supplementary information virtual metagenome ... · supplementary information virtual metagenome...

Supplementary Information

Virtual metagenome reconstruction from 16S rRNA gene sequences

Shujiro Okuda, Yuki Tsuchiya, Chiho Kiriyama, Masumi Itoh, and Hisao Morisaki

Supplementary Figure S1 The universal phylogenetic tree of 16S rRNA gene sequences

from 1137 genomes obtained from KEGG

Supplementary Figure S2 Mapping of a 16S rRNA gene sequence to the universal

phylogenetic tree

Supplementary Figure S3 Functional distributions between virtual and real metagenomes

Supplementary Figure S4 Clustering of a functional module profile

Supplementary Figure S5 Clustering of a functional category profile

Supplementary Figure S6 Flow of biofilm formation

Supplementary Table S1 List of IMG/M metagenome samples

Supplementary Table S2 Biofilm reformation experiments

Supplementary Table S3 Information on the DGGE samples and their sequences

Supplementary Table S4 Relative band intensities for FP1 experiments

Supplementary Table S5 Relative band intensities for FP2 experiments

Supplementary Table S6 Relative band intensities for LW experiments

Supplementary Table S7 Band locations in the DGGE gel image

Supplementary Figure S1. The universal phylogenetic tree of 16S rRNA gene sequences of completely

sequenced genomes.

1137 completely sequenced genomes were obtained from KEGG. The phylogenetic tree was constructed by

using the neighbor-joining method and the maximum composite likelihood model.

ecd:ECDH10B_0182

6904_G

WB:wbe

1000R

WJ:jce1020b:oce3120Z:ece ec

s:ECs5366

2120_51147HCE:fce et

w:ECSP_0200

eok:G2583_0205

ecr:ECIAI1_16S_1

eum:ECUMN_16S_1

ect:ECIAI39_16S_1

eoh:ECO103_rRNA01

ebd:ECBD_R0003

eoi:ECO111_rRNA01

ssn:SSON_0215

ecc:c5600

ecv:APECO1_r01

sdy:SDY_0220

ecm:EcSMS35_0213

ecy:ECSE_16SrRNA01

ecp:ECP_4732

ecg:E2348C_rRNA1

ecq:ECED1_16S_1

eci:UTI89_C0217

ecz:ECS88_16S_1

sfx:S0194

sfv:SFV_0185

ebr:ECB_r00001

efe:EFER_16S_1

ecw:EcE24377A_5003

ecl:EcolC_R0005

ecx:EcHS_A4732

sfl:SF4435

eoj:ECO26_rRNA01

sbo:SBO_0190

eck:EC55989_16S_1

sbc:SbBS512_E0195

cko:CKO_00097

cro:16S_rRNA-1

sei:SPC_r001

sec:SC16Sr1

seh:SeHA_C0288

ses:SARI_00267

spt:SPA0256

sek:SSPAr001

sty:STYr001

stt:t0252

sew:SeSA_A0277

stm:STM0249

see:SNSL254_A0272

sea:SeAg_B0291

sed:SeD_A0272

set:SEN_r001

esa:ESA_00047

ctu:Ctu_R00010

kpe:KPK_0438

kva:Kvar_R0003

kpu:KP1_6001

kpn:KPN_00215

enc:ECL_16S01

ent:Ent638_R0007

pam:PANA_r0001

ebi:EbC_08400_tr01

eta:ETA_r001

epy:EpC_r01

eam:EAMY_r01

eay:EAM_r001

etr:ETAE_R025

pct:PC1_R0001

spe:Spro_R0007

eca:ECAr001

pwa:Pecwa_R0001

sgl:SG16SrRNA01

dda:Dd703_R0005

ddd:Dda3937_04220

ddc:Dd586_R0001

dze:Dd1591_R0001

yen:YEr001

ypy:YPK_R0085

ypb:YPTS_R0084

yps:YPTB_RNA_102

ypi:YpsIP31758_4189

ypk:yr001

ypa:YPA_r001

ypn:YPN_r001

ypp:YPDSF_R0001

ypm:YP_r1

ypz:YPZ3_r1

ype:YPOr01

ypg:YpAngola_A0013

pmr:PMIr001

plu:plur001

pay:PAU_00407a

xbo:XBJ1_rRNA0001

xne:XNC1_rRNA0001

hde:HDEF_1320

wbr:WGLr001

rip:RIEPE_0047

bci:BCI_0154

bfl:Bfl554

bpn:BPEN_572

bab:bbp225

bcc:BCc_153

bas:BUsg618

buc:BU243

bap:BUAP5A_239

bau:BUAPTUC7_241

vch:VCr001

vco:VC0395_A0241

vcj:VCD_rna029

vcm:VCM66_16S01

ppr:PBPRA0068

vfi:VF_AR0001

vfm:VFMJ11_A1267

vsa:VSAL_I3071r

vvu:VV1_r03

vvy:VVAr01

vsp:VS_IIr1243

vex:VEA_rna015

vpa:VPAr01

vha:VIBHAR_00198

apl:APL_2109

apa:APP7_r0001

apj:APJL_R001

hdu:16SrRNA_1

hso:HS_r16S01

hsm:HSM_R0014

msu:MS16S-1

asu:Asuc_R0008

hap:HAPS_0987

aap:NT05HA_2391

aat:D11S_0110

pmu:PM_r01

hin:HI0220.5

hip:CGSHiEE_r09322

hit:NTHIR0003

hiq:CGSHiGG_r10337

tau:Tola_R0001

aha:AHA_0077

asa:ASA_0079

sse:Ssed_R0001

swd:Swoo_R0001

svo:SVI_r001

swp:swp_rRNA10

spl:Spea_R0001

shl:Shal_R0001

slo:Shew_R0001

saz:Sama_R0001

sdn:Sden_R0001

sfr:Sfri_R0001

sbl:Sbal_R0001

sbp:Sbal223_R0001

sbm:Shew185_R0001

sbn:Sbal195_R0001

she:Shewmr4_R0001

shn:Shewana3_R0001

shm:Shewmr7_R0001

son:SO_r001

spc:Sputcn32_R0001

shw:Sputw3181_R0001

ilo:ILr1179.3

cps:CPS_0034

pha:PSHA_arRNA16s1

pin:Ping_R0001

pat:Patl_R0001

amc:MADE_R0001

tcx:Tcr_R0038

mmw:Mmwyl1_R0006

csa:Csal_R0001

par:Psyc_R0018

pcr:Pcryo_R0019

prw:PsycPRwf_R0014

mct:MCR_1955

acd:AOLE_r19636

aci:ACIADrRNA16S_1

acb:A1S_r01

abm:ABSDF_16S_1

abn:AB57_4865

abc:ACICU_rRNA1

aby:ABAYE_16s_1

abb:ABBFA_003544

sde:Sde_R0013

ttu:TERTU_0692

cja:CJA_3859

hch:HCH_10042

maq:Maqu_R0006

abo:ABO_r1

avn:Avin_55000

psb:Psyr_RNA13

psp:PSPPH_0689

pst:PSPTO_r01

pfl:PFL_0119

pfs:PFLUr1

pap:PSPA7_0811

pag:PLES_06472

pae:PA0668.1

pau:PA14_08570

pfo:Pfl01_R1

pmy:Pmen_R

0008

psa:PST_0759

ppw:PputW

619_R0

006

pen:PSEEN

_16s_1

ppg:PputGB1_

R0001

ppu:PP_16SA

ppf:Ppu

t_R0001

rma:Rm

ag_R00

40

vok:CO

SY_0907d

kko:Kkor_R00

03

ftm:FTM

_0530

ftn:FTN_

0472

ftu:FTT_

r04

ftf:FTFr04

ftw:FTW

_2069

ftl:FTL_

R0003

fth:FTH_

r0001

fta:FTA_

2130

afe:Lfer

r_R000

9

afr:AFE_

0384

alv:Alvin_

R0001

lpn:lpg0

302

lpc:LPC_

0381

lpp:lppr0

1

lpf:lplr01

lpa:lpa_0

5016

llo:LLO_

r0001

gpb:HDN

1F_r01

mca:MC

A_Mc16S

A

noc:Noc_

R0010

nwa:Nwa

t_R0016

nhl:Nhal_

R0018

aeh:Mlg_

R0004

hha:Hhal

_R0009

tgr:Tgr7_

R0043

tkm:TK90_

R0007

cbs:COXB

URSA331

_A0275

cbu:CBU_1

6S

cbd:CBUD

_1917

cbg:CbuG_

1829

cbc:CbuK_

0370

hna:Hneap

_R0016

dno:DNO_0

887

xft:PD0048

xfn:XfasM2

3_R0003

xfa:XFr01

xfm:Xfasm1

2_R0003

smt:Smal_R

0002

xal:XALc_Yr

01

xoo:XOO46

92

xom:XOO_r0

1

xop:PXO_rn

a52

xcv:XCVr2

xac:XAC3896

xca:xccb100

_rna003

xcc:XCC3840

xcb:XC_4386

crp:CRP_16S

rRNA

zin:ZICARI_00

6

nma:NMAr03

nme:NMrrnaA16

S

nmi:NMO_rRNA

01

nmc:NMC_r01

ngo:NGO_r03

ngk:NGK_rrna16

s1

cvi:CV_rRNA16s

1lhk:LHK_

r1ajs:Ajs_R

0009dia:Dtpsy

_R0011aav:Aave

_R0006dac:Daci_

R0008ctt:CtCNB

1_R0009vei:Veis_R

0008rfr:Rfer_R0

053vap:Vapar_

R0049pol:Bpro_R

0044pna:Pnap_R

0004mpt:Mpe_A0

326alch:Lcho_R0

001tin:Tint_R004

5eba:ebr03azo:azo_rrn1tmz:Tmz1t_R0

002mfa:Mfla_R0002mei:Msip34_R00

01mmb:Mmol_R000

2meh:M301_R0001neu:RNA_45net:Neut_R0005nmu:Nmul_AR0012dar:Daro_R0002app:CAP2UW1_R0025slt:Slit_R0004gca:Galf_R0001tbd:Tbd_R0009bpa:BPPr01bbr:BBr01bpe:BPr01bpt:Bpetrrna_01bav:BAVr03har:HEAR_16s_1mms:mma_rRNA01hse:Hsero_0477rso:RS00481rsl:RPSI07_16s_rRNA_1rsc:RCFBP_16s_rRNA_1rpi:Rpic_R0045rpf:Rpic12D_R0048reu:Reut_AR0020rme:Rmet_R0054reh:H16_A1659cti:RALTA_A_16S_1pnu:Pnuc_R0002pne:Pnec_R0002bxe:Bxe_AR0025bpy:Bphyt_R0011bge:BC1002_R0011bph:Bphy_R0005bmv:BMASAVP1_0001bml:BMA10229_0003bma:BMAA_Bm16SCbpr:GBP346_A1353bpm:BURPS1710b_0005bpl:BURPS1106A_1337bmn:BMA10247_0450bps:BPSLr01bpd:BURPS668_1328bte:BTH_I1096bgl:bglu_1gr01bmu:Bmul_R0004bmj:BMULJ_00384bvi:Bcep1808_R0003bam:Bamb_R0003bcm:Bcenmc03_R0003bac:BamMC406_R0003bur:Bcep18194_AR0011bcn:Bcen_R0002bch:Bcen2424_R0003mgm:Mmc1_R0003gdi:GDI_r01gdj:Gdia_R0015apt:APA01_25560gox:GOX0224gbe:GbCGDNIH1_R0001

acr:Acry_R0036rri:A1G_r07597rrj:RrIowa_1119rpk:RPR_r07842rco:RCRNA26raf:RAF_RNA26rms:RMA_RNA26rfe:RF_RNA14rbe:RBE_RNA14rbo:A1I_r08027rcm:A1E_r05750

rpr:RPr03rty:RT0602rak:A1C_r06955

ots:OTBS_r01ott:OTT_RNA006

nse:NSE_0973nri:NRI_16SAwol:Wp16SAwri:WRi_r11990

wpi:WPa_r01wbm:Wbm9003

ama:AMr3amf:AMF_1059

acn:ACIS_01352

aph:APH_1000

ecn:Ecaj_R0013

ech:ECH_0919

erg:ERGA_RRNA_16S

eru:Erumr01erw:ERWE_RRNA_16S

pub:SAR11_16S_rRNA

rce:RC1_0374

azl:AZL_r007

mag:amb_r01

rru:Rru_AR0004

apb:SAR116_16S

las:CLIBASIA_r05781

hci:HCDSEM_128

zmo:ZMOr003

zmn:Za10_R0038

swi:Swit_R0031

sjp:SJA_C1-r0010

nar:Saro_R0053

sal:Sala_R0048

eli:ELI_r15155

rsp:RSP_4294

rsk:RSKD131_rrna16s1

rsh:Rsph17029_R0002

rsq:Rsph17025_R0036

rcp:RCAP_rcr00001

pde:Pden_R0002

jan:Jann_R0051

dsh:Dshi_6006

rde:RD1_0727

sil:SPO_Sp16SA

sit:TM1040_R0002

mmr:Mmar10_R0017

hne:HNE_2659

hba:Hbal_R0006

pla:Plav_R0021

pbr:PB2503_r13907

ccr:CC_r03

ccs:CCNA_R0069

cse:Cseg_R0002

cak:Caul_R0005

bsb:Bresu_R0046

bra:BRADO_16S_1

bbt:BBta_rRNA16S1

bja:Bjar01

rpa:RPA_RNA52

rpt:Rpal_R0049

oca:OCAR_7782

nwi:Nwi_R0013

nha:Nham_R0013

rpb:RPB_R0055

rpd:RPD_R0012

rpc:RPC_R0018

rpe:RPE_R0012

bid:Bind_R0005

msl:Msil_R0033

mrd:Mrad2831_R0013

met:M446_R0021

mno:Mnod_R0008

mpo:Mpop_R0013

mch:Mchl_R0015

mex:Mext_R0013

mea:Mex_1p16S1

mdi:METDI_16S_1

xau:Xaut_R0006

azc:AZC_16r01

sno:Snov_R0042

mlo:MAFFr03

mes:Meso_R0044

atu:Atu0053

avi:Avi_4501

btr:BTrrna0003

bgr:Bgr_15510

bhe:BH12670

bqu:BQ09990

bbk:BARBAKC583_0258

rle:RLr01

rlg:Rleg_R0040

rlt:Rleg2_R0042

ret:RHE_CH00059

rec:RHECIAT_CH0000062

ara:Arad_5100

rhi:NGR_c26520

sme:SMc02675

smd:Smed_R0041

oan:Oant_R0010

bmi:BMEA_A1695

bmc:BAbS19_IIr0014

bmt:BSUIS_A1702

bcs:BCAN_A1681

bme:BMEIIr01

bmr:BMI_I1660

bmf:BAB1_2225

bmb:BruAb1_rrna_0003

bms:BRAr03

bov:BOV_1586

nis:NIS_r01

nam:NAMH_0157

hps:HPSH_r08358

hpg:HPG27_rRNA4

hpb:HELPY_16S_1

hpa:HPAG1_r03

hpp:HPP12_r3

hpj:jhpr3

hpy:HPr04

hpl:HPB8_r1

hac:16S_rRNA_copy_I

hhe:HHr03

wsu:WS_r01

tdn:Suden_R0018

sun:SUN_r01

abu:Abu_0841

ant:Arnit_R0003

sdl:Sdel_R0037

cff:CFF8240_0152

cco:CCC13826_2336

cha:CHAB381_1800

cla:Cla_0460

cjr:CJE_Cj16SA

cjd:JJD26997_0032

cje:Cjr01

cjj:CJJ81176_1704

cju:C8J_Cj16SA

bba:Bd_r01

dvu:Dv16SA

dvl:Dvul_R0005

dvm:DvM

F_R0027

dds:Ddes_R0007

dde:Dde_R0001

lip:LI_r03

dma:DM

R_r00010

dsa:Desal_R0003

dba:Dbac_R0011

drt:Dret_R0034

ade:Adeh_R0011

acp:A2cp1_R0012

ank:AnaeK_R0012

afw:Anae109_R0032

mxa:M

XAN_0319

scl:sce_rRNA_16_1

hoh:Hoch_R0002

dol:Dole_R0011

dal:Dalk_R0043

dat:HRM2_22530

sat:SYN_R03878

dps:DPr01

dak:DaAHT2_R0009

sfu:Sfum_R0013

dbr:Deba_R0006

pca:Pcar_R0052

gsu:Gs16SA

gme:Gmet_R0011

ppd:Ppro_R0021

glo:Glov_R0005

gur:Gura_R0015

geo:Geob_R0020

gbm:Gbem

_R0018

gem:GM21_R0018

ddf:DEFD

S_r01

dap:Dacet_R

0028

str:Sterm_R0001

smf:Sm

on_R0009

lba:Lebu_R0003

fnu:FNr03

tex:Teth514_R0007

tpd:Teth39_R0009

tit:Thit_R0007

tmt:Tm

ath_R0007

tte:TTEr01dau:D

aud_R0007

adg:Adeg_R0022

toc:Toce_R0001

dth:DICTH_0617

dtu:Dtur_R

0002

csc:Csac_R

0001

ate:Athe_R0003

cob:COB47_R

0003

chy:CHY_C

h16SA

ttm:Tthe_R

0007

nth:Nther_R

0001

swo:Sw

ol_R0008

slp:Slip_R0008

cth:Cthe_R

0041

cce:Ccel_R

0007

clo:HMPREF0868_1286

vpr:Vpar_R0001

afn:Acfer_R0001

dsy:DSY_16SrR

NA1

dhd:Dhaf_R

0006

hmo:H

M1_0562

drm:Dred_R

0001

dae:Dtox_R

0006

tjr:TherJR_R0009

pth:PTH_r001

mta:M

oth_R0012

cdc:CD196_r01

cdl:CDR20291_r01

cdf:CDr001

amt:Am

et_R0001

aoe:Clos_R

0001hor:H

ore_R0001

aar:Acear_R0001

ckl:CKL_0008

ckr:CKR_16SrR

NA1

clj:CLJU

_c00080cpe:C

PEr001cpf:C

PF_2998cpr:C

PR_r01

cbe:Cbei_R

0001cbk:C

LL_A0008cbt:C

LH_0008

cno:NT01C

X_0156ccb:C

locel_R0001

cac:CA_C

r001ctc:C

TC0r03

cbl:CLK_3816

cby:CLM_0008

cbb:CLD_3805

cbi:CLJ_B0008

cbf:CLI_0009

cba:CLB_0008

cbo:CBOr001

cbh:CLC_0008

eel:EUBELI_00013

ere:EUBREC_0011

bpb:bpr_I3010cpy:C

phy_R0002

fma:FM

G_rrnA

_16SrRNA

1000

R_er

pA:r

pa10

rUU:r

uu71

10_3

APU:

apu

4210

_01RUU:

euu

0200

2EPY

M:ep

m30

r_A

GM:

agm

S61A n

rr_

GM:

egm

10rNP

M:np

m10

rlfM:l

fm

S61-

Anrr

_CS

M:y

mmmcp:M

CAP_0378

acl:ACL_0067

pml:ATP_R0001

pal:PAa_r01

poy:PAM_r01

ayw:AYW

B_r01msy:M

S53_0724mcd:M

CRO_0175

maa:M

AG_r04

mal:M

AGa5770

mat:M

ARTH_R05

mho:M

HO_r02

mpu:M

YPU_RRNA_16S

mmo:M

MOB9320

mhr:M

HR_r001

mhp:M

HP7448_r3

mhy:m

hprRNA-16S

mhj:M

HJ_0709

bcz:rRNA-16SrR

NA_1

bcx:BCA_0007

bca:BCE_5738

ban:Ba16SAbar:Ba16SAbat:rR

NA-16s-1

bai:BAA_0007bah:BAM

EG_0007

bcr:BCAH187_A0007

bcq:BCQ_0007

bcb:BCB4264_A5616

bcg:BCG9842_B0208

bcu:BCAH820_5664

bal:BACI_c00070

btl:BALH_r16S01

bce:BC0007

btk:BT9727_r01btb:BM

B171_C5089

bwe:BcerKBAB4_R

0001

bcy:Bcer98_R0001

bmq:BM

Q_0007

bmd:BM

D_0007

bpu:BPUM_r0001

bli:BL_rrna_0001bld:BLi00008bay:R

BAM_000080

bsu:BSU_rR

NA_1

bss:BSUW23_r20632

oih:OB3546

mcl:M

CCL_rR

NA01

sca:Sca_16S_rRNA_A

sha:SHrRNA01

ssp:SSPr01slg:SLG

D_00852

sep:SEr03ser:SER

P_Se16SA

sah:SaurJH1_R

0005

sao:SAOUHSC_R0001

sae:NWMN_rR

NA01

sax:USA300H

OU_r0001

saw:SAH

V_r0001

saj:SaurJH9_R

0005

sav:SAVrRNA01

sau:SArRNA01

sam:MWrRNA01

sas:SASr001sar:SAR

r001sac:SAC

OL_Sa16SA

saa:SAUSA300_0455

sad:SAAV_0425

sab:SAB_r01

lsg:lse_r001lwe:lw

e_rRNA_0001

lin:linr01lmo:lm

or01lmh:LM

HCC_R001

lmn:LM

5578_rRNA01

lmy:LM

5923_rRNA01

lmf:LM

Of2365_16SA

lmc:Lm

4b_r00001

lsp:Bsph_rRNA0116S

bha:BHr001

bpf:BpOF4_r19933

bcl:ABCr01

bse:Bsel_R0001

afl:Aflv_R001

gwc:GWCH70_R0001

gtn:GTNG

_16s001

gka:GKR001

gyc:GYMC61_R0001

gct:GC56T3_R0001

esi:Exig_R0001

eat:EAT1b_R0019

bbe:BBR47_r0010

gym:GYMC10_R0001

pjd:Pjdr2_R0001

aac:Aaci_R0001

bts:Btus_R0001

lpl:lp_rRNA01

lpj:JDM1_rRNA01

lbr:LVIS_r0082

ppe:PEPE_r0108

lsa:LSAr01

lrh:LGG_03012

lrl:LC705_02985

lcz:LCAZH_r0282

lca:LSEI_r0258

lcb:LCABL_r02

lfe:LAF_16SrRNA01

lre:Lreu_R0003

lrf:LAR_16SrRNA01

lsl:LSL_RNA001

efa:Ef16SA

ljo:LJR007

ljf:FI9785_1813

lga:LGAS_r0449

ldb:Ldb0054

lbu:LBUL_r0045

lac:LBA2001

lhe:lhv_3101

lcr:LCRIS_02033

lme:LEUM_r0019

lci:LCK_r0001

lki:LKI_r10292

lgs:LEGAS_R0022

lla:L200142

llk:LLKF_r0002

llc:LACR_r0552

llm:llmg_rRNA_1

smu:SMUr01

smc:SmuNN2025rRNA0001

spj:MGAS2096_SPYR2218

spb:M28_SpyR0001

spi:MGAS10750SpyR2225

sph:MGAS10270SpyR2220

spk:MGAS9429_SpyR0001

spf:SpyM5r01

spg:SpyM3_r01

sps:SPsr01

spz:M5005_Spy_R0001

spy:SPy_r01

spa:M6_Spys1887

spm:spyM18_r01

soz:Spy49_rRNA16s1

sds:SDEG_0017

sag:Sa16SA

san:gbsr001

sak:SAK_0016sub:SUBr01

sez:Sez_1962

seq:SZO_r01

seu:SEQ__r01

ssu:SSU05_2255

ssv:SSU98_2252

sss:SSUSC84_r0001

ssi:SSUr01

ssb:SSUBM407_r0001

stc:str_r01

stl:stu_r01

ste:STER_r0019

sga:GALLO_r0001

ssa:SSA_2400

sgo:SGO_0611

smb:smi_0016

snc:HMPREF0837_r10003

snp:SPAP_0016

spn:SP_rrnaA16S

spr:sprr01

spp:SPP_0016

spv:SPH_0016

spx:SPG_0016

snm:SP70585_0017

spd:SPD_0016

snt:SPT_0050

spw:SPCG_s01

sne:SPN23F_r01

sjj:SPJ_0016

cya:CYA_1089

cyb:CYB_1377

gvi:gvir003

cyt:cce_RNA045

cyu:UCYN_00080

cyp:PCC8801_R0024

cyh:Cyan8802_R0023

cyc:PCC7424_R0011

syn:6803r03

mar:MAE_r001

syp:SYNPCC7002_A1395

ter:Tery_R0014

npu:Npun_r020

naz:Aazo_R0008

ana:allrr01

ava:Ava_R

0006

tel:rTEr03

cyn:Cyan7425_R0

006

amr:AM

1_6417

syc:syc

RNA02

1_c

syf:Synpcc7942_R

0004

syr:RNA_8

syd:Syncc9605_R

0016

sye:Syncc9902_R

0046

syw:RN

A_40

syx:RN

A_16

pmf:P9303_rrs

1309419

syg:syn

c_0553

pma:Pro

r01

pmj:P9211_rrs

1309438

pmn:PM

N2A_R0

036

pme:NATL1

_rrs1309404

pmm:RN

A_39

pmc:P9515_rrs

1309392

pmi:PM

T9312_R00

09

pmb:A96

01_rrs1

309386

pmg:P93

01_rrs1

309398

pmh:P92

15_rrs1

723409

sru:SRU

_2691

rmr:Rma

r_R000

6

pvi:Cvib_

R0003

plt:Plut_R

0049

cli:Clim_

R0003

pph:Pph

a_R0003

cph:Cph

a266_R0

048

cch:Cag

_r1

cte:CTrrn

aA16S

cpc:Cpa

r_R0003

cpb:Cph

amn1_R

0003

paa:Paes

_R0003

cts:Ctha_

R0011

cpi:Cpin_

R0024

aas:Aasi

_R0009

chu:CHU_

r16S01

phe:Phep

_R0011

dfe:Dfer_R

0013sli:Sl

in_R0004

bfr:BF16S

rRNA01

bfs:BFr04bth:BT_r03

bvu:BVU_0

228pru:P

RU_0182

pmz:HMPR

EF0659_A

5260pgi:P

G16SA

pgn:PGN_r

0001pdi:BD

I_0133

aps:CFPG_

16SrRNA01

smg:SMGW

SS_076

smh:DMIN_0

0720

sum:SMCAR

I_089

sms:SMDSE

M_079bbl:BL

BBGE_305

bpi:BPLAN_3

36fba:FIC

_00421

fjo:Fjoh_R000

5fps:FP

0471coc:Co

ch_R0012

rbi:RB2501_r0

0051

fbc:FB2170_r1

0252cat:CA2

559_r07731

gfo:GFO_0607zpr:ZPR_0693dra:DR_

r01tra:Trad

_R0003tth:TTC3024ttj:TTHAr03

mrb:Mrub_R0005msv:Mesil_R0001fsu:Fisuc_R0016lil:LA_r03lic:LIC110

10lbj:LBJ_1828lbl:LBL_1455lbf:LBF_1040

bhy:BHWA1_02699brm:Bmur_

R0028tpa:TPr01tpp:TPASS_r0001tde:TDE_16SAssm:Spirs_R0021bbu:16Sbbz:BbuZS7_0432bga:BG0433baf:BAPKO_0447bhr:BHR0002btu:BTR0002bdu:BDU_424bre:BRE_428caa:Caka_R0019amu:Amuc_R0019pcu:pcr03wch:wcw_1258cpj:CPjr01cpt:CpBr01cpn:CPnr01cpa:CPr03cca:CCA_r03cab:CABr03cfe:CF16SrRNA01cmu:TCrrnaA16Sctb:CTL_r01ctl:CTLon_0108bctr:CTr01cta:CTA_0804ctj:JALI_r1rsd:TGRD_16SrRNA01sus:Acid_R0010aba:Acid345_R0047aca:ACP_3584tye:THEYE_A0950tai:Taci_R0035aco:Amico_R0001ccu:Ccur_00120

ele:Elen_R0012apv:Apar_R0046ols:Olsu_R0006sth:STH5001rxy:Rxyl_R0022

cwo:Cwoe_R0024afo:Afer_R0023blo:BLr01blj:BLD_r0001bln:Blon_R0026bll:BLJ_1335

bad:BAD_r0003bde:BDP_2rRNA16S

gva:HMPREF0424_1407bla:BLA_r0001blc:Balac_1279blt:Balat_1279tbi:Tbis_R0038sma:SAV_r10

sgr:SGR_16SrRNA1sco:SCOr03

scb:SCAB_r03aau:AAur_0150ach:Achl_R0015art:Arth_R0016

rsa:RSal33209_0430mlu:Mlut_03860krh:KRH_r00030

rmu:RMDY18_r00050

bfa:Bfae_04500

kse:Ksed_07380bcv:Bcav_R0018

ske:Sked_06910xce:Xcel_R0005cfl:Cfla_R0015lxx:Lxx01380

cmi:CMM_RNA_0001a

cms:CMS_r001

twh:TWTRNA11tws:TWr03

mcu:HMPREF0573_r10003

jde:Jden_R0019

ahe:Arch_R0011

fra:Francci3_R0040

fal:FRAAL_16S_1

fre:Franean1_R0015

ace:Acel_R0036

nml:Namu_R0046

cai:Caci_R0035

gob:Gobs_R0004

kra:Krad_R0036

tfu:Tfu_R0025

nda:Ndas_R0002

tcu:Tcur_R0013

sro:Sros_R0017

mau:Micau_R0029

stp:Strop_R0005

saq:Sare_R0005

nca:Noca_R0032

kfl:Kfla_R0040

pac:PPA2417

pak:HMPREF0675_3607

sna:Snas_R0033

cdi:DIP0766.1

cpu:cpfrc_r001

car:cauri_r01

cjk:jk0090a

cur:cur_rRNA01

cef:CErRNA01

cgt:cgR_r01

cgl:NCg1r01

cgb:cgr01

ckp:ckrop_r01

sen:SACE_8101

amd:AMED_R16

svi:Svir_05560

ami:Amir_R0011

srt:Srot_R0018

tpr:Tpau_R0011

rha:RHA1_ro00941

rop:ROP_r0030

rer:RER_r0010

nfa:nfa70010

gbr:Gbro_R0027

mab:MAB_r5051

mmc:Mmcs_R0024

mjl:Mjls_R0021

mkm:Mkms_R0021

msm:MSMEG_3757

mgi:Mflv_R0023

mva:Mvan_R0027

mle:MLr01

mpa:MAP_r02

mav:MAV_1532

mul:MUL_3949

mmi:MMAR_5519

mtb:TBMG_05103

mtc:MTr01

mtu:Rvnr01

mbo:Mbr01

mbb:BCG_r17

mbt:JTY_r0001

mra:MRA_r01

mtf:TBFG_14046

gau:GAU_r0001

nde:NIDE_16S_1

rba:RBr03

psl:Psta_R0021

deh:cbdb_r03

deb:DehaBAV1_R0032

deg:DehalGT_R0032

det:DET_De16S

dev:DhcVS_893

tro:trd_1020

sti:Sthe_R0002

ttr:Tter_R0021

hau:Haur_R0019

rrs:RoseRS_R0016

rca:Rcas_R0039

cag:Cagg_R0009

cau:Caur_R0008

chl:Chy400_R0008

sul:SYO3AOP1_R0017

hya:HY04AAS1_R0033

aae:aq_r03

hth:HTH_r03

tal:Thal_R0033

cpo:COPRO5265_1653

kol:Kole_R0024

fno:Fnod_R0020

tle:Tlet_R0052

tpt:Tpet_R0030

tnp:Tnap_R0019

tna:CTN_rrna16S

tma:TMrrnaA16S

trq:TRQ2_R0030

smr:Smar_R0040

shc:Shell_R0023

dka:DKAM_R0022

tag:Tagg_R0004

ape:APE_rRNA05

hbu:Hbut_1672

asc:ASAC_R0005

iho:Igni_R0022

tpe:Tpen_R0014

cma:Cmaq_R0003

pis:Pisl_R0038

pai:PAErR16S

pcl:Pcal_R0022

pas:Pars_R0008

tne:Tneu_R0010

mse:Msed_R0026

sto:STrRNA02

sai:Saci_1300

sin:YN1551_R0044

sia:M1425_R0006

sid:M164_R0008

sim:M1627_R0006

siy:YG5714_R0045

sii:LD85_R0006

sso:SSOr03

sis:LS215_R0006

kcr:Kcr_R0018

mka:MKr02

neq:NEQ_r03

nmr:Nmar_R0029

pho:PHrRNA01

pab:PABr02

pfu:PF_r001

ton:TON_1979

tko:TKr05

tga:TGAM_r054

tsi:TSIB_R0048

afu:AFrRNA02

apo:Arcpr_R0041

fpl:Ferp_R0032

mif:Metin_R0018

mvu:M

etvu_R0009

mfe:M

efer_R0001

mja:M

J_r02

mfs:M

FS40622_R0003

abi:Aboo_R0037

pto:PTOr02

tac:Tar02

tvo:TVNr04

mae:M

aeo_R0024

mvo:M

vol_R0028

mvn:M

evan_R0001

mmz:MmarC7_R0022

mmq:MmarC5_R0032

mmp:RNA_39

mmx:MmarC6_R0020

msi:M

sm_1801

mru:m

ru_2278

mst:M

sp_0350

mth:M

TH1753

mmg:MTBM

A_c03280

hma:rrs-1

hmu:Hm

uk_R0017

hut:Huta_R0021

hal:VNGr02

hsl:OE_r01

nph:NPr03

hje:HacjB3_r01

htu:Htur_R0015

nmg:Nm

ag_R0001

hla:Hlac_R0001

hwa:HQr01

hvo:HVO_3038

mbn:M

boo_R0046

mpl:M

pal_R0019

mem:Memar_R0043

mhu:M

hun_R0001

mla:M

lab_R0011

mpd:M

CP_r0001

rci:LRCr01

mtp:M

the_R0021

mev:M

etev_R0001

mbu:M

bur_R0023

mmh:M

mah_R

0012

mma:M

M_ZR

NA059

mac:M

A0896

mba:M

bar_AR0023

0.00

0.05

0.10

0.15

0.20

0.25

Supplementary Figure S2. Mapping of a 16S rRNA gene sequence to the universal phylogenetic tree.

In this schematic model, q is a query sequence, t is a leaf or an internal node on the path from the initial

sequence to the root on the universal tree, and s is the sibling node of t. Along with the path from the initial

sequence to the root, the distances were computed between q, t, and s, and the query was mapped as a sister

clade of t.

Supplementary Figure S3. Functional distributions between virtual and real metagenomes.

KEGG BRITE categories at third hierarchical level were counted in the virtual and real metagenomes. The Y-axis indicates coverage of KOs in each category.

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Supplementary Figure S4. Clustering of a functional module profile.

Module enrichments are color coded. The stages of biofilm formation are described at the left side of sample names. Red arrows indicate the final stage. Clustering

of the module transition patterns provides two clusters, and pie charts of functions in the clusters are provided. Red indicates transporter-related modules, blue

indicates metabolism-related modules, and green indicates other functions.

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Supplementary Figure S6. Flow of biofilm formation.

Cells of sample names are separated into three groups: initiation (FP1_0, FP1_7, and FP2_0; green),

growth (FP1_21, FP1_28, and FP2_7; red), and matured (FP1_42 and FP2_21: orange) stages, based on

the clustering results (Fig. 5a and Supplementary Fig. S5).

Supplementary Table S1. List of IMG/M metagenome samples.

Identifiers, names in IMG/M samples, and the similarities with conservation probability threshold zero

(Fig. 3a) are shown. When a virtual metagenome is not reconstructed under the threshold, similarity is

shown as ND.

ID Name Similarity

2000000000 Sludge/US, Phrap Assembly 0.649183206

2000000001 Sludge/Australian, Phrap Assembly 0.716593705

2001000000 Sludge/US, Jazz Assembly 0.763754503

2001200000 Acid Mine Drainage 0.697557628

2001200001 Soil microbial communities from Minnesota Farm 0.726030254

2001200002 Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #1 ND

2001200003 Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 0.743994072

2001200004 Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 0.704683196

2003000006 Air microbial communities Singapore indoor air filters 1 0.699744975

2003000007 Air microbial communities Singapore indoor air filters 2 0.649240768

2004000001 Single-cell genome from subgingival tooth surface TM7c ND

2004002000 Human Gut Community Subject 7 0.673979399

2004002001 Human Gut Community Subject 8 0.55179582

2004080001 Hindgut microbiome of Nasutitermes sp. (Costa Rica) 0.555807789

2004175000 Hindgut microbiome of Nasutitermes sp. (Costa Rica), fosmids 0.213994007

2004175001 Anaerobic methane oxidation (AOM) community from Eel River Basin sediment, California 0.376870967

2004178001 Olavius algarvensis endosymbiont metagenome Delta1 0.690287641

2004178002 Olavius algarvensis endosymbiont metagenome Delta4 ND

2004178003 Olavius algarvensis endosymbiont metagenome Gamma1 0.427388162

2004178004 Olavius algarvensis endosymbiont metagenome Gamma3 0.636924866

2004230000 Mouse Gut Community lean3 ND


2004230002 Mouse Gut Community ob2 ND

2004230003 Mouse Gut Community ob1 ND


2004247000 Guerrero Negro salt ponds hypersaline mat 01(G) 0.624394242

2004247001 Guerrero Negro salt ponds hypersaline mat 02(H) 0.611912737

2004247002 Guerrero Negro salt ponds hypersaline mat 03(I) 0.488413281

2004247003 Guerrero Negro salt ponds hypersaline mat 04(N) 0.495554385

2004247004 Guerrero Negro salt ponds hypersaline mat 05(O) 0.587275233

2004247005 Guerrero Negro salt ponds hypersaline mat 06(P) 0.517801633

2004247006 Guerrero Negro salt ponds hypersaline mat 07(S) 0.500709575

2004247007 Guerrero Negro salt ponds hypersaline mat 08(T) 0.590261513

2004247008 Guerrero Negro salt ponds hypersaline mat 09(Y) 0.550113204

2004247009 Guerrero Negro salt ponds hypersaline mat 10(Z) 0.443833541

2004247010 Single-cell genome from subgingival tooth surface TM7a 0.306724575

2005137000 simHC - Simulated High Complexity Metagenome ND

2005137001 simLC - Simulated Low Complexity Metagenome ND

2005137002 simMC - Simulated Medium Complexity Metagenome ND

2005503000 Single-cell genome from subgingival tooth surface TM7b ND

2006207000 Methylotrophic community from Lake Washington sediment Methane enrichment 0.755168671

2006207001 Methylotrophic community from Lake Washington sediment Methanol enrichment 0.695475315

2006207002 Methylotrophic community from Lake Washington sediment Methylamine enrichment 0.67172153

2006207003 Methylotrophic community from Lake Washington sediment Formaldehyde enrichment 0.68976531

2006207004 Methylotrophic community from Lake Washington sediment Formate enrichment 0.767600394

2006543005 Methylotrophic community from Lake Washington sediment combined (v2) 0.757989872

2006543007 Uranium Contaminated Groundwater FW106 0.73206682

2007300000 Sludge/US Virion (fgenesb) 0.415855383

2007309000 Bath Hot Springs, filamentous community 0.83960483

2007309001 Bath Hot Springs, planktonic community 0.555951435

2007427000 Oak Ridge Pristine Groundwater FRC FW301 0.73957766

2007915000 Wastewater Terephthalate-degrading communities from Bioreactor 0.675130895

2009439000 Bison Hot Spring Pool, Yellowstone (14JAN08 BISONS) 0.644054477

2009439003 Bison Hot Spring Pool, Yellowstone (05DEC07 BISONN) 0.625026858

2010170001 Bison Hot Spring Pool, Yellowstone (11FEB08 BISONR) 0.577458238

2010170002 Bison Hot Spring Pool, Yellowstone (11FEB08 BISONQ) 0.708288636

2010170003 Bison Hot Spring Pool, Yellowstone (11FEB08 BISONP) 0.714709058

2010170004 Obsidian Hot Spring, Yellowstone 0.366087829

2010388001 Poplar biomass decaying microbial community 0.649356642

2010483000 Aquatic microbial communities from Lake Kinneret (08) 0.094421306

2010483001 Aquatic microbial communities from Lake Kinneret (06) ND







2010549000 Endophytic microbiome from Rice 0.765667172

2012990003 DNA Fragments from Six Antarctic Marine (submission_id = 262) 0.049945402

2013338003 Macropus eugenii Gut Microbiome (Macropus_eugenii_combined, MeugComb) 0.657088287

2013505000 DRU (Sample 145) ND

2013505001 VLU (Sample 144) ND

2013515000 Microbial community from Yellowstone Hot Springs (White Creek Site 3) 0.636243518

2013515001 Microbial community from Yellowstone Hot Springs (OSP Spring YNP8) 0.75845226

2013515002 Microbial community from Yellowstone Hot Springs (Bechler Spring) 0.495056455

2013843002 Aquatic dechlorinating community (KB-1) (Sample 10166) 0.697255175

2013843003 Microbial community from Yellowstone Hot Springs (Josephs Coat Springs) 0.834272159

2013954000 Microbial community from Yellowstone Hot Springs (Bath Lake Vista Annex) 0.7561072

2013954001 Microbial community from Yellowstone Hot Springs (OSP Spring YNP14) 0.848600942

2014031002 Microbial community from Yellowstone Hot Springs (Alice Springs, Crater Hills) 0.857597195

2014031003 Microbial community from Yellowstone Hot Springs (Monarch Geyser, Norris Geyser Basin, v1) 0.679348473

2014031004 Microbial community from Yellowstone Hot Springs (Dragon Spring, Norris Geyser Basin) 0.802847495

2014031005 Microbial community from Yellowstone Hot Springs (Calcite Springs, Tower Falls Region) 0.794612978

2014031006 Microbial community from Yellowstone Hot Springs (Chocolate Pots) 0.647811669

2014031007 Microbial community from Yellowstone Hot Springs (Octopus Springs) 0.530926062

2014613002 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (1_Upper_euphotic) 0.477752878

2014613003 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (2_Base_of_chrolophyll_max) 0.40242069

2014642000 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (6_Upper_euphotic) 0.489326973

2014642001 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (3_Below_base_of_euphotic) 0.407096209

2014642002 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (5_Below_upper_mesopelagic) ND

2014642003 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (7_Oxygen_minimum_layer) 0.526349534

2014642004 Marine planktonic communities from Hawaii Ocean Times Series Station (HOT/ALOHA) (4_Deep_abyss) 0.602023875

2014730001 ANAS dechlorinating bioreactor (Sample 196) 0.814280252

2015219000 Microbial community from Yellowstone Hot Springs (Cistern Spring) 0.814907191

2015219001 Microbial community from Yellowstone Hot Springs (NL10 454-Titanium, v1) 0.779105662

2015219002 Microbial community from Yellowstone Hot Springs (Mushroom Spring) 0.675839433

2015219006 Archaeal virus community from Yellowstone Hot Springs (Nymph Lake) ND

2015391000 Archaeal virus community from Yellowstone Hot Springs (Crater Hills) ND

2015391001 Microbial community from Yellowstone Hot Springs (Narrow Gauge - 454-Titanium) 0.784169881

2016842003 Microbial community from Yellowstone Hot Springs (Fairy Spring Red Layer) 0.63142199

2016842004 Microbial community from Yellowstone Hot Springs (Washburn Springs #1) 0.589147193

2016842005 Microbial community from Yellowstone Hot Springs (Obsidian Pool Prime) 0.620763188

2016842008 Microbial community from Yellowstone Hot Springs (Bath Lake Vista Annex - Purple-Sulfur Mats) 0.615370154

2017108002 Marine anaerobic ammonium oxidizing (anammox) community 0.552593053

2019105001 K9gut 0.694936416

2019105002 K9gut2 0.677095044

2020627003 Benzene-Degrading Methanogenic communities from Bioreactor 0.579924765

2021593001 Forestomach microbiome of Macropus eugenii 0.290331998

2021593003 Termite Protist Endosymbiont Community (submission 732b) ND

2021593004 Soil microbial community from switchgrass rhizosphere 0.755384568

2029527000 Compost Minireactor Metagenome (GBAN) (final assembly) 0.75424004

2029527002 Soil microbial communities from FACE and OTC sites 0.723271255

2029527003 Apterostigma dentigerum fungus garden (APTF) 0.814379057

2029527004 Atta cephalotes fungus garden (ACEF) 0.784962433

2029527005 Atta colombica fungus garden (ACOFG) 0.857562335

2029527006 Atta colombica fungus garden (Fungus garden bottom) 0.884411981

2029527007 Dendroctonus ponderosae fungus gallery (MPB hybrid gallery) 0.733172864

2030936003 Anammox bioreactor Anammoxoglobus propionicus 0.682163535

2030936005 Cyphomyrmex longiscapus fungus garden 0.873230543

2030936006 Atta texana internal waste dump (Dump top) 0.774532235

2032320002 Soil microbial communities from FACE and OTC sites (FACENCE) 0.740398602

2032320003 Soil microbial communities from FACE and OTC sites (FACENCT) 0.7424995

2032320004 Soil microbial communities from FACE and OTC sites (Maryland Estuary ambient) 0.780275396

2032320005 Soil microbial communities from FACE and OTC sites (Oak Ridge ambient) 0.755631007

2032320006 Soil microbial communities from FACE and OTC sites (Oak Ridge elevated CO2) 0.742642292

2032320007 Atta texana internal waste dump (Dump bottom) 0.767128571

2032320008 Dendroctonus ponderosae fungus gallery (Lodgepole pine) 0.831369008

2032320009 Dendroctonus ponderosae beetle community (MPB hybrid beetle) 0.763850241

2035918000 Acromyrmex echinatior fungus garden (combined) 0.789261608

2035918001 Wastewater treatment plant Plasmid pool from Switzerland (submission 1086) 0.557639732

2035918002 Wastewater treatment plant Plasmid pool from Switzerland (submission 1087) 0.554117303

2035918003 Dendroctonus ponderosae beetle community (Lodgepole pine) 0.822709841

2035918004 Soil microbial communities from FACE and OTC sites (FACENC) 0.729380304

2035918005 Soil microbial communities from FACE and OTC sites (NTS Crust elevated CO2) 0.76114592

2035918006 Soil microbial communities from FACE and OTC sites (Maryland Estuary elevated) 0.766691349

2038011000 Atta colombica fungus garden and dump (Dump top) 0.804277771

2040502000 Atta colombica fungus garden and dump (Dump bottom) 0.771427615

2040502001 Soil microbial communities from FACE and OTC sites (North Carolina Elevated CO2) 0.736684589

2040502004 Marine bacterioplankton communities from Antarctic (Winter fosmids) ND

2040502005 Marine bacterioplankton communities from Antarctic (Summer fosmids) 0.338822367

2043231000 Xyleborus affinis beetle metagenome (Ambrosia beetle adult) 0.724423933

2044078000 Maize field bulk soil (Bulk soil sample from field growing corn (Zea mays)) 0.684814237

2044078001 Maize rhizosphere soil (Soil sample from rhizosphere of corn (Zea mays)) 0.683417526

2044078002 Miscanthus rhizosphere soil (Rhizosphere soil sample of Miscanthus x giganteus) 0.667865523

2044078003 Miscanthus field bulk soil (Bulk soil sample from field growing Miscanthus x giganteus) 0.710843323

2044078004 Switchgrass rhizosphere soil (Rhizosphere soil sample from switchgrass (Panicum virgatum)) 0.6719134

2044078005 Switchgrass field bulk soil (Bulk soil sample from field growing switchgrass (Panicum virgatum)) 0.634503109

2044078006 Dendroctonus frontalis bacterial community 0.810141653

2044078007 Dendroctonus frontalis fungal community 0.762825377

2044078011 Xyleborus affinis microbiome from Bern, Switzerland (Larvae community) 0.751410765

2046860004

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Anaerobic with added nitrate,

13C SIP) 0.765181166

2046860005

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Aerobic without added nitrate,

SIP additional fraction) 0.670562174

2046860006

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Aerobic with added nitrate, 13C

SIP) 0.74521482

2046860007

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Aerobic without added nitrate,

13C SIP) 0.727853242

2046860008

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Anaerobic without added nitrate,

13C SIP) 0.713079285

2048955003 Poplar biomass decaying microbial community (13 April 2010 assembly with 454 paired-end) 0.814294201

2049941001 Mixed alcohol (MixAlco) bioreactor (40 degree reactor) 0.812243981

2051774008 Saline water microbial communities from Great Salt Lake ND

2053563001 Thermophilic enrichment culture SG0.5Z960 (454-Illumina assembly) ND

2053563014 Sediment and water microbial communities from Great Boiling Spring (Surface sediment) 0.615386334

2058419001 Saline water microbial communities from Great Salt Lake (South Arm Antelope Island) 0.684924217

2058419003 Saline water microbial communities from Great Salt Lake (North Arm Stromatolite) 0.662049673

2058419004 Sediment and water microbial communities from Great Boiling Spring (Water-borne viral community) 0.33342833

2061766000 Benzene-degrading methanogenic communities from Bioreactor (Assembly with PE data) 0.714068188

2061766001 Thermophilic enrichment culture SG0.5JP960 (454-Illumina assembly v2) 0.666169366

2065487013 Fungus-growing Termite Worker 0.810149068

2065487014 Fungus-growing Termite Fungus Garden 0.817520752

2077657006 Freshwater microbial communities from Mississippi River (Itasca #1) ND

2077657007 Freshwater microbial communities from Mississippi River (Minneapolis #1) ND

2077657008 Viral community from bovine rumen (Cow 7887) ND

2077657009 Viral community from bovine rumen (Cow 6993) ND

2081372008

Terephthalate-degrading communities (TA reactor DNA contigs from 4 samples) (Terephthalate degrading reactor

metagenome contigs from 4 samples) ND

2084038000 Viral community from bovine rumen (Cow 7664) 0.475187856

2084038009 Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Flow sorted aerobic no nitrate) 0.78054136

2084038020 Sediment and water microbial communities from Great Boiling Spring (Water borne 27 Oct 2010 assembly) 0.594482177

2088090005 Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Original sample replicate 1) 0.795388762

2088090006

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Original sample replicate 2 12C

fraction) 0.782324882

2088090007

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Flow sorted anaerobic plus

nitrate) 0.782674873

2088090009

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Anaerobic + nitrate SIP Nov

2010 with PE) 0.805564063

2088090012 Coastal water and sediment microbial communities from Arctic (High methane PC12-236-260cm) 0.735951

2088090013

Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Anaerobic no nitrate SIP Nov

2010 with PE) 0.778068027

2088090027 Sediment and water microbial communities from Great Boiling Spring (Cellulolytic enrichment CS 77C sediment) 0.633132628

2100351001 Coastal water and sediment microbial communities from Arctic (Low methane PC12-247-20cm) 0.761708625

2100351006 Coastal water and sediment microbial communities from Arctic (High methane PC12-225-485cm Dec 2010 assembly) 0.74961658

2100351007 Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (Flow sorted aerobic plus nitrate) 0.788023063

2100351009 Sediment and water microbial communities from Great Boiling Spring (GBS Cellulolytic enrichment CS 85C sediment) 0.635200746

2100351010

Groundwater dechlorinating microbial community from Kitchener, Ontario, containing dehalobacter (TCA/MEAL culture

Nov 2010 assembly with PE data) 0.687296203

2100351011 Coastal water and sediment microbial communities from Arctic (Medium methane PC12-240-170cm Sept2010 assembly) 0.747062115

2100351012 Coastal water and sediment microbial communities from Arctic (Low methane PC12-244-90cm Sept2010 assembly) 0.759917138

2124908000 Sediment microbial communities from Lake Washington for Methane and Nitrogen Cycles (WGA anaerobic no nitrate) 0.570120116

Supplementary Table S2. Biofilm reformation experiments.

Date May 19 May 26 June 9 June 16 Jun 30 July 23

Day 0 7 21 28 42 65 FP1

Sample name FP1_0 FP1_7 FP1_21 FP1_28 FP1_42 FP1_65

Day 0 7 21 44 FP2

Sample name FP2_0 FP2_7 FP2_21 FP2_44

Supplementary Table S3. Information on the DGGE samples and their sequences.

Sample name Band number Accession number

FP1_0 1 AB697766 FP1_0 4 AB697767 FP1_0 5 AB697768 FP1_0 7 AB697769 FP1_0 8 AB697770 FP1_0 10 AB697771 FP1_7 1 AB697772 FP1_7 3 AB697773 FP1_7 4 AB697774 FP1_7 5 AB697775 FP1_7 6 AB697776 FP1_7 7 AB697777 FP1_7 8 AB697778 FP1_7 9 AB697779 FP1_7 10 AB697780

FP1_21 2 AB697781 FP1_21 5 AB697782 FP1_21 7 AB697783 FP1_21 8 AB697784 FP1_28 1 AB697785 FP1_28 4 AB697786 FP1_28 5 AB697787 FP1_42 3 AB697788 FP1_42 7 AB697789 FP1_42 8 AB697790 FP1_42 9 AB697791 FP1_65 5 AB697792 FP1_65 10 AB697793 FP1_65 11 AB697794 FP2_0 1 AB697795 FP2_0 3 AB697796 FP2_0 4 AB697797 FP2_0 5 AB697798 FP2_0 7 AB697799 FP2_0 8 AB697800 FP2_0 10 AB697801 FP2_7 2 AB697802 FP2_7 5 AB697803

FP2_21 4 AB697804 FP2_21 7 AB697805 FP2_21 10 AB697806 FP2_44 4 AB697807 FP2_44 6 AB697808 FP2_44 7 AB697809 LW_0 1 AB697810 LW_0 2 AB697811 LW_0 5 AB697812

LW_0 6 AB697813 LW_0 8 AB697814 LW_7 7 AB697815 LW_7 10 AB697816

LW_21 5 AB697817 LW_21 8 AB697818 LW_42 4 AB697819 LW_65 5 AB697820 LW_65 7 AB697821 LW_65 9 AB697822 LW_65 11 AB697823 LW_65 14 AB697824

Supplementary Table S4. Relative band intensities for FP1 experiments.

� � Sample name � � FP1_0 FP1_7 FP1_21 FP1_28 FP1_42 FP1_65

1 0.900778023 0.428092203 0.415310651 0.549579595 0.395819572 0.914599933 2 0.625156085 0.621124263 0.873467878 0.771384283 0.431442861 0.990966222 3 0.749207569 0.936071309 0.814507608 0.935788435 0.547607814 0.794579733 4 1 0.721761633 0.814190617 1 0.516372558 0.786499832 5 0.784170589 0.998897781 0.862320372 0.462680257 0.493866189 0.869094378 6 0.435981174 1 0.483727811 0.529772577 0.807653462 7 0.424214773 0.389514544 0.534182164 0.931065396 1 8 0.389011622 0.39804476 1 0.998726055 0.868140501 9 0.355105177 0.371112283 1 0.85882617

10 0.496013832 0.428906886 0.935192459 11 0.749074178 12 � 13 �

Ban

d nu

mbe

r

14 � � � � � �

Supplementary Table S5. Relative band intensities for FP2 experiments.

� � Sample name � � FP2_0 FP2_7 FP2_21 FP2_44

1 0.769622307 0.573377298 0.641411579 0.82433765 2 0.766376512 0.898098378 0.672698574 0.921109723 3 1.568383004 0.67577578 0.66768138 0.792913023 4 1 0.754821808 0.707480692 0.889356387 5 1.104086751 1 0.618524156 0.813030044 6 0.643405134 0.657211256 0.539940245 0.896259286 7 0.829448215 0.891031062 1 8 0.655724402 0.780145442 0.704884623 9 0.694231337 0.807091719 0.535796463

10 0.766745353 1 � 11 0.41467952 � 12 � 13 �

Ban

d nu

mbe

r

14 � � � �

Supplementary Table S6. Relative band intensities for LW experiments.

� � Sample name � � LW_0 LW_7 LW_21 LW_28 LW_42 LW_65

1 0.838104594 0.398134111 0.431633868 0.4279436 0.477179943 0.413348887 2 1 0.565597668 0.489593376 0.718549716 0.446613629 0.350256124 3 0.63462438 0.83090379 0.844666251 1 0.740605046 0.365725009 4 0.525961269 0.54483965 1 0.57748886 0.972050665 0.616219506 5 0.614089251 0.499533528 0.774116713 0.591405725 0.822045431 0.589186996 6 0.714893816 0.487230321 0.57783701 0.664652384 0.670836386 0.522391845 7 0.63462438 1 0.72273578 0.599218702 1 0.752041386 8 0.561839274 0.625830904 0.801508535 0.918635171 0.561184968 0.538165035 9 0.430863505 0.498542274 0.614699711 0.761643167 0.571077149 0.666379267

10 0.449059781 0.926472303 0.860148585 0.5248613 1 11 0.773365142 0.714909545 0.736522558 0.948115839 12 0.409697216 13 0.515899985

Ban

d nu

mbe

r

14 � � � � � 0.810062383

Supplementary Table S7. Band locations in the DGGE gel image.

� Sample name

�

FP1_

0

FP1_

7

FP1_

21

FP1_

28

FP1_

42

FP1_

65

FP2_

0

FP2_

7

FP2_

21

FP2_

44

LW_0

LW_7

LW_2

1

LW_2

8

LW_4

2

LW_6

5

1 1 1 1 1

1 1 1 1 1 � 2 2 2 1 3 2 1

2 2 1 2 2 1 1 2 3 2 4 2 3 1

3 2 2 2 2 3 4 3 3 5 4 3 � 3 2 6 3 3 � 3

4 4 4 3 3 4 3 4 4 5 4 4 7

5 5 5 4 4 4 3 5 6 5 5 8 6 5 4 5 5 5 4 5

6 6 5 9 6 6 5 6 6 7 6 6 6 7 7

7 � 6 8 7 8 7 10 7 7 8 6 7 7 8 7 7 9 8 9 7 9 � 10 8 5 8 � 8 9 8 10 8 9 11 8 � 6 9 9 9 10 8 12 10 � 9 11 10 � 10 13 11 10 11 9 11 14

8 9

9 11

Ban

d lo

catio

n

10 10

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