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Supporting Information for
Exploration of the Antibiotic Resistome in a Wastewater Treatment Plant by a Nine-Year Longitudinal Metagenomic Study
Xiaole Yina, Yu Denga, Liping Maa,b, Yulin Wanga, Lilian Y.L. Chanc, Tong Zhang*, a,d
a Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
b Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
c High Performance Computing Team, Information Technology Services, The University of Hong Kong, Hong Kong, China.
d International Center for Antibiotic Resistance in the Environment, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
* To whom correspondence should be addressed. E-mail address: [email protected]
Figure S1. Dynamics of ARGs spanning 9 years in AS in the unit of copy of ARGs per copy of 16S rRNA.
Figure S2. Dynamics of ARGs spanning 9 years in AS in the unit of PPM (ARG read per million reads).
Figure S3. Seasonal coloring and PCoA analysis of all samples based on Bray-Curtis distance.
Figure S4. Average abundances of ARGs in four consecutive time range (clustered by PCoA in Figure 1b)
Figure S5. Profile of monthly variations of genes resistant to widely-used antibiotics types.
Figure S6. Temporal variation of relative abundance of core resistome.
Figure S7. A heatmap illustrating the abundance of core resistome in 9 years.
Figure S8. Dynamics of core resistome.
Figure S9. Variation of relative abundance of top 8 phyla or classes of proteobacteria.
Figure S10. Variation of relative abundance of 19 most abundant families.
Figure S11. Correlation analyses. a. RDA analysis of operational parameters with AS resistome; b. VPA analysis based on bacterial community, MGEs and AS resistome
Figure S12. Possibility of horizontal gene transfer on different ARGs-carrying species. Species in the same phyla/class were framed together. Numbers around center point stand for the total occurrence of each predicted ARGs-carrying species which were in proportion to the diameter of the corresponding pies. Potential pathogens were highlighted in red font.
Figure S13. Comparation of abundance of ARGs between this study with other ecotypes listed by (Li et al., 2015). Metagenomic datasets of these ecotypes were retrieved from (Li et al., 2015).
Figure S14. Occurrence patterns in other ecotypes of a list of genes which detected as core resistome in this study.
Figure S15. Temporal variation of the abundance of ereA gene and relevant hosts. b. Regression analysis showed close correlation between Geobacter with ereA gene.
Figure S16. Temporal variation of the abundance of qnrS gene and relevant hosts. b. Regression analysis showed close correlation between Vibrio anguillarum and qnrS gene.
Figure S17. Occurrence of emerging genotypes or genes related to superbugs.
Table S1. Sampling dates since June of 2007 to December of 2015.
Table S2. Bacterial pathogen list (Li et al., 2015a)
Table S3. AS genomes used in analyzing the incidence of ARGs encountering MGEs.
Table S4. Significance of differences among the 4 clusters from Figure 1b. The numbers are the P values from the pair-wise Mann-Whitney test. Those values which are less than 0.05 are highlighted in red.
Table S5. Information of core resistome according to persistency and abundancy detected from 9 years
Figure S1. Dynamics of ARGs spanning 9 years in AS in the unit of copy of ARGs per copy of 16S rRNA.
Figure S2. Dynamics of ARGs spanning 9 years in AS in the unit of PPM (ARG read per million reads).
Figure S3. Seasonal coloring and PCoA analysis of all samples based on Bray-Curtis distance.
Figure S4. Average abundances of ARGs in four consecutive time range (clustered by PCoA in Figure 1b)
Figure S5. Profile of monthly variations of resistance genes to widely-used antibiotics types.
Figure S6. Temporal variation of relative abundance of core resistome
Figure S7. A heatmap illustrating the abundance of core resistome in 9 years.
Figure S8. Dynamics of core resistome (to be continued)
Figure S8. Dynamics of core resistome
Figure S9. Variation of relative abundance of top 8 phyla or classes of proteobacteria.
Figure S10. Variation of relative abundance of 19 most abundant families.
Figure S11. Correlation analyses. a. RDA analysis of operational parameters with AS resistome; b. VPA analysis based on bacterial community, MGEs and AS resistome
Figure S12. Possibility of horizontal gene transfer on different ARGs-carrying species. Species in the same phyla/class were framed together. Numbers around center point stand for the total occurrence of each predicted ARGs-carrying species which were in proportion to the diameter of the corresponding pies. Potential pathogens were highlighted in red font.
Figure S13. Comparation of abundance of ARGs between this study with other ecotypes listed by (Li et al., 2015). Metagenomic datasets of these ecotypes were retrieved from (Li et al., 2015).
Figure S14. Occurrence patterns in other ecotypes of a list of genes which detected as core resistome in this study.
Figure S15. Temporal variation of the abundance of ereA gene and relevant hosts. b. Regression analysis showed close correlation between Geobacter with ereA gene.
Figure S16. Temporal variation of the abundance of qnrS gene and relevant hosts. b. Regression analysis showed close correlation between Vibrio anguillarum and qnrS gene.
Figure S17. Occurrence of emerging genotypes or genes related to superbugs.
Table S1. Sampling dates since June of 2007 to December of 2015.
No.
Date
No.
Date
No.
Date
1
2-Jun-2007
34
20-Jul-2010
67
30-May-2013
2
5-Jul-2007
35
17-Aug-2010
68
26-Jun-2013
3
17-Aug-2007
36
15-Sep-2010
69
22-Jul-2013
4
19-Oct-2007
37
12-Oct-2010
70
28-Aug-2013
5
9-Nov-2007
38
18-Nov-2010
71
3-Oct-2013
6
14-Dec-2007
39
14-Dec-2010
72
31-Oct-2013
7
15-Jan-2008
40
12-Jan-2011
73
27-Nov-2013
8
20-Feb-2008
41
16-Feb-2011
74
31-Dec-2013
9
16-Apr-2008
42
17-Mar-2011
75
27-Jan-2014
10
21-May-2008
43
20-Apr-2011
76
4-Mar-2014
11
11-Jun-2008
44
18-May-2011
77
1-Apr-2014
12
18-Aug-2008
45
21-Jun-2011
78
29-Apr-2014
13
19-Sep-2008
46
21-Jul-2011
79
3-Jun-2014
14
8-Oct-2008
47
16-Aug-2011
80
27-Jun-2014
15
13-Nov-2008
48
19-Sep-2011
81
28-Jul-2014
16
15-Dec-2008
49
21-Oct-2011
82
5-Sep-2014
17
12-Jan-2009
50
17-Nov-2011
83
3-Oct-2014
18
13-Feb-2009
51
16-Dec-2011
84
29-Oct-2014
19
25-Mar-2009
52
11-Jan-2012
85
3-Dec-2014
20
17-Apr-2009
53
15-Feb-2012
86
6-Jan-2015
21
26-May-2009
54
24-Apr-2012
87
3-Feb-2015
22
9-Jun-2009
55
30-May-2012
88
2-Mar-2015
23
20-Jul-2009
56
27-Jun-2012
89
25-Mar-2015
24
24-Aug-2009
57
23-Jul-2012
90
28-Apr-2015
25
10-Sep-2009
58
27-Aug-2012
91
29-May-2015
26
19-Oct-2009
59
24-Sep-2012
92
25-Jun-2015
27
19-Nov-2009
60
22-Oct-2012
93
30-Jul-2015
28
15-Dec-2009
61
27-Nov-2012
94
4-Sep-2015
29
4-Jan-2010
62
20-Dec-2012
95
7-Oct-2015
30
25-Feb-2010
63
22-Jan-2013
96
2-Nov-2015
31
22-Mar-2010
64
21-Feb-2013
97
3-Dec-2015
32
20-Apr-2010
65
21-Mar-2013
33
18-May-2010
66
23-Apr-2013
Table S2. Bacterial pathogen list (Li et al., 2015a)
Abiotrophia defectiva
Anaerococcus prevotii
Bartonella henselae
Achromobacter piechaudii
Anaerococcus vaginalis
Bartonella quintana
Achromobacter xylosoxidans
Arcanobacterium bernardiae
Bergeyella zoohelcum
Acidaminococcus fermentans
Arcanobacterium heamolyticum
Bifidobacterium dentium
Acinetobacter baumannii
Arcanobacterium pyogenes
Bilophila wadsworthia
Acinetobacter calcoaceticus
Arcobacter butzleri
Bordetella avium
Acinetobacter haemolyticus
Arcobacter cryaerophilus
Bordetella bronchiseptica
Acinetobacter johnsonii
Anaplasma phagocytophila
Bordetella parapertussis
Acinetobacter junii
Bacillus anthracis
Bordetella pertussis
Acinetobacter lwoffii
Bacillus cereus
Borrelia brasiliensis
Acinetobacter radioresistens
Bacillus circulans
Borrelia burgdorferi
Actinobacillus actinomycetemcomitans
Bacillus coagulans
Borrelia caucasica
Actinobacillus equuli
Bacillus licheniformis
Borrelia crocidurae
Actinobacillus hominis
Bacillus mycoides
Borrelia duttonii
Actinobacillus lignieresii
Bacillus pumilus
Borrelia hermsii
Actinobacillus pleuropneumoniae
Bacillus sphaericus
Borrelia hispanica
Actinobacillus suis
Bacillus subtilis
Borrelia latyschewii
Actinobacillus ureae
Bacillus thuringiensis
Borrelia mazzottii
Actinomyces georgiae
Bacteroides caccae
Borrelia parkeri
Actinomyces gerencseriae
Bacteroides distasonis
Borrelia persica
Actinomyces israelii
Bacteroides eggerthii
Borrelia recurrentis
Actinomyces meyeri
Bacteroides forsythus
Borrelia turicatae
Actinomyces naeslundii
Bacteroides fragilis
Borrelia venezuelensis
Actinomyces neuii
Bacteroides galacturonicus
Brevibacillus brevis
Actinomyces odontolyticus
Bacteroides merdae
Brevundimonas diminuta
Actinomyces radingae
Bacteroides ovatus
Brevundimonas vesicularis
Actinomyces turicensis
Bacteroides pectinophilus
Brucella melitensis
Aerococcus viridans
Bacteroides splanchnicus
Burkholderia cepacia
Aeromonas caviae
Bacteroides stercoris
Burkholderia mallei
Aeromonas hydrophila
Bacteroides thetaiotaomicron
Burkholderia pseudomallei
Aeromonas sobria
Bacteroides uniformis
Campylobacter coli
Aeromonas veronii
Bacteroides ureolyticus
Campylobacter concisus
Alcaligenes odorans
Bacteroides vulgatus
Campylobacter curvus
Amycolatopsis orientalis
Bartonella bacilliformis
Campylobacter fetus
Anaerococcus lactolyticus
Bartonella elizabethae
Campylobacter gracilis
Table S2. Bacterial pathogen list (Li et al., 2015a) (continued)
Campylobacter hyointestinalis
Clostridium botulinum
Dichelobacter nodosus
Campylobacter jejuni
Clostridium butyricum
Edwardsiella hoshinae
Campylobacter lari
Clostridium chauvoei
Edwardsiella tarda
Campylobacter rectus
Clostridium difficile
Eggerthella lenta
Campylobacter sputorum
Clostridium fallax
Ehrlichia chaffeensis
Campylobacter upsaliensis
Clostridium histolyticum
Ehrlichia ewingii
Capnocytophaga canimorsus
Clostridium novyi
Eikenella corrodens
Capnocytophaga cynodegmi
Clostridium perfringens
Enterobacter aerogenes
Capnocytophaga gingivalis
Clostridium ramosum
Enterobacter amnigenus
Capnocytophaga ochracea
Clostridium septicum
Enterobacter asburiae
Capnocytophaga sputigena
Clostridium sordellii
Enterobacter cancerogenus
Cardiobacterium hominis
Clostridium sporogenes
Enterobacter cloacae
Cedecea davisae
Clostridium tertium
Enterobacter gergoviae
Cedecea lapagei
Clostridium tetani
Enterobacter hormaechei
Cedecea neteri
Collinsella aerofaciens
Enterobacter sakazakii
Cellulomonas cellulans
Comamonas testosteroni
Enterococcus avium
Cellulomonas turbata
Corynebacterium afermentans
Enterococcus casseliflavus
Centipeda periodontii
Corynebacterium amycolatum
Enterococcus durans
Chlamydia trachomatis
Corynebacterium argentoratense
Enterococcus faecalis
Chlamydophila pneumoniae
Corynebacterium bovis
Enterococcus faecium
Chlamydophila psittaci
Corynebacterium diphtheriae
Enterococcus flavescens
Chromobacterium violaceum
Corynebacterium jeikeium
Enterococcus gallinarum
Chryseobacterium balustinum
Corynebacterium kutscheri
Enterococcus hirae
Chryseobacterium meningosepticum
Corynebacterium macginleyi
Enterococcus mundtii
Citrobacter amalonaticus
Corynebacterium minutissimum
Enterococcus raffinosus
Citrobacter braakii
Corynebacterium propinquum
Erysipelothrix rhusiopathiae
Citrobacter farmeri
Corynebacterium pseudodiphthericum
Escherichia coli
Citrobacter freundii
Corynebacterium pseudotuberculosis
Eubacterium brachy
Citrobacter koseri
Corynebacterium striatum
Eubacterium combesii
Citrobacter rodentium
Corynebacterium ulcerans
Eubacterium contortum
Citrobacter sedlakii
Corynebacterium urealyticum
Eubacterium cylindroides
Citrobacter werkmanii
Corynebacterium xerosis
Eubacterium limosum
Citrobacter youngae
Coxiella burnetii
Eubacterium moniliforme
Clostridium baratii
Delftia acidovorans
Eubacterium multiforme
Clostridium bifermentans
Dermatophilus congolensis
Eubacterium nodatum
Table S2. Bacterial pathogen list (Li et al., 2015a) (continued)
Eubacterium rectale
Hafnia alvei
Leptospira meyeri
Eubacterium saburreum
Helicobacter cinaedi
Leptospira noguchii
Eubacterium saphenum
Helicobacter fennelliae
Leptospira santarosai
Eubacterium sulci
Helicobacter heilmannii
Leptospira weilii
Eubacterium tenue
Helicobacter pullorum
Leptotrichia buccalis
Ewingella americana
Helicobacter pylori
Listeria ivanovii
Fibrobacter intestinalis
Kingella denitrificans
Listeria monocytogenes
Filifactor alocis
Kingella kingae
Listeria seeligeri
Finegoldia magna
Klebsiella granulomatis
Listeria welshimeri
Fluoribacter bozemanae
Klebsiella ornithinolytica
Mannheimia haemolytica
Fluoribacter dumoffii
Klebsiella oxytoca
Megamonas hypermegale
Fluoribacter gormanii
Klebsiella pneumoniae
Megasphaera sp.
Francisella tularensis
Kluyvera ascorbata
Micromonas micros
Fusobacterium mortiferum
Kluyvera cryocrescens
Mogibacterium timidum
Fusobacterium necrophorum
Lactobacillus sp.
Moraxella (Branhamella) catarrhalis
Fusobacterium nucleatum
Legionella anisa
Moraxella (Branhamella) caviae
Fusobacterium periodonticum
Legionella birminghamensis
Moraxella (Branhamella) cuniculi
Fusobacterium ulcerans
Legionella cherrii
Moraxella (Branhamella) ovis
Fusobacterium varium
Legionella cincinnatiensis
Moraxella (Moxarella) atlantae
Gardnerella vaginalis
Legionella feeleii
Moraxella (Moxarella) bovis
Gemella morbillorum
Legionella hackeliae
Moraxella (Moxarella) lacunata
Gordonia amarae
Legionella jordanis
Moraxella (Moxarella) liquefaciens
Gordonia bronchialis
Legionella lansingensis
Moraxella (Moxarella) nonliquefaciens
Gordonia rubropertincta
Legionella longbeachae
Moraxella (Moxarella) osloensis
Gordonia sputi
Legionella oakridgensis
Moraxella lincolnii
Gordonia terrae
Legionella pneumophila
Morganella morganii
Granulicatella adjacens
Legionella rubrilucens
Mycobacterium abscessus
Haemophilus aphrophilus
Legionella sainthelensi
Mycobacterium africanum
Haemophilus ducreyi
Legionella tucsonensis
Mycobacterium asiaticum
Haemophilus haemolyticus
Legionella wadsworthii
Mycobacterium avium
Haemophilus influenzae
Leifsonia aquatica
Mycobacterium bovis
Haemophilus parahaemolyticus
Leptospira borgpetersenii
Mycobacterium celatum
Haemophilus parainfluenzae
Leptospira inadai
Mycobacterium chelonae
Haemophilus paraphrophilus
Leptospira interrogans
Mycobacterium conspicuum
Haemophilus segnis
Leptospira kirschneri
Mycobacterium fortuitum
Table S2. Bacterial pathogen list (Li et al., 2015a) (continued)
Mycobacterium genavense
Neisseria subflava
Porphyromonas levii
Mycobacterium gordonae
Neisseria weaveri
Porphyromonas macacae
Mycobacterium haemophilum
Neorickettsia sennetsu
Prevotella bivia
Mycobacterium kansasii
Nocardia asteroides
Prevotella buccae
Mycobacterium leprae
Nocardia brasiliensis
Prevotella buccalis
Mycobacterium malmoense
Nocardia caviae
Prevotella corporis
Mycobacterium marinum
Nocardia farcinica
Prevotella dentalis
Mycobacterium mucogenicum
Nocardia nova
Prevotella denticola
Mycobacterium peregrinum
Nocardia otitidiscaviarum
Prevotella disiens
Mycobacterium porcinum
Nocardia pseudobrasiliensis
Prevotella enoeca
Mycobacterium scrofulaceum
Nocardia transvalensis
Prevotella heparinolytica
Mycobacterium senegalense
Ochrobactrum anthropi
Prevotella intermedia
Mycobacterium shimoidei
Oligella ureolytica
Prevotella loescheii
Mycobacterium simiae
Oligella urethralis
Prevotella melaninogenica
Mycobacterium smegmatis
Orientia tsutsugamushi
Prevotella nigrescens
Mycobacterium szulgai
Paenibacillus alvei
Prevotella oralis
Mycobacterium tuberculosis
Paenibacillus macerans
Prevotella oris
Mycobacterium ulcerans
Pantoea agglomerans
Prevotella oulora
Mycobacterium xenopi
Pasteurella aerogenes
Prevotella ruminicola
Mycoplasma fermentans
Pasteurella caballi
Prevotella tannerae
Mycoplasma genitalium
Pasteurella canis
Prevotella veroralis
Mycoplasma hominis
Pasteurella dagmatis
Prevotella zoogleoformans
Mycoplasma pneumoniae
Pasteurella multocida
Propionibacterium acnes
Mycoplasma salivarium
Pasteurella pneumotropica
Propionibacterium avidum
Myroides odoratus
Pasteurella stomatis
Propionibacterium granulosum
Neisseria cinerea
Peptinophilus asaccharolyticus
Propionibacterium propionicus
Neisseria elongata
Peptococcus niger
Proteus mirabilis
Neisseria flava
Peptostreptococcus anaerobius
Proteus penneri
Neisseria flavescens
Photobacterium damselae
Proteus vulgaris
Neisseria gonorrhoeae
Plesiomonas shigelloides
Providencia alcalifaciens
Neisseria lactamica
Porphyromonas asaccharolytica
Providencia rettgeri
Neisseria meningitidis
Porphyromonas catoniae
Providencia stuartii
Neisseria mucosa
Porphyromonas circumdentaria
Pseudomonas aeruginosa
Neisseria perflava
Porphyromonas endodontalis
Pseudomonas alcaligenes
Neisseria sicca
Porphyromonas gingivalis
Pseudomonas fluorescens
Table S2. Bacterial pathogen list (Li et al., 2015a) (continued)
Pseudomonas pseudoalcaligenes
Selenomonas artemidis
Streptococcus gordonii
Vibrio parahaemolyticus
Pseudomonas putida
Selenomonas dianae
Streptococcus intermedius
Vibrio vulnificus
Pseudomonas stutzeri
Selenomonas flueggei
Streptococcus milleri
Wolinella succinogenes
Pseudonocardia autotrophica
Selenomonas infelix
Streptococcus mitis
Yersinia bercovieri
Pseudoramibacter alactolyticus
Selenomonas noxia
Streptococcus mutans
Yersinia enterocolitica
Psychrobacter phenylpyruvicus
Serratia ficaria
Streptococcus pneumoniae
Yersinia frederiksenii
Rahnella aquatilis
Serratia marcescens
Streptococcus pyogenes
Yersinia intermedia
Ralstonia pickettii
Serratia odorifera
Streptococcus salivarius
Yersinia kristensenii
Rhodococcus equi
Serratia plymuthica
Streptococcus sanguis
Yersinia mollaretii
Rhodococcus erythropolis
Serratia proteamaculans
Streptococcus sobrinus
Yersinia pestis
Rhodococcus fascians
Serratia rubidaea
Streptococcus suis
Yersinia pseudotuberculosis
Rhodococcus rhodnii
Shigella boydii
Streptococcus uberis
Yersinia rohdei
Rhodococcus rhodochrous
Shigella dysenteriae
Sutterella wadsworthensis
Yersinia ruckeri
Rickettsia africae
Shigella flexneri
Suttonella indologenes
Rickettsia akari
Shigella sonnei
Tatlockia maceachernii
Rickettsia australis
Sphingomonas paucimobilis
Tatlockia micdadei
Rickettsia conorii
Spirillum minus
Tatumella ptyseos
Rickettsia felis
Staphylococcus aureus
Treponema carateum
Rickettsia honei
Staphylococcus epidermidis
Treponema pallidum
Rickettsia japonica
Staphylococcus haemolyticus
Tropheryma whippelii
Rickettsia massiliae
Staphylococcus hyicus
Tsukamurella inchonensis
Rickettsia prowazekii
Staphylococcus intermedius
Tsukamurella paurometabola
Rickettsia rickettsii
Staphylococcus lugdunensis
Tsukamurella pulmonis
Rickettsia sibirica
Staphylococcus saprophyticus
Tsukamurella tyrosinosolvens
Rickettsia typhi
Staphylococcus warneri
Ureaplasma urealyticum
Rothia dentocariosa
Stenotrophomonas maltophilia
Veillonella atypica
Ruminococcus productus
Streptobacillus moniliformis
Veillonella dispar
Saccharomonospora viridis
Streptococcus acidominimus
Veillonella parvula
Saccharopolyspora rectivirgula
Streptococcus agalactiae
Vibrio alginolyticus
Salmonella bongori
Streptococcus anginosus
Vibrio cholerae
Salmonella choleraesuis
Streptococcus bovis
Vibrio cincinnatiensis
Salmonella enteritidis
Streptococcus canis
Vibrio fluvialis
Salmonella typhi
Streptococcus constellatus
Vibrio furnissii
Salmonella typhimurium
Streptococcus criceti
Vibrio hollisae
Sebaldella termitidis
Streptococcus equi
Vibrio mimicus
Table S3. AS genomes used in analyzing the incidence of ARGs encountering MGEs.
NCBI.Taxon.ID
Organism.Name
Ecotype
Pathogen
32002
Achromobacter denitrificans
AS
None
56780
Syntrophus aciditrophicus SB
AS
None
62977
Acinetobacter baylyi ADP1
AS
None
265072
Methylobacillus flagellatus KT
AS
None
272564
Desulfitobacterium hafniense DCB-2
AS
None
335543
Syntrophobacter fumaroxidans MPOB
AS
None
337191
Gordonia sp. KTR9
AS
None
338963
Pelobacter carbinolicus Bd1, GraBd1
AS
None
370438
Pelotomaculum thermopropionicum SI
AS
None
381666
Cupriavidus necator H16
AS
None
398578
Delftia acidovorans SPH-1
AS
None
402881
Parvibaculum lavamentivorans DS-1
AS
None
420662
Methylibium petroleiphilum PM1
AS
None
439375
Ochrobactrum anthropi ATCC 49188
AS
None
465721
Steroidobacter denitrificans DSM 18526
AS
None
479431
Nakamurella multipartita Y-104, DSM 44233
AS
None
479434
Sphaerobacter thermophilus 4ac11, DSM 20745
AS
None
522306
Candidatus Accumulibacter phosphatis Type IIA UW-1
AS
None
558173
Corynebacterium doosanense CAU 212, DSM 45436
AS
None
596154
Alicycliphilus denitrificans K601
AS
None
610130
Lachnoclostridium saccharolyticum WM1, DSM 2544
AS
None
635013
Thermincola potens JR
AS
None
643648
Syntrophothermus lipocalidus DSM 12680
AS
None
645991
Syntrophobotulus glycolicus FlGlyR, DSM 8271
AS
None
663278
Ethanoligenens harbinense YUAN-3
AS
None
675635
Pseudonocardia dioxanivorans CB1190
AS
None
706587
Desulfomonile tiedjei DCB-1, DSM 6799
AS
None
720554
Hungateiclostridium clariflavum EBR 45, DSM 19732
AS
None
742013
Delftia acidovorans Cs1-4
AS
None
760192
Haliscomenobacter hydrossis O, DSM 1100
AS
None
868595
Desulfotomaculum carboxydivorans CO-1-SRB, DSM 14880
AS
None
879274
Shinella sp. HZN7
AS
None
880072
Desulfobacca acetoxidans ASRB2, DSM 11109
AS
None
926569
Anaerolinea thermophila UNI-1
AS
None
927704
Selenomonas ruminantium lactilytica TAM6421
AS
None
980445
Desulfoglaeba alkanexedens ALDC
AS
None
983917
Rubrivivax gelatinosus IL144
AS
None
1030157
Sphingomonas sp. KC8
AS
None
1032480
Microlunatus phosphovorus NM-1
AS
None
1118963
Arthrobacter nitroguajacolicus Rue61a
AS
None
1150621
Sulfurospirillum multivorans DSM 12446
AS
None
1209989
Tepidanaerobacter sp. Re1
AS
None
1219035
Novosphingobium tardaugens NBRC 16725
AS
None
1325564
Nitrospira japonica
AS
None
1458492
Myroides sp. ZB35
AS
None
Table S4. Significance of differences among the 4 clusters from Figure 1b. The numbers are the P values from the pair-wise Mann-Whitney test. Those values which are less than 0.05 are highlighted in red.
ARGs
cluster1
cluster2
cluster3
cluster4
Count of Detected ARGs
cluster1
0.000455
0.307646
0.00322
cluster2
0.000455
0.001263
0.342295
cluster3
0.307646
0.001263
0.017629
cluster4
0.00322
0.342295
0.017629
Total abundance
cluster1
0.818736
3.16E-14
7.02E-05
cluster2
0.818736
3.30E-10
0.000532
cluster3
3.16E-14
3.30E-10
0.000135
cluster4
7.02E-05
0.000532
0.000135
aminoglycoside
cluster1
1.31E-07
5.86E-19
1.32E-11
cluster2
1.31E-07
4.31E-08
3.71E-05
cluster3
5.86E-19
4.31E-08
0.94552
cluster4
1.32E-11
3.71E-05
0.94552
bacitracin
cluster1
2.13E-05
0.85181
0.005188
cluster2
2.13E-05
1.68E-06
1.33E-08
cluster3
0.85181
1.68E-06
0.004079
cluster4
0.005188
1.33E-08
0.004079
beta.lactam
cluster1
2.44E-09
1.86E-06
1.32E-11
cluster2
2.44E-09
0.024939
0.002337
cluster3
1.86E-06
0.024939
4.09E-08
cluster4
1.32E-11
0.002337
4.09E-08
chloramphenicol
cluster1
6.67E-10
5.86E-19
1.32E-11
cluster2
6.67E-10
4.80E-09
0.119496
cluster3
5.86E-19
4.80E-09
8.25E-06
cluster4
1.32E-11
0.119496
8.25E-06
fosfomycin
cluster1
0.827717
0.123212
0.812021
cluster2
0.827717
0.127117
0.71118
cluster3
0.123212
0.127117
0.332092
cluster4
0.812021
0.71118
0.332092
fosmidomycin
cluster1
0.339077
0.376661
0.33057
cluster2
0.339077
0.323475
0.036637
cluster3
0.376661
0.323475
0.05612
cluster4
0.33057
0.036637
0.05612
kasugamycin
cluster1
0.033024
0.000247
0.043438
cluster2
0.033024
0.554874
0.904001
cluster3
0.000247
0.554874
0.647833
cluster4
0.043438
0.904001
0.647833
MLS
cluster1
0.007098
0.000305
2.66E-05
cluster2
0.007098
0.673056
0.044784
cluster3
0.000305
0.673056
0.038112
cluster4
2.66E-05
0.044784
0.038112
polymyxin
cluster1
0.006051
0.014271
0.000351
cluster2
0.006051
0.59287
0.044784
cluster3
0.014271
0.59287
0.005701
cluster4
0.000351
0.044784
0.005701
quinolone
cluster1
2.73E-08
1.04E-13
3.96E-10
cluster2
2.73E-08
0.728687
0.598552
cluster3
1.04E-13
0.728687
0.732494
cluster4
3.96E-10
0.598552
0.732494
Table S4. Significance of differences among the 4 clusters from Figure 1b. The numbers are the P values from the pair-wise Mann-Whitney test. Those values which are less than 0.05 are highlighted in red. (continued)
rifamycin
cluster1
1.30E-08
7.79E-07
0.00055
cluster2
1.30E-08
0.004701
0.010577
cluster3
7.79E-07
0.004701
0.646118
cluster4
0.00055
0.010577
0.646118
sulfonamide
cluster1
1.61E-05
1.35E-14
0.014784
cluster2
1.61E-05
0.000257
0.101454
cluster3
1.35E-14
0.000257
2.65E-06
cluster4
0.014784
0.101454
2.65E-06
tetracycline
cluster1
3.22E-10
2.34E-18
1.32E-11
cluster2
3.22E-10
0.021341
0.019174
cluster3
2.34E-18
0.021341
0.604536
cluster4
1.32E-11
0.019174
0.604536
vancomycin
cluster1
0.001495
4.73E-08
1.86E-07
cluster2
0.001495
0.517275
0.16274
cluster3
4.73E-08
0.517275
0.171818
cluster4
1.86E-07
0.16274
0.171818
Table S5. Information of core resistome according to persistency and abundancy detected from 9 years
ARG subtypes
Occurrence frequency (%)
Average abundance
(Copy of ARGs per cell)
Relative abundance (%)
aminoglycoside__aadA
100
0.008257
3.37
aminoglycoside__aph(3'')-I
100
0.005744
2.34
aminoglycoside__aph(6)-I
100
0.004243
1.73
bacitracin__bacA
100
0.031070
12.68
beta-lactam__class A beta-lactamase
100
0.003326
1.36
chloramphenicol__floR
100
0.003257
1.33
fosmidomycin__rosA
100
0.001377
0.56
fosmidomycin__rosB
100
0.001055
0.43
MLS__ereA
100
0.004958
2.02
MLS__macA
96
0.000692
0.28
MLS__macB
100
0.003216
1.31
multidrug__acrB
100
0.007931
3.24
multidrug__adeJ
100
0.000357
0.15
multidrug__ceoB
98
0.000158
0.06
multidrug__mdtB
100
0.000663
0.27
multidrug__mdtC
99
0.000387
0.16
multidrug__mdtF
100
0.000634
0.26
multidrug__mexB
100
0.002494
1.02
multidrug__mexD
100
0.000428
0.17
multidrug__mexF
100
0.002082
0.85
multidrug__mexI
100
0.001577
0.64
multidrug__mexW
100
0.004074
1.66
multidrug__multidrug_ABC_transporter
100
0.002327
0.95
multidrug__multidrug_transporter
100
0.009492
3.87
multidrug__qacEdelta1
100
0.006008
2.45
multidrug__smeB
97
0.000215
0.09
multidrug__smeE
96
0.000120
0.05
polymyxin__arnA
100
0.000561
0.23
rifamycin__ADP-ribosylating transferase_arr
100
0.003623
1.48
sulfonamide__sul1
100
0.023627
9.64
sulfonamide__sul2
99
0.002698
1.10
sulfonamide__sul4
99
0.002514
1.03
tetracycline__tet32
96
0.000218
0.09
tetracycline__tetC
96
0.002511
1.02
tetracycline__tetG
100
0.002959
1.21
tetracycline__tetM
98
0.000476
0.19
tetracycline__tetO
99
0.000372
0.15
tetracycline__tetracycline_resistance_protein
96
0.000635
0.26
tetracycline__tetW
99
0.000618
0.25
unclassified__transcriptional regulatory protein CpxR
100
0.005376
2.19
vancomycin__vanR
97
0.001088
0.44