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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