s 24,756 2829  
   Bin_107_01260 171 Small; acid-soluble spore protein C2 sspC2_1 n/s 16,600 2136  
   Bin_107_00122 186 Small; acid-soluble spore protein C1 sspC1_2 n/s 9026 956  
   Bin_107_00144 234 Glutaredoxin-3 grxC n/s 7124 459  
   Bin_107_01233 258 Peptidase domain protein n/s n/s 1245 65  
   Bin_107_00711 99 Enolase eno 4.2.1.11 87 37  
   Bin_107_01338 1530 4-alpha-glucanotransferase malQ 2.4.1.2 4863 20  
   Bin_107_00018 114 L-cystine import ATP-binding protein tcyN n/s 58 19  
   Bin_107_01344 678 Trehalose import ATP-binding protein sugC 3.6.3.- 1732 19  
   Bin_107_01340 894 Maltose transport system permease protein malG n/s 2415 19  
   Bin_107_01038 531 PTS system, maltose-specific, EIICB component malP n/s 1017 16  
   Bin_107_01656 1002 Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde-3-phosphate dehydrogenase gapN 1.2.1.12 2090 14  
   Bin_107_01134 627 Lysozym acm 3.2.1.17 1086 13  
   Bin_107_00091 1881 Amylopullulanase apu 3.2.1.41 3989 13  
   Bin_107_01040 1335 6-phospho-alpha-glucosidase pagL 3.2.1.- 2015 10  
   Bin_107_00188 624 Thiamine transporter thiT n/s 692 9  
   Bin_107_01547 132 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase gap 1.2.1.9 158 8  
108 Bacteroidales (unclassified genus) T2OLR1500 Bin_108_01400 213 Hypothetical protein n/s n/s 18 1.4 n/s
   Bin_108_00987 726 Alkyl hydroperoxide reductase ahpC 1.11.1.15 85 0.8  
   Bin_108_00986 183 Nitrite reductase [NAD(P)H] nasD 1.7.1.4 4 0.4  
   Bin_108_00047 1140 Hypothetical protein n/s n/s 60 0.3  
   Bin_108_01184 441 50S ribosomal protein L15 rplO n/s 14 0.2  
134 Lachnospirales (Kineothrix sp.) T2OLR1500 Bin_134_02838 177 Transition state regulatory protein abrB n/s 1527 181 Hydrtolysis
   Bin_134_00038 555 Hypothetical protein n/s n/s 491 7  
   Bin_134_00185 291 ATP-dependent Clp protease, proteolytic subunit clpP n/s 81 3  
   Bin_134_00184 1278 ATP-dependent Clp protease, ATP-binding subunit clpX n/s 622 3  
   Bin_134_00305 906 HTH-type transcriptional regulator yofA n/s 324 2  
   Bin_134_02093 1110 Trehalose import ATP-binding protein acm 3.2.1.17 234 1  
   Bin_134_00012 570 Amylopullulanase pulA 3.2.1.41 74 1  
   Bin_134_00958 3558 Pyruvate-flavodoxin oxidoreductase ydbK 1.2.7.1 623 1  
  1. 1 The first five transcripts of each MAG represent the top transcripts of the corresponding MAG
  2. 2 Hydrolysis reactor
  3. 3 Transcripts per million averaged for datasets from two technical replicates
  4. 4 Anaerobic digestion
  5. n/s Not specified
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Environmental Microbiome

ISSN: 2524-6372