Skip to main content

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.