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 |
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 |