Skip to main content

Table 1 Comparison of richness estimates for published viral metagenomes

From: Estimation of viral richness from shotgun metagenomes using a frequency count approach

Virome

CatchAll richness estimate

PHACCS richness estimate

Virome

 

Best parametric model ± SEa

estimate

 
 

All singletons

Empirically discounted

Statistically discounted

Power law model

Reference

Mammalian gut environments

 Nonmedicated swine feces, 21 db

90,576 ± 7,717

20,781 ± 1,054

2,381 ± 203

360

[7]

 Nonmedicated swine feces, 35 d

124,284 ± 11,985

17,581 ± 762

9,693 ± 935

405

[7]

 Nonmedicated swine feces, 38 d

84,524 ± 23,415

14,663 ± 592

4,686 ± 1,298

246

[7]

 Nonmedicated swine feces, 63 d

105,310 ± 48,167

16,267 ± 2,190

5,362 ± 2,452

164

[7]

 Nonmedicated swine feces, 77 d

130,773 ± 44,679

22,879 ± 3,381

5,071 ± 1,733

357

[7]

 Nonmedicated swine feces, 85 d

113,335 ± 7,958

27,650 ± 1,478

1,307 ± 92

787

[7]

 Nonmedicated swine feces, 91 d

154,869 ± 59,005

24,202 ± 1,139

5,386 ± 2,052

703

[7]

 Human infant fecesc

1,087 ± 348

344 ± 74

94 ± 30

8

[11]

 Human adult fecesc

9,576 ± 1,810

2,733 ± 517

NAd

1,930

[12]

Aquatic environments

 Reclaimed fresh water, potable

59,741 ± 5,150

14,259 ± 803

2,388 ± 206

184

[9]

 Reclaimed fresh water, effluent

128,778 ± 10,752

29,882 ± 1,833

1,617 ± 135

764

[9]

 Reclaimed fresh water, nursery

204,571 ± 75,474

37,260 ± 7,320

4,477 ± 1,652

1,754

[9]

 Reclaimed fresh water, park

185,739 ± 15,756

42,854 ± 2,899

1,043 ± 88

98,603

[9]

 Salt water, Gulf of Mexicoc

246,019 ± 90,045

59,696 ± 21,341

103 ± 37

15,400

[6]

 Salt water, British Columbiac

320,708 ± 73,575

81,644 ± 18,730

NA

129,000

[6]

 Salt water, Sargasso Seac

108,264 ± 14,870

28,701 ± 3,942

NA

5,140

[6]

 Salt water, Arctic Oceanc

NA

NA

NA

532

[6]

Pooled viromes

 The seven swine fecal viromes

155,469 ± 16,052

34,512 ± 2,360

1,990 ± 206

NDe

[7]

 The four reclaimed fresh water viromes

183,920 ± 18,009

41,751 ± 3,284

1,428 ± 140

ND

[9]

 Nonmedicated swine feces, 85 d, mixed with reclaimed fresh water, effluent

196,069 ± 23,490

43,205 ± 3,865

1,958 ± 235

ND

[7, 9]

 The four saltwater viromesc

668,901 ± 269,866

151,974 ± 54,948

1,272 ± 513

57, 600 [16]

[6]

  1. aSE, standard error.
  2. bd, days old.
  3. cThe contig spectra published in the corresponding reference were run in CatchAll.
  4. dNA, not available because the contig spectra did not contain enough data to perform the calculation.
  5. eND, not determined.