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Table 2 Abundance of reads (TPM) and abundance of transcripts (Depth) per fungal species detected with metatranscriptomics. True members of the mock community – at species level – are shown in bold

From: Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions

Speciesa

TPM (read-level)

Depth (transcript-level)

Relative abundance (transcript-level %)

Cryptococcus neoformans

149,692.28

11,049.04

22.464

Candida tropicalis

142,496.47

9424.30

19.161

Pichia kudriavzevii

62,133.74

9234.05

18.774

Clavispora lusitaniae

57,317.81

7107.80

14.451

Candida auris

13,402.41

3354.39

6.820

Candida dubliniensis

52,027.94

1706.41

3.469

Pichia membranifaciens

10,860.75

1498.26

3.046

Candida albicans

42,948.69

1441.56

2.931

Yarrowia lipolytica

52,376.03

1384.29

2.814

Candida orthopsilosis

44,531.25

1308.09

2.660

Candida glabrata

50,404.11

992.55

2.018

Cryptococcus gattii VGI

9350.81

463.71

0.943

Candida glycerinogenes

2345.13

41.51

0.084

Nakaseomyces delphensis

12,821.76

35.45

0.072

Candida parapsilosis

15,989.78

31.11

0.063

Candida nivariensis

1411.36

12.72

0.026

Kluyveromyces marxianus

47.70

8.90

0.018

Torulaspora delbrueckii

15.01

6.00

0.012

Kluyveromyces lactis

9.24

3.93

0.008

Saccharomyces cerevisiae

22.84

3.77

0.008

Eremothecium sinecaudum

25.93

3.67

0.008

Pichia cecembensis

751.23

3.60

0.007

Lodderomyces elongisporus

34.30

3.59

0.007

Uncultured Candida

885.35

3.13

0.006

Eremothecium gossypii

10.13

3.04

0.006

Naumovozyma dairenensis

17.37

2.80

0.006

Suhomyces tanzawaensis

30.87

2.25

0.005

Dipodascaceae sp. LM136

24,286.11

2.16

0.004

Cyberlindnera jadinii

12.32

2.04

0.004

Metschnikowia bicuspidata

16.02

1.29

0.003

Brettanomyces naardenensis

96.13

1.19

0.002

Pichia norvegensis

783.06

1.11

0.002

Debaryomyces fabryi

22.87

0.92

0.002

Candida neerlandica

487.65

0.69

0.001

Melanotaenium endogenum

262.12

0.59

0.001

Pichia kluyveri

51,814.00

0.55

0.001

Candida pseudohaemulonis b

560.14

0.49

0.001

Candida sp. (in: Saccharomycetales)

330.15

0.49

0.001

Pichia sp. 2 TMS-2011

0.00

0.45

0.001

Cryptococcus neoformans AD hybrid

0.00

0.44

0.001

Saccharomycetales sp. LM594

2.60

0.30

0.001

Naumovozyma castellii

4.56

0.29

0.001

Saccharomyces pastorianus

0.81

0.26

0.001

Cryptococcus gattii VGIII

0.48

0.21

0.000

Other Eukaryotes

936.75

18.83

0.038

Bacteria

423.36

15.79

0.032

Unclassified

198,000.57

8.00

0.016

TOTAL

1,000,000

49,186

100

  1. a Species defined according to the NCBI taxonomy database. Strain numbers may indicate vouchers rather than genetically different lineages. bCandida pseudohaemulonis is also referred to as C. pseudohaemulonii
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