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Table 2 Glycosyl hydrolase homologues found in metagenome samples

From: Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

Metagenome sourcea Genome size (bp) Gene countb Glycosyl hydrolase matchesc Glycosyl hydrolase matches/total genes (%)d Matches/million base pairsd
Marine archaeal anaerobic methane oxidation community (methane oxidation, sulfate reducer) [62] 2,116,255 2,332 3 0.13 1.42
Acid mine drainage (acidic, metal tolerance, pink biofilm) [12] 10,830,886 12,559 73 0.58 6.74
Human gut community (gut microbiome of human) [63] 36,304,498 46,503 705 1.52 19.42
Hypersaline mat (marine microbial communities) [64] 84,253,870 135,922 786 0.58 9.33
Lake Washington formaldehyde enrichment (13C-labeled formaldehyde; 13C-labeled DNA isolated by CsCl purification) [21] 57,622,063 89,729 397 0.44 6.89
Lake Washington formate enrichment (13C-labeled formate; 13C-labeled DNA isolated by CsCl purification) [21] 17,570,569 28,700 114 0.40 6.49
Lake Washington methane enrichment (13C-labeled methane; 13C-labeled DNA isolated by CsCl purification) [21] 52,164,993 81,076 428 0.53 8.20
Lake Washington methanol enrichment (13C-labeled methanol; 13C-labeled DNA isolated by CsCl purification) [21] 50,245,961 77,229 373 0.49 7.42
Lake Washington methylamine enrichment (13C-labeled methylamine; 13C-labeled DNA isolated by CsCl purification) [21] 37,225,208 54,340 285 0.52 7.66
Mouse gut community (lean mouse) [65] 6,511,633 8,510 119 1.40 18.27
Mouse gut community (obese mouse) [65] 4,200,364 5,382 58 1.08 13.81
Olavius algarvensis microbiome delta (sulfate reducer, symbiont) [66] 19,918,898 15,092 41 0.27 2.06
Olavius algarvensis microbiome gamma (sulfate reducer, symbiont) [66] 9,964,793 6,026 16 0.27 1.61
Singapore air sample [67] 75,598,288 91,635 514 0.56 6.80
Sludge Australian Phrap assembly (phosphate removal) [68] 53,048,954 30,590 177 0.58 3.34
Sludge US Jazz assembly (phosphate removal) [68] 41,128,538 16,840 126 0.75 3.06
Sludge US Phrap assembly (phosphate removal) [68] 56,608,360 34,254 260 0.76 4.59
Soil diversa silage (farm silage surface soil) [69] 152,406,385 184,374 1,078 0.58 7.07
TM7 (human oral microflora) [70] 3,451,819 3,908 14 0.36 4.06
Termite gut (cellulolytic, cellulose degrader, lignin degrader, symbiont) [55] 61,992,778 83,225 1,267 1.52 20.44
Uranium-contaminated groundwater (acidophile) 9,554,544 12,335 71 0.58 7.43
Whalefall sample (barophile) [69, 71] 94,937,484 122,145 433 0.35 4.56
Total (or average for glycosyl hydrolase matches/total genes and matches/million base pairs) 937,657,141 1,142,706 7,338 0.64 7.83
  1. aData source: IMG/M [18]; bonly protein coding sequences were included (no RNA genes); ctranslated sequences from all 43 environmental metagenome projects were blast-searched against the CAZy sequences for homologues of glycosyl hydrolases using an e value < 10-40 as a cut-off threshold; dGlycosyl hydrolase matches/total genes and matches per million base pairs provides an indication for the relative abundance of glycosyl hydrolases in the microbial community.