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- Supplemental 1 -
Supplemental Figures Supplemental Figure 1 - ESOM Showing Best Blast Hit of Scaffolds ESOM showing the clustering of de novo assembled metagenomic data. Each point represents a fragment of an assembled scaffold. Clustering of data points is based on the time series abundance pattern of each assembled scaffold. Dark lines between clusters show definitive separation of genome bins. Data points are colored based on the best BLAST hit of each scaffold compared against the NCBI NT database (coloring is independent of the assembly and binning).
UnknownHit not specified
Veillonella parvulaEscherichia coli
Enterococcus faecalisEnterococcus plasmids
Finegoldia magnaLeuconostoc citreum
ClostridiumPropionibacterium acnes
Staphylococcus phage
Staphylococcus aureusStaphylococcus aureus plasmidsStaphylococcus epidermidisStaphylococcus epidermidis plasmidsStaphylococcus hominisStaphylococcus lugdunensisStreptococcusIsoptericolaShigellaCellulomonasStreptococcus phage
12, 13
8, 9
1
45, 21
14
2
17, 2515
6, 227
23, 24
10
20
3, 16
18, 19
Actinomyces urogenitalis
Clostridium bartlettii
Clostridium butyricum
Enterococcus faecalisEscherichia coli - Strain A
Escherichia coli - Strain B
Leuconostoc sp.
Negativicoccus succinicivoransPropionibacterium sp.
Staphylococcus sp.Streptococcus anginosus
Streptococcus parasanguinis
Streptococcus sp.
Varibaculum cambriense
Veillonella sp. - Species A
Veillonella sp. - Species B
11Veillonella dispar
:::::::::::::::::
BinGenome :2
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3 3
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18 18
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2 2
1
1 1
1
- Supplemental 2 -
Supplemental Figure 2 - Phylogeny of EMIRGE 16S rRNA Genes Reconstructed 16S rRNA gene sequences were aligned along with sequences from their closest relatives in addition to species previously identified in the infant gut. Sequences were aligned with PyNAST using the GreenGenes {DeSantis:2006ii} alignment of OTUs classified at 97% sequence similarity as a template. The phylogenetic tree was constructed with FastTree2 using the generalized time-reversible model for nucleotide evolution and the CAT approximation. Local support values were calculated with the Shimodaira-Hasegawa test. The tree was rooted with the 16S sequence for Halobacterium salinarum and formatted using FigTree. Sequences reconstructed with EMIRGE from the microbial community are shown in blue, and reference sequences with an associated sequenced genome are shown in red.
0.1
Arcanobacterium haemolyticum str. 708 (Finished)
Actinomyces massiliensis str. 4401292
Mobiluncus mulieris str. ATCC 35243 (Draft)
Veillonella parvula DSM 2008 (Finished)
Microbes on human vaginal epithelium clone rRNA307
Actinobaculum schaalii str. BD04-00146
Escherichia coli ABU 83972 (Finished)
Arcanobacterium sp. str. NML 06501
Actinomyces gerencseriae str. DSM 6844
Actinomyces cf. urogenitalis M560/98/1
Veillonella sp. - Species B (Bin 18 and 19)
Veillonella parvula (Finished)
Actinomyces coleocanis str. CCUG 41708 (Draft)
Varibaculum sp. str. CCUG 45456
Varibaculum cambriense
Actinomyces urogenitalis (Bin 12 and 13)
Actinomyces israelii str. A1
Bifidobacterium sp. S18-11 (Draft)
Proteus myxofaciens
Streptococcus parasanguinis (Bin 23 and 24)
Clostridium butyricum (Draft)
Clostridium sp. MDA2315 (Finished)
Microbes on human vaginal epithelium clone rRNA275Varibaculum cambriense str. M124
Varibaculum cambriense str. M398
Actinomyces urogenitalis (Draft)
Enterococcus faecalis (Bin 4)
Actinomyces funkei str. CCUG 42773
Actinomyces turicensis str. APL11
Yersinia sp. SL0604Citrobacter freundii
Arcanobacterium pyogenes HC-H 10
Actinomyces sp str. APL10
Arcanobacterium haemolyticum str. CIP 103370 (Finished)
Actinomyces oricola str. CCUG 46090
Actinomyces naeslundii
Varibaculum cambriense str. CCUG 44998
Streptococcus agalactiae (Finished)
Propionibacterium avidum
Escherichia coli O83 H1 str. NRG 857C (Finished)
Veillonella sp. - Species A (Bin 3 and 16)
Propionibacterium propionicum
Varibaculum cambriense CCUG 44998T
Actinobaculum urinale str. CCUG 46093T
Actinobaculum massiliae str. CIP 107404
Klebsiella pneumoniae subsp. pneumoniae (Finished)
Varibaculum cambriense str. M397
Actinomyces meyeri str. C.I.P. 103148T
Staphylococcus sp. (Bin 6 and 22)
Arcanobacterium hippocoleae str. CCUG 44697 equine vaginal secretion
Shigella dysenteriae (Finished)
Arcanobacterium phocae str. DSM 10004
occupant source house floor dust clone FC04F06
Arcanobacterium bernardiae str. LCDC 89/0504 = DSM 9152
Streptococcus parasanguinis (Finished)
Actinomyces ruminocola str. D471
Veillonella sp. oral taxon 158 (Draft)
occupant source house mattress dust clone MB05D09
Actinomyces odontolyticus str. ATCC 17982 (Draft)
Actinomyces europaeus CCUG 32789AT
Streptococcus parasanguinis ATCC 15912 (Finished)
Arcanobacterium pluranimalium str. 1128
Actinomyces neuii subsp. anitratus DSM 8577T
Clostridium sp. 6-44 (Finished)
Actinomyces suimastitidis str. CCUG 39276
Actinomyces georgiae str. 6843 DSM
Actinomyces howellii str. NCTC 11636
Actinomyces hongkongensis str. HKU8
Jonesia sp. str. TUT1016
Actinomyces sp. str. 7400942 (Draft)
Clostridium bartlettii (Bin 8 and 9)
Actinomyces urogenitalis str. DSM 15434 (Draft)
Ruminococcus obeum A2-162 (Finished)
Actinomyces hyovaginalis str. E6
Actinomyces viscosus str. ChDC OS34 (Draft)
Enterococcus faecalis OG1RF (Finished)
Actinomyces marimammalium str. CCUG 41710
Actinomyces genomosp. C1
Actinomyces slackii str. CCUG 32792
Actinomyces radicidentis str. CCUG 36733T
Propionibacterium sp. H456 (Draft)
Actinomyces lingnae str. CCUG 32865
Salmonella sp. AHL 6
Streptococcus anginosus (Draft)
Clostridiaceae bacterium DJF VP56
Actinomyces radingae str. APL1
Actinomyces odontolyticus str. F0309 (Draft)
Escherichia coli BL21 DE3 (Finished)
Actinomyces viscosus str. CCUG 33710 (Draft)
Actinobaculum sp. VA15-2004 VA15 2004
Serratia proteamaculans (Finished)
Actinomyces denticolens str. KM1298 04
Actinomyces bovis str. NCTC 11535
Varibaculum cambriense (Bin 20)
Mobiluncus subsp. curtisii str. CCUG 21018 subsp.
Negativicoccus succinicivorans
Actinomyces suis
Escherichia coli - Strain A (Bin 5 and 21)
occupant source house mattress dust clone MA03A07
Escherichia coli ATCC 8739 (Finished)
Staphylococcus epidermidis ATCC 12228 (Finished)
Erwinia sp. Xb2 (Finished)
Clostridium butyricum (Bin 1)
Streptococcus anginosus (Bin 7)
Actinomyces subsp. neuii DSM 8576
Actinomyces graevenitzii str. CCUG 27294
Veillonella dispar (Bin 11)
Actinomyces sp. oral taxon 848 str. F0332 (Draft)
Staphylococcus epidermidis RP62A (Finished)
Clostridiales bacterium 80/4
Negativicoccus succinicivorans (Bin 17 and 25)
Escherichia coli UMNF18 (Finished)
Ruminococcus sp. 5 (Finished)
Veillonella dispar (Draft)
Enterococcus sp. CSL 7544-3 (Finished)
Actinomyces canis
Halobacterium salinarum (Finished)
Arcanobacterium haemolyticum str. NCTC 9697 (Finished)
Mobiluncus curtisii str. ATCC 43063 (Finished)
Escherichia coli (Finished)
Bacteroides fragilis (Finished)
Varibaculum cambriense str. M380
Propionibacterium sp. (Bin 15)
Arcanobacterium suiabortus str. Murakami
Actinomyces vaccimaxillae str. R10176T
Actinomyces catuli str. CCUG 41709
Actinomyces sp. oral taxon 180 str. F0310 (Draft)
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1
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0.96
0.97
0.97
1
1
0.93
0.59
0.93
0.89
0.99
1
0.35
0.94
0.76
0.64
1
0.97
0.03
0.99
0.75
0.71
0.85
0.98
0.47
0.92
1
0.34
0.99
0.75
0.73
0.99
0.78
0.89
0.99
0.87
0.98
0.96
1
0.97
0.89
1
0.34
0.76
0.57
1
1
1
0.68
0.95
0.97
0.98
0.86
0.91
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0.34
0.92
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0.96
0.37
0.79
0.77
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1
1
0.98
0.93
1
0.47
0.92
0.74
0.95
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0.57
0.86
0.77
0.99
0.11
0.71
1
0.78
1
1
0.84
1
0.97
0.99
0.76
0.93
0.95
0.98
0.90
0.93
1
0.99
0.17
1
0.41
0.89
0.76
1
0.89 0.96
0.97
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1
0.80
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0.97
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0.87
- Supplemental 3 -
Supplemental Figure 3 - Phylogeny of Plasmid Replication Protein Genes Plasmid novelty and diversity represented by plasmid replication proteins. Protein sequences were aligned using MUSCLE and the phylogenetic tree was constructed using FastTree2 with the Jones-Taylor-Thornton model of amino acid evolution and the CAT approximation. Local support values were calculated with the Shimodaira-Hasegawa test. Sequences from plasmids reconstructed from the microbial community are shown in red.
0.5
UniRef90 P17492 Replication protein n=3 Tax=Neisseria RepID=REPA NEIGO
UniRef90 C3DUG1 Replication initiation protein n=1 Tax=Bacillus thuringiensis serovar sotto RepID=C3DUG1 BACTS
UniRef90 Q8EQS6 Transcriptional regulator GntR family n=1 Tax=Oceanobacillus iheyensis HTE831 RepID=Q8EQS6 OCEIH
UniRef90 C9BR53 Initiator replication protein Fragment n=1 Tax=Enterococcus faecium 1 231 502 RepID=C9BR53 ENTFC
Staphylococcus sp. - Plasmid B - I9.NODE 778 length 2473 cov 68.247879 1 100.00 150 3e-102 300 UniRef90 P06735
Staphylococcus aureus gi 188039006 ref YP 001901403.1 rep protein [Staphylococcus aureus]
UniRef90 I1DRZ7 Putative helix-turn-helix motif protein n=3 Tax=Campylobacter RepID=I1DRZ7 9PROT
UniRef90 B1B3J8 Replication protein Rep n=43 Tax=Staphylococcus aureus RepID=B1B3J8 STAAU
UniRef90 A3MAA6 Putative uncharacterized protein n=1 Tax=Acinetobacter baumannii ATCC 17978 RepID=A3MAA6 ACIBT
UniRef90 F5VFX2 Putative RepB protein n=1 Tax=Lactobacillus salivarius NIAS840 RepID=F5VFX2 9LACO
UniRef90 E3Q0R2 RepA protein n=1 Tax=Lactobacillus rennini RepID=E3Q0R2 9LACO
UniRef90 B9ECE7 Plasmid replication initiation protein n=1 Tax=Macrococcus caseolyticus JCSC5402 RepID=B9ECE7 MACCJ
UniRef90 UPI0002492734 Rep n=1 Tax=Lactobacillus acidipiscis KCTC 13900 RepID=UPI0002492734
UniRef90 H7WT32 Replication initiation protein n=5 Tax=Campylobacter RepID=H7WT32 CAMCO
UniRef90 G2RYC8 Replication initiator protein n=1 Tax=Bacillus megaterium WSH-002 RepID=G2RYC8 BACME
UniRef90 Q1CR19 Replication initiation protein A n=5 Tax=Helicobacter pylori RepID=Q1CR19 HELPH
UniRef90 H7XV03 Replication initiation protein n=3 Tax=Campylobacter jejuni subsp. jejuni RepID=H7XV03 CAMJU
UniRef90 H4E426 Replication initiation factor family protein n=1 Tax=Staphylococcus aureus subsp. aureus CIG2018 RepID=H4E426 STAAU
UniRef90 H4GDG7 Replication initiation factor Fragment n=1 Tax=Staphylococcus aureus subsp. aureus IS-189 RepID=H4GDG7 STAAU
UniRef90 A7HZC8 Putative RepE n=1 Tax=Campylobacter hominis ATCC BAA-381 RepID=A7HZC8 CAMHC
UniRef90 Q83ZX8 Replication protein n=1 Tax=Pasteurella multocida RepID=Q83ZX8 PASMD
Escherichia coli - Strain A / B Plasmid - I1.NODE 26 length 3137 cov 2140.327148 1 1 86.36 22 1e-04 41.6 UniRef90 E8A5F4
UniRef90 Q52051 Plasmid replication control protein n=1 Tax=Butyrivibrio fibrisolvens RepID=Q52051 BUTFI
UniRef90 C2V4G0 Putative uncharacterized protein n=2 Tax=Bacillus cereus group RepID=C2V4G0 BACCE
UniRef90 H3WKQ8 Replication initiation factor domain protein Fragment n=1 Tax=Staphylococcus epidermidis VCU128 RepID=H3WKQ8 STAEP
UniRef90 D1WIH1 Initiator RepB protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WIH1 STAEP
UniRef90 O50587 Plasmid pONE430 DNA complete sequence n=1 Tax=Selenomonas ruminantium RepID=O50587 SELRU
UniRef90 C2LYR6 Replication protein n=2 Tax=Staphylococcus RepID=C2LYR6 STAHO
UniRef90 H3WGV0 Replication initiation family protein n=1 Tax=Staphylococcus epidermidis VCU128 RepID=H3WGV0 STAEP
UniRef90 E4I4L2 Initiator RepB protein n=5 Tax=Enterococcus faecium RepID=E4I4L2 ENTFC
UniRef90 C3S7V4 Rep n=1 Tax=Streptococcus parasanguinis RepID=C3S7V4 STRPA
n/a gi 449265372 ref YP 007419102.1 plasmid replication protein [Staphylococcus hyicus]
UniRef90 B0LSK6 Rep n=2 Tax=Enterococcus faecium RepID=B0LSK6 ENTFC
UniRef90 Q16A85 Malonyl-CoA decarboxylase n=1 Tax=Roseobacter denitrificans OCh 114 RepID=Q16A85 ROSDO
UniRef90 D6CW34 Initiator Replication protein n=1 Tax=Salinibacter ruber M8 RepID=D6CW34 SALRM
UniRef90 E3VVN2 Replication protein A n=1 Tax=Lactobacillus casei RepID=E3VVN2 LACCA
UniRef90 H3WGY9 Firmicute plasmid replication protein RepL domain protein n=3 Tax=Staphylococcus epidermidis RepID=H3WGY9 STAEP
UniRef90 F6BEP1 Transcriptional regulator ArsR family n=1 Tax=Methanotorris igneus Kol 5 RepID=F6BEP1 METIK
UniRef90 D1WPL6 Initiator RepB protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WPL6 STAEP
UniRef90 F5MQM0 Putative uncharacterized protein n=5 Tax=Enterobacteriaceae RepID=F5MQM0 SHIFL
UniRef90 Q93CK6 Putative replication protein n=2 Tax=Enterococcus faecalis RepID=Q93CK6 ENTFL
UniRef90 D9SSY3 Replication initiation factor n=1 Tax=Clostridium cellulovorans 743B RepID=D9SSY3 CLOC7
UniRef90 H9C6J0 RepB n=1 Tax=Psychrobacter sp. DAB AL43B RepID=H9C6J0 9GAMM
UniRef90 D1WJI2 Initiator RepB protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WJI2 STAEP
UniRef90 F2B588 MarR family protein n=13 Tax=Streptococcus RepID=F2B588 STRPN
UniRef90 C2GPE0 Replication initiator protein n=3 Tax=Lactobacillus reuteri RepID=C2GPE0 LACRE
UniRef90 G9XF59 Putative uncharacterized protein n=1 Tax=Eubacteriaceae bacterium CM5 RepID=G9XF59 9FIRM
UniRef90 H1M1G1 Initiator RepB protein n=2 Tax=Bacteria RepID=H1M1G1 9BACT
UniRef90 D1WIU2 Replication initiation family protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WIU2 STAEP
UniRef90 H3Z533 Conserved domain protein Fragment n=1 Tax=Staphylococcus epidermidis VCU081 RepID=H3Z533 STAEP
UniRef90 G8P7H4 Replication initiation protein n=2 Tax=Lactococcus lactis subsp. cremoris RepID=G8P7H4 LACLC
UniRef90 H3VE05 Replication initiation factor n=4 Tax=Staphylococcus RepID=H3VE05 STAEP
UniRef90 Q53U45 Putative repliccation protein B n=1 Tax=Campylobacter lari RepID=Q53U45 CAMLA
UniRef90 Q58793 Uncharacterized HTH-type transcriptional regulator MJ1398 n=1 Tax=Methanocaldococcus jannaschii DSM 2661 RepID=Y1398 METJA
UniRef90 C2FE88 Plasmid replication protein RepB family n=2 Tax=Lactobacillus casei group RepID=C2FE88 LACPA
UniRef90 P08115 Replication initiation protein n=4 Tax=Staphylococcus RepID=REP STAAU
UniRef90 G4XGN5 Replication protein n=1 Tax=Selenomonas ruminantium RepID=G4XGN5 SELRU
UniRef90 UPI00020A9AE5 UPI00020A9AE5 related cluster n=1 Tax=unknown RepID=UPI00020A9AE5
UniRef90 D1P806 Replication and maintenance protein n=1 Tax=Providencia rustigianii DSM 4541 RepID=D1P806 9ENTR
UniRef90 H3ULV8 Replication initiation family protein n=5 Tax=Staphylococcus epidermidis RepID=H3ULV8 STAEP
UniRef90 E8A5F4 Putative uncharacterized protein n=1 Tax=Salmonella enterica subsp. enterica serovar Montevideo str. 366867 RepID=E8A5F4 SALMO
UniRef90 D0T033 Replicase n=3 Tax=Acinetobacter RepID=D0T033 ACILW
UniRef90 Q3Y1H3 Replication initiation factor n=2 Tax=Enterococcus faecium DO RepID=Q3Y1H3 ENTFC
Enterococcus faecalis ATCC 4200 gi 256619590 ref ZP 05476436.1 initiator Replication protein [Enterococcus faecalis ATCC 4200]
UniRef90 D2J655 Replication initiation protein n=1 Tax=Staphylococcus aureus RepID=D2J655 STAAU
UniRef90 F4HFW8 Replication protein RepA n=1 Tax=Gallibacterium anatis UMN179 RepID=F4HFW8 GALAU
UniRef90 F2J4U9 Transcriptional regulator MarR family n=1 Tax=Polymorphum gilvum SL003B-26A1 RepID=F2J4U9 POLGS
UniRef90 UPI0002492749 replication protein n=1 Tax=Lactobacillus acidipiscis KCTC 13900 RepID=UPI0002492749
UniRef90 UPI0002193484 hypothetical protein LcorcK3 06922 partial n=1 Tax=Lactobacillus coryniformis subsp. coryniformis KCTC 3167 RepID=UPI0002193484
n/a gi 425280919 ref ZP 18672111.1 putative plasmid replication initiation protein [Escherichia coli ARS4.2123]
UniRef90 D4RTC4 Replication protein n=2 Tax=Enterococcus faecium RepID=D4RTC4 ENTFC
UniRef90 F8LU10 Replication initiator protein n=1 Tax=Streptococcus thermophilus JIM 8232 RepID=F8LU10 STRTR
Streptococcus parasanguinis - Plasmid - I10.NODE 3378 length 8927 cov 50.796909 3 100.00 270 0.0 560 UniRef90 C3S7V4
UniRef90 C7YFW9 Predicted protein n=1 Tax=Enterococcus faecalis T8 RepID=C7YFW9 ENTFL
UniRef90 Q83YJ2 RepB n=1 Tax=Bifidobacterium longum RepID=Q83YJ2 BIFLN
UniRef90 E8KKR2 Replication protein n=1 Tax=Actinobacillus ureae ATCC 25976 RepID=E8KKR2 9PAST
UniRef90 B9ECF4 Plasmid replication initiation protein n=1 Tax=Macrococcus caseolyticus JCSC5402 RepID=B9ECF4 MACCJ
UniRef90 C2PNY6 Rep14-4 n=4 Tax=Bacillus RepID=C2PNY6 BACCE
n/a gi 444922101 ref ZP 21241876.1 putative plasmid replication initiation protein [Escherichia coli 09BKT078844]
UniRef90 O54428 Replication protein n=5 Tax=Lactococcus lactis RepID=O54428 9LACT
UniRef90 Q8GFD5 RepA n=2 Tax=Enterococcus faecalis RepID=Q8GFD5 ENTFL
UniRef90 Q1EL65 Putative firmicute plasmid replication protein n=1 Tax=uncultured bacterium RepID=Q1EL65 9BACT
UniRef90 P14490 Replication initiation protein n=7 Tax=root RepID=REPM STAAU
UniRef90 D2J7W9 Replication initiation protein n=6 Tax=root RepID=D2J7W9 STAAU
UniRef90 C0WUU3 Replication initiator protein n=1 Tax=Lactobacillus buchneri ATCC 11577 RepID=C0WUU3 LACBU
UniRef90 B3ZYI7 Putative replication initiator protein n=1 Tax=Bacillus cereus 03BB108 RepID=B3ZYI7 BACCE
UniRef90 D3S7D7 Transcriptional regulator ArsR family n=1 Tax=Methanocaldococcus sp. FS406-22 RepID=D3S7D7 METSF
UniRef90 D3G1X2 Initiator RepB protein n=1 Tax=Bacillus pseudofirmus OF4 RepID=D3G1X2 BACPE
UniRef90 A1IVP1 Replication protein n=1 Tax=Bifidobacterium longum RepID=A1IVP1 BIFLN
UniRef90 C5DB17 Initiator RepB protein n=1 Tax=Geobacillus sp. WCH70 RepID=C5DB17 GEOSW
UniRef90 Q007S8 Replication initiation protein A n=2 Tax=Helicobacter pylori RepID=Q007S8 HELPX
UniRef90 UPI0002492743 replication protein A1 n=1 Tax=Lactobacillus acidipiscis KCTC 13900 RepID=UPI0002492743
UniRef90 I0EZ50 Uncharacterized protein n=1 Tax=Helicobacter pylori HUP-B14 RepID=I0EZ50 HELPX
UniRef90 A0MVT0 Putative RepE n=1 Tax=Campylobacter fetus subsp. venerealis RepID=A0MVT0 CAMFE
n/a gi 420342852 ref ZP 14844324.1 putative plasmid replication initiation protein [Shigella flexneri K-404]
UniRef90 E5CPW5 Replication protein n=1 Tax=Staphylococcus caprae C87 RepID=E5CPW5 9STAP
UniRef90 D1WM26 Conserved domain protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WM26 STAEP
UniRef90 E5CQ05 Replication initiation protein n=1 Tax=Staphylococcus caprae C87 RepID=E5CQ05 9STAP
UniRef90 F8EQU9 Initiator RepB protein n=1 Tax=Runella slithyformis DSM 19594 RepID=F8EQU9 RUNSL
UniRef90 Q52204 Putative plasmid replication protein n=1 Tax=Plasmid pRJF2 RepID=Q52204 9ZZZZ
UniRef90 E0G0H9 Replication initiation factor n=2 Tax=Enterococcus faecalis RepID=E0G0H9 ENTFL
UniRef90 H7G1N7 Replication protein n=1 Tax=Lactobacillus salivarius SMXD51 RepID=H7G1N7 9LACO
UniRef90 C5QLN2 Replication protein Rep n=3 Tax=Staphylococcus RepID=C5QLN2 STAEP
UniRef90 F5RHC4 Putative uncharacterized protein n=1 Tax=Methyloversatilis universalis FAM5 RepID=F5RHC4 9RHOO
UniRef90 H2AM28 Putative replication initiator protein n=1 Tax=Lactococcus garvieae RepID=H2AM28 9LACT
Macrococcus caseolyticus JCSC5402 gi 222143326 ref YP 002561361.1 plasmid replication initiation protein [Macrococcus caseolyticus JCSC5402]
UniRef90 P71455 ORF1 protein n=1 Tax=Oenococcus oeni RepID=P71455 OENOE
UniRef90 Q17V39 Replication A protein n=1 Tax=Helicobacter acinonychis str. Sheeba RepID=Q17V39 HELAH
UniRef90 C7WV09 RepE replication protein Fragment n=1 Tax=Enterococcus faecalis ARO1/DG RepID=C7WV09 ENTFL
UniRef90 UPI0002192B7D replicase n=1 Tax=Leuconostoc inhae KCTC 3774 RepID=UPI0002192B7D
UniRef90 A0S0I0 DNA replication protein n=4 Tax=Bacteria RepID=A0S0I0 9GAMM
UniRef90 D2QVX6 Initiator RepB protein n=1 Tax=Spirosoma linguale DSM 74 RepID=D2QVX6 SPILD
UniRef90 C7C2U9 Plasmid replication protein n=1 Tax=Staphylococcus aureus subsp. aureus ST398 RepID=C7C2U9 STAA5
UniRef90 G6LHT2 Replication initiation protein n=2 Tax=Streptococcus RepID=G6LHT2 STRPN
UniRef90 D4CRM3 Putative replication protein rep n=1 Tax=Fusobacterium periodonticum ATCC 33693 RepID=D4CRM3 9FUSO
UniRef90 B9ECE1 Plasmid replication initiation protein n=1 Tax=Macrococcus caseolyticus JCSC5402 RepID=B9ECE1 MACCJ
UniRef90 A3IZU1 Putative uncharacterized protein n=1 Tax=Cyanothece sp. CCY0110 RepID=A3IZU1 9CHRO
UniRef90 A1IGF7 Replication Protein A n=5 Tax=Enterococcus faecium RepID=A1IGF7 ENTFC
UniRef90 E6JQ18 Initiator Replication family protein n=1 Tax=Staphylococcus epidermidis FRI909 RepID=E6JQ18 STAEP
UniRef90 D2JCH6 Replication protein Rep n=2 Tax=Staphylococcus epidermidis RepID=D2JCH6 STAEP
Staphylococcus sp. - Plasmid A - I9.NODE 928 length 2490 cov 54.558231 2 100.00 314 0.0 651 UniRef90 C5QD25
UniRef90 E4IM21 Replication initiation factor Fragment n=1 Tax=Enterococcus faecium TX0082 RepID=E4IM21 ENTFC
UniRef90 H1HIK2 Putative uncharacterized protein n=2 Tax=Fusobacterium RepID=H1HIK2 FUSNU
UniRef90 D6JZ60 Putative uncharacterized protein n=1 Tax=Acinetobacter sp. SH024 RepID=D6JZ60 ACIG3
UniRef90 E9FPE3 Replication initiation factor family protein n=3 Tax=Streptococcus RepID=E9FPE3 9STRE
UniRef90 Q1ENI4 RepB n=1 Tax=Lactobacillus plantarum RepID=Q1ENI4 LACPN
UniRef90 E4PYH4 Replication protein n=1 Tax=Staphylococcus aureus RepID=E4PYH4 STAAU
UniRef90 UPI0002191AAA replication initiator protein n=1 Tax=Lactobacillus coryniformis subsp. coryniformis KCTC 3167 RepID=UPI0002191AAA
UniRef90 Q9RHE5 RepA n=1 Tax=Erysipelothrix rhusiopathiae RepID=Q9RHE5 ERYRH
UniRef90 F2HQ97 Replication protein n=1 Tax=Lactococcus lactis subsp. lactis CV56 RepID=F2HQ97 LACLV
UniRef90 I0TN76 Uncharacterized protein Fragment n=1 Tax=Staphylococcus aureus subsp. aureus IS-250 RepID=I0TN76 STAAU
UniRef90 F7QX45 Replication protein n=2 Tax=Lactobacillus salivarius RepID=F7QX45 9LACO
UniRef90 Q2PZL5 RepA n=1 Tax=Bifidobacterium sp. A24 RepID=Q2PZL5 9BIFI
UniRef90 C5ZV43 Response regulator receiver domain protein n=1 Tax=Helicobacter canadensis MIT 98-5491 RepID=C5ZV43 9HELI
UniRef90 E4IA29 Initiator RepB protein n=5 Tax=Enterococcus faecium RepID=E4IA29 ENTFC
UniRef90 G0ID38 Rep n=1 Tax=Streptococcus pseudopneumoniae IS7493 RepID=G0ID38 STRES
UniRef90 Q3ZFU4 RepC n=1 Tax=Lactobacillus johnsonii FI9785 RepID=Q3ZFU4 LACJF
UniRef90 B2I3S2 Replicase n=1 Tax=Acinetobacter baumannii ACICU RepID=B2I3S2 ACIBC
UniRef90 F9H9U1 Initiator RepB protein n=1 Tax=Streptococcus mitis SK1073 RepID=F9H9U1 STRMT
UniRef90 Q1T717 Putative repliccation protein B n=1 Tax=Campylobacter lari RepID=Q1T717 CAMLA
UniRef90 E7S7B6 Initiator RepB protein n=1 Tax=Streptococcus agalactiae ATCC 13813 RepID=E7S7B6 STRAG
UniRef90 F9NGX5 Replication initiation factor n=4 Tax=Streptococcus RepID=F9NGX5 STREQ
UniRef90 D4RFJ6 Replication protein Fragment n=1 Tax=Enterococcus faecium E1679 RepID=D4RFJ6 ENTFC
Enterococcus faecalis T2 gi 255976344 ref ZP 05426930.1 replication protein [Enterococcus faecalis T2]
UniRef90 H0DS20 Replication initiation family protein Fragment n=1 Tax=Staphylococcus epidermidis VCU071 RepID=H0DS20 STAEP
UniRef90 G9SNX1 Putative replication protein rep n=1 Tax=Enterococcus faecium E4453 RepID=G9SNX1 ENTFC
UniRef90 P06735 Replication and maintenance protein n=33 Tax=root RepID=REMA STAEP
UniRef90 Q3SAX5 RepA n=1 Tax=Carnobacterium divergens RepID=Q3SAX5 CARDV
UniRef90 A8UD54 Replication protein n=1 Tax=Carnobacterium sp. AT7 RepID=A8UD54 9LACT
UniRef90 H1M1G9 Replication initiation factor n=1 Tax=Prevotella dentalis DSM 3688 RepID=H1M1G9 9BACT
UniRef90 D0T0I6 DNA replication protein n=1 Tax=Acinetobacter lwoffii SH145 RepID=D0T0I6 ACILW
UniRef90 B0LSK9 RepA n=2 Tax=Enterococcus faecium RepID=B0LSK9 ENTFC
UniRef90 E3R7A8 Replication initiation protein n=1 Tax=Lactobacillus crispatus CTV-05 RepID=E3R7A8 9LACO
UniRef90 B9W3U8 Initiation protein repA n=6 Tax=Lactobacillales RepID=B9W3U8 PEDPE
UniRef90 Q93NB4 RepB n=2 Tax=Lactobacillales RepID=Q93NB4 9LACT
UniRef90 F0VWN3 Replication initiation protein n=2 Tax=Streptococcus gallolyticus subsp. gallolyticus RepID=F0VWN3 STRG2
Staphylococcus aureus gi 71558997 ref YP 271814.1 RepL [Staphylococcus aureus]
UniRef90 C2K1S1 Plasmid replication initiation protein n=2 Tax=Lactobacillus RepID=C2K1S1 LACRH
UniRef90 E5Z8K0 Aminoacyl-histidine dipeptidase n=62 Tax=Campylobacter jejuni RepID=E5Z8K0 CAMJU
UniRef90 UPI00004A2E95 UPI00004A2E95 related cluster n=1 Tax=unknown RepID=UPI00004A2E95
UniRef90 G9ST47 Putative replication protein rep n=1 Tax=Enterococcus faecium E4453 RepID=G9ST47 ENTFC
UniRef90 UPI0002492987 replication protein A1 n=1 Tax=Lactobacillus acidipiscis KCTC 13900 RepID=UPI0002492987
UniRef90 E3EY75 Transcriptional regulator GntR family n=2 Tax=Ketogulonicigenium vulgare RepID=E3EY75 KETVY
UniRef90 Q2JEC3 Transcriptional regulator ArsR family n=1 Tax=Frankia sp. CcI3 RepID=Q2JEC3 FRASC
UniRef90 H3Z5J2 Conserved domain protein Fragment n=1 Tax=Staphylococcus epidermidis VCU081 RepID=H3Z5J2 STAEP
UniRef90 C3ICZ9 Initiator RepB protein n=3 Tax=Bacillus cereus group RepID=C3ICZ9 BACTU
UniRef90 E6JRH5 Initiator Replication family protein n=5 Tax=Staphylococcus RepID=E6JRH5 STAEP
UniRef90 A3W9G0 Putative uncharacterized protein n=1 Tax=Erythrobacter sp. NAP1 RepID=A3W9G0 9SPHN
UniRef90 UPI0001BCE2AC putative RepE n=1 Tax=Campylobacter fetus subsp. venerealis str. Azul-94 RepID=UPI0001BCE2AC
UniRef90 Q84FN9 Putative uncharacterized protein n=1 Tax=Weissella cibaria RepID=Q84FN9 9LACT
UniRef90 C6E4J9 Response regulator receiver protein n=1 Tax=Geobacter sp. M21 RepID=C6E4J9 GEOSM
UniRef90 Q1WRF7 Replication protein n=6 Tax=Lactobacillus salivarius RepID=Q1WRF7 LACS1
UniRef90 Q4F8N0 RepA n=1 Tax=Lactobacillus plantarum RepID=Q4F8N0 LACPN
UniRef90 Q47816 ORF1 n=1 Tax=Enterococcus faecium RepID=Q47816 ENTFC
UniRef90 Q2B8G7 Replication initiator protein n=1 Tax=Bacillus sp. NRRL B-14911 RepID=Q2B8G7 9BACI
UniRef90 P12053 Replication initiation protein n=4 Tax=Bacilli RepID=REPE STAAU
UniRef90 Q47742 Rep B n=1 Tax=Enterococcus faecium RepID=Q47742 ENTFC
UniRef90 C7UIY7 Initiator Replication protein n=1 Tax=Enterococcus faecalis ATCC 4200 RepID=C7UIY7 ENTFL
UniRef90 E0GF30 Replication initiation factor n=4 Tax=Bacilli RepID=E0GF30 ENTFL
UniRef90 H1TH98 Firmicute plasmid replication protein RepL n=6 Tax=Staphylococcus RepID=H1TH98 STAAU
UniRef90 F0P513 Replication initiation protein truncated n=1 Tax=Staphylococcus pseudintermedius ED99 RepID=F0P513 STAPE
UniRef90 H8H8J4 Replication initiation protein A n=1 Tax=Helicobacter pylori ELS37 RepID=H8H8J4 HELPX
UniRef90 C0MM89 Replication protein B-1 n=2 Tax=Lactobacillus paracasei subsp. paracasei RepID=C0MM89 LACPA
UniRef90 Q0I4Q2 Putative uncharacterized protein n=1 Tax=Haemophilus somnus 129PT RepID=Q0I4Q2 HAES1
UniRef90 E6HNI1 Plasmid recombination enzyme n=1 Tax=Enterococcus faecalis TX2137 RepID=E6HNI1 ENTFL
UniRef90 H7SBB7 Replication initiation protein n=2 Tax=Campylobacter coli RepID=H7SBB7 CAMCO
UniRef90 C0IMI9 Rep n=3 Tax=Pasteurellaceae RepID=C0IMI9 PASMD
UniRef90 D4YIW4 Replication initiation protein n=1 Tax=Aerococcus viridans ATCC 11563 RepID=D4YIW4 9LACT
UniRef90 Q9F7U5 RepA n=2 Tax=Helicobacter pylori RepID=Q9F7U5 HELPX
UniRef90 C6RJX9 DNA replication protein n=1 Tax=Acinetobacter radioresistens SK82 RepID=C6RJX9 ACIRA
UniRef90 F7SHN7 Putative uncharacterized protein n=1 Tax=Lactobacillus johnsonii pf01 RepID=F7SHN7 LACJH
UniRef90 H9C6J6 RepB n=1 Tax=Psychrobacter sp. DAB AL43B RepID=H9C6J6 9GAMM
UniRef90 C9BRX0 Replication protein n=2 Tax=Enterococcus faecium RepID=C9BRX0 ENTFC
UniRef90 F6ITL9 Replication protein A n=4 Tax=Lactobacillaceae RepID=F6ITL9 LACPE
UniRef90 F0VYJ2 Replication protein n=1 Tax=Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069 RepID=F0VYJ2 STRG2
UniRef90 E8QRR4 Replication initiation protein A n=3 Tax=Helicobacter pylori RepID=E8QRR4 HELPR
UniRef90 F1SZJ6 Plasmid replication protein n=2 Tax=Tetragenococcus RepID=F1SZJ6 TETHA
UniRef90 D0T0E6 DNA replication protein n=1 Tax=Acinetobacter lwoffii SH145 RepID=D0T0E6 ACILW
UniRef90 D4RUJ3 Replication protein n=2 Tax=Enterococcus faecium RepID=D4RUJ3 ENTFC
UniRef90 D0C5D0 DNA replication protein n=2 Tax=Acinetobacter RepID=D0C5D0 9GAMM
UniRef90 E6FPQ0 Initiator RepB protein Fragment n=1 Tax=Enterococcus faecalis TX1346 RepID=E6FPQ0 ENTFL
UniRef90 C2E7V5 Replication protein n=1 Tax=Lactobacillus johnsonii ATCC 33200 RepID=C2E7V5 LACJH
UniRef90 D2JC78 Replication protein n=1 Tax=Staphylococcus epidermidis RepID=D2JC78 STAEP
UniRef90 C5QTZ6 Replication initiation protein DnaA n=4 Tax=Staphylococcus epidermidis RepID=C5QTZ6 STAEP
UniRef90 D6PG14 Putative uncharacterized protein n=1 Tax=uncultured phage MedDCM-OCT-S08-C582 RepID=D6PG14 9VIRU
UniRef90 B5YI76 Catabolite gene activator n=1 Tax=Thermodesulfovibrio yellowstonii DSM 11347 RepID=B5YI76 THEYD
UniRef90 C2Q5I8 Initiator RepB protein n=7 Tax=Bacillus cereus group RepID=C2Q5I8 BACCE
UniRef90 Q7X3Y5 RepB n=2 Tax=Lactobacillales RepID=Q7X3Y5 PEDAC
UniRef90 H3UTK3 Initiator RepB protein Fragment n=1 Tax=Staphylococcus epidermidis VCU065 RepID=H3UTK3 STAEP
UniRef90 Q2VHU2 Replication protein RepB n=4 Tax=Lactococcus lactis RepID=Q2VHU2 9LACT
UniRef90 D5E3Q9 Replication initiator protein n=1 Tax=Bacillus megaterium QM B1551 RepID=D5E3Q9 BACMQ
UniRef90 G8PF60 Plasmid replication protein n=4 Tax=Lactobacillaceae RepID=G8PF60 PEDCP
UniRef90 C9C8I5 Replication initiator protein Fragment n=1 Tax=Enterococcus faecium 1 231 410 RepID=C9C8I5 ENTFC
UniRef90 Q4VGM0 RepB n=7 Tax=Campylobacter RepID=Q4VGM0 CAMCO
UniRef90 E5W9M1 Crp/Fnr family protein n=4 Tax=Bacillus RepID=E5W9M1 9BACI
UniRef90 G5H6T4 Putative uncharacterized protein n=1 Tax=Alistipes indistinctus YIT 12060 RepID=G5H6T4 9BACT
UniRef90 E6LJ28 Putative uncharacterized protein Fragment n=1 Tax=Enterococcus italicus DSM 15952 RepID=E6LJ28 9ENTE
UniRef90 B0S461 Replication protein n=1 Tax=Finegoldia magna ATCC 29328 RepID=B0S461 FINM2
UniRef90 C9CGX5 Plasmid replication protein n=8 Tax=Enterococcus RepID=C9CGX5 ENTFC
UniRef90 D0T089 DNA replication protein n=1 Tax=Acinetobacter lwoffii SH145 RepID=D0T089 ACILW
UniRef90 Q52216 Putative uncharacterized protein n=1 Tax=Plasmid pRJF1 RepID=Q52216 9ZZZZ
UniRef90 F6ITM4 RepB n=1 Tax=Lactobacillus pentosus MP-10 RepID=F6ITM4 LACPE
UniRef90 Q02VJ2 Replication initiator protein n=1 Tax=Lactococcus lactis subsp. cremoris SK11 RepID=Q02VJ2 LACLS
UniRef90 B0VXM4 Rep n=1 Tax=Geobacillus stearothermophilus RepID=B0VXM4 GEOSE
UniRef90 C0L9E7 RepB n=1 Tax=Leuconostoc mesenteroides RepID=C0L9E7 LEUME
UniRef90 B5RSD3 Plasmid replication protein RepB family n=3 Tax=Lactobacillus RepID=B5RSD3 LACRH
UniRef90 G8PA02 Plasmid replication protein n=2 Tax=Lactococcus lactis RepID=G8PA02 LACLC
UniRef90 I0EZ54 Replication initiation protein A n=1 Tax=Helicobacter pylori HUP-B14 RepID=I0EZ54 HELPX
UniRef90 H3Z5R2 Replication initiation factor domain protein Fragment n=1 Tax=Staphylococcus epidermidis VCU081 RepID=H3Z5R2 STAEP
UniRef90 D7AER5 Response regulator n=1 Tax=Geobacter sulfurreducens KN400 RepID=D7AER5 GEOSK
UniRef90 C6RSQ0 Replicase n=3 Tax=Acinetobacter RepID=C6RSQ0 ACIRA
UniRef90 Q629K5 Replication protein n=1 Tax=Haemophilus somnus 129PT RepID=Q629K5 HAES1
UniRef90 F1YSK2 Replication and maintenance protein n=1 Tax=Acetobacter pomorum DM001 RepID=F1YSK2 9PROT
UniRef90 F8ERE5 Initiator RepB protein n=1 Tax=Runella slithyformis DSM 19594 RepID=F8ERE5 RUNSL
Enterococcus faecalis gi 32470454 ref NP 863355.1 RepE replication protein [Enterococcus faecalis]
UniRef90 A8UX05 Replication initiator protein n=1 Tax=Hydrogenivirga sp. 128-5-R1-1 RepID=A8UX05 9AQUI
UniRef90 E0WUJ6 Plasmid replication protein n=1 Tax=Candidatus Regiella insecticola LSR1 RepID=E0WUJ6 9ENTR
UniRef90 D2JC87 Replication protein Rep n=1 Tax=Staphylococcus epidermidis RepID=D2JC87 STAEP
UniRef90 Q663F3 Plasmid replication protein n=1 Tax=Yersinia pseudotuberculosis RepID=Q663F3 YERPS
UniRef90 H8G345 Initiator Replication family protein n=1 Tax=Pediococcus pentosaceus IE-3 RepID=H8G345 PEDPE
UniRef90 Q6TV38 Putative replication initiator protein n=1 Tax=Bacillus methanolicus RepID=Q6TV38 BACMT
UniRef90 Q93GF3 Rep n=12 Tax=Staphylococcus RepID=Q93GF3 STAAU
UniRef90 Q1PHH6 PCZ2.1 n=1 Tax=Planococcus sp. ZOYM RepID=Q1PHH6 9BACL
UniRef90 G2M6Z2 Replication initiation protein A n=2 Tax=Helicobacter pylori RepID=G2M6Z2 HELPX
UniRef90 F9H9U7 Initiator RepB protein n=1 Tax=Streptococcus mitis SK1073 RepID=F9H9U7 STRMT
UniRef90 C9C883 Replication initiation protein n=5 Tax=Enterococcus faecium RepID=C9C883 ENTFC
UniRef90 UPI0001BCE2A8 replication protein B n=1 Tax=Campylobacter fetus subsp. venerealis str. Azul-94 RepID=UPI0001BCE2A8
UniRef90 C6BEC1 Transcriptional regulator TrmB n=1 Tax=Ralstonia pickettii 12D RepID=C6BEC1 RALP1
UniRef90 C5QCS9 Replication protein Rep n=4 Tax=Staphylococcus RepID=C5QCS9 STAEP
UniRef90 Q3D3I5 Replication initiation protein putative n=4 Tax=Streptococcus agalactiae RepID=Q3D3I5 STRAG
UniRef90 F9H9U4 Initiator RepB protein Fragment n=1 Tax=Streptococcus mitis SK1073 RepID=F9H9U4 STRMT
UniRef90 E7GPP4 Putative uncharacterized protein n=1 Tax=Clostridium symbiosum WAL-14163 RepID=E7GPP4 CLOSY
UniRef90 C9N206 Putative replication protein rep n=1 Tax=Leptotrichia hofstadii F0254 RepID=C9N206 9FUSO
UniRef90 D2BP94 Plasmid replication initiator protein n=1 Tax=Lactococcus lactis subsp. lactis KF147 RepID=D2BP94 LACLK
UniRef90 O68171 Replication protein n=4 Tax=Lactococcus lactis RepID=O68171 9LACT
UniRef90 D2J5U9 Replication protein Rep n=1 Tax=Staphylococcus sp. 693-2 RepID=D2J5U9 9STAP
n/a gi 425246132 ref ZP 18639383.1 putative plasmid replication initiation protein [Escherichia coli 5905]
UniRef90 C4FFL8 Putative uncharacterized protein n=1 Tax=Bifidobacterium angulatum DSM 20098 = JCM 7096 RepID=C4FFL8 9BIFI
UniRef90 E6FIQ3 Conserved domain protein Fragment n=1 Tax=Enterococcus faecalis TX4244 RepID=E6FIQ3 ENTFL
UniRef90 Q2RYM1 Initiator replication protein RepB n=1 Tax=Salinibacter ruber DSM 13855 RepID=Q2RYM1 SALRD
UniRef90 E5CPV0 Replication protein n=4 Tax=Staphylococcus RepID=E5CPV0 9STAP
UniRef90 F2M3W8 Replication initiation factor family protein n=1 Tax=Lactobacillus amylovorus GRL 1112 RepID=F2M3W8 LACAR
UniRef90 C5Q196 Replication initiation protein n=34 Tax=Staphylococcus aureus RepID=C5Q196 STAAU
UniRef90 C0SQL8 Putative plasmid replication protein n=1 Tax=Lactobacillus brevis RepID=C0SQL8 LACBR
UniRef90 D1WIU1 Replication initiation family protein n=1 Tax=Staphylococcus epidermidis SK135 RepID=D1WIU1 STAEP
UniRef90 Q84EX4 Putative RepB protein n=1 Tax=Lactobacillus fermentum RepID=Q84EX4 LACFE
UniRef90 D0T0I5 DNA replication protein n=1 Tax=Acinetobacter lwoffii SH145 RepID=D0T0I5 ACILW
UniRef90 I0TKQ9 Initiator RepB protein n=1 Tax=Staphylococcus aureus subsp. aureus IS-K RepID=I0TKQ9 STAAU
UniRef90 I1EVF0 Uncharacterized protein n=2 Tax=Amphimedon queenslandica RepID=I1EVF0 AMPQE
UniRef90 D6DCB4 Protein involved in initiation of plasmid replication n=4 Tax=Bifidobacterium longum RepID=D6DCB4 BIFLN
UniRef90 C2RWN8 Putative uncharacterized protein n=1 Tax=Bacillus cereus BDRD-ST24 RepID=C2RWN8 BACCE
UniRef90 Q0QVX3 PNL18.2 p1 n=2 Tax=Neisseria lactamica RepID=Q0QVX3 NEILA
UniRef90 D1WM25 Replication initiation factor n=5 Tax=Staphylococcus epidermidis RepID=D1WM25 STAEP
UniRef90 D2J993 Replication and maintenance protein n=1 Tax=Staphylococcus aureus RepID=D2J993 STAAU
UniRef90 B9VWK0 Putative replication protein n=1 Tax=Pseudomonas sp. CG21 RepID=B9VWK0 9PSED
UniRef90 C6ZNM0 Replication initiation protein n=1 Tax=Staphylococcus simulans bv. staphylolyticus RepID=C6ZNM0 STAST
UniRef90 D0SRM6 Replicase n=1 Tax=Acinetobacter junii SH205 RepID=D0SRM6 ACIJU
UniRef90 B0VVE6 DNA replication protein n=2 Tax=Acinetobacter RepID=B0VVE6 ACIBS
UniRef90 G2MFU0 Replication initiation protein A n=1 Tax=Helicobacter pylori SNT49 RepID=G2MFU0 HELPX
UniRef90 P03064 Replication initiation protein n=29 Tax=root RepID=REPC STAAU
UniRef90 Q53J10 Replication initiation protein n=1 Tax=Staphylococcus sciuri subsp. sciuri RepID=Q53J10 STASC
UniRef90 F0VYI5 Putative replication protein rep n=2 Tax=Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069 RepID=F0VYI5 STRG2
UniRef90 O87353 Replication protein Rep n=1 Tax=Staphylococcus aureus RepID=O87353 STAAU
Enterococcus casseliflavus EC30 gi 257868406 ref ZP 05648059.1 plasmid replication initiation protein [Enterococcus casseliflavus EC30]
Veillonella sp. - Species A - Plasmid - I8.NODE 8 length 47555 cov 69.285919.1.47631 40 39.19 222 4e-47 170 UniRef90 C7UIY7
UniRef90 O69440 Replicase n=1 Tax=Leuconostoc mesenteroides subsp. mesenteroides RepID=O69440 LEUME
UniRef90 Q03N27 Plasmid replication initiation protein n=4 Tax=Lactobacillaceae RepID=Q03N27 LACBA
UniRef90 C9A1Q4 Replication protein n=4 Tax=Enterococcus RepID=C9A1Q4 ENTGA
UniRef90 H3WGV1 Replication initiation factor n=1 Tax=Staphylococcus epidermidis VCU128 RepID=H3WGV1 STAEP
UniRef90 UPI0001850A4B hypothetical protein Bcoam 03434 n=1 Tax=Bacillus coahuilensis m4-4 RepID=UPI0001850A4B
UniRef90 E4Z838 Replication protein n=1 Tax=Staphylococcus aureus RepID=E4Z838 STAAU
UniRef90 F0V0I9 Replication protein n=1 Tax=Staphylococcus hyicus RepID=F0V0I9 STAHY
UniRef90 E6IQC7 Replication initiation factor n=1 Tax=Enterococcus faecalis TX2141 RepID=E6IQC7 ENTFL
UniRef90 I0CE77 RepB n=1 Tax=Psychrobacter sp. DAB AL43B RepID=I0CE77 9GAMM
UniRef90 P19529 Replication initiation protein n=5 Tax=root RepID=REPN STAAU
UniRef90 H1L6V3 Response regulator receiver protein n=2 Tax=Geobacter metallireducens RepID=H1L6V3 GEOME
UniRef90 G6FG06 Putative uncharacterized protein n=1 Tax=Lactococcus lactis subsp. cremoris CNCM I-1631 RepID=G6FG06 LACLC
UniRef90 F7JS68 Putative uncharacterized protein n=1 Tax=Lachnospiraceae bacterium 1 4 56FAA RepID=F7JS68 9FIRM
UniRef90 C7D4Z3 Replication protein n=6 Tax=Enterococcus faecalis RepID=C7D4Z3 ENTFL
UniRef90 UPI000225B524 transcriptional regulator n=1 Tax=Ornithinibacillus scapharcae TW25 RepID=UPI000225B524
UniRef90 D0T8U0 Replicase n=1 Tax=Acinetobacter radioresistens SH164 RepID=D0T8U0 ACIRA
UniRef90 C7WV03 Initiator Replication protein n=5 Tax=Lactobacillales RepID=C7WV03 ENTFL
UniRef90 D4QMP5 Putative uncharacterized protein Fragment n=1 Tax=Enterococcus faecium E980 RepID=D4QMP5 ENTFC
UniRef90 Q9S392 FNR-like protein n=6 Tax=Lactococcus lactis RepID=Q9S392 9LACT
UniRef90 D6HBL4 Replication protein n=5 Tax=Staphylococcus aureus RepID=D6HBL4 STAAU
UniRef90 C2MUB6 Plasmid replication control protein n=1 Tax=Bacillus cereus m1293 RepID=C2MUB6 BACCE
UniRef90 Q8L2W1 Replication initiation protein A n=4 Tax=Helicobacter pylori RepID=Q8L2W1 HELPX
UniRef90 H0AIL5 Firmicute plasmid replication protein RepL n=6 Tax=Staphylococcus RepID=H0AIL5 STAAU
UniRef90 F9GWV6 Rep n=1 Tax=Haemophilus haemolyticus M21127 RepID=F9GWV6 HAEHA
UniRef90 E4I4K9 Initiator RepB protein n=5 Tax=Enterococcus faecium RepID=E4I4K9 ENTFC
UniRef90 C5QD25 Replication protein n=12 Tax=Bacilli RepID=C5QD25 STAEP
UniRef90 D4R2S4 Replication protein n=1 Tax=Enterococcus faecium E1162 RepID=D4R2S4 ENTFC
UniRef90 Q5QCI9 Replication initiator protein n=2 Tax=Leuconostoc citreum RepID=Q5QCI9 LEUCI
UniRef90 D4QSW4 Replication initiation protein n=1 Tax=Enterococcus faecium E1071 RepID=D4QSW4 ENTFC
UniRef90 G9SP94 Replication initiation protein Fragment n=1 Tax=Enterococcus faecium E4453 RepID=G9SP94 ENTFC
UniRef90 E3IJA7 Initiator RepB protein n=2 Tax=Geobacillus RepID=E3IJA7 GEOS0
UniRef90 H4AW83 Initiator Replication family protein Fragment n=1 Tax=Staphylococcus aureus subsp. aureus CIG1150 RepID=H4AW83 STAAU
UniRef90 E9DP28 Replication initiator protein n=3 Tax=Streptococcus RepID=E9DP28 9STRE
UniRef90 D2JCJ9 Replication initiation protein n=3 Tax=Staphylococcus epidermidis RepID=D2JCJ9 STAEP
UniRef90 Q8RSQ6 Replication protein n=2 Tax=Pasteurellaceae RepID=Q8RSQ6 9PAST
UniRef90 D0WD49 Initiator RepB protein n=10 Tax=Neisseria RepID=D0WD49 NEILA
UniRef90 B7KZW6 Putative uncharacterized protein n=1 Tax=Methylobacterium chloromethanicum CM4 RepID=B7KZW6 METC4
Halalkalicoccus jeotgali B3 gi 300712718 ref YP 003738531 1 orc1 cdc6 family replication initiation protein Halalkalicoccus jeotgali B3
UniRef90 E6JNP2 Replication initiation protein n=1 Tax=Staphylococcus epidermidis FRI909 RepID=E6JNP2 STAEP
UniRef90 C2Z1F6 Putative uncharacterized protein n=1 Tax=Bacillus cereus AH1271 RepID=C2Z1F6 BACCE
UniRef90 P97059 Putative replication initiation protein n=1 Tax=Streptococcus agalactiae RepID=P97059 STRAG
Enterococcus faecalis - Plasmid - I2.NODE 11 length 5143 cov 203.251801 4 100.00 240 2e-174 490 UniRef90 C7D4Z3
UniRef90 G9SSL5 Replication protein n=2 Tax=Enterococcus faecium RepID=G9SSL5 ENTFC
UniRef90 E5Y197 Initiator Replication protein n=3 Tax=Bifidobacterium RepID=E5Y197 9BIFI
UniRef90 G6W7A3 Replication initiation protein n=9 Tax=Streptococcus pneumoniae RepID=G6W7A3 STRPN
UniRef90 G6A5X5 Putative uncharacterized protein n=1 Tax=Streptococcus intermedius F0395 RepID=G6A5X5 STRIT
UniRef90 Q7MRU6 Putative uncharacterized protein n=1 Tax=Wolinella succinogenes RepID=Q7MRU6 WOLSU
UniRef90 E0H0K9 Initiator RepB protein Fragment n=1 Tax=Enterococcus faecalis TX0109 RepID=E0H0K9 ENTFL
UniRef90 C5Q197 Replication initiator protein n=34 Tax=Staphylococcus aureus RepID=C5Q197 STAAU
Streptococcus parasanguinis gi 229587268 ref YP 002860116.1 Rep [Streptococcus parasanguinis]
UniRef90 C1HTV0 RepA n=1 Tax=Escherichia sp. 3 2 53FAA RepID=C1HTV0 9ESCH
UniRef90 E6ZVQ4 Putative uncharacterized protein n=1 Tax=Sporisorium reilianum SRZ2 RepID=E6ZVQ4 SPORE
UniRef90 Q53621 Replication protein n=2 Tax=root RepID=Q53621 STAAU
UniRef90 G2HXL3 Putative uncharacterized protein n=1 Tax=Arcobacter sp. L RepID=G2HXL3 9PROT
UniRef90 Q8KSC4 Rm protein n=1 Tax=Bacillus thuringiensis serovar entomocidus RepID=Q8KSC4 BACTE
UniRef90 Q3EUV0 Hypothetical cytosolic protein n=2 Tax=Bacillus thuringiensis RepID=Q3EUV0 BACTI
UniRef90 G5GSC4 Putative uncharacterized protein n=6 Tax=Selenomonas infelix ATCC 43532 RepID=G5GSC4 9FIRM
UniRef90 F5SU89 Replication protein n=1 Tax=Psychrobacter sp. 1501 2011 RepID=F5SU89 9GAMM
UniRef90 G2M6Y5 Putative uncharacterized protein n=1 Tax=Helicobacter pylori Puno120 RepID=G2M6Y5 HELPX
Enterococcus faecalis DS5 gi 256959310 ref ZP 05563481.1 initiator Replication protein [Enterococcus faecalis DS5]
UniRef90 Q4L2Y4 Replication protein Rep n=3 Tax=Staphylococcus RepID=Q4L2Y4 STAHJ
UniRef90 Q9ZN83 Replication protein n=1 Tax=Streptococcus equinus RepID=Q9ZN83 STREI
UniRef90 D2J6M2 Replication protein Rep n=2 Tax=Staphylococcus RepID=D2J6M2 9STAP
UniRef90 Q6WAV8 RepB n=1 Tax=Avibacterium paragallinarum RepID=Q6WAV8 HAEGA
UniRef90 H7G1Q9 Replication initiator protein n=1 Tax=Lactobacillus salivarius SMXD51 RepID=H7G1Q9 9LACO
Staphylococcus aureus gi 188039009 ref YP 001901401.1 rep protein [Staphylococcus aureus]
UniRef90 C9C889 Initiator replication protein n=5 Tax=Enterococcus faecium RepID=C9C889 ENTFC
UniRef90 E0GZ88 Replication initiation factor n=2 Tax=Enterococcus faecalis RepID=E0GZ88 ENTFL
UniRef90 H3UQF8 Initiator RepB protein n=5 Tax=Staphylococcus epidermidis RepID=H3UQF8 STAEP
UniRef90 C8PWL8 DNA replication protein n=1 Tax=Enhydrobacter aerosaccus SK60 RepID=C8PWL8 9GAMM
UniRef90 Q9ZF12 Putative uncharacterized protein ORF1 n=1 Tax=Oenococcus oeni RepID=Q9ZF12 OENOE
UniRef90 H7VRZ9 Plasmid replication control protein n=4 Tax=Campylobacter coli RepID=H7VRZ9 CAMCO
UniRef90 H7SJ62 Putative replication protein B n=3 Tax=Campylobacter RepID=H7SJ62 CAMCO
UniRef90 C2PPD1 Replication and maintenance protein n=6 Tax=Bacillus cereus RepID=C2PPD1 BACCE
UniRef90 Q2HWD8 Replication protein n=1 Tax=Tetragenococcus halophilus RepID=Q2HWD8 TETHA
UniRef90 C5QCS7 Replication protein n=7 Tax=Staphylococcus RepID=C5QCS7 STAEP
UniRef90 E8K922 Replication protein Rep n=1 Tax=Streptococcus parasanguinis ATCC 903 RepID=E8K922 STRPA
UniRef90 F2CAR2 Replication initiator protein n=26 Tax=Streptococcus RepID=F2CAR2 STRSA
UniRef90 F3STJ7 Replication initiation factor n=2 Tax=Bacteria RepID=F3STJ7 STAWA
UniRef90 E6FIQ5 Replication initiation factor Fragment n=1 Tax=Enterococcus faecalis TX4244 RepID=E6FIQ5 ENTFL
UniRef90 H4GDU5 Replication initiation family protein n=1 Tax=Staphylococcus aureus subsp. aureus IS-189 RepID=H4GDU5 STAAU
UniRef90 E8SFH9 Replication initiation protein topisomerase n=2 Tax=Staphylococcus pseudintermedius RepID=E8SFH9 STAPH
UniRef90 Q848T4 Replication inititation protein RepM n=1 Tax=Enterococcus faecium RepID=Q848T4 ENTFC
UniRef90 H4HIC6 Initiator Replication family protein n=1 Tax=Staphylococcus aureus subsp. aureus CIG290 RepID=H4HIC6 STAAU
UniRef90 Q93T03 Replication protein n=1 Tax=Lactobacillus fermentum RepID=Q93T03 LACFE
UniRef90 G9SNZ6 Replication initiation protein Fragment n=1 Tax=Enterococcus faecium E4453 RepID=G9SNZ6 ENTFC
UniRef90 D0T0G9 Replicase n=2 Tax=Acinetobacter RepID=D0T0G9 ACILW
UniRef90 Q9ZIR9 Replication protein A n=1 Tax=Helicobacter pylori RepID=Q9ZIR9 HELPX
UniRef90 P95772 RepL n=1 Tax=Staphylococcus lugdunensis RepID=P95772 STALU
UniRef90 E6L7J0 Putative uncharacterized protein n=2 Tax=Campylobacter upsaliensis RepID=E6L7J0 CAMUP
UniRef90 H8LFE1 Replication initiation factor n=3 Tax=Enterococcus faecium RepID=H8LFE1 ENTFU
Enterococcus faecium 1 231 410 gi 257892067 ref ZP 05671720.1 initiator replication protein [Enterococcus faecium 1 231 410]
UniRef90 B9M1K3 Response regulator receiver protein n=1 Tax=Geobacter sp. FRC-32 RepID=B9M1K3 GEOSF
UniRef90 A0ES89 RepA n=10 Tax=Bifidobacterium RepID=A0ES89 BIFLN
UniRef90 B5Z5Q1 Replication and maintenance protein n=3 Tax=Bacillus cereus RepID=B5Z5Q1 BACCE
UniRef90 D0U573 Replication initiation protein RepB-like protein n=1 Tax=Psychrobacter sp. J466 RepID=D0U573 9GAMM
Enterococcus faecalis 62 gi 384519691 ref YP 005706994.1 initiator Replication family protein [Enterococcus faecalis 62]
UniRef90 Q68BL4 Replication protein n=1 Tax=Lactobacillus casei RepID=Q68BL4 LACCA
UniRef90 C9CG04 Predicted protein n=1 Tax=Enterococcus faecium 1 230 933 RepID=C9CG04 ENTFC
UniRef90 D0UHC6 Putative replicase Fragment n=1 Tax=Acinetobacter baumannii RepID=D0UHC6 ACIBA
UniRef90 Q48654 RepB protein n=1 Tax=Lactococcus lactis RepID=Q48654 9LACT
UniRef90 Q8SVH3 Putative uncharacterized protein ECU05 1300 n=1 Tax=Encephalitozoon cuniculi GB-M1 RepID=Q8SVH3 ENCCU
UniRef90 E4IMU5 Initiator RepB protein Fragment n=1 Tax=Enterococcus faecium TX0082 RepID=E4IMU5 ENTFC
UniRef90 Q2A6M6 Replication protein B n=2 Tax=Pasteurellaceae RepID=Q2A6M6 PASTR
UniRef90 E1PXW8 Replication initiation protein A n=1 Tax=Helicobacter pylori Sat464 RepID=E1PXW8 HELPT
UniRef90 H4GDG4 Replication initiation factor domain protein Fragment n=1 Tax=Staphylococcus aureus subsp. aureus IS-189 RepID=H4GDG4 STAAU
UniRef90 F7STL2 Replication protein n=1 Tax=Halomonas sp. TD01 RepID=F7STL2 9GAMM
UniRef90 C9BRW7 Replication protein n=6 Tax=Enterococcus faecium RepID=C9BRW7 ENTFC
UniRef90 Q8GN33 Probable replication protein rep n=1 Tax=Bifidobacterium longum NCC2705 RepID=REP BIFLO
UniRef90 D4XK18 DNA replication protein n=3 Tax=Acinetobacter RepID=D4XK18 ACIHA
UniRef90 C3AXF3 Initiator RepB protein n=2 Tax=Bacillus mycoides RepID=C3AXF3 BACMY
UniRef90 E3VVN6 Replication protein A1 n=2 Tax=Lactobacillus RepID=E3VVN6 LACCA
UniRef90 F6ITA7 Replication protein A n=6 Tax=Lactobacillaceae RepID=F6ITA7 LACPE
UniRef90 G4XGN6 Replication protein n=2 Tax=Selenomonas ruminantium RepID=G4XGN6 SELRU
UniRef90 Q5JGN9 Riboflavin kinase n=1 Tax=Thermococcus kodakarensis KOD1 RepID=RIFK PYRKO
UniRef90 D4FMJ6 Replication protein Rep n=1 Tax=Staphylococcus epidermidis M23864 W2 grey RepID=D4FMJ6 STAEP
Staphylococcus simulans bv. staphylolyticus gi 254732689 ref YP 003084326.1 replication initiation protein [Staphylococcus simulans bv. staphylolyticus]
UniRef90 D0T8W6 DNA replication protein n=1 Tax=Acinetobacter radioresistens SH164 RepID=D0T8W6 ACIRA
0.987
0.459
0.646
0.622
0.988
1
0.998
0.913
0.519
0.863
0.933
1
0.923
0.999
1
0.997
0.944
0.89
0.752
0.498
1
0.826
0.991
0.996
0.991
0.981
0.735
0.915
0.121
0.884
1
0.895
0.824
0.996
0.988
1
0.973
0.978
0.748
0.935
1
0.936
0.442
0.998
0.911
0.793
0.014
0.841
0.938
0.778
0.897
0.845
0.46
0.817
0.639
0.997
0.416
0.668
0.999
0.885
0.687
0.993
0.629
0
0.663
0.972
0.625
0.905
0.967
0.906
0.07
0.621
0.854
0.8780.979
0.904
0.953
0.119
1
0.776
0.985
0.906
0.978
0.768
0.711
0.655
0.807
0
1
0.715
0.077
0.685
0.917
0.995
0.722
0.697
1
0.997
0.723
0.759
0.83
0.999
0.547
1
0.993
0.98
0.786
0.331
1
0.764
0.899
0.981
0.125
0.521
0.984
0.703 0.585
0.735
0.995
0.424
0.497
0.698
0.816
0.999
0.997
1
0.813
0.71
0.079
1
0.95
0.477
1
0.957
1
0.57
0.776
1
0.717
0.822
0.756
0.43
0.999
0.904
0.595
0.428
0.944
0.992
1
1
1
1
0.453
0.846
0.897
0.442
0.004
0.68
0.785
0.908
0.987
0.957
0.339
0.76
0.708
0.897
0.967
1
0.192
0.709
0.755
0.823
0.706
0.99
0.847
0.961
0.939
0.998
0.765
0.795
0.999
0.987
0.987
0.999
0.979
0.543
0.9
1
0.939
0.396
0.891
0.672
0.994
0.967
0.929
0.938
0.609
1
1
1
0.175
0.913
0.93
0.577
0.91
0.88
0.952
0.995
0.74
0.728
0.834
0.993
0.386
0.951
0.983
0.992
0.526
0.996
0.108
0.189
0.988
0.974
0.892
1
0
0.73
0.966
0.23
0.934
0
0.855
0.875
0.772
0.947
0.321
0.866
0.987
0.404
0.771
0.532
0.991
0.979
0.31
0.61
0.986
0.852
0.749
0.959
0.97
0.533
0.8
0.366
0.984
1
1
0.968
0.814
0.936
0.203
0
0.986
0.934
0.872
0.572
0.843
0.76
0.991
0.997
0.563
0.403
0.837
0.58
0.957
0.894
0.998
0.684
1
0.223
0.191
1
1
0.998
1
0.483
0.725
0.972
0.64
0.904
0.757
0.7180.485
0.876
0.844
0.807
0
0.997
0.853
0.282
0.763
0.748
0.882
0.9
0.74
0.897
0.92
0.925
0.827
0.952
0.959
0.612
0.969
0.978
0.977
0.442
0.729
0.937
0.438
0.603
0.992
0.991
0.52
1
0.912
1
0.096
0.999
0.076
0.968
0.116
1
0.984
0.187
0.3
0.139
0.531
0.996
0.97
1
0.907
0.724
0.77
0.859
0.929
0.993
0.89
0.497
0.937
0.983
0.842
0.927
0.911
0.993
0.846
0.14
0.771
0.992
1
0.63
0.993
0.907
0.933
0.985
0.851
0.925
0.976
0.873
1
0.68
0.148
0.836
0.192
0.883
0.964
0.401
1
0.806
0.848
0.442
0.368
0.97
0.962
0.507
1
0.444
0.52
0.993
0.901
0.791
- Supplemental 4 -
Supplemental Figure 4 - Phylogenetic Analysis of the Catalytic Subunits of the Nitrate Reductase and Dimethyl Dulfoxide (DMSO) Reductase Superfamilies Genes newly assigned to the nitrate reductase and DMSO reductase superfamilies (this study) are shown in red.
Cytoplasmic Nitrite oxidoreductase (NxrA)Pseudomonas stutzeri
Pseudomonas fluorescens
Escherichia coli
Halomonas maura
Aeropyrum pernix
Pyrobaculum aerophilum
Haloarcula marismortui
Haloferax mediterranei
Haemophilus influenza sp P45004
Actinobacillus succinogenes
Escherichia coli sp P18775
Alkalilimnicola ehrlichii ABI5
ArxA Ectothiorhodospira sp PHS
Halorhodospira halophila
Alternative complex III (ACTB)Wolinella succinogenes
Escherichia coli
99
9558
97
100
98
9998
79
96
97
99
99
76
49
71
51
91
85
79
95
100
91
90
100
81100
82
99
81
80
45
76
0.5
Varibaculum cambriense Nar
Varibaculum cambriense DmsA
Periplasmic Nitrite oxidoreductase (NxrA)
Nitrate reductase (NarG)
Dimethyl Sulfoxide reductase (DmsA)
Trimethylamine N-oxide reductase (TorA)Tetrathionate reductase (TtrA)
Thiosulphate/polysulphide reductases (PhsA and PsrA)Arsenate reductase (ArrA)
Anaerobic arsenite oxidase (ArxA)
Formate Dehydrogenase (FdhA)Formate Dehydrogenase (FdhN)
Periplasmic and Assimilatory Nitrate reductase (NapA/NarB/NasA)Arsenite oxidase (AroA/AroA-like)
- Supplemental 5 -
Supplemental Figure 5 - Relative Abundance of Varibaculum in Human Microbiome Project Data The relative abundance of Varibaculum was determined for each sample analyzed by the Human Microbiome Project. These samples were characterized by sequencing the V13 (a) and V35 (b) regions of the 16S rRNA gene.
Rel
ativ
e A
bund
ance
(% T
otal
Rea
ds)
0.0
0.5
1.0
1.5
2.0
2.5
OTU 97 11349 Root;p Actinobacteria;c Actinobacteria;o Actinomycetales;f Actinomycetaceae;g VaribaculumOTU 97 1933 Root;p Actinobacteria;c Actinobacteria;o Actinomycetales;f Actinomycetaceae;g VaribaculumOTU 97 29022 Root;p Actinobacteria;c Actinobacteria;o Actinomycetales;f Actinomycetaceae;g Varibaculum
Rel
ativ
e A
bund
ance
(% T
otal
Rea
ds)
0.0
0.5
1.0
1.5
2.0
2.5
OTU_97.11029 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.15054 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.1737 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.1786 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.36329 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.4074 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum OTU_97.4225 Root;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum
a)
b)
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:7
6414
3897
sam
ple:
7000
2387
6si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:764
1438
97 sa
mpl
e:70
0023
876
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:7
6489
2411
sam
ple:
7000
3834
2si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:764
8924
11 sa
mpl
e:70
0038
342
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:763
7595
25 sa
mpl
e:70
0023
818
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:763
7595
25 sa
mpl
e:70
0023
818
site
:Rig
ht A
ntec
ubita
l fos
sa p
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nt:7
6509
4712
sam
ple:
7001
0361
9si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:765
0947
12 sa
mpl
e:70
0103
619
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:1
6084
5950
sam
ple:
7000
9584
8si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:160
8459
50 sa
mpl
e:70
0095
848
site
:Lef
t Ret
roau
ricul
ar c
reas
e pa
tient
:764
5889
59 sa
mpl
e:70
0024
733
site
:Lef
t Ret
roau
ricul
ar c
reas
e pa
tient
:764
5889
59 sa
mpl
e:70
0024
733
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:764
1438
97 sa
mpl
e:70
0023
875
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:764
1438
97 sa
mpl
e:70
0023
875
site
:Mid
vag
ina
patie
nt:7
6384
0445
sam
ple:
7001
1412
2si
te:M
id v
agin
a pa
tient
:763
8404
45 sa
mpl
e:70
0114
122
site:V
agin
al in
troitu
s pat
ient
:763
7595
25 sa
mpl
e:70
0103
669
site:V
agin
al in
troitu
s pat
ient
:763
7595
25 sa
mpl
e:70
0103
669
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:7
6434
6198
sam
ple:
7000
2423
8si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:764
3461
98 sa
mpl
e:70
0024
238
site:V
agin
al in
troitu
s pat
ient
:764
0629
76 sa
mpl
e:70
0023
640
site:V
agin
al in
troitu
s pat
ient
:764
0629
76 sa
mpl
e:70
0023
640
site:V
agin
al in
troitu
s pat
ient
:160
5829
58 sa
mpl
e:70
0108
549
site:V
agin
al in
troitu
s pat
ient
:160
5829
58 sa
mpl
e:70
0108
549
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:160
6031
88 sa
mpl
e:70
0034
923
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:160
6031
88 sa
mpl
e:70
0034
923
site
:Mid
vag
ina
patie
nt:4
1451
9462
sam
ple:
7001
1183
1si
te:M
id v
agin
a pa
tient
:414
5194
62 sa
mpl
e:70
0111
831
site
:Mid
vag
ina
patie
nt:6
5085
3796
sam
ple:
7000
9888
6si
te:M
id v
agin
a pa
tient
:650
8537
96 sa
mpl
e:70
0098
886
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:7
6525
6553
sam
ple:
7000
3729
8si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:765
2565
53 sa
mpl
e:70
0037
298
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:160
8661
80 sa
mpl
e:70
0109
333
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:160
8661
80 sa
mpl
e:70
0109
333
site:V
agin
al in
troitu
s pat
ient
:650
8537
96 sa
mpl
e:70
0110
372
site:V
agin
al in
troitu
s pat
ient
:650
8537
96 sa
mpl
e:70
0110
372
site
:Mid
vag
ina
patie
nt:1
5900
5010
sam
ple:
7000
1605
6si
te:M
id v
agin
a pa
tient
:159
0050
10 sa
mpl
e:70
0016
056
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:5
1781
0313
sam
ple:
7001
0641
0si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:517
8103
13 sa
mpl
e:70
0106
410
site
:Ant
erio
r nar
es p
atie
nt:1
6050
2038
sam
ple:
7000
3425
0si
te:A
nter
ior n
ares
pat
ient
:160
5020
38 sa
mpl
e:70
0034
250
site:V
agin
al in
troitu
s pat
ient
:160
7043
39 sa
mpl
e:70
0108
237
site:V
agin
al in
troitu
s pat
ient
:160
7043
39 sa
mpl
e:70
0108
237
site
:Lef
t Ret
roau
ricul
ar c
reas
e pa
tient
:161
4730
83 sa
mpl
e:70
0110
235
site
:Lef
t Ret
roau
ricul
ar c
reas
e pa
tient
:161
4730
83 sa
mpl
e:70
0110
235
site:V
agin
al in
troitu
s pat
ient
:160
6436
49 sa
mpl
e:70
0095
232
site:V
agin
al in
troitu
s pat
ient
:160
6436
49 sa
mpl
e:70
0095
232
site:V
agin
al in
troitu
s pat
ient
:763
7212
71 sa
mpl
e:70
0111
315
site:V
agin
al in
troitu
s pat
ient
:763
7212
71 sa
mpl
e:70
0111
315
site:V
agin
al in
troitu
s pat
ient
:763
4560
73 sa
mpl
e:70
0105
682
site:V
agin
al in
troitu
s pat
ient
:763
4560
73 sa
mpl
e:70
0105
682
site
:Rig
ht A
ntec
ubita
l fos
sa p
atie
nt:1
6058
2958
sam
ple:
7000
3478
9si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:160
5829
58 sa
mpl
e:70
0034
789
site:V
agin
al in
troitu
s pat
ient
:158
2362
65 sa
mpl
e:70
0098
951
site:V
agin
al in
troitu
s pat
ient
:158
2362
65 sa
mpl
e:70
0098
951
site:V
agin
al in
troitu
s pat
ient
:763
8404
45 sa
mpl
e:70
0023
243
site:V
agin
al in
troitu
s pat
ient
:763
8404
45 sa
mpl
e:70
0023
243
site
:Lef
t Ant
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ital f
ossa
pat
ient
:764
3057
38 sa
mpl
e:70
0037
448
site
:Lef
t Ant
ecub
ital f
ossa
pat
ient
:764
3057
38 sa
mpl
e:70
0037
448
site:V
agin
al in
troitu
s pat
ient
:158
2767
26 sa
mpl
e:70
0099
078
site:V
agin
al in
troitu
s pat
ient
:158
2767
26 sa
mpl
e:70
0099
078
site:V
agin
al in
troitu
s pat
ient
:370
4259
37 sa
mpl
e:70
0098
688
site:V
agin
al in
troitu
s pat
ient
:370
4259
37 sa
mpl
e:70
0098
688
site
:Mid
vag
ina
patie
nt:7
6375
9525
sam
ple:
7001
0367
0si
te:M
id v
agin
a pa
tient
:763
7595
25 sa
mpl
e:70
0103
670
site:V
agin
al in
troitu
s pat
ient
:764
6496
50 sa
mpl
e:70
0024
852
site:V
agin
al in
troitu
s pat
ient
:764
6496
50 sa
mpl
e:70
0024
852
site
:Mid
vag
ina
patie
nt:1
5827
6726
sam
ple:
7000
9907
9si
te:M
id v
agin
a pa
tient
:158
2767
26 sa
mpl
e:70
0099
079
site:V
agin
al in
troitu
s pat
ient
:638
7544
22 sa
mpl
e:70
0109
249
site:V
agin
al in
troitu
s pat
ient
:638
7544
22 sa
mpl
e:70
0109
249
site
:Mid
vag
ina
patie
nt:1
6100
7791
sam
ple:
7001
0897
4si
te:M
id v
agin
a pa
tient
:161
0077
91 sa
mpl
e:70
0108
974
site
:Rig
ht A
ntec
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l fos
sa p
atie
nt:1
6096
7330
sam
ple:
7001
0849
0si
te:R
ight
Ant
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ital f
ossa
pat
ient
:160
9673
30 sa
mpl
e:70
0108
490
site
:Rig
ht A
ntec
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l fos
sa p
atie
nt:4
1451
9462
sam
ple:
7001
1182
8si
te:R
ight
Ant
ecub
ital f
ossa
pat
ient
:414
5194
62 sa
mpl
e:70
0111
828
site
:Mid
vag
ina
patie
nt:7
6384
0445
sam
ple:
7000
2324
4si
te:M
id v
agin
a pa
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:763
8404
45 sa
mpl
e:70
0023
244
site:V
agin
al in
troitu
s pat
ient
:763
8404
45 sa
mpl
e:70
0114
121
site:V
agin
al in
troitu
s pat
ient
:763
8404
45 sa
mpl
e:70
0114
121
site
:Mid
vag
ina
patie
nt:1
5833
7416
sam
ple:
7000
9785
7si
te:M
id v
agin
a pa
tient
:158
3374
16 sa
mpl
e:70
0097
857
site
:Mid
vag
ina
patie
nt:1
6147
3083
sam
ple:
7000
9750
1si
te:M
id v
agin
a pa
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:161
4730
83 sa
mpl
e:70
0097
501
site
:Rig
ht A
ntec
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sa p
atie
nt:1
5949
0532
sam
ple:
7001
0237
3si
te:R
ight
Ant
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ital f
ossa
pat
ient
:159
4905
32 sa
mpl
e:70
0102
373
site:V
agin
al in
troitu
s pat
ient
:650
8537
96 sa
mpl
e:70
0098
885
site:V
agin
al in
troitu
s pat
ient
:650
8537
96 sa
mpl
e:70
0098
885
site:V
agin
al in
troitu
s pat
ient
:160
3199
67 sa
mpl
e:70
0109
640
site:V
agin
al in
troitu
s pat
ient
:160
3199
67 sa
mpl
e:70
0109
640
site:V
agin
al in
troitu
s pat
ient
:158
7420
18 sa
mpl
e:70
0015
236
site:V
agin
al in
troitu
s pat
ient
:158
7420
18 sa
mpl
e:70
0015
236
site
:Rig
ht R
etro
auric
ular
cre
ase
patie
nt:1
6147
3083
sam
ple:
7001
1023
6si
te:R
ight
Ret
roau
ricul
ar c
reas
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tient
:161
4730
83 sa
mpl
e:70
0110
236
site:V
agin
al in
troitu
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ient
:763
7190
65 sa
mpl
e:70
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396
site:V
agin
al in
troitu
s pat
ient
:763
7190
65 sa
mpl
e:70
0023
396
site
:Mid
vag
ina
patie
nt:7
3705
2003
sam
ple:
7001
0606
3si
te:M
id v
agin
a pa
tient
:737
0520
03 sa
mpl
e:70
0106
063
site
:Rig
ht A
ntec
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sa p
atie
nt:4
1451
9462
sam
ple:
7001
0213
0si
te:R
ight
Ant
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ital f
ossa
pat
ient
:414
5194
62 sa
mpl
e:70
0102
130
site
:Ant
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r nar
es p
atie
nt:7
6495
3101
sam
ple:
7001
1438
6si
te:A
nter
ior n
ares
pat
ient
:764
9531
01 sa
mpl
e:70
0114
386
site
:Mid
vag
ina
patie
nt:1
6064
3649
sam
ple:
7000
9523
3si
te:M
id v
agin
a pa
tient
:160
6436
49 sa
mpl
e:70
0095
233
site
:Mid
vag
ina
patie
nt:1
6149
3313
sam
ple:
7000
9743
5si
te:M
id v
agin
a pa
tient
:161
4933
13 sa
mpl
e:70
0097
435
site
:Rig
ht R
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auric
ular
cre
ase
patie
nt:1
6147
3083
sam
ple:
7000
9749
6si
te:R
ight
Ret
roau
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ar c
reas
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tient
:161
4730
83 sa
mpl
e:70
0097
496
site
:Ant
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es p
atie
nt:7
6450
8039
sam
ple:
7000
2468
8si
te:A
nter
ior n
ares
pat
ient
:764
5080
39 sa
mpl
e:70
0024
688
site
:Ant
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r nar
es p
atie
nt:1
6005
6975
sam
ple:
7001
0794
8si
te:A
nter
ior n
ares
pat
ient
:160
0569
75 sa
mpl
e:70
0107
948
site
:Mid
vag
ina
patie
nt:7
6418
4357
sam
ple:
7000
2397
4si
te:M
id v
agin
a pa
tient
:764
1843
57 sa
mpl
e:70
0023
974
site
:Sto
ol p
atie
nt:7
6414
3897
sam
ple:
7000
2387
2si
te:S
tool
pat
ient
:764
1438
97 sa
mpl
e:70
0023
872
site
:Mid
vag
ina
patie
nt:7
6414
3897
sam
ple:
7000
2387
9si
te:M
id v
agin
a pa
tient
:764
1438
97 sa
mpl
e:70
0023
879
site
:Rig
ht A
ntec
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sa p
atie
nt:1
5928
8231
sam
ple:
7001
0286
5si
te:R
ight
Ant
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pat
ient
:159
2882
31 sa
mpl
e:70
0102
865
site
:Lef
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ient
:638
7544
22 sa
mpl
e:70
0109
246
site
:Lef
t Ant
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pat
ient
:638
7544
22 sa
mpl
e:70
0109
246
site:V
agin
al in
troitu
s pat
ient
:465
5787
59 sa
mpl
e:70
0105
988
site:V
agin
al in
troitu
s pat
ient
:465
5787
59 sa
mpl
e:70
0105
988
site
:Mid
vag
ina
patie
nt:6
5085
3796
sam
ple:
7001
1037
3si
te:M
id v
agin
a pa
tient
:650
8537
96 sa
mpl
e:70
0110
373
site
:Lef
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pat
ient
:160
3199
67 sa
mpl
e:70
0109
637
site
:Lef
t Ant
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pat
ient
:160
3199
67 sa
mpl
e:70
0109
637
site
:Rig
ht R
etro
auric
ular
cre
ase
patie
nt:8
7284
8689
sam
ple:
7001
1176
0si
te:R
ight
Ret
roau
ricul
ar c
reas
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tient
:872
8486
89 sa
mpl
e:70
0111
760
site:V
agin
al in
troitu
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ient
:763
7595
25 sa
mpl
e:70
0023
821
site:V
agin
al in
troitu
s pat
ient
:763
7595
25 sa
mpl
e:70
0023
821
site:V
agin
al in
troitu
s pat
ient
:256
7894
58 sa
mpl
e:70
0105
093
site:V
agin
al in
troitu
s pat
ient
:256
7894
58 sa
mpl
e:70
0105
093
site:V
agin
al in
troitu
s pat
ient
:763
6988
34 sa
mpl
e:70
0023
067
site:V
agin
al in
troitu
s pat
ient
:763
6988
34 sa
mpl
e:70
0023
067
site
:Mid
vag
ina
patie
nt:5
3324
7696
sam
ple:
7000
9812
9si
te:M
id v
agin
a pa
tient
:533
2476
96 sa
mpl
e:70
0098
129
site:V
agin
al in
troitu
s pat
ient
:764
8114
90 sa
mpl
e:70
0106
873
site:V
agin
al in
troitu
s pat
ient
:764
8114
90 sa
mpl
e:70
0106
873
site:V
agin
al in
troitu
s pat
ient
:764
3461
98 sa
mpl
e:70
0113
548
site:V
agin
al in
troitu
s pat
ient
:764
3461
98 sa
mpl
e:70
0113
548
site:V
agin
al in
troitu
s pat
ient
:160
6436
49 sa
mpl
e:70
0110
108
site:V
agin
al in
troitu
s pat
ient
:160
6436
49 sa
mpl
e:70
0110
108
site:P
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orni
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:158
2564
96 sa
mpl
e:70
0097
709
site:P
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rior f
orni
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tient
:158
2564
96 sa
mpl
e:70
0097
709
site:V
agin
al in
troitu
s pat
ient
:160
5020
38 sa
mpl
e:70
0034
251
site:V
agin
al in
troitu
s pat
ient
:160
5020
38 sa
mpl
e:70
0034
251
site
:Mid
vag
ina
patie
nt:1
5898
4779
sam
ple:
7000
1576
2si
te:M
id v
agin
a pa
tient
:158
9847
79 sa
mpl
e:70
0015
762
site
:Mid
vag
ina
patie
nt:1
6064
3649
sam
ple:
7001
1010
9si
te:M
id v
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:160
6436
49 sa
mpl
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0110
109
site
:Lef
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ient
:604
8120
05 sa
mpl
e:70
0110
435
site
:Lef
t Ant
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pat
ient
:604
8120
05 sa
mpl
e:70
0110
435
site
:Lef
t Ret
roau
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:160
8459
50 sa
mpl
e:70
0109
520
site
:Lef
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roau
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:160
8459
50 sa
mpl
e:70
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520
site:P
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:158
4587
97 sa
mpl
e:70
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776
site:P
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:158
4587
97 sa
mpl
e:70
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776
site
:Lef
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:160
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39 sa
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232
site
:Lef
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tient
:160
7043
39 sa
mpl
e:70
0108
232
site
:Lef
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pat
ient
:161
4730
83 sa
mpl
e:70
0110
237
site
:Lef
t Ant
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pat
ient
:161
4730
83 sa
mpl
e:70
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237
site:V
agin
al in
troitu
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:158
4587
97 sa
mpl
e:70
0014
770
site:V
agin
al in
troitu
s pat
ient
:158
4587
97 sa
mpl
e:70
0014
770
site:V
agin
al in
troitu
s pat
ient
:159
0859
30 sa
mpl
e:70
0016
498
site:V
agin
al in
troitu
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ient
:159
0859
30 sa
mpl
e:70
0016
498
site
:Mid
vag
ina
patie
nt:1
3290
2142
sam
ple:
7001
0348
6si
te:M
id v
agin
a pa
tient
:132
9021
42 sa
mpl
e:70
0103
486
site:P
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rior f
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tient
:159
7332
94 sa
mpl
e:70
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151
site:P
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tient
:159
7332
94 sa
mpl
e:70
0033
151
site:P
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tient
:158
7420
18 sa
mpl
e:70
0015
242
site:P
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:158
7420
18 sa
mpl
e:70
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242
site
:Lef
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pat
ient
:158
9847
79 sa
mpl
e:70
0110
770
site
:Lef
t Ant
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pat
ient
:158
9847
79 sa
mpl
e:70
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770
site:V
agin
al in
troitu
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ient
:159
4703
02 sa
mpl
e:70
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493
site:V
agin
al in
troitu
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ient
:159
4703
02 sa
mpl
e:70
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493
site:P
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:132
9021
42 sa
mpl
e:70
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487
site:P
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tient
:132
9021
42 sa
mpl
e:70
0103
487
site
: Ant
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nt: 1
5924
7771
sam
ple:
700
0330
33si
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id v
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: 763
8404
45 sa
mpl
e: 7
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4122
site
: Rig
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nt: 7
6390
1136
sam
ple:
700
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: 764
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01 sa
mpl
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4385
site:
Vag
inal
intro
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nt: 7
6345
6073
sam
ple:
700
1056
82sit
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agin
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troitu
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ient
: 763
8404
45 sa
mpl
e: 7
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4121
site:
Vag
inal
intro
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nt: 7
6418
4357
sam
ple:
700
1060
15si
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ntec
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0005
sam
ple:
700
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: 159
2275
41 sa
mpl
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2602
site:
Vag
inal
intro
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atie
nt: 7
6406
2976
sam
ple:
700
1140
64sit
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agin
al in
troitu
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ient
: 763
7595
25 sa
mpl
e: 7
0002
3821
site:
Vag
inal
intro
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atie
nt: 1
6147
3083
sam
ple:
700
1102
40sit
e: Po
ster
ior f
orni
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tient
: 375
4504
39 sa
mpl
e: 7
0011
4806
site
: Mid
vag
ina
patie
nt: 1
5827
6726
sam
ple:
700
0990
79si
te: R
ight
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: 763
5976
84 sa
mpl
e: 7
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8009
site:
Vag
inal
intro
itus p
atie
nt: 1
5823
6265
sam
ple:
700
0989
51sit
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agin
al in
troitu
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ient
: 764
1438
97 sa
mpl
e: 7
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6806
site:
Vag
inal
intro
itus p
atie
nt: 1
5874
2018
sam
ple:
700
0152
36sit
e: V
agin
al in
troitu
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ient
: 159
0050
10 sa
mpl
e: 7
0001
6055
site:
Vag
inal
intro
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atie
nt: 7
6464
9650
sam
ple:
700
0248
52si
te: M
id v
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: 159
0050
10 sa
mpl
e: 7
0001
6056
site
: Ant
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nt: 7
6414
3897
sam
ple:
700
1068
05sit
e: V
agin
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troitu
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ient
: 158
2767
26 sa
mpl
e: 7
0009
9078
site
: Mid
vag
ina
patie
nt: 5
5335
9145
sam
ple:
700
1064
92si
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atie
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6180
sam
ple:
700
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33si
te: R
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Ret
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- Supplemental 6 -
Supplemental Tables Supplemental Table 1 - ESOM bins. Assembly and classification of scaffolds clustered into bins using an ESOM. Each bin was compared to a sequenced microbial genome by identifying orthologs. Orthologs were identified by finding reciprocral best hits from pair-wise protein sequence searches between each bin and the genome of a sequenced relative.
Genome Bin Phylum Bin Size (bp) Bin Coverage N50Number of
ORFsPredicted % Single
Copy Genes Closest Relative with Sequenced GenomeClosest Relative
Genome Size (bp)
% ORFs Orthologous to
ReferenceAverage % AA ID
of OrthologsActinomyces urogenitalis 13 Actinobacteria 116,128.00 1,982.48 2,487 156 3.70 Actinomyces urogenitalis DSM 15434 uid55459 2,702,812 51.92 94.34
Escherichia coli - Strain A 5 Proteobacteria 1,704,074.00 1,829.54 3,509 2,503 11.11 Escherichia coli S88 uid62979 5,032,268 55.21 95.00Streptococcus anginosus 7 Firmicutes 2,108,491.00 1,714.41 537,826 2,252 100.00 Streptococcus anginosus 1 2 62CV uid62163 1,821,055 67.67 95.22
Escherichia coli - Strain A 21 Proteobacteria 3,962,046.00 1,563.00 6,305 4,906 37.04 Escherichia coli S88 uid62979 5,032,268 60.44 97.38Veillonella dispar 11 Firmicutes 2,445,194.00 1,331.29 53,688 2,693 100.00 Veillonella dispar ATCC 17748 uid55331 2,118,767 60.04 91.57
Clostridium butyricum 1 Firmicutes 4,350,784.00 724.59 103,127 4,094 100.00 Clostridium butyricum 5521 uid54843 4,540,699 73.47 96.52Actinomyces urogenitalis 12 Actinobacteria 2,491,825.00 704.73 3,400 2,883 92.59 Actinomyces urogenitalis DSM 15434 uid55459 2,702,812 69.48 98.64Veillonella sp. - Species A 3 Firmicutes 2,173,194.00 373.08 4,666 2,727 37.04 Veillonella oral taxon 158 F0412 uid61047 2,176,752 56.33 92.59
Enterococcus faecalis 4 Firmicutes 2,960,721.00 255.03 235,714 2,906 100.00 Enterococcus faecalis OG1RF uid54927 2,739,625 79.11 98.82Veillonella sp. - Species A 16 Firmicutes 539,200.00 230.21 3,983 756 7.41 Veillonella dispar ATCC 17748 uid55331 2,118,767 64.29 92.45Escherichia coli - Strain B 14 Proteobacteria 641,540.00 207.93 4,041 883 3.70 Escherichia coli S88 uid62979 5,032,268 52.66 82.25Veillonella sp. - Species B 18 Firmicutes 109,076.00 158.19 1,316 174 22.22 Veillonella dispar ATCC 17748 uid55331 2,118,767 79.31 91.53Varibaculum cambriense 20 Actinobacteria 2,247,641.00 122.51 240,417 1,954 100.00 Mobiluncus mulieris ATCC 35239 uid52345 2,533,633 58.19 53.79
Staphylococcus sp. 22 Firmicutes 490,354.00 75.43 7,348 564 18.52 Staphylococcus epidermidis ATCC 12228 uid57861 2,499,279 74.82 94.85Veillonella sp. - Species B 19 Firmicutes 530,104.00 75.38 2,283 705 7.41 Veillonella dispar ATCC 17748 uid55331 2,118,767 63.12 85.29
Clostridium bartlettii 9 Firmicutes 2,444,327.00 60.98 12,184 2,342 92.59 Clostridium bartlettii DSM 16795 uid54809 2,972,256 89.03 98.53Clostridium bartlettii 8 Firmicutes 241,119.00 56.99 17,901 291 0.00 Clostridium bartlettii DSM 16795 uid54809 2,972,256 51.20 64.62
Negativicoccus succinicivorans 17 Negativicoccus 1,341,981.00 33.59 17,543 1,448 100.00 Bacillus coagulans 36D1 uid54335 3,552,226 50.28 43.78Negativicoccus succinicivorans 25 Negativicoccus 166,917.00 32.97 1,766 238 3.70 Bacillus coagulans 36D1 uid54335 3,552,226 23.11 36.62
Streptococcus parasanguinis 23 Firmicutes 2,017,810.00 32.00 5,231 2,366 77.78 Streptococcus parasanguinis ATCC 15912 uid49313 2,153,652 68.43 94.96Staphylococcus sp. 6 Firmicutes 1,039,864.00 31.23 10,033 1,102 18.52 Staphylococcus epidermidis ATCC 12228 uid57861 2,499,279 84.94 98.43
Propionibacterium sp. 15 Propionibacterium 336,576.00 22.16 1,117 565 18.52 Propionibacterium 5 U 42AFAA uid75117 2,532,807 46.37 82.40Leuconostoc sp. 2 Firmicutes 566,369.00 19.44 1,603 874 25.93 Leuconostoc citreum KM20 uid58481 1,796,284 66.70 96.03
Streptococcus sp. 10 Firmicutes 1,915,777.00 16.17 11,008 2,114 55.56 Streptococcus M334 uid62529 2,207,013 67.64 93.88Streptococcus parasanguinis 24 Firmicutes 829,730.00 8.19 1,343 1,318 14.81 Streptococcus parasanguinis ATCC 15912 uid49313 2,153,652 59.03 70.58
Supplemental Table 2 - Absolute abundance of reconstructed genomes. Percent of total reads used in the metagenome assembly that could be mapped to reconstructed genomes at each time point and as a total.
Genome DOL 14 DOL 15 DOL 15 DOL 18 DOL 18 DOL 19 DOL 19 DOL 20 DOL 20 TotalEscherichia coli - Strain A 58.860 44.566 36.751 29.765 17.912 22.821 26.512 33.088 36.597 33.447
Unassembled and Unbinned 18.582 16.636 16.092 13.071 10.374 12.357 12.489 13.682 14.552 14.012Streptococcus anginosus 0.044 0.197 0.206 20.935 15.970 21.174 19.276 20.431 15.224 13.016
Veillonella dispar 4.596 10.642 13.491 14.499 7.331 15.952 17.137 12.572 11.219 11.722Clostridium butyricum 0.092 4.917 9.954 5.376 39.871 14.426 9.686 3.120 4.781 11.352
Actinomyces urogenitalis 2.283 6.018 9.913 8.936 3.681 7.049 8.455 9.991 9.811 7.135Veillonella sp. - Species A 7.836 6.820 6.841 1.621 1.076 1.247 1.444 1.949 2.306 3.298
Enterococcus faecalis 4.844 4.937 3.321 2.175 1.443 2.491 2.318 1.799 1.609 2.719Varibaculum cambriense 0.071 1.638 0.387 1.942 1.067 0.579 0.887 1.143 0.898 0.992
Clostridium bartlettii 0.409 0.794 0.972 0.582 0.458 0.760 0.618 0.406 0.405 0.586Escherichia coli - Strain B 0.608 0.717 0.295 0.143 0.159 0.131 0.121 0.204 0.178 0.281Veillonella sp. - Species B 0.111 0.181 0.205 0.240 0.104 0.201 0.220 0.328 0.305 0.206
Streptococcus parasanguinis 0.006 0.016 0.016 0.053 0.025 0.133 0.180 0.497 1.014 0.205Negativicoccus succinicivorans 0.457 0.324 0.290 0.111 0.077 0.113 0.143 0.087 0.091 0.182
Staphylococcus sp. 0.114 0.166 0.116 0.173 0.140 0.193 0.108 0.223 0.252 0.164Escherichia coli - Strain A / B - Plasmid 0.352 0.304 0.159 0.114 0.075 0.118 0.107 0.117 0.133 0.162
Streptococcus sp. 0.026 0.419 0.429 0.022 0.012 0.041 0.019 0.043 0.093 0.112Veillonella sp. - Species A - Phage 0.102 0.096 0.102 0.054 0.034 0.042 0.066 0.101 0.204 0.086Escherichia coli - Strain A - Phage 0.139 0.107 0.084 0.069 0.048 0.057 0.064 0.068 0.077 0.078Veillonella sp. - Species A - Plasmid 0.242 0.226 0.139 0.009 0.005 0.008 0.006 0.006 0.007 0.069Veillonella sp. - Species B - Phage 0.038 0.036 0.035 0.035 0.021 0.027 0.048 0.068 0.140 0.048
Leuconostoc sp. 0.028 0.048 0.093 0.017 0.078 0.019 0.035 0.006 0.031 0.040Enterococcus faecalis - Plasmid 0.060 0.106 0.037 0.025 0.016 0.029 0.025 0.025 0.019 0.038
Propionibacterium sp. 0.088 0.065 0.046 0.011 0.009 0.007 0.007 0.008 0.010 0.027Actinomyces urogenitalis - Phage 0.006 0.018 0.023 0.019 0.010 0.017 0.022 0.023 0.022 0.017
Streptococcus parasanguinis - Plasmid 0.000 0.000 0.000 0.000 0.000 0.002 0.003 0.010 0.016 0.003Staphylococcus sp. - Plasmid B 0.002 0.003 0.001 0.001 0.001 0.002 0.001 0.003 0.004 0.002Staphylococcus sp. - Plasmid A 0.002 0.003 0.001 0.001 0.001 0.001 0.001 0.002 0.003 0.002
Staphylococcus sp. - Phage 0.002 0.001 0.001 0.002 0.002 0.001 0.001 0.001 0.001 0.001
- Supplemental 7 -
Supplemental Table 3 - Coverage of reconstructed genomes. Coverage of reconstructed genomes at each time point and as a total.
Genome DOL 14 DOL 15 DOL 15 DOL 18 DOL 18 DOL 19 DOL 19 DOL 20 DOL 20 TotalEscherichia coli - Strain A / B - Plasmid 3,310.53 3,006.34 1,139.91 1,148.89 958.28 1,041.67 1,026.07 1,127.07 1,150.90 13,909.65
Escherichia coli - Strain A - Phage 1,074.53 866.54 496.74 574.85 506.76 413.92 504.95 541.55 550.77 5,530.63Enterococcus faecalis - Plasmid 347.35 645.56 165.90 157.22 126.40 158.52 147.64 147.28 101.04 1,996.92
Streptococcus anginosus 0.63 2.97 2.26 323.78 312.81 285.34 282.81 301.64 202.17 1,714.41Escherichia coli - Strain A 315.09 250.71 150.33 171.42 130.65 114.52 144.85 181.91 180.98 1,640.47
Actinomyces urogenitalis - Phage 57.29 186.51 177.61 210.95 142.71 164.47 232.03 237.30 208.64 1,617.51Veillonella dispar 56.97 138.64 127.79 193.36 123.83 185.37 216.81 160.05 128.47 1,331.29
Veillonella sp. - Species A - Phage 151.54 149.00 115.57 86.39 68.37 58.96 100.50 154.19 279.74 1,164.27Veillonella sp. - Species B - Phage 69.35 69.17 48.50 69.94 52.17 46.84 88.93 128.20 237.07 810.17
Actinomyces urogenitalis 26.56 73.59 88.14 111.86 58.35 76.88 100.41 119.40 105.45 760.65Clostridium butyricum 0.64 36.00 52.99 40.30 378.49 94.21 68.87 22.32 30.77 724.59
Veillonella sp. - Species A - Plasmid 154.11 151.29 67.74 5.89 4.57 4.57 3.76 4.02 3.95 399.91Veillonella sp. - Species A 89.13 81.53 59.46 19.83 16.67 13.30 16.77 22.77 24.24 343.69
Enterococcus faecalis 49.59 53.11 25.98 23.96 20.13 23.91 24.22 18.92 15.22 255.03Staphylococcus sp. - Plasmid B 27.47 40.68 12.85 12.42 19.30 20.04 14.18 31.35 39.36 217.65Staphylococcus sp. - Plasmid A 28.46 31.18 7.79 11.22 12.01 15.54 17.04 23.88 33.56 180.68
Staphylococcus sp. - Phage 19.83 17.89 10.31 21.14 27.86 9.33 8.39 10.60 14.48 139.83Escherichia coli - Strain B 29.11 36.07 10.78 7.36 10.39 5.87 5.91 10.01 7.85 123.35Varibaculum cambriense 0.96 23.22 3.99 28.18 19.62 7.32 12.21 15.83 11.18 122.51
Streptococcus parasanguinis - Plasmid 0.01 0.04 0.09 1.70 1.16 7.64 10.92 33.18 50.03 104.78Veillonella sp. - Species B 5.25 9.01 7.44 12.24 6.72 8.94 10.63 15.95 13.35 89.51
Clostridium bartlettii 4.62 9.42 8.38 7.07 7.04 8.04 7.12 4.71 4.22 60.62Negativicoccus succinicivorans 9.18 6.84 4.45 2.41 2.10 2.12 2.93 1.79 1.69 33.52
Staphylococcus sp. 2.28 3.50 1.77 3.73 3.83 3.64 2.21 4.61 4.67 30.23Propionibacterium sp. 7.95 6.18 3.16 1.09 1.05 0.58 0.60 0.73 0.82 22.16
Streptococcus parasanguinis 0.07 0.18 0.13 0.61 0.36 1.34 1.97 5.48 10.07 20.21Leuconostoc sp. 1.52 2.69 3.82 0.96 5.72 0.95 1.93 0.31 1.54 19.44
Streptococcus sp. 0.42 6.97 5.18 0.38 0.26 0.61 0.31 0.70 1.35 16.17
Supplemental Table 4 - Relative abunance of reconstructed genomes. Relative abundance of reconstructed genomes at each time point and as a total.
Genome DOL 14 DOL 15 DOL 15 DOL 18 DOL 18 DOL 19 DOL 19 DOL 20 DOL 20 TotalEscherichia coli - Strain A / B - Plasmid 56.68 50.91 40.72 35.36 31.76 37.54 33.59 33.89 33.72 41.67
Escherichia coli - Strain A - Phage 18.40 14.68 17.75 17.69 16.79 14.92 16.53 16.28 16.13 16.57Enterococcus faecalis - Plasmid 5.95 10.93 5.93 4.84 4.19 5.71 4.83 4.43 2.96 5.98
Streptococcus anginosus 0.01 0.05 0.08 9.97 10.37 10.28 9.26 9.07 5.92 5.14Escherichia coli - Strain A 5.39 4.25 5.37 5.28 4.33 4.13 4.74 5.47 5.30 4.91
Actinomyces urogenitalis - Phage 0.98 3.16 6.35 6.49 4.73 5.93 7.60 7.14 6.11 4.85Veillonella dispar 0.98 2.35 4.57 5.95 4.10 6.68 7.10 4.81 3.76 3.99
Veillonella sp. - Species A - Phage 2.59 2.52 4.13 2.66 2.27 2.13 3.29 4.64 8.19 3.49Veillonella sp. - Species B - Phage 1.19 1.17 1.73 2.15 1.73 1.69 2.91 3.85 6.94 2.43
Actinomyces urogenitalis 0.45 1.25 3.15 3.44 1.93 2.77 3.29 3.59 3.09 2.28Clostridium butyricum 0.01 0.61 1.89 1.24 12.54 3.40 2.25 0.67 0.90 2.17
Veillonella sp. - Species A - Plasmid 2.64 2.56 2.42 0.18 0.15 0.16 0.12 0.12 0.12 1.20Veillonella sp. - Species A 1.53 1.38 2.12 0.61 0.55 0.48 0.55 0.68 0.71 1.03
Enterococcus faecalis 0.85 0.90 0.93 0.74 0.67 0.86 0.79 0.57 0.45 0.76Staphylococcus sp. - Plasmid B 0.47 0.69 0.46 0.38 0.64 0.72 0.46 0.94 1.15 0.65Staphylococcus sp. - Plasmid A 0.49 0.53 0.28 0.35 0.40 0.56 0.56 0.72 0.98 0.54
Staphylococcus sp. - Phage 0.34 0.30 0.37 0.65 0.92 0.34 0.27 0.32 0.42 0.42Escherichia coli - Strain B 0.50 0.61 0.39 0.23 0.34 0.21 0.19 0.30 0.23 0.37Varibaculum cambriense 0.02 0.39 0.14 0.87 0.65 0.26 0.40 0.48 0.33 0.37
Streptococcus parasanguinis - Plasmid 0.00 0.00 0.00 0.05 0.04 0.28 0.36 1.00 1.47 0.31Veillonella sp. - Species B 0.09 0.15 0.27 0.38 0.22 0.32 0.35 0.48 0.39 0.27
Clostridium bartlettii 0.08 0.16 0.30 0.22 0.23 0.29 0.23 0.14 0.12 0.18Negativicoccus succinicivorans 0.16 0.12 0.16 0.07 0.07 0.08 0.10 0.05 0.05 0.10
Staphylococcus sp. 0.04 0.06 0.06 0.11 0.13 0.13 0.07 0.14 0.14 0.09Propionibacterium sp. 0.14 0.10 0.11 0.03 0.03 0.02 0.02 0.02 0.02 0.07
Streptococcus parasanguinis 0.00 0.00 0.00 0.02 0.01 0.05 0.06 0.16 0.29 0.06Leuconostoc sp. 0.03 0.05 0.14 0.03 0.19 0.03 0.06 0.01 0.05 0.06
Streptococcus sp. 0.01 0.12 0.19 0.01 0.01 0.02 0.01 0.02 0.04 0.05
- Supplemental 8 -
Supplemental Table 5 - Relative abundance of bacterial genomes. Relative abundance of reconstructed bacterial genomes at each time point and as a total.
Genome DOL 14 DOL 15 DOL 15 DOL 18 DOL 18 DOL 19 DOL 19 DOL 20 DOL 20 TotalStreptococcus anginosus 0.10 0.40 0.41 34.13 28.49 34.26 31.40 34.00 27.17 23.46
Escherichia coli - Strain A 52.52 33.85 27.04 18.07 11.90 13.75 16.08 20.51 24.32 22.45Veillonella dispar 9.50 18.72 22.98 20.39 11.28 22.25 24.08 18.04 17.27 18.22
Actinomyces urogenitalis 4.43 9.94 15.85 11.79 5.31 9.23 11.15 13.46 14.17 10.41Clostridium butyricum 0.11 4.86 9.53 4.25 34.47 11.31 7.65 2.52 4.14 9.92
Veillonella sp. - Species A 14.86 11.01 10.69 2.09 1.52 1.60 1.86 2.57 3.26 4.70Enterococcus faecalis 8.27 7.17 4.67 2.53 1.83 2.87 2.69 2.13 2.05 3.49
Escherichia coli - Strain B 4.85 4.87 1.94 0.78 0.95 0.70 0.66 1.13 1.06 1.69Varibaculum cambriense 0.16 3.14 0.72 2.97 1.79 0.88 1.36 1.78 1.50 1.68Veillonella sp. - Species B 0.87 1.22 1.34 1.29 0.61 1.07 1.18 1.80 1.79 1.22
Clostridium bartlettii 0.77 1.27 1.51 0.75 0.64 0.97 0.79 0.53 0.57 0.83Negativicoccus succinicivorans 1.53 0.92 0.80 0.25 0.19 0.26 0.33 0.20 0.23 0.46
Staphylococcus sp. 0.38 0.47 0.32 0.39 0.35 0.44 0.25 0.52 0.63 0.41Propionibacterium sp. 1.33 0.83 0.57 0.11 0.10 0.07 0.07 0.08 0.11 0.30
Streptococcus parasanguinis 0.01 0.02 0.02 0.06 0.03 0.16 0.22 0.62 1.35 0.28Leuconostoc sp. 0.25 0.36 0.69 0.10 0.52 0.11 0.21 0.04 0.21 0.27
Streptococcus sp. 0.07 0.94 0.93 0.04 0.02 0.07 0.03 0.08 0.18 0.22
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