TABLE 2

Numbers of sequences for 12 pathogenic OTUs observed in wild rodents, negative controls, and positive controls, together with TCC and TFA threshold valuesd

OTUTotal no. of sequencesWild rodents (n = 711)Negative controlsPositive controlsThreshold
NCPCRNCextNCmusPCBartonnela_tPCBorrelia_bPCMycoplasma_m
Total no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTotal no. of sequencesMaximum no. of sequences in one PCRTCCaTFAb
Run 1
    Whole data set7,960,5337,149,44464,72245,9008,00239,3088,74168,35026,211137,42473,134239,465120,552280,64282,933//
    Mycoplasma_OTU_11,410,2181,410,18961,8072132953386436282
    Mycoplasma_OTU_3507,376507,36936,3352100002211222101
    Ehrlichia_OTU649,451649,42363,13742327411111266130
    Borrelia_OTU345,873345,84528,528447494110073469
    Orientia_OTU279,965279,95729,503114100220011256
    Bartonella_OTU202,12767,97316,145111111134,12471,16374209940
    PCMycoplasma_m_OTUc280,1513382800002234202418279,75382,767//
    PCBorrelia_b_OTUc238,772420430000003821238,238119,5867623//
Run 2
    Whole data set6,687,0606,525,10742,32661,2319,14553,3347,669//12,1427,51813,3787,16421,8686,520//
    Mycoplasma_OTU_1155,486155,4867,7030000//000000031
    Mycoplasma_OTU_21,036,0841,035,89023,58811192115//000011115207
    Mycoplasma_OTU_3127,591127,5905,0721100//000000126
    Mycoplasma_OTU_485,59685,58320,146001313//0000001317
    Mycoplasma_OTU_556,32456,32410,7600000//000000011
    Mycoplasma_OTU_613,35613,3561,4820000//00000003
    Ehrlichia_OTU74,01774,01719,6510000//000000015
    Borrelia_OTU21,63621,6363,0850000//00000004
    Orientia_OTU3073071810000//00000000
    Bartonella_OTU1,559,0281,547,65214,5151122//11,2976,71422745959312
    Streptobacillus_OTU32,39932,3996,2450000//00000006
    Rickettsia_OTU5895893290000//00000000
    PCMycoplasma_m_OTUc16,854210000//000016,8525,766//
    PCBorrelia_b_OTUc12,197000000//0012,1976,42600//
  • a Threshold TCC data are based on the maximum number of sequences observed in a negative or positive control for a particular OTU in each run.

  • b Threshold TFA data are based on the false-assignment rate (0.02%) weighted by the total number of sequences of each OTU in each run.

  • c Mycoplasma mycoides and Borrelia burgdorferi bacterial isolates were added as positive controls for PCR and indexing (i.e., PCalien) (see Fig. 1).

  • d Data are given for the two MiSeq runs separately. NCPCR, negative controls for PCR; NCext, negative controls for extraction; NCmus, negative controls for dissection; PCBartonella_t, positive controls for PCR; PCBorrelia_b and PCMycoplsma_m, positive controls for PCR and positive controls for indexing; TCC and TFA, thresholds for positivity for a particular bacterium according to bacterial OTU and MiSeq run (see also Fig. 1).