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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)1Assumed taxonomic affiliationAnalyzed HR2 biofilm sampleGene transcripts involved in carbohydrate or protein utilizationPredicted functional role in AD4
GenIDGene lengthPutative gene productGeneEC numberTranscripts mappedNormalized number of transcripts [TPM]3
17Bacteroidales (Prevotella sp.)T1OLR1500Bin_17_01477366Deoxyguanosinetriphosphate triphosphohydrolasedgt3.1.5.11413.9n/s
  Bin_17_01805171Hypothetical proteinn/sn/s283.4 
  Bin_17_0060217750S ribosomal proteinrpmDn/s101.5 
  Bin_17_00172651   750.8 
  Bin_17_0060351950S ribosomal proteinrpsEn/s530.8 
  Bin_17_008621041L-3,5-diaminohexanoate dehydrogenasekdd1.4.1.11920.6 
  Bin_17_00014579N-acetylhexosamine 1-kinasenahK2.7.1.162380.5 
18Clostridiales (Acetivibrio sp.)M1OLR1500Bin_18_02374207Small; acid-soluble spore protein C2sspC 4876619Hydrolysis
  Bin_18_01750144Hypothetical proteinn/sn/s462145 
  Bin_18_01164192Hypothetical proteinn/sn/s38458 
  Bin_18_00189786SulfurtransferasetusA2.8.1.-393853 
  Bin_18_01827108Hypothetical proteinn/sn/s7446 
  Bin_18_02918711Glycerol uptake facilitator proteinglpFn/s5739 
  Bin_18_01829912Lactose transport system permease proteinlacFn/s7609 
  Bin_18_018311377Beta-glucosidase AbglA3.2.1.217986 
  Bin_18_013011272Peptidoglycan binding domain protein n/s6785 
  Bin_18_01830858L-arabinose transport system permease proteinaraQn/s4135 
  Bin_18_010161119D-galactose-binding periplasmic protein precursormglBn/s3093 
40Lachnospirales (Herbinix sp.)M1OLR1500Bin_40_01523225Acid-soluble spore protein C2sspC_1n/s42,0762942Hydrolysis
  Bin_40_01017114Manganese containing catalasen/sn/s51561711 
  Bin_40_00454147Hypothetical proteinn/sn/s55081017 
  Bin_40_00073246Hypothetical proteinn/sn/s17,2991006 
  Bin_40_01138228Acid-soluble spore protein C2sspC_2n/s14,627994 
  Bin_40_000331770Oligopeptide-binding proteinoppAn/s14,44550 
  Bin_40_00081819Maritimacinn/sn/s491542 
  Bin_40_00131681Thiamine transporterthiTn/s352238 
  Bin_40_005191116Trehalose import ATP-binding proteinsugCn/s638537 
  Bin_40_005051008Glyceraldehyde-3-phosphate dehydrogenasegapN1.2.1.12416327 
  Bin_40_015901329Maltose/maltodextrin-binding protein precursormalXn/s563827 
107Clostridiales (Clostridium sp.)T2OLR1500Bin_107_01262183Small; acid-soluble spore protein C1sspC1_1n/s29,6693262Hydrolysis
  Bin_107_01261180Small; acid-soluble spore protein C2sspC2_2n/s24,7562829 
  Bin_107_01260171Small; acid-soluble spore protein C2sspC2_1n/s16,6002136 
  Bin_107_00122186Small; acid-soluble spore protein C1sspC1_2n/s9026956 
  Bin_107_00144234Glutaredoxin-3grxCn/s7124459 
  Bin_107_01233258Peptidase domain proteinn/sn/s124565 
  Bin_107_0071199Enolaseeno4.2.1.118737 
  Bin_107_0133815304-alpha-glucanotransferasemalQ2.4.1.2486320 
  Bin_107_00018114L-cystine import ATP-binding proteintcyNn/s5819 
  Bin_107_01344678Trehalose import ATP-binding proteinsugC3.6.3.-173219 
  Bin_107_01340894Maltose transport system permease proteinmalGn/s241519 
  Bin_107_01038531PTS system, maltose-specific, EIICB componentmalPn/s101716 
  Bin_107_016561002Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde-3-phosphate dehydrogenasegapN1.2.1.12209014 
  Bin_107_01134627Lysozymacm3.2.1.17108613 
  Bin_107_000911881Amylopullulanaseapu3.2.1.41398913 
  Bin_107_0104013356-phospho-alpha-glucosidasepagL3.2.1.-201510 
  Bin_107_00188624Thiamine transporterthiTn/s6929 
  Bin_107_01547132NADP-dependent glyceraldehyde-3-phosphate dehydrogenasegap1.2.1.91588 
108Bacteroidales (unclassified genus)T2OLR1500Bin_108_01400213Hypothetical proteinn/sn/s181.4n/s
  Bin_108_00987726Alkyl hydroperoxide reductaseahpC1.11.1.15850.8 
  Bin_108_00986183Nitrite reductase [NAD(P)H]nasD1.7.1.440.4 
  Bin_108_000471140Hypothetical proteinn/sn/s600.3 
  Bin_108_0118444150S ribosomal protein L15rplOn/s140.2 
134Lachnospirales (Kineothrix sp.)T2OLR1500Bin_134_02838177Transition state regulatory proteinabrBn/s1527181Hydrtolysis
  Bin_134_00038555Hypothetical proteinn/sn/s4917 
  Bin_134_00185291ATP-dependent Clp protease, proteolytic subunitclpPn/s813 
  Bin_134_001841278ATP-dependent Clp protease, ATP-binding subunitclpXn/s6223 
  Bin_134_00305906HTH-type transcriptional regulatoryofAn/s3242 
  Bin_134_020931110Trehalose import ATP-binding proteinacm3.2.1.172341 
  Bin_134_00012570AmylopullulanasepulA3.2.1.41741 
  Bin_134_009583558Pyruvate-flavodoxin oxidoreductaseydbK1.2.7.16231 
  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