Literature DB >> 32478153

Data relating to sequencing statistics and the reads and genomic coverage aligning to Taenia solium in the cerebrospinal fluid.

Xiaofei Fei1, Chaoyang Li1, Yun Zhang1, Hongya Zhang1, Xuewu Liu1, Xinchao Ji1, Yajun Shi1, Na Liu1, Mengli Wu1, Fang Du1, Yining Yang1, Wen Dai1, TingTing Liu1, Ying He1, Ting Bian1, Huimin Zhou1, Xingyue An1, Zheng Cai1, Jian Shi2, Guodong Feng3, Ming Shi1, Gang Zhao1.   

Abstract

This data can serve as a reference for other next-generation sequencing (NGS) of the cerebrospinal fluid (CSF). In the related research article, entitled "Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Neurocysticercosis", we reported NGS of the CSF might be an auxiliary method for neurocysticercosis (NCC) patients who have complicated manifestations and courses to receive early diagnosis and treatment. In this article, we retrieved the available data about the sequencing statistics of the CSF samples and the number of unique reads and genomic coverage aligning to microorganic sequences. The data were generated by the Illumina MiniSeq system for sequencing and computational subtraction of the human host sequences was performed. Finally, the remaining sequencing data were aligned to the Microbial Genome Databases. This data can serve as a reference for other NGS of the CSF.
© 2020 Published by Elsevier Inc.

Entities:  

Keywords:  DNA Sequence Analyses; High-Throughput Nucleotide Sequencing; Sequence Analysis; Taenia solium

Year:  2020        PMID： 32478153      PMCID： PMC7248648          DOI： 10.1016/j.dib.2020.105700

Source DB:  PubMed          Journal:  Data Brief        ISSN： 2352-3409


Specifications Table

Value of the Data

This data provide raw reads aligning to human and the number of reads and genomic coverage aligning to Taenia solium and other microorganic sequences in the CSF. This data can serve as a reference for the diagnosis of neurocysticercosis by the next-generation sequencing (NGS) of the CSF. This data can be also used by further NGS of the CSF to identify common contaminated or non-pathogenic biological sequences.

Data Description

The reads aligned to human/primate, non-human/primate and NCBI (National Center for Biotechnology Information) NT (Nucleotide Sequence) database (ftp://ftp.ncbi.nlm.nih.gov/genomes) in the CSF are given in Table 1. The Microbial Genome Databases are composed of 2700 whole genome sequences of viral taxa, 1494 bacterial genomes or scaffolds, 73 fungi and 48 parasites associated with human infectivity. The reference genomes were downloaded from NCBI. The coverage of each species was calculated using Soap Coverage (http://soap.genomics.org.cn). The number of unique reads and genomic coverage of Taenia solium and other microorganisms in the CSF and the “no-template” controls are given in Table 2.
Table 1

. The Sequencing statistics aligned to human/primate, non-human/primate and NCBI NT database in the cerebrospinal fluid

Sample% Reads Passing Quality Control# of Raw Reads# of Reads after Quality Filtering and Adapter Trimming# of Reads Aligned to Human / Primate# of Non-Human / Primate Reads% Human / Primate Reads# of Reads Aligned to NCBI NT database*
Case 1-191.73985%693159635903626181972298.47115%5997
Case 1-279.77807%10636728485778231812539697.00723%7339
Case 1-390.39721%1067117964644957545709999.26408%3215
Case 1-486.63103%9021197815157120636945291.11316%23107
Case 2-291.10832%1175863107130910088916241894.17367%48977
Case 2-391.60472%856970785025778762626399.20219%4459
Case 3-192.24918%122609011310581127120393899.65183%1208
Case 3-291.37044%159695314591431454141500299.65720%2467
Case 3-392.91249%127539911850051180024498199.57966%2063
Case 3-493.21982%120210711206021112667793599.29190%4804
Case 3-579.97971%106436585127672680212447485.37795%95282
Case 491.39075%6511955951325770961803696.96941%9493
Case 591.86937%155919114324191424446797399.44339%4581
Case 690.16523%10291959279769065992137797.69638%11589
Case 791.74785%74146768028048437419590671.20215%186639

Reads Aligned to NCBI NT database refer to the filtered reads aligning to the microbial genomes.

Table 2

The reads aligning to microbial genomes only in the cerebrospinal fluid and the non-template controls

Data of Case 1-1
speciescoverageunique reads
bacteria
Mesorhizobium sp. UASWS10091.07102%928
Ralstonia sp. NT800.71621%422
Staphylococcus hominis0.44053%136
Propionibacterium acnes0.37285%142
Moraxella osloensis0.36310%110
Ralstonia sp. MD270.27996%98
Burkholderia sp. A90.23270%4
Staphylococcus warneri0.21697%66
Staphylococcus epidermidis0.20439%40
Burkholderia ubonensis0.20348%34
Burkholderia multivorans0.19835%92
Ralstonia sp. 5_2_56FAA0.19063%48
Asinibacterium sp. OR530.17729%86
Burkholderia sp. lig300.16949%24
Acidovorax sp. KKS1020.14422%30
Pantoea sp. 91400.10644%70
Pantoea sp. aB0.05827%4
Pantoea agglomerans0.05721%2
Pseudomonas oryzihabitans0.02842%20
Pseudomonas sp. RIT-PI-a0.02804%18
Erwinia gerundensis0.02618%18
Atopobium vaginae0.02097%4
Arthrobacter sp. Leaf2340.02086%8
Lactobacillus agilis0.02012%6
Sanguibacter sp. Leaf30.01839%10
viruses
Burkholderia phage KS100.41185%2
Staphylococcus phage StB270.32942%2
Staphylococcus phage SPbeta-like0.27011%8
Human gammaherpesvirus 40.08682%2
Paramecium bursaria Chlorella virus A10.07004%2
Parasite
Taenia solium0.14226%2614
Wuchereria bancrofti0.00581%58
Acanthamoeba palestinensis0.00207%4
Taenia saginata0.00198%0
Enterocytozoon bieneusi0.00194%0
Taenia multiceps0.00143%2
Entamoeba histolytica0.00103%2
Hammondia hammondi0.00096%4
Plasmodium gallinaceum0.00089%0
Theileria equi0.00064%0
Gregarina niphandrodes0.00054%0
Plasmodium malariae0.00022%0
Anncaliia algerae0.00109%0
fungi
Malassezia globosa0.00787%10
Albugo laibachii0.00068%2
Aspergillus fischeri0.00047%0
Fusarium verticillioides0.00019%2
Data of NTC 1-1
speciescoverageunique reads
bacteria
Bradyrhizobium elkanii21.88930%28096
Mesorhizobium sp. UASWS100916.55630%18192
Ralstonia sp. NT8014.52210%9754
Staphylococcus hominis10.42230%3698
Ralstonia sp. MD278.87976%4906
Moraxella osloensis7.18657%2434
Corynebacterium jeikeium5.98909%1270
Ralstonia sp. 5_2_56FAA4.20281%1410
Propionibacterium acnes3.72993%1482
Asinibacterium sp. OR533.17341%1474
Corynebacterium afermentans3.10861%666
Streptomyces purpurogeneiscleroticus3.10289%3072
Paracoccus sphaerophysae2.93074%1418
Comamonadaceae bacterium CCH4-C52.64042%352
Corynebacterium sp. HMSC034A012.48935%376
Ralstonia pickettii2.45672%580
Comamonadaceae bacterium CCH12-A102.45636%64
Acidovorax temperans2.31626%278
Staphylococcus warneri2.29655%684
Burkholderia sp. A92.28783%62
Staphylococcus haemolyticus2.19982%760
Burkholderia ubonensis2.19935%532
Corynebacterium tuberculostearicum2.19913%356
Psychrobacter sp. 1501(2011)2.16726%994
Burkholderia sp. lig302.05547%408
Brevundimonas vesicularis1.96955%336
Afipia broomeae1.89598%1128
Herbaspirillum frisingense1.85754%1566
Acidovorax sp. CCH12-A41.79300%66
Staphylococcus epidermidis1.79137%384
Acidovorax delafieldii1.78164%240
alpha proteobacterium L41A1.73341%178
Corynebacterium aurimucosum1.72909%176
Burkholderia multivorans1.71611%876
Acidovorax sp. KKS1021.61235%180
Kocuria palustris1.59043%674
Pseudomonas fluorescens1.58135%1664
Brevundimonas nasdae1.56017%212
Sphingomonas sp. Ant H111.50154%686
Azospira oryzae1.46515%812
Acidovorax sp. Root701.42366%266
Burkholderia pseudomultivorans1.23697%170
Asticcacaulis excentricus1.19113%452
Burkholderia dolosa1.14323%128
Burkholderia territorii1.03587%80
Acidovorax sp. Root4021.02996%156
Burkholderia cenocepacia1.01921%74
Caulobacter vibrioides1.00835%654
Burkholderia vietnamiensis0.88260%98
Burkholderia cepacia0.87995%76
Burkholderia contaminans0.86850%66
Burkholderia paludis0.85199%86
Burkholderia latens0.81089%58
Methylotenera versatilis0.76310%204
Acinetobacter johnsonii0.70205%346
Burkholderia oklahomensis0.51224%66
Acinetobacter baumannii0.03004%2
Tepidiphilus thermophilus0.02925%6
Peptoniphilus lacrimalis0.02125%4
Gardnerella vaginalis0.01717%4
Serratia marcescens0.00894%2
viruses
Burkholderia phage KS1012.39273%42
Flavobacterium phage Fpv20.45320%4
Paramecium bursaria Chlorella virus A10.35670%5
Staphylococcus phage IME-SA414.68467%67
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%35
Staphylococcus phage PH1512.20680%42
Staphylococcus phage Ipla78.94998%18
Staphylococcus phage CNPx4.27783%10
Staphylococcus phage StB123.47691%6
Staphylococcus phage StB20-like1.07450%3
Staphylococcus phage StB270.85037%3
Staphylococcus phage PT10280.83317%1
Staphylococcus phage SPbeta-like0.80453%19
Parasite
Acanthamoeba palestinensis0.00880%34
Wuchereria bancrofti0.00770%46
Hammondia hammondi0.00330%6
Cryptosporidium hominis0.00210%4
Acanthamoeba mauritaniensis0.00180%2
Trypanosoma cruzi0.00080%2
Toxoplasma gondii0.00220%4
Enterobius vermicularis0.00030%3
Hammondia hammondi0.00070%4
Leishmania mexicana0.00130%4
fungi
Malassezia globosa0.00938%6
Neurospora crassa0.00170%4
Neurospora tetrasperma0.00147%3
Sordaria macrospora0.00085%1
Talaromyces marneffei0.00061%1
Aspergillus oryzae0.00120%6
Albugo laibachii0.00090%5
Data of Case 1-2
speciescoverageunique reads
bacteria
Burkholderia contaminans2.21054%2372
Burkholderia sp. A91.46819%32
Propionibacterium acnes1.22233%476
Burkholderia ubonensis1.12679%258
Burkholderia sp. lig301.05198%184
Burkholderia multivorans0.86904%476
Burkholderia pseudomultivorans0.62819%104
Burkholderia cenocepacia0.59451%50
Burkholderia cepacia0.59443%48
Burkholderia dolosa0.58867%66
Burkholderia territorii0.52705%28
Burkholderia vietnamiensis0.44917%36
Burkholderia paludis0.44871%40
Burkholderia latens0.41821%36
Burkholderia oklahomensis0.27370%20
Candidatus Kinetoplastibacterium crithidii0.03528%0
Burkholderiales bacterium YL450.01796%0
Candidatus Profftella armatura0.01656%0
Streptococcus sp. oral taxon 0580.01412%0
Formosa sp. Hel3_A1_480.00878%0
[Eubacterium] nodatum0.00765%0
Deinococcus puniceus0.00690%0
Streptococcus sp. HMSC034E030.00663%0
Streptococcus pasteurianus0.00654%0
Streptococcus macedonicus0.00630%0
viruses
Burkholderia phage KS101.76432%0
Staphylococcus phage Slt0.15137%0
Staphylococcus phage phiMR110.15112%0
Staphylococcus phage phiJB0.15112%0
Staphylococcus phage 710.15076%0
Burkholderia virus phiE1250.12178%0
Parasite
Taenia solium0.02478%334
Enterocytozoon bieneusi0.00531%0
Wuchereria bancrofti0.00307%28
Entamoeba histolytica0.00111%0
Taenia multiceps0.00072%0
Anncaliia algerae0.00054%0
Acanthamoeba palestinensis0.00045%0
Taenia saginata0.00036%0
Toxoplasma gondii0.00029%0
Hammondia hammondi0.00028%0
Vitrella brassicaformis0.00019%0
Trypanosoma congolense0.00016%0
Hymenolepis nana0.00012%0
fungi
Malassezia globosa0.00135%2
Albugo laibachii0.00037%2
Sordaria macrospora0.00019%0
Data of NTC 1-2
Speciescoverageunique reads
bacteria
Burkholderia contaminans70.71390%192162
Burkholderia sp. A918.34850%698
Propionibacterium acnes9.69150%4508
Burkholderia ubonensis9.52910%4152
Burkholderia cepacia9.48444%778
Streptomyces purpurogeneiscleroticus9.26422%11520
Burkholderia sp. lig308.61528%3324
Paracoccus sphaerophysae8.27434%4748
Burkholderia multivorans7.99355%10438
Burkholderia cenocepacia7.77753%722
Burkholderia pseudomultivorans6.56730%1360
Burkholderia paludis6.23575%752
Burkholderia territorii5.93721%810
Burkholderia dolosa5.70962%1008
Brevundimonas vesicularis5.46127%1098
alpha proteobacterium L41A5.36417%960
Burkholderia vietnamiensis5.00986%758
Burkholderia latens4.81704%550
Moraxella osloensis4.48765%1750
Brevundimonas nasdae4.26600%620
Ralstonia sp. MD273.95541%3814
Methylobacterium sp. Leaf923.33116%1984
Burkholderia oklahomensis2.55266%532
Burkholderia sp. MSMB02662.39555%502
Burkholderia thailandensis2.36199%356
Mitsuaria chitosanitabida2.30286%1550
Burkholderia pseudomallei2.15821%394
Polynucleobacter duraquae2.03233%242
Mesorhizobium sp. UASWS10092.02916%2578
Staphylococcus epidermidis1.75235%464
Delftia sp. 6701.59035%350
beta proteobacterium CB1.47058%160
Rhizobiales bacterium CCH3-A51.44322%1258
Delftia tsuruhatensis1.39544%136
Comamonadaceae bacterium CCH4-C51.34171%152
Burkholderia sp. TSV851.26039%206
Limnohabitans sp. Rim471.25771%524
Comamonadaceae bacterium CCH12-A101.22388%28
Sphingopyxis sp. LC811.21113%646
Methylobacterium sp. AMS51.17324%160
Paraburkholderia graminis1.11557%100
Cupriavidus metallidurans1.07216%148
Polynucleobacter sp. MWH-Adler-W81.06592%154
Polynucleobacter yangtzensis1.06532%116
Acidovorax sp. CCH12-A41.06181%22
Acidovorax temperans1.05237%140
Rhodoluna lacicola1.00760%172
Acidovorax sp. KKS1021.00036%100
Burkholderia glumae0.92570%164
Burkholderia plantarii0.90366%156
Acidovorax delafieldii0.85833%102
Acinetobacter johnsonii0.70257%396
Serratia marcescens0.60362%398
Staphylococcus warneri0.59456%284
Methylobacterium populi0.51600%72
Methylobacterium sp. MB2000.45124%106
Brevundimonas diminuta0.32852%38
Pseudomonas putida0.30588%34
Brevundimonas naejangsanensis0.23745%4
Cellvibrio sp. pealriver0.23255%36
Luteimonas huabeiensis0.21588%4
Paracoccus sp. S44930.19800%24
Paracoccus sp. 2280.17676%18
Thermomonas hydrothermalis0.13133%2
Caldimonas manganoxidans0.11231%6
Deinococcus geothermalis0.06766%14
Pseudomonas pseudoalcaligenes0.05742%8
Tetrasphaera elongata0.05497%12
Microbacterium aurum0.05443%14
Dietzia sp. 111N12-10.04864%24
Gordonia sputi0.04593%18
Brevibacterium casei0.02841%10
Xanthomonas sp. Mitacek010.02604%4
viruses
Burkholderia phage KS1012.46273%45
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Staphylococcus phage IME-SA414.67467%87
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%45
Staphylococcus phage PH1512.88680%42
Staphylococcus phage Ipla78.89998%23
Staphylococcus phage CNPx4.65783%11
Staphylococcus phage StB123.47691%8
Staphylococcus phage PT10280.43317%0
Staphylococcus phage SPbeta-like0.80953%21
Parasite
Acanthamoeba palestinensis0.00760%36
Wuchereria bancrofti0.00660%55
Hammondia hammondi0.00330%10
Cryptosporidium hominis0.00240%5
Acanthamoeba mauritaniensis0.00100%1
Enterobius vermicularis0.00020%3
Hammondia hammondi0.00030%1
Leishmania mexicana0.00150%4
fungi
Malassezia globosa0.00945%7
Neurospora crassa0.00168%5
Neurospora tetrasperma0.00147%5
Sordaria macrospora0.00085%1
Albugo laibachii0.00110%5
Data of Case 1-3
speciescoverageunique reads
bacteria
Mesorhizobium sp. UASWS10090.60169%520
Burkholderia sp. A90.25588%4
Comamonadaceae bacterium CCH4-C50.22380%28
Burkholderia sp. lig300.22198%44
Moraxella osloensis0.20637%84
Acidovorax temperans0.20151%16
Comamonadaceae bacterium CCH12-A100.20112%4
Burkholderia ubonensis0.20000%42
Burkholderia multivorans0.18438%92
Asinibacterium sp. OR530.16400%82
Methylotenera versatilis0.15945%26
Acidovorax delafieldii0.14580%20
Acidovorax sp. CCH12-A40.13736%0
Burkholderia dolosa0.12890%6
Acidovorax sp. KKS1020.12711%20
Buchnera aphidicola0.03577%4
Candidatus Methylopumilus planktonicus0.01526%2
Streptococcus suis0.01360%2
Streptococcus sp. HMSC063B030.01279%2
Streptococcus sp. X13SY080.00962%0
Candidatus Nitrosotenuis cloacae0.00926%2
Coriobacteriales bacterium DNF008090.00883%2
Lactobacillus frumenti0.00865%2
Fenollaria timonensis0.00862%0
Ezakiella massiliensis0.00861%0
viruses
Propionibacterium phage P1.10.51111%2
Rhodoferax phage P262180.20653%0
Burkholderia phage KS100.19928%0
Paramecium bursaria Chlorella virus A10.05417%2
Parasite
Wuchereria bancrofti0.01117%138
Taenia solium0.00129%20
Entamoeba histolytica0.00060%0
Acanthamoeba palestinensis0.00055%0
Anncaliia algerae0.00054%0
Acanthamoeba mauritaniensis0.00038%0
Hammondia hammondi0.00033%0
Toxoplasma gondii0.00023%0
Vitrella brassicaformis0.00020%0
Sordaria macrospora0.00018%0
Spirometra erinaceieuropaei0.00016%16
Sarcocystis neurona0.00009%2
Acanthamoeba lugdunensis0.00008%0
Taenia saginata0.00007%0
Taenia multiceps0.00005%0
fungi
[Candida] glabrata0
Fusarium verticillioides0.00061%4
Aspergillus oryzae0.00050%2
Phytophthora ramorum0.00031%0
Data of NTC 1-3
speciescoverageunique reads
bacteria
Propionibacterium acnes34.04003%11554
Burkholderia sp. A912.28355%582
Burkholderia ubonensis9.00584%5830
Burkholderia sp. lig308.51874%4474
Moraxella osloensis7.97496%1552
Acidovorax sp. CCH12-A47.68344%209
Comamonadaceae bacterium CCH4-C57.43362%1213
Mesorhizobium sp. UASWS10096.71863%3682
Acidovorax temperans6.18504%1086
Comamonadaceae bacterium CCH12-A106.17620%400
Burkholderia multivorans5.28967%8881
Acidovorax sp. KKS1024.38349%1422
Burkholderia pseudomultivorans4.29995%2234
Acidovorax delafieldii4.23114%1467
Burkholderia dolosa3.80671%1668
Streptomyces purpurogeneiscleroticus3.78001%1982
Staphylococcus epidermidis3.26394%669
Burkholderia territorii3.21927%1242
Burkholderia vietnamiensis3.03225%1214
Burkholderia cepacia2.84271%1257
Burkholderia cenocepacia2.83904%1263
Burkholderia latens2.67585%835
Burkholderia paludis2.64373%1292
Burkholderia contaminans2.43925%1041
Methylophilus sp. 422.14890%308
Paludibacter propionicigenes1.97348%582
Cutibacterium granulosum1.92545%253
Burkholderia oklahomensis1.88096%855
Acidovorax sp. Root701.77776%481
Chryseobacterium gambrini1.70283%610
Acidovorax sp. Root4021.68536%480
Paraburkholderia graminis1.67921%33
Staphylococcus hominis1.61241%287
Methyloversatilis universalis1.59867%470
Burkholderia sp. MSMB02661.57836%636
Burkholderia thailandensis1.56916%539
Burkholderia pseudomallei1.53337%617
[Propionibacterium] namnetense1.52591%278
Limnohabitans sp. Rim471.47593%235
Corynebacterium sp. KPL18601.45035%265
Sphingomonas sp. CCH10-B31.26080%47
Pelomonas sp. Root14441.23576%169
Cupriavidus metallidurans1.23463%206
Curvibacter delicatus1.14647%148
Acidovorax sp. GW101-3H111.11543%293
Bosea vaviloviae0.96862%404
Xenophilus azovorans0.92828%16
Propionibacterium humerusii0.85206%190
Dyella jiangningensis0.75250%502
Acinetobacter johnsonii0.58676%176
Micrococcus luteus0.56357%61
Corynebacterium aurimucosum0.50558%72
Neisseria sp. HMSC073B070.47438%65
viruses
Burkholderia phage KS1012.46273%45
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Staphylococcus phage IME-SA414.67467%87
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%45
Staphylococcus phage PH1512.88680%42
Staphylococcus phage Ipla78.89998%23
Staphylococcus phage CNPx4.65783%11
Staphylococcus phage StB123.47691%8
Staphylococcus phage PT10280.43317%0
Propionibacterium phage P1.10.80953%21
Parasite
Acanthamoeba palestinensis0.00680%30
Wuchereria bancrofti0.00970%66
Hammondia hammondi0.00330%6
Cryptosporidium hominis0.00210%5
Acanthamoeba mauritaniensis0.00180%2
Trypanosoma cruzi0.00190%3
Toxoplasma gondii0.00220%4
Enterobius vermicularis0.00030%3
fungi
Malassezia globosa0.00938%7
Neurospora crassa0.00170%4
Neurospora tetrasperma0.00177%5
Sordaria macrospora0.00085%1
Albugo laibachii0.00120%8
Data of Case 1-4
speciescoverageunique reads
bacteria
Burkholderia sp. A97.81720%124
Burkholderia ubonensis4.04034%1367
Burkholderia sp. lig303.77586%1022
Burkholderia contaminans3.77353%2157
Burkholderia multivorans2.76210%2158
Mesorhizobium sp. UASWS10092.74414%1415
Burkholderia pseudomultivorans1.71037%506
Burkholderia dolosa1.49604%440
Ralstonia sp. MD271.33630%558
Propionibacterium acnes1.29076%248
Burkholderia territorii1.22983%291
Burkholderia vietnamiensis1.14219%260
Burkholderia cepacia1.03080%316
Burkholderia cenocepacia1.01151%324
Burkholderia latens0.97577%197
Candidatus Kinetoplastibacterium galatii0.06556%0
Lactobacillus crispatus0.02790%4
Cellulosimicrobium sp. I38E0.02219%4
Leuconostoc lactis0.02120%4
Pantoea septica0.01996%6
Brackiella oedipodis0.01800%0
Gardnerella vaginalis0.01685%1
Corynebacterium genitalium0.01596%0
Nitrosomonas eutropha0.01455%0
Salmonella enterica0.00303%1
viruses
Burkholderia phage KS109.18294%19
Propionibacterium phage Kubed0.50915%1
Propionibacterium phage PHL0090.39318%1
Propionibacterium phage PHL1160.27897%1
Propionibacterium phage BruceLethal0.25642%0
Propionibacterium phage Lauchelly0.25409%0
Burkholderia virus phiE1250.23982%1
Rhodoferax phage P262180.20653%0
Staphylococcus phage StB120.16773%0
Acinetobacter bacteriophage AP220.16168%0
Burkholderia virus Bcepil020.15945%0
Pseudomonas phage PMG10.13883%0
Burkholderia virus Bcep220.11740%0
Salmonella phage SJ460.07250%0
Invertebrate iridescent virus 310.06130%1
Paramecium bursaria Chlorella virus A10.02335%0
Parasite
Wuchereria bancrofti0.00406%21
Acanthamoeba palestinensis0.00088%5
Hammondia hammondi0.00071%2
Anisakis simplex0.00047%3
Toxoplasma gondii0.00045%1
Enterobius vermicularis0.00015%0
Acanthamoeba mauritaniensis0.00012%1
Necator americanus0.00008%1
Spirometra erinaceieuropaei0.00008%5
Daphnia pulex0.00008%0
Cimex lectularius0.00001%0
fungi
Malassezia globosa8
Sordaria macrospora0.01104%1
Aspergillus oryzae0.00075%1
Aspergillus terreus0.00040%0
Talaromyces stipitatus0.00026%1
Data of NTC 1-4
speciescoverageunique reads
bacteria
Burkholderia contaminans17.06165%12499
Propionibacterium acnes14.79645%3213
Burkholderia sp. A913.71155%416
Moraxella osloensis10.41486%1926
Burkholderia ubonensis7.25759%3932
Ralstonia sp. MD277.19944%3495
Burkholderia sp. lig306.79520%2965
Mesorhizobium sp. UASWS10096.36419%3543
Staphylococcus capitis5.54523%1036
Burkholderia multivorans4.57565%6074
Burkholderia pseudomultivorans3.34007%1486
Burkholderia dolosa2.94948%1156
Acinetobacter johnsonii2.75123%784
Burkholderia territorii2.45843%865
Burkholderia vietnamiensis2.31264%812
Burkholderia cepacia2.23127%888
Streptomyces purpurogeneiscleroticus2.19861%1174
Burkholderia cenocepacia2.18833%914
Burkholderia latens2.07107%558
Sphingomonas sp. Ant H112.05460%689
Burkholderia paludis2.01034%885
Methylotenera versatilis1.68798%291
Paraburkholderia graminis1.48860%22
Pseudomonas sp. NBRC 1111261.47376%592
Burkholderia oklahomensis1.47342%588
Kocuria polaris1.44637%399
Acidovorax sp. Leaf1601.33441%358
Acidovorax delafieldii1.33048%365
Enterobacter hormaechei1.20764%433
Burkholderia sp. MSMB02661.20270%459
Burkholderia thailandensis1.18905%403
Limnohabitans sp. Rim471.18635%218
Burkholderia pseudomallei1.17267%430
Acidovorax sp. CCH12-A41.16758%25
Acidovorax sp. Root701.15159%282
Acidovorax sp. KKS1021.13274%273
Cupriavidus metallidurans1.10643%156
Polynucleobacter duraquae1.04787%64
Azospira oryzae0.98796%277
Acinetobacter ursingii0.96935%249
Xenophilus azovorans0.86198%9
Methylobacterium sp. Leaf920.84496%332
Dyella jiangningensis0.73064%362
Cupriavidus necator0.71804%301
Comamonadaceae bacterium CCH12-A100.65781%18
Ralstonia sp. NT800.65181%210
Comamonadaceae bacterium CCH4-C50.62873%74
Hydrogenophaga sp. Root2090.59192%53
Acinetobacter pittii0.54572%149
Acidovorax temperans0.48750%59
Serratia marcescens0.27563%87
viruses
Burkholderia phage KS1012.43273%53
Flavobacterium phage Fpv20.40320%4
Paramecium bursaria Chlorella virus A10.36670%6
Staphylococcus phage IME-SA417.78467%67
Staphylococcus phage CNPH8214.21050%78
Staphylococcus phage Ipla518.78080%78
Staphylococcus phage PH1514.20680%35
Staphylococcus phage Ipla78.94998%22
Staphylococcus phage CNPx4.27783%9
Propionibacterium phage Kubed3.48991%7
Propionibacterium phage PHL0091.67450%5
Propionibacterium phage PHL1160.78037%3
Propionibacterium phage BruceLethal0.84517%5
Propionibacterium phage Lauchelly0.70453%12
Parasite
Acanthamoeba palestinensis0.00890%37
Wuchereria bancrofti0.00670%42
Hammondia hammondi0.00330%6
Cryptosporidium hominis0.00210%5
Acanthamoeba mauritaniensis0.00190%2
Trypanosoma cruzi0.00080%2
Toxoplasma gondii0.00340%5
Enterobius vermicularis0.00040%4
Hammondia hammondi0.00120%6
Leishmania mexicana0.00140%5
fungi
Malassezia globosa0.00937%6
Neurospora crassa0.00168%5
Talaromyces marneffei0.00061%6
Aspergillus oryzae0.00150%1
Albugo laibachii0.00130%4
Data of Case 2-2
speciescoverageunique reads
bacteria
Burkholderia sp. A93.07628%86
Burkholderia ubonensis2.83859%660
Burkholderia sp. lig302.64866%570
Burkholderia multivorans2.15804%1208
Burkholderia pseudomultivorans1.56057%202
Burkholderia dolosa1.49231%162
Burkholderia territorii1.37086%92
Burkholderia cenocepacia1.33809%108
Burkholderia cepacia1.24686%102
Burkholderia vietnamiensis1.20625%118
Burkholderia paludisj1.11181%134
Burkholderia latens1.10139%70
Mesorhizobium sp. UASWS10091.08090%1114
Burkholderia contaminans1.04647%112
Paracoccus sphaerophysae0.81007%356
Kinetoplastibacterium blastocrithidii0.04780%0
Actinomyces sp. HMSC08A010.02886%10
Candidatus Profftella armatura0.02216%0
Candidatus Kinetoplastibacterium crithidii0.01995%0
Corynebacterium variabile0.01992%4
Aerococcus viridans0.01991%0
Weissella jogaejeotgali0.01973%0
Candidatus Kinetoplastibacterium galatii0.01934%0
Candidatus Kinetoplastibacterium oncopeltii0.01851%0
Streptococcus macedonicus0.01668%0
viruses
Burkholderia phage KS104.26465%16
Propionibacterium phage PHL060L000.50823%2
Staphylococcus phage StB270.37434%2
Burkholderia virus phiE1250.32226%2
Staphylococcus phage IME-SA40.17924%0
Flavobacterium phage Fpv20.08875%2
Paramecium bursaria Chlorella virus A10.02335%0
Parasite
Taenia solium3.03254%45972
Taenia saginata0.05191%18
Taenia multiceps0.03624%62
Wuchereria bancrofti0.01077%74
Acanthamoeba palestinensis0.00174%8
Hymenolepis nana0.00150%0
Entamoeba histolytica0.00119%0
Acanthamoeba mauritaniensis0.00103%2
Echinococcus multilocularis0.00085%0
Trypanosoma cruzi0.00062%0
Hammondia hammondi0.00058%2
Anncaliia algerae0.00054%0
Toxoplasma gondii0.00046%0
Schistosoma mansoni0.00039%0
fungi
Malassezia globosa0.00238%4
Pneumocystis carinii0.00196%0
Sordaria macrospora0.00094%0
Albugo laibachii0.00060%2
Data of NTC 2-2
speciescoverageunique reads
bacteria
Staphylococcus hominis12.19550%4564
Ralstonia sp. MD2710.70210%9644
Burkholderia ubonensis8.40481%3698
Moraxella osloensis7.84991%2552
Burkholderia sp. A97.76343%466
Burkholderia sp. lig307.68243%2762
Paracoccus sphaerophysae7.61451%3744
Rothia sp. ND6WE1A7.30648%2784
Staphylococcus haemolyticus6.01573%2306
Burkholderia multivorans5.80606%6370
Staphylococcus epidermidis5.25386%1058
Burkholderia pseudomultivorans5.06785%1126
alpha proteobacterium L41A4.88849%798
Brevundimonas vesicularis4.87511%854
Burkholderia dolosa4.71681%818
Mesorhizobium sp. UASWS10094.62789%5248
Propionibacterium acnes4.58402%1860
Burkholderia cenocepacia4.31558%560
Burkholderia territorii4.26066%582
Burkholderia vietnamiensis3.87120%662
Burkholderia cepacia3.86708%616
Brevundimonas nasdae3.81090%514
Burkholderia latens3.56392%356
Burkholderia paludis3.52522%598
Burkholderia contaminans3.43589%548
Corynebacterium appendicis3.31193%994
Streptomyces purpurogeneiscleroticus3.21604%3336
Acinetobacter johnsonii2.93549%1556
Staphylococcus warneri2.91993%878
Burkholderia oklahomensis2.19710%456
Burkholderia thailandensis2.03216%256
Burkholderia sp. MSMB02661.90831%434
Burkholderia pseudomallei1.85903%332
Acidovorax delafieldii1.46921%190
Ralstonia sp. NT801.45625%246
Sphingomonas sp. Ant H111.45307%756
Methylotenera versatilis1.38689%204
Corynebacterium tuberculostearicum1.34973%220
Acidovorax sp. KKS1021.31939%164
Corynebacterium aurimucosum1.27600%200
Acidovorax sp. Leaf1601.25323%654
Acidovorax sp. Root701.12287%230
Burkholderia sp. TSV851.07564%164
Cupriavidus metallidurans1.05755%198
Comamonadaceae bacterium CCH12-A101.05171%16
Comamonadaceae bacterium CCH4-C51.02252%96
Acidovorax sp. CCH12-A40.88438%32
Acidovorax sp. Root4020.87451%136
Burkholderia plantarii0.80571%130
Acidovorax temperans0.76659%74
Ralstonia pickettii0.75577%246
Bradyrhizobium elkanii0.71983%762
Limnohabitans sp. Rim470.69754%252
Ralstonia sp. 5_2_56FAA0.57599%66
Acinetobacter lwoffii0.52177%168
Cloacibacterium normanense0.16745%54
Prevotella disiens0.01169%2
Serratia marcescens0.00786%6
viruses
Burkholderia phage KS1012.39273%42
Flavobacterium phage Fpv20.45320%4
Paramecium bursaria Chlorella virus A10.35670%5
Staphylococcus phage IME-SA414.68467%67
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%35
Staphylococcus phage PH1512.20680%42
Staphylococcus phage Ipla78.94998%18
Staphylococcus phage CNPx4.27783%10
Staphylococcus phage StB123.47691%6
Staphylococcus phage StB20-like1.07450%3
Staphylococcus phage StB270.85037%3
Staphylococcus phage PT10280.83317%1
Staphylococcus phage SPbeta-like0.80453%19
Parasite
Acanthamoeba palestinensis0.01080%44
Wuchereria bancrofti0.01070%76
Hammondia hammondi0.00350%5
Cryptosporidium hominis0.00160%3
Acanthamoeba mauritaniensis0.00210%5
Trypanosoma cruzi0.00070%9
Toxoplasma gondii0.00200%3
Enterobius vermicularis0.00130%11
Hammondia hammondi0.00120%8
Leishmania mexicana0.00050%1
fungi
Malassezia globosa0.00938%7
Neurospora crassa0.00173%5
Neurospora tetrasperma0.00144%4
Sordaria macrospora0.00082%2
Talaromyces marneffei0.00061%1
Aspergillus oryzae0.00150%7
Albugo laibachii0.00130%8
Data of Case 2-3
speciescoverageunique reads
bacteria
Mesorhizobium sp. UASWS10090.91784%812
Moraxella osloensis0.50888%156
Burkholderia sp. A90.33967%4
Burkholderia ubonensis0.25409%58
Burkholderia multivorans0.24535%138
Burkholderia sp. lig300.22921%34
Comamonadaceae bacterium CCH4-C50.22088%22
Staphylococcus hominis0.21209%64
Comamonadaceae bacterium CCH12-A100.20514%4
Staphylococcus warneri0.19807%52
Propionibacterium acnes0.19807%68
Acidovorax temperans0.19201%22
Acidovorax delafieldii0.17649%28
Acidovorax sp. KKS1020.16566%20
Herbaspirillum frisingense0.16484%128
Candidatus Kinetoplastibacterium crithidii0.02737%0
Buchnera aphidicola0.01413%2
Streptococcus gordonii0.01386%2
Thermus scotoductus0.01274%2
Leptotrichia shahii0.01268%4
Candidatus Methylopumilus planktonicus0.01106%0
Candidatus Aquiluna sp. IMCC130230.01103%0
Lactobacillus iners0.01049%2
Atopobium vaginae0.01049%2
Mycobacterium hassiacum0.00152%2
viruses
Burkholderia phage KS100.71476%4
Staphylococcus phage Ipla70.24452%0
Staphylococcus phage CNPx0.23791%0
Staphylococcus phage CNPH820.23722%0
Staphylococcus phage Ipla50.23634%0
Rhodoferax phage P262180.20653%0
Burkholderia virus phiE1250.14052%0
Paramecium bursaria Chlorella virus A10.07004%2
Parasite
Wuchereria bancrofti0.01086%118
Taenia solium0.00910%162
Acanthamoeba palestinensis0.00137%2
Toxoplasma gondii0.00068%4
Entamoeba histolytica0.00060%0
Hammondia hammondi0.00055%4
Leishmania mexicana0.00046%0
Acanthamoeba mauritaniensis0.00030%0
Daphnia magna0.00023%0
Daphnia pulex0.00019%0
Taenia multiceps0.00008%0
Taenia saginata0.00007%0
Trichobilharzia regenti0.00001%0
fungi
Candida glabrata0.00098%2
Sordaria macrospora0.00088%2
Malassezia globosa0.00087%2
Fusarium graminearum0.00039%2
Aspergillus oryzae0.00029%2
Data of NTC 2-3
speciescoverageunique reads
bacteria
Burkholderia ubonensis12.17370%7912
Burkholderia contaminans12.10940%10322
Mesorhizobium sp. UASWS100911.83390%13442
Burkholderia sp. lig3011.40910%6560
Burkholderia sp. A911.29790%910
Propionibacterium acnes9.16155%3460
Burkholderia multivorans8.55849%17058
Burkholderia pseudomultivorans7.80365%2686
Burkholderia dolosa7.34465%1902
Burkholderia cenocepacia7.00066%1386
Burkholderia territorii6.74042%1392
Burkholderia cepacia6.33014%1264
Burkholderia vietnamiensis6.17856%1488
Burkholderia latens5.73374%926
Burkholderia paludis5.59031%1366
Ralstonia sp. MD274.20060%3402
Burkholderia oklahomensis3.58476%976
Acidovorax delafieldii3.58468%538
Burkholderia thailandensis3.36727%574
Acidovorax sp. KKS1023.27177%364
Burkholderia sp. MSMB02663.22183%928
Streptomyces purpurogeneiscleroticus3.17552%3042
Burkholderia pseudomallei3.13012%752
Sphingomonas sp. Ant H113.04975%1640
Acidovorax sp. Root702.79418%558
Methylotenera versatilis2.75240%486
Methylobacterium sp. Leaf922.45321%1300
Acidovorax sp. Leaf1602.42142%1122
Limnohabitans sp. Rim472.21576%802
Acidovorax sp. Root4022.13516%284
Moraxella osloensis2.12775%646
Thermomonas hydrothermalis1.82230%588
Burkholderia sp. TSV851.78087%384
Rhizobiales bacterium CCH3-A51.71232%1246
Methyloversatilis universalis1.42668%474
Polynucleobacter duraquae1.41796%154
Polynucleobacter sp. MWH-Adler-W81.20835%186
Bradyrhizobium elkanii1.20446%1270
Kocuria palustris0.88080%378
Arthrobacter sp. LS160.78653%434
Serratia marcescens0.62863%350
Aerococcus urinaeequi0.57963%86
Staphylococcus capitis0.49754%188
Sphingomonas paucimobilis0.48782%36
Methylophilus sp. 50.31586%32
Streptococcus cristatus0.03968%4
Neisseria sp. HMSC073B070.03618%2
Neisseria sp. HMSC074B070.03480%2
Streptococcus sp. M3340.03407%2
Streptococcus mitis0.03110%2
Streptococcus gordonii0.02959%4
Corynebacterium matruchotii0.02556%10
Streptococcus sanguinis0.02546%2
Streptococcus pseudopneumoniae0.02475%2
Streptococcus oralis0.00757%2
Staphylococcus xylosus0.00656%4
viruses
Burkholderia phage KS1012.46273%45
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Staphylococcus phage IME-SA414.67467%87
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%45
Staphylococcus phage PH1512.88680%42
Staphylococcus phage StB123.47691%8
Staphylococcus phage PT10280.43317%0
Propionibacterium phage P1.10.80953%21
Parasite
Acanthamoeba palestinensis0.00680%30
Wuchereria bancrofti0.01270%106
Hammondia hammondi0.00330%6
Cryptosporidium hominis0.00210%5
Acanthamoeba mauritaniensis0.00170%4
Trypanosoma cruzi0.00180%3
Toxoplasma gondii0.00220%5
Enterobius vermicularis0.00120%6
fungi
Malassezia globosa0.00956%8
Neurospora crassa0.00179%5
Neurospora tetrasperma0.00177%6
Sordaria macrospora0.00065%2
Albugo laibachii0.00120%4
Data of Case 3-1
speciescoverageunique reads
bacteria
Burkholderia sp. A90.10084%2
Moraxella osloensis0.06874%24
Burkholderia multivorans0.04319%32
Pandoraea thiooxydans0.04222%0
Burkholderia sp. b140.03558%0
Burkholderia ubonensis0.03458%6
Burkholderia sp. lig300.03346%14
Polynucleobacter duraquae0.03168%4
Methylotenera versatilis0.02709%0
Burkholderia contaminans0.02371%12
Paraburkholderia rhizoxinica0.02211%0
Lactobacillus acidophilus0.02088%2
Polynucleobacter sp. MWH-Adler-W80.01885%4
Burkholderia dolosa0.01842%2
beta proteobacterium CB0.01809%0
Lactobacillus gasseri0.00792%2
Gemella morbillorum0.00725%2
Megasphaera micronuciformis0.00663%2
Bergeyella zoohelcum0.00643%0
Erysipelotrichaceae bacterium MTC70.00605%0
Alloprevotella rava0.00578%2
Negativicoccus massiliensis0.00544%0
Prevotella stercorea0.00484%0
Chryseobacterium antarcticum0.00480%0
viruses
Parasite
Taenia solium0.08346%1114
Wuchereria bancrofti0.01755%134
Taenia saginata0.00105%0
Taenia multiceps0.00069%0
Toxoplasma gondii0.00046%2
Entamoeba histolytica0.00030%0
Plasmodium vivax0.00028%2
Plasmodium malariae0.00022%0
Spirometra erinaceieuropaei0.00012%10
Eimeria mitis0.00010%0
Clonorchis sinensis0.00003%0
fungi
Hamiltosporidium tvaerminnensis0.00057%0
Sclerotinia sclerotiorum0.00020%0
Allomyces macrogynus0.00013%0
Data of NTC 3-1
speciescoverageunique reads
bacteria
Moraxella osloensis4.60267%1602
Propionibacterium acnes2.02756%940
Acinetobacter johnsonii1.78572%1074
Staphylococcus epidermidis1.47129%328
Polynucleobacter duraquae1.02221%118
beta proteobacterium CB0.91454%124
Staphylococcus warneri0.88221%370
Staphylococcus hominis0.75899%284
Polynucleobacter sp. MWH-Adler-W80.73046%114
Chryseobacterium haifense0.71781%282
Burkholderia sp. A90.71542%40
Burkholderia contaminans0.53869%572
Burkholderia multivorans0.51537%628
Polynucleobacter yangtzensis0.49462%60
Burkholderia ubonensis0.48325%210
Methylotenera versatilis0.45982%32
Staphylococcus haemolyticus0.42115%160
Burkholderia sp. lig300.40663%216
Staphylococcus capitis0.34395%90
Burkholderia sp. b140.28547%4
Acinetobacter lwoffii0.25894%86
Burkholderia territorii0.25855%34
Burkholderia cepacia0.25659%34
Burkholderia dolosa0.25389%50
Burkholderia pseudomultivorans0.25365%54
Burkholderia latens0.24669%16
Burkholderia cenocepacia0.22793%30
Ralstonia sp. MD270.21679%200
Polynucleobacter sp. MWH-Weng1-10.21435%2
[Propionibacterium] namnetense0.19896%18
Burkholderia paludis0.19189%20
Moraxella atlantae0.19034%4
Burkholderia vietnamiensis0.18418%26
Staphylococcus caprae0.15180%22
Psychrobacter sp. SHUES10.12428%52
Veillonella atypica0.11949%4
Rhodoluna lacicola0.11787%18
Acinetobacter radioresistens0.11707%4
Burkholderia oklahomensis0.10138%14
Corynebacterium sp. KPL18600.09916%20
Staphylococcus cohnii0.09633%18
Acinetobacter schindleri0.07833%16
Acinetobacter indicus0.07579%6
Acinetobacter nosocomialis0.06862%2
Psychrobacter sp. P11F60.06282%22
Cloacibacterium normanense0.04807%12
Dolosigranulum pigrum0.04253%10
Psychrobacter sp. P11G50.03984%2
Acinetobacter harbinensis0.03611%6
Corynebacterium singulare0.03190%6
Corynebacterium accolens0.02429%6
Bradyrhizobium elkanii0.02394%28
Psychrobacter sp. G0.01795%4
Neisseria sp. oral taxon 0140.01650%2
Acinetobacter pittii0.01196%2
viruses
Burkholderia phage KS1012.46273%45
Flavobacterium phage Fpv20.44520%5
Staphylococcus phage PT10280.43317%0
Staphylococcus phage SPbeta-like0.80953%21
Parasite
Acanthamoeba palestinensis0.00760%36
Wuchereria bancrofti0.01560%96
Hammondia hammondi0.00360%12
Cryptosporidium hominis0.00130%3
Acanthamoeba mauritaniensis0.00100%1
Enterobius vermicularis0.00100%5
Hammondia hammondi0.00030%1
Leishmania mexicana0.00210%6
fungi
Malassezia globosa0.00979%8
Neurospora crassa0.00168%5
Neurospora tetrasperma0.00146%6
Sordaria macrospora0.00085%1
Albugo laibachii0.00150%8
Data of Case 3-2
speciescoverageunique reads
bacteria
Burkholderia sp. A90.36836%6
Burkholderia ubonensis0.34902%54
Burkholderia sp. lig300.29985%44
Bradyrhizobium elkanii0.29244%318
Burkholderia multivorans0.24832%120
Burkholderia pseudomultivorans0.18167%20
Burkholderia dolosa0.17946%12
Burkholderia territorii0.16482%18
Burkholderia cenocepacia0.16120%6
Burkholderia cepacia0.14259%12
Burkholderia paludis0.12624%12
Burkholderia contaminans0.11931%24
Burkholderia latens0.11872%16
Burkholderia vietnamiensis0.11297%4
Burkholderia oklahomensis0.07175%10
Kinetoplastibacterium blastocrithidii0.02915%0
Candidatus Kinetoplastibacterium galatii0.02907%0
Sphingopyxis sp. LPB01400.00754%0
Streptococcus sp. I-P160.00741%2
Rhodospirillum rubrum0.00690%0
Thermus scotoductus0.00534%2
Staphylococcus agnetis0.00522%0
Actinomyces sp. ICM470.00479%2
Brochothrix thermosphacta0.00419%2
Solemya pervernicosa gill symbiont0.00415%0
viruses
Burkholderia phage KS100.61911%4
Parasite
Taenia solium0.07672%1026
Wuchereria bancrofti0.02276%180
Leishmania mexicana0.00339%18
Taenia saginata0.00170%0
Taenia multiceps0.00126%6
Toxoplasma gondii0.00072%2
Entamoeba histolytica0.00030%0
Trichuris suis0.00023%0
Acanthamoeba mauritaniensis0.00023%0
Hammondia hammondi0.00022%0
Spirometra erinaceieuropaei0.00022%18
Enterobius vermicularis0.00016%2
Daphnia pulex0.00008%0
Fasciola hepatica0.00001%0
fungi
Malassezia globosa0.00168%2
Data of NTC 3-2
speciescoverageunique reads
bacteria
Burkholderia ubonensis9.57853%4852
Burkholderia sp. lig308.86285%3832
Burkholderia sp. A98.67200%542
Mesorhizobium sp. UASWS10098.00531%9484
Burkholderia multivorans6.60315%9182
Burkholderia pseudomultivorans5.84032%1584
Burkholderia dolosa5.33883%1148
Burkholderia cenocepacia4.99446%792
Burkholderia territorii4.97842%806
Burkholderia vietnamiensis4.51675%854
Burkholderia cepacia4.41761%682
Burkholderia latens4.15117%500
Burkholderia paludis4.06631%822
Burkholderia contaminans4.03285%808
Propionibacterium acnes3.98345%1658
Burkholderia oklahomensis2.57198%602
Burkholderia thailandensis2.36005%434
Burkholderia sp. MSMB02662.30809%476
Streptomyces purpurogeneiscleroticus2.23613%2526
Burkholderia pseudomallei2.20894%474
Sphingomonas sp. Ant H112.17519%1192
Acidovorax delafieldii2.15278%326
Acidovorax sp. KKS1022.08157%270
Brevundimonas vesicularis2.05936%362
alpha proteobacterium L41A2.02106%278
Comamonadaceae bacterium CCH4-C51.97819%226
Rhizobiales bacterium CCH3-A51.94178%1568
Acidovorax sp. Root701.71866%352
Methylotenera versatilis1.60144%232
Moraxella osloensis1.49328%528
Acidovorax sp. Leaf1601.26938%682
Bradyrhizobium elkanii1.26822%1444
Sphingomonas echinoides0.81389%76
Methyloversatilis discipulorum0.74241%352
Staphylococcus hominis0.51032%196
Acinetobacter johnsonii0.49428%232
Afipia broomeae0.38927%84
Sphingomonas paucimobilis0.27656%14
Brevundimonas sp. BAL30.25902%56
Methylobacterium populi0.23710%10
Afipia sp. OHSU_I-C60.23504%16
Brevundimonas sp. DS200.20330%20
Staphylococcus warneri0.17526%46
Paracoccus sp. 2280.08994%10
Comamonas thiooxydans0.04206%6
Rothia mucilaginosa0.02486%2
Serratia marcescens0.01072%10
Kocuria flava0.00951%4
viruses
Burkholderia phage KS1011.16273%39
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Staphylococcus phage IME-SA412.37467%66
Propionibacterium phage P1.10.75953%15
Parasite
Acanthamoeba palestinensis0.00770%43
Wuchereria bancrofti0.02170%130
Hammondia hammondi0.00300%7
Cryptosporidium hominis0.00210%5
Acanthamoeba mauritaniensis0.00160%5
Trypanosoma cruzi0.00180%3
Toxoplasma gondii0.00310%8
Enterobius vermicularis0.00120%6
fungi
Malassezia globosa0.00967%6
Neurospora crassa0.00179%5
Neurospora tetrasperma0.00217%7
Sordaria macrospora0.00065%2
Albugo laibachii0.00120%5
Data of Case 3-3
speciescoverageunique reads
bacteria
Burkholderia sp. A90.43787%6
Burkholderia ubonensis0.38464%74
Burkholderia sp. lig300.36030%64
Burkholderia multivorans0.30223%132
Burkholderia pseudomultivorans0.21531%34
Burkholderia dolosa0.21283%20
Burkholderia territorii0.17445%22
Burkholderia cenocepacia0.17331%14
Burkholderia paludis0.14703%10
Burkholderia vietnamiensis0.14694%16
Burkholderia cepacia0.14440%10
Burkholderia contaminans0.13599%10
Burkholderia latens0.12709%4
Burkholderia oklahomensis0.10530%10
Burkholderia thailandensis0.09303%4
Bartonella ancashensis0.01247%0
bacterium endosymbiont of Mortierella elongata0.01073%0
Solemya pervernicosa gill symbiont0.00850%4
Bartonella bacilliformis0.00747%0
Fulvimarina pelagi0.00678%0
Clostridiales bacterium KLE16150.00492%2
Helicobacter heilmannii0.00467%0
Mageeibacillus indolicus0.00448%0
Burkholderia sp. Leaf1770.00441%0
Candidatus Glomeribacter gigasporarum0.00434%0
viruses
Burkholderia phage KS100.79713%2
Burkholderia virus Bcepil020.11959%0
Parasite
Taenia solium0.04368%592
Wuchereria bancrofti0.01555%108
Leishmania mexicana0.00162%4
Taenia saginata0.00133%2
Toxoplasma gondii0.00084%4
Trichuris suis0.00084%4
Taenia multiceps0.00074%0
Trichinella zimbabwensis0.00029%0
Plasmodium vivax0.00027%0
Leptomonas seymouri0.00027%0
Trichuris muris0.00018%0
Eimeria tenella0.00014%0
Sarcoptes scabiei0.00013%0
fungi
Malassezia globosa0.00256%4
Sordaria macrospora0.00019%0
Data of NTC 3-3
speciescoverageunique reads
bacteria
Bradyrhizobium elkanii10.70770%12942
Burkholderia ubonensis9.14576%3794
Burkholderia sp. A98.60309%408
Burkholderia sp. lig308.47525%3010
Burkholderia multivorans6.32021%6692
Burkholderia pseudomultivorans5.51548%1166
Burkholderia dolosa5.10665%916
Burkholderia territorii4.77273%672
Burkholderia cenocepacia4.73794%620
Burkholderia vietnamiensis4.32945%660
Burkholderia cepacia4.19702%614
Ralstonia sp. MD274.19666%3488
Burkholderia latens4.00264%452
Burkholderia paludis3.85719%650
Burkholderia contaminans3.65830%488
Mesorhizobium sp. UASWS10092.92958%2972
Burkholderia oklahomensis2.42164%484
Burkholderia thailandensis2.26419%276
Burkholderia sp. MSMB02662.18351%350
Streptomyces purpurogeneiscleroticus2.14049%2136
Burkholderia pseudomallei2.04635%318
Propionibacterium acnes2.03909%802
Bacillus sp. VT-16-641.89532%3728
Phyllobacterium sp. UNC302MFCol5.21.63491%412
Burkholderia sp. TSV851.12836%124
Phyllobacterium sp. YR5310.99762%426
Cupriavidus metallidurans0.87224%124
Burkholderia glumae0.84774%150
Burkholderia plantarii0.84727%140
Paraburkholderia graminis0.82195%30
Moraxella osloensis0.76100%254
Limnohabitans sp. Rim470.75291%274
Dyella jiangningensis0.67286%466
Methylotenera versatilis0.64078%68
Acidovorax temperans0.50702%54
Acinetobacter johnsonii0.21199%110
[Eubacterium] angustum0.16539%6
Thermomonas hydrothermalis0.13901%28
Chryseobacterium sp. FF120.12517%8
Paracoccus sphaerophysae0.11972%46
[Propionibacterium] namnetense0.11688%20
Comamonas aquatica0.11633%36
Cloacibacterium normanense0.07579%22
Leifsonia sp. Leaf3360.06631%14
Micrococcus luteus0.06260%14
Paenarthrobacter nicotinovorans0.03381%8
Arthrobacter sp. LS160.03111%16
Kocuria polaris0.01722%10
Corynebacterium stationis0.00790%2
viruses
Burkholderia phage KS1012.39273%42
Flavobacterium phage Fpv20.45320%4
Paramecium bursaria Chlorella virus A10.35670%5
Staphylococcus phage IME-SA414.68467%67
Staphylococcus phage CNPH8213.21050%45
Staphylococcus phage Ipla512.78080%35
Staphylococcus phage PH1512.20680%42
Staphylococcus phage Ipla78.94998%18
Parasite
Acanthamoeba palestinensis0.01080%44
Wuchereria bancrofti0.01270%96
Hammondia hammondi0.00350%5
Cryptosporidium hominis0.00170%4
Acanthamoeba mauritaniensis0.00210%5
Trypanosoma cruzi0.00080%9
Toxoplasma gondii0.00200%6
Enterobius vermicularis0.00100%11
Hammondia hammondi0.00140%8
Leishmania mexicana0.00130%5
fungi
Malassezia globosa0.00943%8
Neurospora crassa0.00182%9
Neurospora tetrasperma0.00140%3
Sordaria macrospora0.00082%2
Data of Case 3-4
speciescoverageunique reads
bacteria
Burkholderia sp. A91.00709%14
Burkholderia ubonensis0.98022%228
Burkholderia sp. lig300.79173%146
Burkholderia multivorans0.74839%354
Propionibacterium acnes0.73383%256
Ralstonia sp. MD270.51143%414
Burkholderia pseudomultivorans0.50465%66
Burkholderia dolosa0.48257%58
Burkholderia territorii0.44845%42
Burkholderia cenocepacia0.41857%30
Burkholderia vietnamiensis0.37598%44
Burkholderia paludis0.35834%20
Burkholderia cepacia0.35464%30
Burkholderia latens0.34386%20
Burkholderia contaminans0.31135%24
Candidatus Profftella armatura0.02302%0
Propionibacterium sp. oral taxon 1920.01623%0
Buchnera aphidicola0.01274%2
Brochothrix thermosphacta0.01155%6
Exiguobacterium sp. AT1b0.01100%2
Weissella confusa0.01046%4
Atopobium deltae0.01033%2
Bergeyella zoohelcum0.00917%0
Granulicatella elegans0.00860%2
Pseudomonas luteola0.00778%6
viruses
Burkholderia phage KS101.93171%12
Propionibacterium phage Procrass10.39868%2
Burkholderia virus phiE1250.14052%0
Escherichia virus EC60.13104%0
Escherichia virus AYO145A0.12933%0
Salmonella virus HB20140.12913%0
Salmonella virus UAB870.12899%0
Paramecium bursaria Chlorella virus A10.02335%0
Parasite
Wuchereria bancrofti0.01744%124
Taenia solium0.00647%78
Toxoplasma gondii0.00114%2
Entamoeba histolytica0.00089%0
Endotrypanum monterogeii0.00046%0
Leishmania mexicana0.00043%0
Trichuris trichiura0.00040%0
Vitrella brassicaformis0.00031%0
Cyclospora cayetanensis0.00029%2
Naegleria fowleri0.00025%0
Acanthamoeba palestinensis0.00024%0
Acanthamoeba mauritaniensis0.00023%0
Trichuris muris0.00009%0
Chromera velia0.00004%0
Trichobilharzia regenti0.00001%0
fungi
Malassezia globosa0.00166%2
Aspergillus niger0.00022%0
Sordaria macrospora0.00020%2
Data of NTC 3-4
speciescoverageunique reads
bacteria
Ralstonia sp. MD2754.07490%75456
Propionibacterium acnes26.50730%12352
Moraxella osloensis17.82990%6552
Burkholderia ubonensis11.38230%6708
Burkholderia sp. lig3010.67190%5064
Burkholderia sp. A910.40340%786
Burkholderia multivorans7.74574%11594
Burkholderia pseudomultivorans7.10555%2222
Ralstonia sp. NT807.04594%374
Burkholderia dolosa6.72714%1400
Burkholderia territorii6.17956%1116
Burkholderia cenocepacia6.16325%1008
Burkholderia vietnamiensis5.59079%1100
Burkholderia cepacia5.53351%942
Burkholderia contaminans5.29455%1500
Burkholderia latens5.20924%642
Burkholderia paludis5.02586%990
Chryseobacterium haifense4.52775%1546
Mesorhizobium sp. UASWS10094.42173%4836
Burkholderia oklahomensis3.26041%804
Staphylococcus epidermidis3.19298%804
Streptomyces purpurogeneiscleroticus3.01688%2892
Burkholderia thailandensis3.00964%492
Burkholderia sp. MSMB02662.88301%594
Paracoccus sphaerophysae2.82150%1420
Burkholderia pseudomallei2.81857%542
Bradyrhizobium elkanii2.80009%3180
Ralstonia pickettii2.67821%1448
alpha proteobacterium L41A2.50307%374
Brevundimonas vesicularis2.50114%448
Acinetobacter johnsonii2.21033%1150
Desulfocarbo indianensis2.13641%16
Ralstonia sp. 5_2_56FAA2.02035%206
Brevundimonas nasdae2.00738%256
Chryseobacterium sp. FF121.80377%234
Micrococcus luteus1.73076%34
Burkholderia sp. TSV851.50398%248
[Propionibacterium] namnetense1.45034%294
Staphylococcus hominis1.36621%490
Cupriavidus metallidurans1.34057%126
Limnohabitans sp. Rim471.28398%454
Burkholderia plantarii1.19460%184
Paraburkholderia graminis1.09001%50
Burkholderia glumae1.08947%196
Streptococcus sp. CCH8-G70.86913%68
Thermomonas hydrothermalis0.86666%278
Dyella jiangningensis0.74234%708
Corynebacterium tuberculostearicum0.73242%134
Corynebacterium aurimucosum0.56701%72
Actinomyces oris0.55522%152
Actinomyces odontolyticus0.46989%130
Veillonella parvula0.46043%108
Corynebacterium afermentans0.33454%80
Porphyromonas somerae0.22141%28
Ottowia sp. oral taxon 8940.21324%68
Bacillus sp. VT-16-640.19344%74
Phyllobacterium sp. UNC302MFCol5.20.12524%6
Phyllobacterium sp. YR5310.10552%12
Corynebacterium ureicelerivorans0.08345%12
Corynebacterium striatum0.05518%6
Paramesorhizobium deserti0.03794%2
Serratia marcescens0.03624%28
viruses
Burkholderia phage KS1011.26273%34
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Staphylococcus phage IME-SA413.56467%77
Staphylococcus phage CNPH8213.21050%67
Staphylococcus phage Ipla514.78080%23
Staphylococcus phage PH1513.88680%66
Parasite
Acanthamoeba palestinensis0.00830%44
Wuchereria bancrofti0.01560%109
Hammondia hammondi0.00330%11
Cryptosporidium hominis0.00270%6
Acanthamoeba mauritaniensis0.00100%1
Enterobius vermicularis0.00050%6
Hammondia hammondi0.00030%1
Leishmania mexicana0.00160%5
fungi
Malassezia globosa0.00947%7
Neurospora crassa0.00168%6
Neurospora tetrasperma0.00144%3
Sordaria macrospora0.00085%1
Albugo laibachii0.00100%4
Data of Case 3-5
speciescoverageunique reads
bacteria
Burkholderia contaminans18.70960%21516
Burkholderia sp. A910.11700%480
Burkholderia ubonensis9.44550%3918
Burkholderia sp. lig308.71094%3184
Burkholderia multivorans6.83204%8176
Streptomyces purpurogeneiscleroticus6.57775%6694
Burkholderia pseudomultivorans5.75880%1272
Burkholderia cenocepacia5.36565%658
Burkholderia dolosa5.31402%972
Burkholderia territorii4.98050%654
Burkholderia cepacia4.94573%726
Burkholderia vietnamiensis4.54066%736
Burkholderia paludis4.27915%724
Burkholderia latens4.14980%416
Mesorhizobium sp. UASWS10093.08087%3280
Lactobacillus coryniformis0.09456%2
Candidatus Kinetoplastibacterium crithidii0.06375%0
Atopobium vaginae0.04516%8
Gardnerella vaginalis0.03952%0
Aerococcus viridans0.03527%6
Streptococcus oralis0.03409%4
Enterococcus malodoratus0.03193%18
Corynebacterium lowii0.02990%10
Propionibacteriaceae bacterium P6A170.02940%0
Atopococcus tabaci0.02646%0
viruses
Burkholderia phage KS1013.10220%94
Enterobacteria phage HK6292.33675%0
Escherichia virus Lambda2.27826%0
Burkholderia phage KS51.03932%6
Propionibacterium phage PHL1160.51031%0
Propionibacterium phage Pirate0.46372%0
Propionibacterium phage QueenBey0.46356%0
Propionibacterium phage P104A0.46304%0
Human mastadenovirus C0.41740%0
Shigella phage Sf60.30992%0
Shigella phage SfII0.29174%0
Burkholderia virus phiE1250.27729%4
Propionibacterium phage BruceLethal0.25642%0
Propionibacterium phage Moyashi0.25638%0
Propionibacterium phage PHL0410.25500%0
Parasite
Acanthamoeba palestinensis0.00881%34
Wuchereria bancrofti0.00765%46
Entamoeba histolytica0.00470%0
Enterocytozoon bieneusi0.00451%0
Hammondia hammondi0.00330%6
Cryptosporidium hominis0.00209%4
Acanthamoeba mauritaniensis0.00181%2
Vitrella brassicaformis0.00092%0
Trypanosoma cruzi0.00079%2
Babesia bigemina0.00054%0
fungi
Sordaria macrospora0.00231%2
Malassezia globosa0.00212%4
Batrachochytrium dendrobatidis0.00159%0
Talaromyces marneffei0.00129%0
Aspergillus nidulans0.00097%2
Albugo laibachii0.00090%2
Sporisorium reilianum0.00065%2
Talaromyces stipitatus0.00062%0
Fusarium verticillioides0.00036%2
Aspergillus terreus0.00026%0
Coccidioides posadasii0.00027%0
Data of NTC 3-5
speciescoverageunique reads
bacteria
Burkholderia contaminans56.80650%109638
Streptomyces purpurogeneiscleroticus24.69500%30704
Burkholderia sp. A916.05410%896
Burkholderia ubonensis11.90740%7644
Burkholderia sp. lig3011.14240%6124
Burkholderia multivorans9.38219%17226
Burkholderia cepacia8.52934%1194
Burkholderia cenocepacia8.03225%1264
Burkholderia pseudomultivorans7.77659%2452
Burkholderia dolosa7.20618%1822
Propionibacterium acnes6.98045%2948
Burkholderia territorii6.88786%1242
Burkholderia paludis6.50903%1362
Burkholderia vietnamiensis6.26256%1434
Burkholderia latens5.81930%844
Serratia marcescens5.64359%3652
Mesorhizobium sp. UASWS10094.28548%4730
Burkholderia oklahomensis3.49623%980
Burkholderia thailandensis3.21669%660
Burkholderia sp. MSMB02663.14893%732
Delftia tsuruhatensis3.05396%392
Delftia sp. 6703.03026%460
Burkholderia pseudomallei2.97279%656
Mitsuaria chitosanitabida2.36550%1322
Ralstonia sp. MD272.22214%1752
Moraxella osloensis2.11922%710
Brevundimonas vesicularis1.76609%298
Limnohabitans sp. Rim471.74668%648
Burkholderia sp. TSV851.72213%346
Paracoccus sphaerophysae1.63158%772
alpha proteobacterium L41A1.60633%230
Delftia acidovorans1.60317%210
Methylobacterium radiotolerans1.59919%654
Comamonadaceae bacterium CCH4-C51.55371%180
Acidovorax sp. KKS1021.46956%160
Comamonadaceae bacterium CCH12-A101.40673%32
Acidovorax delafieldii1.38893%178
Brevundimonas nasdae1.36767%180
Polynucleobacter duraquae1.33801%170
Burkholderia plantarii1.27188%228
Acidovorax temperans1.26872%174
Cupriavidus metallidurans1.26008%246
Methylobacterium sp. Leaf921.23582%600
Burkholderia glumae1.19595%284
Paraburkholderia graminis1.18886%54
Acidovorax sp. CCH12-A41.18354%32
Rhizobiales bacterium CCH3-A51.12968%878
Methylobacterium sp. B341.12402%186
Methylotenera versatilis1.08952%144
Acidovorax sp. Root701.03090%212
beta proteobacterium CB1.02751%114
Sphingopyxis sp. LC811.00728%518
Methyloversatilis universalis0.99189%392
Burkholderia gladioli0.98735%698
Polynucleobacter sp. MWH-Adler-W80.95063%176
Sphingomonas sp. Ant H110.90814%438
Acinetobacter johnsonii0.78364%424
Staphylococcus warneri0.27879%88
Tetrasphaera elongata0.06735%34
Chryseobacterium haifense0.03634%6
Klebsiella pneumoniae0.01997%12
viruses
Burkholderia phage KS1013.36273%44
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Propionibacterium phage PHL11614.67467%87
Propionibacterium phage Pirate17.21050%43
Propionibacterium phage QueenBey15.78080%34
Propionibacterium phage P104A16.88680%41
Staphylococcus phage StB123.47691%8
Staphylococcus phage PT10280.43317%0
Propionibacterium phage P1.11.10953%10
Parasite
Acanthamoeba palestinensis0.00660%33
Wuchereria bancrofti0.00870%56
Hammondia hammondi0.00330%7
Cryptosporidium hominis0.00220%5
Acanthamoeba mauritaniensis0.00240%4
Trypanosoma cruzi0.00180%2
Toxoplasma gondii0.00230%5
Enterobius vermicularis0.00120%5
fungi
Malassezia globosa0.00957%9
Neurospora crassa0.00199%6
Neurospora tetrasperma0.00177%6
Sordaria macrospora0.00078%8
Albugo laibachii0.00120%4
Data of Case 4
speciescoverageunique reads
bacteria
Staphylococcus hominis1.84954%670
Burkholderia sp. A91.83276%44
Burkholderia ubonensis1.70182%392
Burkholderia sp. lig301.50086%284
Burkholderia multivorans1.29341%680
Burkholderia pseudomultivorans0.94778%128
Ralstonia sp. MD270.93673%716
Burkholderia dolosa0.85274%98
Burkholderia territorii0.77720%70
Burkholderia cenocepacia0.76887%66
Burkholderia cepacia0.66769%60
Burkholderia vietnamiensis0.65960%70
Burkholderia paludis0.62014%74
Mesorhizobium sp. UASWS10090.58649%588
Burkholderia latens0.55086%32
Lactococcus piscium0.05453%16
Lactococcus raffinolactis0.03024%8
Pelobacter propionicus0.02021%0
Exiguobacterium sp. RIT3410.01928%2
Candidatus Profftella armatura0.01699%0
Dermacoccus nishinomiyaensis0.01693%0
Bacillus cellulosilyticus0.01636%0
Helcobacillus massiliensis0.01443%0
Candidatus Glomeribacter gigasporarum0.01372%0
Arthrobacter sp. Leaf2340.01274%6
viruses
Burkholderia phage KS102.51096%8
Staphylococcus phage StB120.53451%4
Staphylococcus phage SPbeta-like0.48228%0
Enterobacteria phage SfI0.33603%0
Enterobacteria phage HK5420.33108%0
Enterobacteria phage HK5440.32126%0
Escherichia virus Lambda0.26597%0
Burkholderia virus phiE1250.14052%0
Pseudomonas phage PaMx740.12791%0
Flavobacterium phage Fpv20.11909%2
Paramecium bursaria Chlorella virus A10.04669%2
Parasite
Wuchereria bancrofti0.00513%42
Acanthamoeba palestinensis0.00197%20
Hammondia hammondi0.00065%0
Trypanosoma cruzi0.00062%0
Anncaliia algerae0.00054%0
Trypanosoma grayi0.00036%0
Taenia solium0.00032%6
Toxoplasma gondii0.00026%4
Leishmania sp. MAR LEM24940.00024%0
Anisakis simplex0.00012%0
Daphnia magna0.00012%0
Vitrella brassicaformis0.00010%0
Spirometra erinaceieuropaei0.00009%6
Necator americanus0.00006%0
fungi
Sordaria macrospora0.00104%2
Albugo laibachii0.00046%2
Blastocystis hominis0.00040%0
Data of NTC 4
speciescoverageunique reads
bacteria
Staphylococcus hominis12.19550%4564
Ralstonia sp. MD2710.70210%9644
Burkholderia ubonensis8.40481%3698
Moraxella osloensis7.84991%2552
Burkholderia sp. A97.76343%466
Burkholderia sp. lig307.68243%2762
Paracoccus sphaerophysae7.61451%3744
Rothia sp. ND6WE1A7.30648%2784
Staphylococcus haemolyticus6.01573%2306
Burkholderia multivorans5.80606%6370
Staphylococcus epidermidis5.25386%1058
Burkholderia pseudomultivorans5.06785%1126
alpha proteobacterium L41A4.88849%798
Brevundimonas vesicularis4.87511%854
Burkholderia dolosa4.71681%818
Mesorhizobium sp. UASWS10094.62789%5248
Propionibacterium acnes4.58402%1860
Burkholderia cenocepacia4.31558%560
Burkholderia territorii4.26066%582
Burkholderia vietnamiensis3.87120%662
Burkholderia cepacia3.86708%616
Brevundimonas nasdae3.81090%514
Burkholderia latens3.56392%356
Burkholderia paludis3.52522%598
Burkholderia contaminans3.43589%548
Corynebacterium appendicis3.31193%994
Streptomyces purpurogeneiscleroticus3.21604%3336
Acinetobacter johnsonii2.93549%1556
Staphylococcus warneri2.91993%878
Burkholderia oklahomensis2.19710%456
Burkholderia thailandensis2.03216%256
Burkholderia sp. MSMB02661.90831%434
Burkholderia pseudomallei1.85903%332
Acidovorax delafieldii1.46921%190
Ralstonia sp. NT801.45625%246
Sphingomonas sp. Ant H111.45307%756
Methylotenera versatilis1.38689%204
Corynebacterium tuberculostearicum1.34973%220
Acidovorax sp. KKS1021.31939%164
Corynebacterium aurimucosum1.27600%200
Acidovorax sp. Leaf1601.25323%654
Acidovorax sp. Root701.12287%230
Burkholderia sp. TSV851.07564%164
Cupriavidus metallidurans1.05755%198
Comamonadaceae bacterium CCH12-A101.05171%16
Comamonadaceae bacterium CCH4-C51.02252%96
Acidovorax sp. CCH12-A40.88438%32
Acidovorax sp. Root4020.87451%136
Burkholderia plantarii0.80571%130
Acidovorax temperans0.76659%74
Ralstonia pickettii0.75577%246
Bradyrhizobium elkanii0.71983%762
Limnohabitans sp. Rim470.69754%252
Ralstonia sp. 5_2_56FAA0.57599%66
Acinetobacter lwoffii0.52177%168
Cloacibacterium normanense0.16745%54
Prevotella disiens0.01169%2
Serratia marcescens0.00786%6
viruses
Burkholderia phage KS1010.96273%34
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Enterobacteria phage SfI12.37467%67
Enterobacteria phage HK54211.21050%34
Enterobacteria phage HK54416.78080%65
Propionibacterium phage P1.10.80953%19
Parasite
Acanthamoeba palestinensis0.00670%31
Wuchereria bancrofti0.08700%46
Hammondia hammondi0.00330%8
Cryptosporidium hominis0.00190%6
Acanthamoeba mauritaniensis0.00170%5
Trypanosoma cruzi0.00150%4
Toxoplasma gondii0.00230%3
Enterobius vermicularis0.00120%6
fungi
Malassezia globosa0.00876%7
Neurospora crassa0.00179%5
Neurospora tetrasperma0.00178%7
Sordaria macrospora0.00045%1
Albugo laibachii0.00140%3
Data of Case 5
speciescoverageunique reads
bacteria
Burkholderia sp. A90.82290%14
Burkholderia ubonensis0.74907%158
Burkholderia sp. lig300.70272%124
Burkholderia multivorans0.56438%236
Burkholderia pseudomultivorans0.45016%44
Corynebacterium jeikeium0.36015%54
Burkholderia dolosa0.35464%32
Burkholderia cenocepacia0.34338%14
Burkholderia territorii0.33098%24
Burkholderia cepacia0.30341%24
Burkholderia latens0.30035%20
Burkholderia vietnamiensis0.28130%32
Burkholderia contaminans0.27948%26
Burkholderia paludis0.26410%18
Mesorhizobium sp. UASWS10090.22014%234
Gardnerella vaginalis0.01983%2
Candidatus Kinetoplastibacterium galatii0.01825%2
Corynebacterium sp. HMSC065H090.01801%2
Candidatus Profftella armatura0.01699%0
Turicella sp. HMSC034H070.01514%0
Corynebacterium sp. HMSC062A030.01339%0
Corynebacterium sp. HMSC066C020.01326%0
Trueperella sp. HMSC08B050.01225%0
Geothrix fermentans0.01222%0
viruses
Burkholderia phage KS100.99641%0
Burkholderia virus phiE1250.14052%0
Parasite
Taenia solium0.04556%626
Wuchereria bancrofti0.02155%186
Enterocytozoon bieneusi0.00194%0
Taenia saginata0.00103%2
Leptomonas seymouri0.00066%0
Entamoeba histolytica0.00060%0
Anncaliia algerae0.00054%0
Taenia multiceps0.00049%2
Acanthamoeba palestinensis0.00047%2
Toxoplasma gondii0.00039%2
Leishmania tarentolae0.00024%0
Spirometra erinaceieuropaei0.00019%24
Hammondia hammondi0.00015%0
Dracunculus medinensis0.00007%0
fungi
Malassezia globosa0.03473%28
Sordaria macrospora0.00041%2
Data of NTC 5
speciescoverageunique reads
bacteria
Paracoccus sphaerophysae13.91450%7542
Burkholderia ubonensis10.91620%6322
Burkholderia sp. lig3010.28230%4788
Burkholderia sp. A99.93702%698
Ralstonia sp. MD278.91267%8016
Burkholderia multivorans7.51153%10518
Moraxella osloensis6.85012%2348
Burkholderia pseudomultivorans6.83803%1920
Burkholderia dolosa6.36310%1392
Brevundimonas vesicularis5.95865%1122
Burkholderia territorii5.94944%1030
Burkholderia cenocepacia5.93886%982
alpha proteobacterium L41A5.87010%960
Burkholderia vietnamiensis5.41452%1092
Burkholderia cepacia5.25421%964
Streptomyces purpurogeneiscleroticus5.14750%5328
Burkholderia latens5.02917%708
Brevundimonas nasdae4.88906%742
Burkholderia paludis4.85164%1048
Burkholderia contaminans4.73254%1012
Staphylococcus hominis4.18608%1598
Bradyrhizobium elkanii3.61955%4378
Burkholderia oklahomensis3.10360%726
Burkholderia thailandensis2.95443%448
Mesorhizobium sp. UASWS10092.86955%3198
Burkholderia sp. MSMB02662.74114%650
Burkholderia pseudomallei2.69440%562
Thermomonas hydrothermalis1.90140%628
Ralstonia sp. NT801.61419%420
Burkholderia sp. TSV851.47854%242
Acinetobacter johnsonii1.40778%718
Comamonadaceae bacterium CCH4-C51.27388%146
Propionibacterium acnes1.21901%528
Burkholderia plantarii1.18824%182
Acidovorax delafieldii1.18208%166
Methyloversatilis universalis1.15586%474
Acidovorax sp. KKS1021.11858%120
Comamonadaceae bacterium CCH12-A101.10651%30
Burkholderia glumae1.09671%178
Cupriavidus metallidurans1.06383%166
Limnohabitans sp. Rim471.04516%322
Sphingomonas paucimobilis1.04005%586
Methyloversatilis discipulorum1.02565%442
Rhizobiales bacterium CCH3-A51.02316%774
Staphylococcus epidermidis0.97893%214
Staphylococcus haemolyticus0.96417%342
Acidovorax sp. Root700.84761%150
Sphingomonas sp. Ant H110.81704%336
Methylotenera versatilis0.67421%68
Acidovorax sp. Root4020.67300%106
Acidovorax sp. Leaf1600.35953%148
Rothia sp. ND6WE1A0.20422%78
Streptococcus sp. CCH8-G70.01582%2
Streptococcus sp. HMSC073F110.01440%2
Serratia marcescens0.01119%8
Streptococcus oralis0.00698%2
viruses
Burkholderia phage KS1010.66273%33
Flavobacterium phage Fpv20.44520%4
Paramecium bursaria Chlorella virus A10.23770%3
Staphylococcus phage IME-SA410.37467%30
Propionibacterium phage P1.10.65953%12
Parasite
Acanthamoeba palestinensis0.00800%45
Wuchereria bancrofti0.02370%150
Hammondia hammondi0.00300%7
Cryptosporidium hominis0.00220%6
Acanthamoeba mauritaniensis0.00160%4
Trypanosoma cruzi0.00180%3
Toxoplasma gondii0.00120%9
Enterobius vermicularis0.00120%6
fungi
Malassezia globosa0.00988%12
Neurospora crassa0.00189%6
Neurospora tetrasperma0.00227%7
Sordaria macrospora0.00065%2
Albugo laibachii0.00190%8
Data of Case 6
speciescoverageunique reads
bacteria
Acinetobacter junii3.67362%1552
Propionibacterium acnes1.86082%666
Burkholderia sp. A91.63337%32
Burkholderia ubonensis1.46515%330
Burkholderia sp. lig301.30212%234
Burkholderia multivorans1.16087%636
Burkholderia pseudomultivorans0.82146%104
Burkholderia dolosa0.74319%46
Burkholderia cenocepacia0.68609%60
Burkholderia territorii0.68137%62
Burkholderia cepacia0.58838%38
Burkholderia contaminans0.58263%110
Burkholderia vietnamiensis0.57924%60
Burkholderia paludis0.54351%52
Burkholderia latens0.54190%36
Pseudomonas putida0.50566%368
Marinomonas aquimarina0.08951%2
Acinetobacter venetianus0.03138%0
Atopobium sp. oral taxon 1990.02702%0
Gardnerella vaginalis0.02238%0
Lactobacillus mucosae0.02029%0
Arthrobacter sp. Leaf2340.01969%8
Candidatus Liberibacter asiaticus0.01929%0
Shewanella sp. MR-40.01895%4
viruses
Burkholderia phage KS102.24791%10
Human gammaherpesvirus 40.45727%2
Pseudomonas phage PaMx740.25581%2
Pseudomonas phage MP14120.24523%2
Lactobacillus phage Sha10.18693%2
Staphylococcus phage StB200.18085%0
Parasite
Taenia solium0.20137%2642
Wuchereria bancrofti0.01339%100
Taenia saginata0.00331%2
Taenia multiceps0.00154%2
Acanthamoeba palestinensis0.00122%10
Toxoplasma gondii0.00121%2
Babesia bigemina0.00108%0
Vitrella brassicaformis0.00041%0
fungi
Pneumocystis jirovecii0.00596%6
Schizosaccharomyces pombe0.00297%0
Fusarium verticillioides0.00207%12
Malassezia globosa0.00336%4
Yarrowia lipolytica0.00073%2
Saccharomyces cerevisiae0.00062%0
Sordaria macrospora0.00037%0
Data of NTC 6
speciescoverageunique reads
bacteria
Propionibacterium acnes12.19170%5332
Burkholderia ubonensis7.63207%3072
Burkholderia sp. A97.38595%396
Burkholderia sp. lig307.13174%2426
Moraxella osloensis6.44270%2288
Burkholderia multivorans5.39103%5470
Burkholderia pseudomultivorans4.57937%984
Burkholderia dolosa4.22517%708
Burkholderia cenocepacia3.98858%534
Burkholderia territorii3.90938%532
Burkholderia contaminans3.73823%1410
Burkholderia cepacia3.51458%502
Burkholderia vietnamiensis3.44614%568
Burkholderia latens3.30098%370
Burkholderia paludis3.22433%518
Thermomonas hydrothermalis2.40415%890
Burkholderia oklahomensis1.98692%442
Burkholderia thailandensis1.90333%280
Rhizobiales bacterium CCH3-A51.86148%1518
Burkholderia sp. MSMB02661.78302%282
Burkholderia pseudomallei1.71428%288
Methyloversatilis universalis1.52909%620
Pseudomonas sp. CFT91.22869%810
Acinetobacter johnsonii1.19179%636
Comamonadaceae bacterium CCH4-C51.18539%152
Sphingopyxis sp. LC811.11632%568
Comamonadaceae bacterium CCH12-A101.04177%26
beta proteobacterium CB1.04169%146
Polynucleobacter duraquae1.02675%110
Acidovorax temperans1.00990%134
Micrococcus luteus1.00961%4
Pseudomonas putida0.97041%912
Burkholderia sp. TSV850.95026%196
Cupriavidus metallidurans0.87502%142
Acidovorax sp. CCH12-A40.86398%28
Methyloversatilis discipulorum0.83134%376
Xylophilus ampelinus0.79146%576
[Propionibacterium] namnetense0.77477%198
Polynucleobacter sp. MWH-Adler-W80.74921%108
Staphylococcus epidermidis0.73200%182
Mesorhizobium sp. UASWS10090.68557%824
Ralstonia sp. MD270.60947%490
Sphingomonas sp. Ant H110.45496%220
Propionibacterium humerusii0.42515%56
Kocuria palustris0.35688%162
Cutibacterium granulosum0.33911%108
Bradyrhizobium elkanii0.22595%266
Delftia sp. 6700.21119%50
Delftia tsuruhatensis0.20858%4
Afipia broomeae0.10435%32
Kocuria polaris0.08646%50
Psychrobacter sp. 1501(2011)0.08235%12
Stenotrophomonas sp. SKA140.05745%2
Prevotella intermedia0.05031%20
Pseudomonas aeruginosa0.02379%18
Serratia marcescens0.01451%10
viruses
Burkholderia phage KS1012.39273%42
Flavobacterium phage Fpv20.45320%4
Paramecium bursaria Chlorella virus A10.35670%5
Staphylococcus phage IME-SA414.68467%67
Staphylococcus phage PH1512.20680%42
Staphylococcus phage Ipla78.94998%18
Parasite
Acanthamoeba palestinensis0.01130%45
Wuchereria bancrofti0.01340%106
Hammondia hammondi0.00350%6
Cryptosporidium hominis0.00170%4
Acanthamoeba mauritaniensis0.00210%4
Trypanosoma cruzi0.00080%9
Toxoplasma gondii0.00200%7
Enterobius vermicularis0.00100%11
fungi
Malassezia globosa0.00988%11
Neurospora crassa0.00182%10
Fusarium verticillioides0.00188%10
Sordaria macrospora0.00098%5
Data of Case 7
speciescoverageunique reads
bacteria
Bradyrhizobium elkanii2.63972%2874
Ralstonia sp. MD272.25852%1758
Burkholderia sp. A91.89506%42
Burkholderia ubonensis1.88076%392
Burkholderia sp. lig301.66429%314
Burkholderia multivorans1.50462%786
Burkholderia pseudomultivorans1.00124%112
Burkholderia dolosa0.97612%100
Moraxella osloensis0.89112%262
Burkholderia cenocepacia0.88388%72
Burkholderia territorii0.82892%62
Burkholderia cepacia0.75835%70
Burkholderia vietnamiensis0.75451%68
Burkholderia paludis0.68078%88
Burkholderia latens0.66739%28
Microlunatus phosphovorus0.11110%86
Candidatus Kinetoplastibacterium galatii0.03406%0
Weissella hellenica0.02400%4
Knoellia subterranea0.02260%10
bacterium endosymbiont of Mortierella elongata0.02204%0
Candidatus Profftella armatura0.02130%0
Streptococcus sp. HMSC063B030.02032%0
Bacteroides sp. Marseille-P31660.01886%0
Blattabacterium sp. (Nauphoeta cinerea)0.01692%0
Blattabacterium sp. (Periplaneta americana)0.01655%0
viruses
Burkholderia phage KS102.84044%8
Human mastadenovirus C0.66784%4
Enterobacteria phage HK6290.16283%0
Gordonia phage Schwabeltier0.15993%0
Escherichia virus Lambda0.15876%0
Burkholderia virus phiE1250.15738%2
Salmonella phage SJ460.11890%2
Paramecium bursaria Chlorella virus A10.02335%0
Parasite
Taenia solium14.80790%261064
Taenia saginata0.23011%112
Taenia multiceps0.15579%212
Acanthamoeba palestinensis0.00688%68
Wuchereria bancrofti0.00473%28
Hymenolepis nana0.00428%4
Cimex hemipterus0.00281%0
Enterocytozoon bieneusi0.00194%0
Echinococcus multilocularis0.00156%2
Trypanosoma cruzi0.00145%0
Cryptosporidium hominis0.00128%2
261492
fungi
Malassezia globosa0.01876%22
[Candida] glabrata0.01215%24
Pneumocystis carinii0.00196%0
Saccharomyces cerevisiae0.00123%2
Data of NTC 7
speciescoverageunique reads
bacteria
Bradyrhizobium elkanii25.93500%34192
Ralstonia sp. MD2720.62190%19060
Burkholderia ubonensis10.47360%4914
Burkholderia sp. A99.70348%580
Burkholderia sp. lig309.69313%4120
Burkholderia multivorans7.12847%9434
Burkholderia pseudomultivorans6.53222%1622
Burkholderia dolosa5.98695%1218
Burkholderia cenocepacia5.61033%816
Burkholderia territorii5.56941%856
Burkholderia vietnamiensis5.08144%832
Burkholderia cepacia5.03973%736
Burkholderia contaminans4.74377%1074
Burkholderia latens4.66839%534
Burkholderia paludis4.59436%834
Mesorhizobium sp. UASWS10093.34627%3464
Propionibacterium acnes3.28747%1292
Streptomyces purpurogeneiscleroticus2.95533%2780
Burkholderia oklahomensis2.87800%584
Burkholderia thailandensis2.76245%384
Burkholderia sp. MSMB02662.56173%526
Burkholderia pseudomallei2.42884%428
Ralstonia sp. NT802.09376%88
Thermomonas hydrothermalis1.59071%466
Burkholderia sp. TSV851.36560%184
Cupriavidus gilardii1.19640%692
Limnohabitans sp. Rim471.13696%364
Ralstonia pickettii1.12647%316
Cupriavidus metallidurans1.09302%158
Burkholderia plantarii1.08915%148
Acidovorax delafieldii1.00982%106
Moraxella osloensis1.00614%330
Paraburkholderia graminis0.97890%32
Burkholderia glumae0.96302%130
Acidovorax sp. KKS1020.87773%80
Methylobacterium sp. Leaf920.87767%408
alpha proteobacterium L41A0.84148%126
Ralstonia sp. 5_2_56FAA0.83787%56
Sphingomonas sp. Ant H110.82602%314
Brevundimonas vesicularis0.80243%156
Burkholderia gladioli0.78890%514
Desulfocarbo indianensis0.78396%8
Acidovorax sp. Root700.72725%170
Brevundimonas nasdae0.71617%116
Xenophilus azovorans0.70860%10
Methylotenera versatilis0.70601%58
Comamonadaceae bacterium CCH12-A100.69941%14
Comamonadaceae bacterium CCH4-C50.69602%46
Paracoccus sphaerophysae0.68723%342
Dyella jiangningensis0.67789%590
Acidovorax sp. CCH12-A40.63535%24
Ralstonia mannitolilytica0.62904%98
Polynucleobacter duraquae0.60213%72
Comamonas testosteroni0.59597%8
Afipia broomeae0.58748%130
Paraburkholderia acidipaludis0.56997%150
beta proteobacterium CB0.54665%52
Acidovorax sp. Root4020.53293%104
Paraburkholderia rhizoxinica0.50318%2
Paraburkholderia ferrariae0.48933%244
Limnohabitans sp. 103DPR20.47128%144
Polynucleobacter sp. MWH-Adler-W80.46562%66
Burkholderia sp. SRS-W-2-20160.46524%66
Staphylococcus epidermidis0.39120%84
Staphylococcus hominis0.35611%126
Staphylococcus haemolyticus0.09685%36
Micrococcus luteus0.03479%4
Rothia sp. ND6WE1A0.01490%4
viruses
Burkholderia phage KS1013.36273%44
Flavobacterium phage Fpv20.44520%5
Paramecium bursaria Chlorella virus A10.36770%4
Propionibacterium phage PHL11614.67467%87
Propionibacterium phage Pirate17.21050%43
Propionibacterium phage QueenBey15.78080%34
Propionibacterium phage P104A16.88680%41
Staphylococcus phage StB123.47691%8
Staphylococcus phage PT10280.43317%0
Propionibacterium phage P1.11.10953%10
Parasite
Acanthamoeba palestinensis0.00860%45
Wuchereria bancrofti0.00770%46
Hammondia hammondi0.00330%7
Cryptosporidium hominis0.00220%6
Acanthamoeba mauritaniensis0.00240%4
Trypanosoma cruzi0.00180%3
Toxoplasma gondii0.00230%5
Enterobius vermicularis0.00120%7
fungi
Malassezia globosa0.00988%16
Neurospora crassa0.00126%6
Neurospora tetrasperma0.00157%4
Sordaria macrospora0.00078%9
Albugo laibachii0.00120%2

NTC = no template control; coverage means genomic coverage.

. The Sequencing statistics aligned to human/primate, non-human/primate and NCBI NT database in the cerebrospinal fluid Reads Aligned to NCBI NT database refer to the filtered reads aligning to the microbial genomes. The reads aligning to microbial genomes only in the cerebrospinal fluid and the non-template controls NTC = no template control; coverage means genomic coverage.

Experimental Design, Materials, and Methods [2,3]

Sample Collection and DNA Extraction

CSF samples (300 µl) were collected from 7 patients. “No-template” controls (NTCs) are sterile water which are used as negative controls. Before the extraction of DNA, 300ul sterile water was added to a sterile centrifuge tube. The operations of NTCs were identical to that of CSF samples. All operations are performed in horizontal laminar flow clean bench. DNA was extracted using the TIANamp Micro DNA Kit (DP316, Tiangen Biotech, Beijing, China). When DNA extraction reagent was added to CSF, the same reagent was added to 300ul sterile water. All operations are performed in the workbench. Proteinase K (10mL) and buffer GB (with carrier RNA; 300mL) were added in the CSF samples and NTCs. The sample was incubated at 56°C for 10 min. After adding 300 µL of cold absolute ethyl alcohol, the tube was incubated for 5min at room temperature. The liquid was transferred to a new adsorption column and washed with buffer GD and buffer PW. Finally, the DNA was dissolved with 40mL of Tris-ethylenediaminetetraacetic acid buffer.

Library construction and sequencing

The extracted DNA was sonicated into 200–300 bp fragments using a Bioruptor Pico. DNA libraries were constructed via end-repair adaptation overnight and the use of polymerase chain reaction (PCR) amplification of the extracted DNA. The purified library was diluted, mixed, denatured, re-diluted, mixed with PhiX (equal to 1% of the final DNA amount) as described in the MiniSeq System Denature and Dilute Libraries Guide, and then applied to an Illumina MiniSeq system for sequencing with the High Output Reagent Kit (150 cycles), as described in the MiniSeq Local Run Manager Software Guide.

Data analysis

High-quality sequencing data were generated after removing short (<35 bp), low-quality, and low-complexity reads and computational subtraction of the human host sequences was performed using a Burrows-Wheeler Alignment tool [1]. Finally, the remaining sequencing data were aligned to the Microbial Genome Databases, which are composed of 2700 whole genome sequences of viral taxa, 1494 bacterial genomes or scaffolds, 73 fungi and 48 parasites associated with human infectivity. The reference genomes were downloaded from the National Center for Biotechnology Information (ftp://ftp.ncbi.nlm.nih.gov/genomes). The mapped data were further processed; the depth and coverage of each species was calculated using Soap Coverage (http://soap.genomics.org.cn).

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
SubjectBiochemistry, Genetics and Molecular Biology (General)
Specific subject areaMolecular Biology
Type of dataTable
How data were acquiredIllumina MiniSeq system for sequencing, computational subtraction, Burrows-Wheeler Alignment tool, Finally, Microbial Genome Databases.
Data formatRaw and filtered
Parameters for data collectionThe sequencing statistics of the cerebrospinal fluid (CSF) samples and the number of unique reads and genomic coverage aligning to microorganic sequences.
Description of data collectionThe data were generated by the Illumina MiniSeq system for sequencing and computational subtraction of the human host sequences was performed using a Burrows-Wheeler Alignment tool. Finally, the remaining sequencing data were aligned to the Microbial Genome Databases (ftp://ftp.ncbi.nlm.nih.gov/genomes), which are composed of 2700 whole genome sequences of viral taxa, 1494 bacterial genomes or scaffolds, 73 fungi and 48 parasites associated with human infectivity.
Data source locationDepartment of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an 710032, China
Data accessibilityData are presented in this article
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