Figures and figure supplements - eLife · 2016. 8. 31. · Figures and figure supplements...

Figures and figure supplements

Phylogenomic analysis supports the ancestral presence of LPS-outer membranes inthe Firmicutes

Luisa CS Antunes et al

Antunes et al. eLife 2016;5:e14589. DOI: 10.7554/eLife.14589 1 of 18

RESEARCH ARTICLE

http://dx.doi.org/10.7554/eLife.14589

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Figure 1. Transmission electron microscopy of a member of Negativicutes and a member of Halanaerobiales. Ultrathin sections of high-pressure frozen

cells of the Negativicutes member Megamonas rupellensis (A,C), and the Halanerobiales member Halanaerobium saccharolyticum (B,D). A Gram-

negative like cell wall architecture is visible for both taxa (A,B): a cytoplasmic membrane (CM) surrounding the cytoplasm (C), a thin peptidoglycan layer

(PG), and an outer membrane (OM). Pili-like structures (P) are also visible in M. rupelllensis. In some cases and due to a preparation artifact caused by

swelling of the cells, the OM detaches from the IM creating an enlarged periplasmic space (PP) between two dividing cells (C,D). In these cases, the

peptidoglycan becomes more apparent as it is also the case for an electron dense surface coat (SC), which might represent lipopolysaccharide (LPS) or

a potential S-layer. Scale bars: 200 nm (A,C) and 100 nm (B,D).

DOI: 10.7554/eLife.14589.003


Research article Cell Biology Genomics and Evolutionary Biology

http://dx.doi.org/10.7554/eLife.14589.003


0.5

Negativicutes

Clostridiales

Thermoanaerobacterales

Lactobacillales

Bacillales

Natranaerobiales

Halanaerobiales

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0.98

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0.96

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0.93

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0.67

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1

0.53

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1

1

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11

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0.65

1

0.98

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0.96

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0.99

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0.99

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0.99

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0.78

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1

1

0.99

0.97

0.61

1

1

1

1

1

1

0.99

0.99

1

1

1

1

1

1

1

1

1

1

0.83

1

1

1

1

0.96

0.99

0.87

0.88

1

0.99

1

1

0.86

1

1

1

1

1

1

1

0.57

1

1

1

1

1

1

0.82

1

1

1

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1

1

0.79

1

1

1

1

0.96

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0.73

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0.99

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Selenomonas noxia ATCC 43541

Bacillus atrophaeus 1942

Chlamydia trachomatis D_UW-3_CX

Listeria monocytogenes 07PF0776

Amphibacillus xylanus NBRC 15112

Lactobacillus sanfranciscensis TMW 1.1304

Lactobacillus plantarum JDM1

Enterococcus faecalis D32

Bacillus halodurans C-125

Nostoc punctiforme PCC 73102

Streptomyces coelicolor A32

Selenomonas sputigena ATCC 35185

Clostridium perfringens str. 13

Megasphaera sp. UPII 135-E

Ruminococcus albus 7

Bacillus pseudofirmus OF4

Paenibacillus sp. Y412MC10

Anaerococcus prevotii DSM 20548

Paenibacillus mucilaginosus 3016

Orenia marismortui DSM 5156

Selenomonas infelix ATCC 43532

Streptococcus sanguinis SK36

Natranaerobius thermophilus JW_NM-WN-LF

Veillonella ratti ACS-216-V-Col6b

Eubacterium siraeum 70_3

Syntrophomonas wolfei subsp. wolfei str. Goettingen

Megamonas rupellensis DSM 19944

Megasphaera genomosp. type_1 str. 28L

Caldicellulosiruptor obsidiansis OB47

Lactobacillus delbrueckii subsp. bulgaricus 2038

Megasphaera micronuciformis F0359

Ethanoligenens harbinense YUAN-3

Thermosediminibacter oceani DSM 16646

Centipeda periodontii DSM 2778

Deinococcus radiodurans R1

Geobacillus sp. WCH70

Streptococcus pneumoniae 670-6B

Streptococcus salivarius CCHSS3

Thermosinus carboxydivorans Nor1

Selenomonas sp. oral taxon 138 str. F0429

Acidaminococcus fermentans DSM 20731

Selenomonas bovis DSM 23594

Thermobacillus composti KWC4

Thermoanaerobacter wiegelii Rt8.B1

Veillonella atypica KON

Eubacterium infirmum F0142

Veillonella parvula DSM 2008

Thermoanaerobacter italicus Ab9

Halanaerobium hydrogeniformans

Eubacterium rectale ATCC 33656

Solibacillus silvestris StLB046

Lactococcus garvieae ATCC 49156

Clostridium lentocellum DSM 5427

Dialister succinatiphilus YIT 11850

Selenomonas ruminantium subsp. lactilytica TAM6421

Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

Selenomonas artemidis F0399

Staphylococcus epidermidis ATCC 12228

Bacillus sp. 1NLA3E

Streptococcus oralis Uo5

Ruegeria pomeroyi DSS-3

Oceanobacillus iheyensis HTE831

Candidatus Arthromitus sp. SFB-mouse-Japan

Clostridium beijerinckii NCIMB 8052

Clostridium botulinum A2 str. Kyoto

Lactobacillus buchneri NRRL B-30929

Bacillus licheniformis 9945A

Clostridium saccharolyticum WM1

Streptococcus pyogenes A20

Desulfitobacterium hafniense DCB-2

Desulfotomaculum kuznetsovii DSM 6115

Bacillus pumilus SAFR-032

Desulfotomaculum gibsoniae DSM 7213

Butyrivibrio fibrisolvens 16_4

Clostridium difficile 630

Streptococcus mutans GS-5

Bacteroides thetaiotaomicron VPI-5482

Dialister invisus DSM 15470

Coprococcus catus GD_7

Desulfotomaculum carboxydivorans CO-1-SRB

Mitsuokella sp. oral taxon 131 str. W9106

Halobacillus halophilus DSM 2266

Carboxydothermus hydrogenoformans Z-2901

Clostridium ljungdahlii DSM 13528

Lactococcus lactis subsp. cremoris A76

Clostridium pasteurianum BC1

Moorella thermoacetica ATCC 39073

Lactobacillus casei ATCC 334

Listeria ivanovii subsp. ivanovii PAM 55

Bacillus cereus 03BB102

Aerococcus urinae ACS-120-V-Col10a

Roseburia intestinalis M50_1

Phascolarctobacterium sp. CAG:266

Thermoanaerobacter tengcongensis MB4

Enterococcus casseliflavus EC20

Oenococcus oeni PSU-1

Geobacillus kaustophilus HTA426

Bacillus selenitireducens MLS10

Carnobacterium maltaromaticum LMA28

Macrococcus caseolyticus JCSC5402

Thermaerobacter marianensis DSM 12885

Lactobacillus reuteri DSM 20016

Filifactor alocis ATCC 35896

Lactobacillus johnsonii DPC 6026

Acetobacterium woodii DSM 1030

Candidatus Desulforudis audaxviator MP104C

Clostridium thermocellum ATCC 27405

Thermincola potens JR

Bacillus cellulosilyticus DSM 2522

Desulfotomaculum ruminis DSM 2154

Lactobacillus helveticus CNRZ32

Syntrophobotulus glycolicus DSM 8271

Desulfotomaculum reducens MI-1

Bacillus clausii KSM-K16

Desulfotomaculum acetoxidans DSM 771

Gemella bergeriae ATCC 700627

Alkaliphilus metalliredigens QYMF

Clostridium novyi NT

Bacillus coagulans 2-6

Sporolactobacillus inulinus CASD

Anaeromusa acidaminophila DSM 3853

Listeria innocua Clip11262

Veillonella dispar ATCC 17748

Eubacterium limosum KIST612

Desulfosporosinus acidiphilus SJ4

Clostridium cellulolyticum H10

Alkaliphilus oremlandii OhILAs

Mahella australiensis 50-1 BON

Halanaerobium saccharolyticum subsp. saccharolyticum DSM 6643

Lysinibacillus sphaericus C3-41

Flavobacterium johnsoniae UW101

Caldicellulosiruptor bescii DSM 6725

Succinispira mobilis DSM 6222

Zymophilus raffinosivorans DSM 20765

Faecalibacterium prausnitzii L2-6

Heliobacterium modesticaldum Ice1

Paenibacillus polymyxa E681

Lactobacillus sakei subsp. sakei 23K

Clostridium sticklandii DSM 519

Lactobacillus ruminis ATCC 27782

Thermoanaerobacterium xylanolyticum LX-11

Acetonema longum DSM 6540

Ruminococcus bromii L2-63

Bacillus subtilis subsp. subtilis str. 168

Anaeroglobus geminatus F0357

Pediococcus pentosaceus ATCC 25745

Clostridium cellulovorans 743B

Desulfitobacterium dehalogenans ATCC 51507

Sporomusa ovata DSM 2662

Bacillus cytotoxicus NVH 391-98

Tepidanaerobacter acetatoxydans Re1

Pediococcus claussenii ATCC BAA-344

Rhodopirellula baltica SH 1

Lactobacillus brevis ATCC 367

Anoxybacillus flavithermus WK1

Bacillus megaterium DSM 319

Alicyclobacillus acidocaldarius LAA1

Enterococcus hirae ATCC 9790

Clostridium phytofermentans ISDg

Bacillus anthracis str. Ames Ancestor

Staphylococcus haemolyticus JCSC1435

Exiguobacterium sibiricum 255-15

Mitsuokella multacida DSM 20544

Staphylococcus aureus 04-02981

Brevibacillus brevis NBRC 100599

Megasphaera elsdenii DSM 20460

Halothermothrix orenii H 168

Enterococcus sp. 7L76

Cohnella laeviribosi DSM 21336

Leuconostoc gasicomitatum LMG 18811

Pelosinus fermentans DSM 17108

Bacillus weihenstephanensis KBAB4

Halobacteroides halobius DSM 5150

Ammonifex degensii KC4

Exiguobacterium sp. AT1b

Pelotomaculum thermopropionicum SI

Clostridium tetani E88

Butyrivibrio proteoclasticus B316

Halanaerobium praevalens DSM 2228

Bacillus thuringiensis str. Al Hakam

Finegoldia magna ATCC 29328

Thermoanaerobacter brockii subsp. finnii Ako-1

Phascolarctobacterium succinatutens YIT 12067

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293

Sulfobacillus acidophilus DSM 10332

Clostridium sp. SY8519

Roseburia hominis A2-183

Lactobacillus fermentum IFO 3956

Tetragenococcus halophilus NBRC 12172

Weissella koreensis KACC 15510

Clostridium saccharoperbutylacetonicum N1-4HMT

Dialister micraerophilus DSM 19965

Thermoanaerobacterium thermosaccharolyticum DSM 571

Bacillus amyloliquefaciens DSM 7

Clostridium acetobutylicum ATCC 824

Enterococcus faecium Aus0004

Syntrophothermus lipocalidus DSM 12680

Megamonas funiformis YIT 11815

Acetohalobium arabaticum DSM 5501

Desulfitobacterium dichloroeliminans LMG P-21439


Veillonella sp. oral taxon 780 str. F0422

Desmospora sp. 8437

Chlorobium limicola DSM 245

Symbiobacterium thermophilum IAM 14863

Melissococcus plutonius ATCC 35311

Corynebacterium glutamicum ATCC 13032

Geobacillus thermoglucosidasius C56-YS93

Clostridium kluyveri DSM 555

Acidaminococcus intestini RyC-MR95

Oscillibacter valericigenes

Selenomonas flueggei ATCC 43531

Desulfosporosinus meridiei DSM 13257

Trichodesmium erythraeum IMS101

Desulfosporosinus orientis DSM 765

Lactobacillus salivarius CECT 5713

Vibrio fischeri ES114

Eubacterium eligens ATCC 27750

CLASS CLOSTRIDIA

CLASS BACILLI

CLASS CLOSTRIDIA

OUTGROUP

Peptococcaceae

Figure 2. Phylum-level phylogeny of the Firmicutes. Bayesian phylogeny of the Firmicutes based on a concatenation of 47 orthologous ribosomal

proteins comprising 5551 amino acid positions and the CAT+GTR+G4 model. Values at nodes represent Bayesian posterior probabilities. The scale bar

represents the average number of substitutions per site. For details on analyses, see Materials and methods.

DOI: 10.7554/eLife.14589.004





0.5

Negativicutes

Clostridiales

Thermoanaerobacterales

Lactobacillales

Bacillales

Natranaerobiales

Halanaerobiales

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0.53

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11

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0.65

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0.98

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0.96

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0.99

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0.78

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0.99

0.97

0.61

1

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1

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1

1

0.99

0.99

1

1

1

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1

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0.83

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0.96

0.99

0.87

0.88

1

0.99

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0.86

1

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0.57

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0.82

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0.79

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0.96

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Bacillus atrophaeus 1942

Chlamydia trachomatis D_UW-3_CX

Listeria monocytogenes 07PF0776

Amphibacillus xylanus NBRC 15112

Lactobacillus sanfranciscensis TMW 1.1304

Lactobacillus plantarum JDM1

Enterococcus faecalis D32

Bacillus halodurans C-125

Nostoc punctiforme PCC 73102

Streptomyces coelicolor A32


Clostridium perfringens str. 13

Megasphaera sp. UPII 135-E

Ruminococcus albus 7

Bacillus pseudofirmus OF4

Paenibacillus sp. Y412MC10

Anaerococcus prevotii DSM 20548

Paenibacillus mucilaginosus 3016



Streptococcus sanguinis SK36

Natranaerobius thermophilus JW_NM-WN-LF

Veillonella ratti ACS-216-V-Col6b

Eubacterium siraeum 70_3

Syntrophomonas wolfei subsp. wolfei str. Goettingen


Megasphaera genomosp. type_1 str. 28L

Caldicellulosiruptor obsidiansis OB47

Lactobacillus delbrueckii subsp. bulgaricus 2038


Ethanoligenens harbinense YUAN-3

Thermosediminibacter oceani DSM 16646


Deinococcus radiodurans R1

Geobacillus sp. WCH70

Streptococcus pneumoniae 670-6B

Streptococcus salivarius CCHSS3





Thermobacillus composti KWC4

Thermoanaerobacter wiegelii Rt8.B1

Veillonella atypica KON

Eubacterium infirmum F0142


Thermoanaerobacter italicus Ab9


Eubacterium rectale ATCC 33656

Solibacillus silvestris StLB046

Lactococcus garvieae ATCC 49156

Clostridium lentocellum DSM 5427



Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130


Staphylococcus epidermidis ATCC 12228

Bacillus sp. 1NLA3E

Streptococcus oralis Uo5

Ruegeria pomeroyi DSS-3

Oceanobacillus iheyensis HTE831

Candidatus Arthromitus sp. SFB-mouse-Japan

Clostridium beijerinckii NCIMB 8052

Clostridium botulinum A2 str. Kyoto

Lactobacillus buchneri NRRL B-30929

Bacillus licheniformis 9945A

Clostridium saccharolyticum WM1

Streptococcus pyogenes A20

Desulfitobacterium hafniense DCB-2

Desulfotomaculum kuznetsovii DSM 6115

Bacillus pumilus SAFR-032

Desulfotomaculum gibsoniae DSM 7213

Butyrivibrio fibrisolvens 16_4

Clostridium difficile 630

Streptococcus mutans GS-5

Bacteroides thetaiotaomicron VPI-5482


Coprococcus catus GD_7

Desulfotomaculum carboxydivorans CO-1-SRB


Halobacillus halophilus DSM 2266

Carboxydothermus hydrogenoformans Z-2901

Clostridium ljungdahlii DSM 13528

Lactococcus lactis subsp. cremoris A76

Clostridium pasteurianum BC1

Moorella thermoacetica ATCC 39073

Lactobacillus casei ATCC 334

Listeria ivanovii subsp. ivanovii PAM 55

Bacillus cereus 03BB102

Aerococcus urinae ACS-120-V-Col10a

Roseburia intestinalis M50_1


Thermoanaerobacter tengcongensis MB4

Enterococcus casseliflavus EC20

Oenococcus oeni PSU-1

Geobacillus kaustophilus HTA426

Bacillus selenitireducens MLS10

Carnobacterium maltaromaticum LMA28

Macrococcus caseolyticus JCSC5402

Thermaerobacter marianensis DSM 12885

Lactobacillus reuteri DSM 20016

Filifactor alocis ATCC 35896

Lactobacillus johnsonii DPC 6026

Acetobacterium woodii DSM 1030

Candidatus Desulforudis audaxviator MP104C

Clostridium thermocellum ATCC 27405

Thermincola potens JR

Bacillus cellulosilyticus DSM 2522

Desulfotomaculum ruminis DSM 2154

Lactobacillus helveticus CNRZ32

Syntrophobotulus glycolicus DSM 8271

Desulfotomaculum reducens MI-1

Bacillus clausii KSM-K16

Desulfotomaculum acetoxidans DSM 771

Gemella bergeriae ATCC 700627

Alkaliphilus metalliredigens QYMF

Clostridium novyi NT

Bacillus coagulans 2-6

Sporolactobacillus inulinus CASD


Listeria innocua Clip11262


Eubacterium limosum KIST612

Desulfosporosinus acidiphilus SJ4

Clostridium cellulolyticum H10

Alkaliphilus oremlandii OhILAs

Mahella australiensis 50-1 BON


Lysinibacillus sphaericus C3-41

Flavobacterium johnsoniae UW101

Caldicellulosiruptor bescii DSM 6725


Zymophilus raffinosivorans DSM 20765

Faecalibacterium prausnitzii L2-6

Heliobacterium modesticaldum Ice1

Paenibacillus polymyxa E681

Lactobacillus sakei subsp. sakei 23K

Clostridium sticklandii DSM 519

Lactobacillus ruminis ATCC 27782

Thermoanaerobacterium xylanolyticum LX-11


Ruminococcus bromii L2-63

Bacillus subtilis subsp. subtilis str. 168


Pediococcus pentosaceus ATCC 25745

Clostridium cellulovorans 743B

Desulfitobacterium dehalogenans ATCC 51507


Bacillus cytotoxicus NVH 391-98

Tepidanaerobacter acetatoxydans Re1

Pediococcus claussenii ATCC BAA-344


Lactobacillus brevis ATCC 367

Anoxybacillus flavithermus WK1

Bacillus megaterium DSM 319

Alicyclobacillus acidocaldarius LAA1

Enterococcus hirae ATCC 9790

Clostridium phytofermentans ISDg

Bacillus anthracis str. Ames Ancestor

Staphylococcus haemolyticus JCSC1435

Exiguobacterium sibiricum 255-15


Staphylococcus aureus 04-02981

Brevibacillus brevis NBRC 100599



Enterococcus sp. 7L76

Cohnella laeviribosi DSM 21336

Leuconostoc gasicomitatum LMG 18811


Bacillus weihenstephanensis KBAB4


Ammonifex degensii KC4

Exiguobacterium sp. AT1b

Pelotomaculum thermopropionicum SI

Clostridium tetani E88

Butyrivibrio proteoclasticus B316


Bacillus thuringiensis str. Al Hakam

Finegoldia magna ATCC 29328

Thermoanaerobacter brockii subsp. finnii Ako-1


Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293

Sulfobacillus acidophilus DSM 10332

Clostridium sp. SY8519

Roseburia hominis A2-183

Lactobacillus fermentum IFO 3956

Tetragenococcus halophilus NBRC 12172

Weissella koreensis KACC 15510

Clostridium saccharoperbutylacetonicum N1-4HMT


Thermoanaerobacterium thermosaccharolyticum DSM 571

Bacillus amyloliquefaciens DSM 7

Clostridium acetobutylicum ATCC 824

Enterococcus faecium Aus0004

Syntrophothermus lipocalidus DSM 12680



Desulfitobacterium dichloroeliminans LMG P-21439


Veillonella sp. oral taxon 780 str. F0422

Desmospora sp. 8437

Chlorobium limicola DSM 245

Symbiobacterium thermophilum IAM 14863

Melissococcus plutonius ATCC 35311

Corynebacterium glutamicum ATCC 13032

Geobacillus thermoglucosidasius C56-YS93

Clostridium kluyveri DSM 555


Oscillibacter valericigenes


Desulfosporosinus meridiei DSM 13257


Desulfosporosinus orientis DSM 765

Lactobacillus salivarius CECT 5713

Vibrio fischeri ES114

Eubacterium eligens ATCC 27750

CLASS CLOSTRIDIA

CLASS BACILLI

CLASS CLOSTRIDIA

OUTGROUP

Peptococcaceae




Figure 2—figure supplement 1. Results of IC congruence test for the 47 ribosomal proteins. IC values were mapped onto the ribosomal protein

concatenation phylogeny shown in Figure 2. Branches in red indicate congruence among markers according to IC tests. Raw results of the test are

provided as Additional Data in Dryad (Antunes et al., 2016).

DOI: 10.7554/eLife.14589.005





0.3

Ruminococcus bromii L2-63@fusion

Streptococcus oralis Uo5@fusionLactobacillus casei ATCC 334@fusion

Enterococcus casseliflavus EC20@fusion

Clostridium pasteurianum BC1@fusion

Acetonema longum DSM 6540@fusion

Desulfotomaculum reducens MI-1@fusion

Gemella bergeriae ATCC 700627@fusion

Veillonella atypica KON@fusion

Bacillus selenitireducens MLS10@fus

Faecalibacterium prausnitzii L2-6@fusion

Clostridium cellulovorans 743B@fusion

Thermoanaerobacterium xylanolyticum LX-11@fusion

Brevibacillus brevis NBRC 100599@fusion

Enterococcus faecalis D32@fusion

Centipeda periodontii DSM 2778@fusion

Carnobacterium maltaromaticum LMA28@fusi

Selenomonas flueggei ATCC 43531@fusion

Ruegeria pomeroyi DSS-3@fusion

Halothermothrix orenii H 168@fusion

Anaerococcus prevotii DSM 20548@fusion

Orenia marismortui DSM 5156@fusion

Bacillus pseudofirmus OF4@fusion

Candidatus Arthromitus sp. SFB-mouse-Japan@fusion

Pelosinus fermentans DSM 17108@fusion

Zymophilus raffinosivorans DSM 20765@fus

Clostridium lentocellum DSM 5427@fusion

Tepidanaerobacter acetatoxydans Re1@fusion

Clostridium beijerinckii NCIMB 8052@fusion

Listeria innocua Clip11262@fusion

Lactobacillus johnsonii DPC 6026@fusion

Megamonas rupellensis DSM 19944@fusion

Mitsuokella multacida DSM 20544@fusion

Halanaerobium praevalens DSM 2228@fusion

Staphylococcus haemolyticus JCSC1435@fusion

Lactococcus garvieae ATCC 49156@fusion

Candidatus Desulforudis audaxviator MP104C@fusion

Bacillus coagulans 2-6@fusion

Natranaerobius thermophilus JW_NM-WN-LF@fusion

Trichodesmium erythraeum IMS101@fusion

Veillonella parvula DSM 2008@fusion

Acetohalobium arabaticum DSM 5501@fusion

Ethanoligenens harbinense YUAN-3@fusion

Acetobacterium woodii DSM 1030@fusion

Bacillus sp. 1NLA3E@fusion

Alkaliphilus metalliredigens QYMF@fusi

Clostridium acetobutylicum ATCC 824@fusio

Desulfitobacterium dichloroeliminans LMG P-21439@fu

Geobacillus sp. WCH70@fusion

Bacillus licheniformis 9945A@fusion

Vibrio fischeri ES114@fusion

Streptococcus sanguinis SK36@fusion

Leuconostoc gasicomitatum LMG 18811@fusion

Amphibacillus xylanus NBRC 15112@fusion

Halobacillus halophilus DSM 2266@fusion

Moorella thermoacetica ATCC 39073@fusion

Bacillus halodurans C-125@fusion

Bacteroides thetaiotaomicron VPI-5482@fusio

Carboxydothermus hydrogenoformans Z-2901@fus

Selenomonas artemidis F0399@fusion

Lactobacillus reuteri DSM 20016@fusion

Eubacterium siraeum 70_3@fusion

Paenibacillus mucilaginosus 3016@fusio

Caldicellulosiruptor bescii DSM 6725@fusion

Lactobacillus brevis ATCC 367@fusionPediococcus pentosaceus ATCC 25745@fusion

Selenomonas sp. oral taxon 138 str. F0429@fusion

Dialister succinatiphilus YIT 11850@fusi

Succinispira mobilis DSM 6222@fusion

Chlorobium limicola DSM 245@fusion

Heliobacterium modesticaldum Ice1@fusion

Desulfosporosinus acidiphilus SJ4@fusion

Geobacillus kaustophilus HTA426@fusion

Caldicellulosiruptor obsidiansis OB47@fusion

Clostridium kluyveri DSM 555@fusion

Pelotomaculum thermopropionicum SI@fu

Pediococcus claussenii ATCC BAA-344@fusion

Clostridium saccharolyticum WM1@fusi

Lactobacillus sakei subsp. sakei 23K@fusion

Mahella australiensis 50-1 BON@fusion

Clostridium perfringens str. 13@fusion

Anoxybacillus flavithermus WK1@fusion

Clostridium sp. SY8519@fusion

Roseburia intestinalis M50_1@fusion

Lactobacillus salivarius CECT 5713@fusion

Syntrophothermus lipocalidus DSM 12680@fusion

Thermosediminibacter oceani DSM 16646@fusion

Selenomonas infelix ATCC 43532@fusion

Staphylococcus epidermidis ATCC 12228@fusion

Desulfotomaculum carboxydivorans CO-1-SRB@fusi

Thermoanaerobacter brockii subsp. finnii Ako-1@fusion

Exiguobacterium sibiricum 255-15@fusion

Lactococcus lactis subsp. cremoris A76@fusion

Bacillus anthracis str. Ames Ancestor@fusion

Dialister micraerophilus DSM 19965@fusio

Bacillus pumilus SAFR-032@fusion

Lactobacillus delbrueckii subsp. bulgaricus 2038@fusion

Megasphaera micronuciformis F0359@fusi

Clostridium novyi NT@fusion

Thermoanaerobacterium thermosaccharolyticum DSM 571@fusion

Filifactor alocis ATCC 35896@fusion

Thermobacillus composti KWC4@fusion

Lactobacillus buchneri NRRL B-30929@fusion

Alkaliphilus oremlandii OhILAs@fusion

Selenomonas bovis DSM 23594@fusion

Clostridium cellulolyticum H10@fusio

Paenibacillus polymyxa E681@fusion

Bacillus cytotoxicus NVH 391-98@fusion

Clostridium ljungdahlii DSM 13528@fusion

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293@fusion

Oscillibacter valericigenes@fusion

Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130@fusion

Desulfotomaculum ruminis DSM 2154@fusion

Eubacterium infirmum F0142@fusion

Nostoc punctiforme PCC 73102@fusion

Listeria monocytogenes 07PF0776@fusio

Megasphaera genomosp. type_1 str. 28L@fusion

Sporolactobacillus inulinus CASD@fusion

Thermoanaerobacter italicus Ab9@fusion

Flavobacterium johnsoniae UW101@fusion

Corynebacterium glutamicum ATCC 13032@fusion

Veillonella ratti ACS-216-V-Col6b@fusion

Butyrivibrio fibrisolvens 16_4@fusion

Sporomusa ovata DSM 2662@fusionAnaeromusa acidaminophila DSM 3853@fusi

Thermoanaerobacter tengcongensis MB4@fusion

Desulfitobacterium dehalogenans ATCC 51507@fusion

Bacillus megaterium DSM 319@fusion

Eubacterium limosum KIST612@fusion

Oceanobacillus iheyensis HTE831@fusion

Bacillus weihenstephanensis KBAB4@f

Streptococcus salivarius CCHSS3@fusion

Enterococcus faecium Aus0004@fusion

Clostridium tetani E88@fusion

Sulfobacillus acidophilus DSM 10332@fusion

Desulfotomaculum gibsoniae DSM 7213@fusion

Selenomonas sputigena ATCC 35185@fusion

Lactobacillus plantarum JDM1@fusion

Bacillus amyloliquefaciens DSM 7@fu

Bacillus thuringiensis str. Al Hakam@fusion

Ammonifex degensii KC4@fusion

Deinococcus radiodurans R1@fusion

Desulfotomaculum kuznetsovii DSM 6115@fusion

Roseburia hominis A2-183@fusion

Coprococcus catus GD_7@fusion

Thermaerobacter marianensis DSM 12885@fusion

Chlamydia trachomatis 434_Bu@fusion

Megasphaera elsdenii DSM 20460@fusion

Acidaminococcus fermentans DSM 20731@fusion

Mitsuokella sp. oral taxon 131 str. W9106@fusion

Selenomonas noxia ATCC 43541@fusion

Enterococcus hirae ATCC 9790@fusion

Lactobacillus fermentum IFO 3956@fusion

Macrococcus caseolyticus JCSC5402@fusion

Thermoanaerobacter wiegelii Rt8.B1@fusion

Syntrophomonas wolfei subsp. wolfei str. Goettingen@fusion

Megamonas funiformis YIT 11815@fusion

Veillonella dispar ATCC 17748@fusion

Solibacillus silvestris StLB046@fusion

Butyrivibrio proteoclasticus B316@fusi

Bacillus subtilis subsp. subtilis str. 168@fusion

Aerococcus urinae ACS-120-V-Col10a@fusion

Halanaerobium hydrogeniformans@fus

Paenibacillus sp. Y412MC10@fusion

Alicyclobacillus acidocaldarius LAA1@fusioDesmospora sp. 8437@fusion

Desulfosporosinus meridiei DSM 13257@fusion

Megasphaera sp. UPII 135-E@fusion

Rhodopirellula baltica SH 1@fusion

Bacillus clausii KSM-K16@fusion

Desulfitobacterium hafniense DCB-2@fusion

Phascolarctobacterium sp. CAG 207@fusion

Anaeroglobus geminatus F0357@fusion

Lysinibacillus sphaericus C3-41@fusion

Weissella koreensis KACC 15510@fusion

Finegoldia magna ATCC 29328@fusion

Lactobacillus sanfranciscensis TMW 1.1304@fus

Enterococcus sp. 7L76@fusion

Dialister invisus DSM 15470@fusion

Eubacterium eligens ATCC 27750@fusion

Veillonella sp. oral taxon 780 str. F0422@fusion

Listeria ivanovii subsp. ivanovii PAM 55@fusion

Clostridium phytofermentans ISDg@fusi

Clostridium sticklandii DSM 519@fusion

Bacillus atrophaeus 1942@fusion

Streptomyces coelicolor A32@fusion

Exiguobacterium sp. AT1b@fusion

Streptococcus pneumoniae 670-6B@fusion

Lactobacillus helveticus CNRZ32@fusion

Clostridium thermocellum ATCC 27405@fusion

Bacillus cereus 03BB102@fusion

Streptococcus mutans GS-5@fusion

Phascolarctobacterium succinatutens YIT 12067@fusion

Desulfosporosinus orientis DSM 765@fusion

Bacillus cellulosilyticus DSM 2522@fus

Thermosinus carboxydivorans Nor1@fusi

Melissococcus plutonius ATCC 35311@fusion

Halanaerobium saccharolyticum subsp. saccharolyticum DSM 6643@fus

Cohnella laeviribosi DSM 21336@fusion

Clostridium saccharoperbutylacetonicum N1-4HMT@fusion

Selenomonas ruminantium subsp. lactilytica TAM6421@fusion

Eubacterium rectale ATCC 33656@fusion

Acidaminococcus intestini RyC-MR95@fusion

Tetragenococcus halophilus NBRC 12172@fusion

Lactobacillus ruminis ATCC 27782@fusion

Clostridium difficile 630@fusion

Thermincola potens JR@fusion

Halobacteroides halobius DSM 5150@fusion

Geobacillus thermoglucosidasius C56-YS93@

Oenococcus oeni PSU-1@fusion

Phascolarctobacterium sp. CAG 266@fusion

Clostridium botulinum A2 str. Kyoto@fusion

Ruminococcus albus 7@fusion

Staphylococcus aureus 04-02981@fusion

Streptococcus pyogenes A20@fusion

Syntrophobotulus glycolicus DSM 8271@fusion

Desulfotomaculum acetoxidans DSM 771@fusion

Symbiobacterium thermophilum IAM 14863@fusion

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Figure 2—figure supplement 2. Maximum likelihood phylogeny of the Firmicutes. The tree was obtained by PhyML 3.0 based from the same

concatenation of 47 orthologous ribosomal proteins as the Bayesian tree in Figure 2 and the LG+G4 model. Values at nodes represent non-parametric

bootstrap values calculated on 100 replicates of the original dataset. The scale bar represents the average number of substitutions per site.

DOI: 10.7554/eLife.14589.006





Figure 2—figure supplement 3. Results of AU test for 12 alternative topologies. Full results of the test are provided as Additional Data in

Dryad (Antunes et al., 2016).

Figure 2—figure supplement 3 continued on next page




Figure 2—figure supplement 3 continued

DOI: 10.7554/eLife.14589.007





Perm

ease

ATPas

e

kdsB

kdsA

kdsD

kdsC

waa

M

lptC

lptA

lptB

lptF

G

lpxA

lpxC

waa

M

skp

skp

lepB

fabZ

hypoth

etic

al

hypoth

etic

al (C

OG08

16)

hypoth

etic

al (C

OG43

72)

mre

B-li

ke

murA

tolC

Perm

ease

Hyp

othet

ical

(COG 0

750)

carb

oxyla

se

epsL

tam

B

bamA/ta

mA

skp

lpxD

lpxB

msb

A

lpxK

lpxI

waa

A

ompM

ompM

ompM

skp

skp

spoIID

murA

Peptid

ase

M23

tam

Bsk

plp

xDlp

xB

msb

Alp

xK

kdsB

kdsA

kdsD

kdsC

waa

Mlp

tClp

tAlp

tB

lptF

Glp

xAlp

xCfa

bZ

lpxI

waa

A

hypoth

etic

alflg

Fflg

Aflg

I

hypoth

etic

al

flgG

Hyp

othet

ical

(COG 0

750)

flgH

flgJ

spoIII

Dgln

Qsm

c

hypoth

etic

al (C

OG43

72)

hypoth

etic

al (C

OG08

16)

YkuD

Peptid

ase

S8lp

tGlp

tF

ostA d

omai

n

conta

inin

gprote

in lptC

ostA

HALANAEROBIALESAcetohalobium arabaticum DSM 5501

NEGATIVICUTESAcidaminococcus fermentans DSM 20731

NEGATIVICUTESVeillonella parvula DSM 2008

HALANAEROBIALESHalobacteroides halobius DSM 5150CP003359 REGION: 2416970..246956

NC_014378 REGION: 2287090..2329181

NC_013740 REGION: 1843921..1889918

NC_013520 REGION: 631051..677624

ompM

ompM

bamA/ta

mA

Figure 3. Conserved genomic locus for cell envelope components. Co-localization of the genes coding for LPS synthesis and transport, OMP assembly

and structural OMPs in the Negativicutes and the Halanaerobiales. Representatives of the 2 families of Negativicutes and the 2 families of

Halanaerobiales are shown (for full distribution and accession numbers see Supplementary file 1). Genes are colored according to their functional

class: LPS synthesis and transport (green), OMP assembly (blue), flagellum (light pink), OM-PG attachment (red), hypothetical (brown), efflux (purple)

(see text for discussion). White boxes indicate proteins not known to being related to the OM or non-conserved proteins whose connection with the

OM is unclear. The figure was obtained by EasyFig (Sullivan et al., 2011), where vertical lines represent BLAST hits with a cutoff of 0.0001.

DOI: 10.7554/eLife.14589.008





A

Negativicutes

Halanaerobiales

Cyanobacteria

Armatimonadetes

Synergistetes

Atribacteria

Dictyoglomi

Deinococcus -Thermus

Spirochaetes

Fusobacteria

Epsilonproteobacteria

Gammaproteobacteria / Betaproteobacteria

Alphaproteobacteria

Chrysiogenetes

Deltaproteobacteria

Thermodesulfobacteria

Deltaproteobacteria

Acidobacteria

Nitrospirae

Deferribacteres

Aquificae

Bacteroidetes/Chlorobi group

Planctomycetes

Chlamydiae/Verrucomicrobia group

Halanaerobiales

Natranaerobiales

Lactobacillales Bacillales

Other Thermoanaerobacterales Other Clostridiales

Clostridiales Family XVIII. Incertae Sedis Clostridiales Family XVII. Incertae Sedis

Negativicutes

Peptococcaceae Thermoanaerobacteraceae

B

0.5

0.91

0.99

0.63

0.92

0.53

1

1

0.83

0.65

1

1

0.63

0.99

1

0.58

1

0.83

1

0.76

1

0.62

1

1

1

0.96

0.99

1

1

1

1

1

0.93

0.52

1

0.99

1

1

0.95

0.99

1

0.95

1

0.93

1

1

1

1

1

1

1

0.53

1

1

1

0.83

0.95

1

1

1

1

1

0.94

1

1

0.59

0.99

1

1

1

0.57

1

1

0.99

0.99

1

0.91

0.7

0.98

0.66

1

0.99

1

1

0.94

0.66

0.99

0.86

0.73

1

0.73

0.53

1

1

1

0.89

0.51

0.62

0.72

0.99

1

1

1

1

1

1

0.98

1

0.99

1

0.99

1

1

1

1

0.88

1

1

1

1

0.99

0.56

0.67

1

0.72

1

0.95

1

1

1

1

Gemmatimonas aurantiaca T-27-Gemmatimonadetes

Leptotrichia buccalis C-1013-b

Leptospirillum ferrooxidans C2-3


Candidatus Protochlamydia amoebophila UWE25

Thiobacillus denitrificans ATCC 25259

Desulfurispirillum indicum S5


Propionispira raffinosivorans DSM 20765

Phascolarctobacterium CAG207

Anabaena variabilis ATCC 29413

Cytophaga hutchinsonii ATCC 33406


Thermanaerovibrio acidaminovorans DSM 6589

Pelodictyon phaeoclathratiforme BU-1


Rubinisphaera brasiliensis DSM 5305

Chlamydia muridarum str. Nigg

Hahella chejuensis KCTC 2396

Megasphaera UPII 135

Dictyoglomus turgidum DSM 6724

Aquifex aeolicus VF5

Acetobacter pasteurianus IFO 3283-01

Thermodesulfobacterium geofontis OPF15

Acaryochloris marina MBIC11017

Truepera radiovictrix DSM 17093

Candidatus Solibacter usitatus Ellin6076



Marinithermus hydrothermalis DSM 14884

Pseudomonas aeruginosa PAO1

Melioribacter roseus P3M-2

Microcystis aeruginosa NIES-843


Simkania negevensis Z



Rickettsia prowazekii str. Madrid E


Chromobacterium violaceum ATCC 12472

Nitrospira defluvii

Prosthecochloris aestuarii DSM 271

Fimbriimonas ginsengisoli Gsoil 348

Bartonella bacilliformis KC583



Syntrophobacter fumaroxidans MPOB

Opitutus terrae PB90-1


Akkermansia muciniphila ATCC BAA-835

Nautilia profundicola AmH

Granulicella mallensis MP5ACTX8

Vibrio cholerae O1 biovar El Tor str. N16961

Desulfurobacterium thermolithotrophum DSM 11699




Cyanothece sp. PCC 7424

Phycisphaera mikurensis NBRC 102666


Dictyoglomus thermophilum H-6-12

Porphyromonas gingivalis ATCC 33277

Chthonomonas calidirosea T49

Pelobacter carbinolicus DSM 2380


Candidatus Caldatribacterium saccharofermentans OP9-77CS

Chitinivibrio alkaliphilus ACht1-Unclassified Bacteria


Ignavibacterium album JCM 16511

Dinoroseobacter shibae DFL 12 = DSM 16493


Synechococcus elongatus PCC 6301

Leptospira biflexa serovar Patoc strain Patoc 1 Ames

Desulfobulbus propionicus DSM 2032



Candidatus Caldatribacterium californiense OP9-cSCG



Myxococcus xanthus DK 1622

Allochromatium vinosum DSM 180



Pedobacter heparinus DSM 2366

Waddlia chondrophila WSU 86-1044

Nitrospina gracilis 3_211 - Nitrospinae


Isosphaera pallida ATCC 43644

Fusobacterium nucleatum subsp. nucleatum ATCC 25586

Arcobacter butzleri ED-1

Meiothermus ruber DSM 1279

Deferribacter desulfuricans SSM1Flexistipes sinusarabici DSM 4947


Veillonella oral taxon 780

Acinetobacter baumannii 1656-2



Thermodesulfatator indicus DSM 15286

Veillonella atypica KONVeillonella ratti ACS-216-V-Col6b

Megasphaera genomosp type_1 28L

Burkholderia ambifaria AMMD



Chlorobaculum parvum NCIB 8327

Bacteroides fragilis 638R

Helicobacter pylori 26695

Stigmatella aurantiaca DW4_3-1

Helicobacter acinonychis str. Sheeba


Chrysiogenes arsenatis DSM 11915

Calditerrivibrio nitroreducens DSM 19672

Agrobacterium radiobacter K84

Escherichia coli str. K-12 substr. MG1655

Geobacter uraniireducens Rf4

Alteromonas macleodii str. Black Sea 11

Anaerobaculum mobile DSM 13181

Campylobacter jejuni subsp. jejuni NCTC 11168

Thermodesulfovibrio yellowstonii DSM 11347

Methylacidiphilum infernorum V4


Candidatus Cloacimonas acidaminovorans str. Evry-Cloacimonetes



Brachyspira hyodysenteriae WA1

Bordetella parapertussis Bpp5


Aminobacterium colombiense DSM 12261

Acidobacterium capsulatum ATCC 51196



Turneriella parva DSM 21527

Legionella longbeachae NSW150

Coraliomargarita akajimensis DSM 45221

Persephonella marina EX-H1

Gloeobacter violaceus PCC 7421


Ilyobacter polytropus DSM 2926

Figure 4. Phylogenetic tree of core LPS components. (A) Bayesian phylogeny based on a concatenation of orthologs of the four core components of

the LPS biosynthesis pathway (lpxABCD), comprising 898 amino acid positions and the CAT+GTR+G4 model. Values at nodes represent Bayesian

Figure 4 continued on next page




Figure 4 continued

posterior probabilities. The scale bar represents the average number of substitutions per site. For details on analyses, see Materials and methods. (B)

Schematic representation of the Firmicutes phylum-level phylogeny from Figure 2, onto which putative losses of the OM are mapped (red crosses). See

text for discussion.

DOI: 10.7554/eLife.14589.009





A

Negativicutes

Halanaerobiales

Cyanobacteria

Armatimonadetes

Synergistetes

Atribacteria

Dictyoglomi

Deinococcus -Thermus

Spirochaetes

Fusobacteria

Epsilonproteobacteria

Gammaproteobacteria / Betaproteobacteria

Alphaproteobacteria

Chrysiogenetes

Deltaproteobacteria

Thermodesulfobacteria

Deltaproteobacteria

Acidobacteria

Nitrospirae

Deferribacteres

Aquificae

Bacteroidetes/Chlorobi group

Planctomycetes

Chlamydiae/Verrucomicrobia group

Halanaerobiales

Natranaerobiales

Lactobacillales Bacillales

Other Thermoanaerobacterales Other Clostridiales

Clostridiales Family XVIII. Incertae Sedis Clostridiales Family XVII. Incertae Sedis

Negativicutes

Peptococcaceae Thermoanaerobacteraceae

B

0.5

1

0.99

0.62

1

0.52

0.95

1

1

1

1

1

0.57

1

1

0.99

1

0.7

1

1

1

1

1

1

0.88

1

1

0.99

1

1

1

Gemmatimonas aurantiaca T-27-Gemmatimonadetes

Leptotrichia buccalis C-1013-b

Leptospirillum ferrooxidans C2-3


Candidatus Protochlamydia amoebophila UWE25

Thiobacillus denitrificans ATCC 25259

Desulfurispirillum indicum S5


Propionispira raffinosivorans DSM 20765


Anabaena variabilis ATCC 29413

Cytophaga hutchinsonii ATCC 33406


Thermanaerovibrio acidaminovorans DSM 6589

Pelodictyon phaeoclathratiforme BU-1


Rubinisphaera brasiliensis DSM 5305

Chlamydia muridarum str. Nigg

Hahella chejuensis KCTC 2396

Megasphaera UPII 135

Dictyoglomus turgidum DSM 6724

Aquifex aeolicus VF5

Acetobacter pasteurianus IFO 3283-01

Thermodesulfobacterium geofontis OPF15

Acaryochloris marina MBIC11017

Truepera radiovictrix DSM 17093

Candidatus Solibacter usitatus Ellin6076



Marinithermus hydrothermalis DSM 14884

Pseudomonas aeruginosa PAO1

Melioribacter roseus P3M-2

Microcystis aeruginosa NIES-843


Simkania negevensis Z



Rickettsia prowazekii str. Madrid E


Chromobacterium violaceum ATCC 12472

Nitrospira defluvii

Prosthecochloris aestuarii DSM 271

Fimbriimonas ginsengisoli Gsoil 348

Bartonella bacilliformis KC583



Syntrophobacter fumaroxidans MPOB

Opitutus terrae PB90-1


Akkermansia muciniphila ATCC BAA-835

Nautilia profundicola AmH

Granulicella mallensis MP5ACTX8

Vibrio cholerae O1 biovar El Tor str. N16961

Desulfurobacterium thermolithotrophum DSM 11699




Cyanothece sp. PCC 7424

Phycisphaera mikurensis NBRC 102666


Dictyoglomus thermophilum H-6-12

Porphyromonas gingivalis ATCC 33277

Chthonomonas calidirosea T49

Pelobacter carbinolicus DSM 2380


Candidatus Caldatribacterium saccharofermentans OP9-77CS

Chitinivibrio alkaliphilus ACht1-Unclassified Bacteria


Ignavibacterium album JCM 16511

Dinoroseobacter shibae DFL 12 = DSM 16493


Synechococcus elongatus PCC 6301

Leptospira biflexa serovar Patoc strain Patoc 1 Ames

Desulfobulbus propionicus DSM 2032



Candidatus Caldatribacterium californiense OP9-cSCG



Myxococcus xanthus DK 1622

Allochromatium vinosum DSM 180



Pedobacter heparinus DSM 2366

Waddlia chondrophila WSU 86-1044

Nitrospina gracilis 3_211 - Nitrospinae


Isosphaera pallida ATCC 43644

Fusobacterium nucleatum subsp. nucleatum ATCC 25586

Arcobacter butzleri ED-1

Meiothermus ruber DSM 1279

Deferribacter desulfuricans SSM1Flexistipes sinusarabici DSM 4947


Veillonella oral taxon 780

Acinetobacter baumannii 1656-2



Thermodesulfatator indicus DSM 15286

Veillonella atypica KONVeillonella ratti ACS-216-V-Col6b

Megasphaera genomosp type_1 28L

Burkholderia ambifaria AMMD



Chlorobaculum parvum NCIB 8327

Bacteroides fragilis 638R

Helicobacter pylori 26695

Stigmatella aurantiaca DW4_3-1

Helicobacter acinonychis str. Sheeba


Chrysiogenes arsenatis DSM 11915

Calditerrivibrio nitroreducens DSM 19672

Agrobacterium radiobacter K84

Escherichia coli str. K-12 substr. MG1655

Geobacter uraniireducens Rf4

Alteromonas macleodii str. Black Sea 11

Anaerobaculum mobile DSM 13181

Campylobacter jejuni subsp. jejuni NCTC 11168

Thermodesulfovibrio yellowstonii DSM 11347

Methylacidiphilum infernorum V4


Candidatus Cloacimonas acidaminovorans str. Evry-Cloacimonetes



Brachyspira hyodysenteriae WA1

Bordetella parapertussis Bpp5


Aminobacterium colombiense DSM 12261

Acidobacterium capsulatum ATCC 51196



Turneriella parva DSM 21527

Legionella longbeachae NSW150

Coraliomargarita akajimensis DSM 45221

Persephonella marina EX-H1

Gloeobacter violaceus PCC 7421


Ilyobacter polytropus DSM 2926

0.92

0.66

1

1

1

10.99

0.76

0.56 1

1

11

1

1

0.67

0.95

0.95

1

1

0.94

1

1

0.99

0.99

1

1

0.99

0.83

1

1

1

1

0.99

0.99

1

0.73

0.72

1

0.99

1

1

0.53

1

11

1

0.98

0.530.65

11

0.991

1

11

1

1

1

0.83

0.86

0.58

0.89

1

1

0.63

1

0.73

1

0.53

1

0.94

0.95

10.93

0.66

0.93

0.99

0.62

0.83

0.63

1

0.51

1

0.91

1

1

1

0.99

0.720.99

1

0.591

1

0.98

1

1




Figure 4—figure supplement 1. Results of IC congruence test for the 4 LPS core proteins. IC values were mapped onto the LPS core proteins

concatenation phylogeny shown in Figure 3. Branches in red indicate congruence among markers (IC values>1). Full results of the test are provided as

Additional Data in Dryad (Antunes et al., 2016).

DOI: 10.7554/eLife.14589.010





LptE

LptA

LptF MsbA

LptCLolA

LolB

LolELolDLolD

LolC

ATP

ADP+Pi

ATP

ADP+Pi

ATP

ADP+Pi

ATP

ADP+Pi

LptB

LptG

LptB

LspALgt Lnt

LpxALpxC/FabZLpxD

ATP

ADP+Pi

UDP-GlcNAc UDP-2,3-

diacylglucosamine LpxILipid X

LpxB

Disaccharide

-1-phosphate

LpxK

Lipid A

UDPUMP

D-Arabinose-5PKdsDKdsAKdsCKdsB

CMP-3-deoxy-D-manno-octulosonate (KDO)

WaaA

Lauroyl-(KDO)2-Lipid

(KDO)2-Lipid A

WaaMLauroyl-ACP

ACP

Skp

Sec

PilQ

LptD

BamDBamE

BamC

BamA

BamB

TamB

OmpM

ATP

ADP+PiFlgH FlgI

FlgA

PilQ

Figure 5. Sketched diagram of inferred characteristics of the diderm Firmicutes cell envelope. The main processes discussed in the text are shown

schematically. Components that were not detected in the genomes of Negativicutes and Halanaerobiales are indicated with a dashed outline and grey

font.

DOI: 10.7554/eLife.14589.011





NEGATIVICUTES(Pelosinus fermentans

DSM 17108)

NEGATIVICUTES(Selenomonas ruminantium

subs. lactilytica TAM6421)

HALANAEROBIALES(Acetohalobium

arabaticum DSM 5501)

HALANAEROBIALES(Halothermothrix

orenii H 168)

hslV

hsiU

codY

flgB

flgCfli

Efli

Ffli

Gfli

Hfli

Ifli

J

hslV

hsiU

codY

flgB

flgC

fliE

fliF

fliG

fliH

fliI

fliJ

hslV

hsiU

codY

flgB

fliE

fliH

fliI

fliJ

flgB

flgC

fliE

fliF

fliG

fliH

fliI

fliJ

mgtE

fliF

fliG

mgtE

mgtE

mgtE

flgE

flgE

flgE

flgD

fliK

flgD

fliK

flgD

fliK

flbD

flbD

flbD

flbD

amiC

norM

fliL

fliM

fliY

cheY

fliO

fliP

fliQ

fliR

flhB

fliL

fliM

fliY

cheY

fliO

flhB

fliL

fliM

fliY

fliO

fliP

fliQ

fliR

flhB

fliL

fliM

fliY

fliO

fliP

fliQ

fliR

flhB

motA

motB

motA

motB

flhA

flhF

flhG

pilZ

flhA

flhF

flhG

pilZ

flhA

flhF

flhG

pilZ

flhA

flhF

flhG

pilZ

cheB

cheA

cheB

cheA

cheW

cheC

cheD

cheW

cheC

cheD

cheC

cheD

fliA

fliA

BACILLALES

(Bacillus subtilis

subs. subtilis 6051 HGW)

GAMMA-PROTEOBACTERIA(Escherichia coli str. K-12

MG1655)

fliE

fliF

fliG

fliH

fliI

fliJ

mgtE

flgC

yecT

argSch

eY

cheZ

cheB

cheR

tap

tar

cheW

cheA

motA

flhD

motB

flhC

insA

insBfli

Ffli

Gfli

Hfli

I fliJ

emrE

ybcM

ybcL

dsrB

codY

fliA

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

fliA

Hyp

othet

ical

Hyp

othet

ical

Polym

eras

e

Polym

eras

e

neuB

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

flgC

Hyp

othet

ical

Hyp

othet

ical

fliP

fliQ

fliR

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

flgB

hsiU

hsiV

flgE

flgD

fliK

flbDfli

Lfli

Mfli

Ych

eY

fliO

fliP

fliQ

fliR

flhB

flhA

flhF

flhG

cheB

cheA

cheW

cheC

cheD

fliA

ylxL

rpsB

fliK fli

Lfli

Mfli

Nfli

Zrc

sAfli

Pfli

Qfli

R

fliE flh

Bflh

Aflh

E

CLOSTRIDIALES(Thermincola potens JR)

hsiU

codY

fliE

fliF

fliG

fliH

fliI

fliJ

mgtE

flgE

flgD

fliK

flbDfli

Lfli

Mfli

Ych

eY

fliO

fliP

fliQ

fliR

flhB

flhA

flhF

flhG

pilZ cheB

cheA

cheW

cheC

cheD

fliA

napC

hslV

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

flgBflg

C

NATRANAEROBIALES

(Natranaerobius

thermophilus JW/NM-WN-LF)

flgB

flgC

fliE

fliF

fliG

fliH

fliI

fliJ

mgtE

flgE

flgD

fliK

Hyp

othet

ical

flbD

fliL

fliM

fliY

cheY

fliO

fliP

fliQ

fliR

flhB

motA

motB

flhA

flhF

flhG

pilZ cheB

cheA

cheW

cheC

cheD

codY

Polym

eras

e

fliA

Hyp

othet

ical

Hyp

othet

ical

Figure 5—figure supplement 1. Flagellar gene cluster of Negativicutes and Halanaerobiales. Structure of the region coding for flagellar components

in representative members of Negativicutes and Halanaerobiales, and its conservation with respect to their closely related monoderm relatives

Therminicola potens, and Natranaerobius thermophiles, respectively. By comparison is shown the structure of the operon in Escherichia coli as

representative of a classical diderm. Colors are only meant to highlight synteny.

DOI: 10.7554/eLife.14589.012





HALANAEROBIALES(Halothermothrix orenii H 168)

HALANAEROBIALES(Acetohalobium arabaticum DSM 5501)

flgH

flgI

flgJ

flgF

flgG

flgE

flgA

flgD

flgB

flgC

flgN

flgM

mvi

M

mvi

Nflg

Kflg

L

rne

pilZ fliA

Polym

eras

e

GAMMA-PROTEOBACTERIA(Escherichia coli str. K-12 substr. MG1655)

csaB

spoVT

flgJ

mre

B

flgG

Hyp

othet

ical

atpD

spoIII

D

spoIID

atpG

atpB


flgF

flgH

flgI

flgJ

flgF

flgG

flgA

murA

NEGATIVICUTES(Pelonsinus fermentans DSM 17108)

mre

BPepitd

ase

M23

spoIII

D

spoIID

spoIV

B

ldh

sucD

sucC

Putativ

e

Transp

onase

flgH

flgI

flgJ

flgF

flgG

flgA

NEGATIVICUTES(Selonomonas ruminantium subsp. lactilytica TAM6421)

mre

B

spoIV

B

murA

Acr

iflav

in re

sist

ance

prote

in

Inte

grase

cat

alyt

ic re

gion

Transp

osase

flgF

flgG

murA

NATRANAEROBIALES(Natranaerobius thermophilus JW/NM-WN-LF)

mre

BPepitd

ase

M23

spoIII

D

spoIID

flgJ

M

g

tran

sport

er

Rev

erse

Transc

ripta

se

flgH

flgI

flgJ

flgF

flgG

flgA

murA Pep

itdas

e

M23

spoIII

D

spoIID

spoIV

B

atpD

Hyp

othet

ical

atpB

flgH

flgI

flgJ

flgF

flgG

flgA

rapD fa

bZm

scL

flgF

flgG

mbl

Hyp

othet

ical

ywoH usd

ywoGpucI

ywoF

ywpD yw

pE

ywpFyw

pG

ssbB

BACILLALES(Bacillus subtilis subs subtilis 6051 HGW)

Hyp

othet

ical

S-laye

r pro

tein

lytR

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Am

inodeo

xy-

choris

mat

e ly

ae

Hyp

othet

ical

pfkB

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Hyp

othet

ical

Figure 5—figure supplement 2. Genomic context of the genes coding for flagellar rings in Halanaerobiales and Negativicutes. Structure of the region

coding for components of the flagellar rings (flgA, flgH, flgI) in representative members of Negativicutes and Halanaerobiales, in comparison with their

closely related monoderm relatives Therminicola potens, and Natranaerobius thermophiles, respectively. The genomic structures in Bacillus subtilis and

Escherichia coli are also shown as the most studied models for monoderm and diderm flagella. Colors are only meant to highlight synteny.

DOI: 10.7554/eLife.14589.013





pilC pilA pilDpilB pilT pfkA

Phosphogly

cero

muta

se

aroK

Hyp

othet

ical

Pro

tein

Enolase

Hyp

othet

ical

Pro

tein

Hyp

othet

ical

Pro

tein

Phage

Inte

grase

pilMTriosp

hosphat

e is

omer

ase

pilB pilT pilC pilDNucl

eosi

der R

ecogniti

on

prote

in

aroE

rhaT

pilV

pilTpilB pilC pilA pilApilD

O-a

ntigen

Poly

mer

ase

pilT pilW pilin li

ke h

ypoth

etic

al

pilMpilNpilOmre

R

aroE

pilTpilB pilC pilA pilD pilin li

ke h

ypoth

etic

al

Hyp

othet

ical

Pro

tein

HAD h

ydro

lase

HAD h

ydro

lase

aroE

pilQ pilW li

ke p

rote

in

com

F

pilM pilNpilT

pilTpilB pilC pilM pilN pilO pilA pilA pilin li

ke h

ypoth

etic

al

pilin li

ke h

ypoth

etic

al

ATPas

e

Hyp

othet

ical

Pro

tein

Hyp

othet

ical

Pro

tein

Cu a

min

e oxi

dase

Hyp

othet

ical

Pro

tein

pilTpilB pilC pilA pilDaroE

rhaT

Car

DHyp

othet

ical

Pro

tein

pilM pilN pilO pilQ aroK

dhqS

pilin li

ke h

ypoth

etic

al

pilP

aroK

dhqS

aroC

aroC

pilM pilN pilO pilQpilP aroK

dhqS

aroC

pilin li

ke h

ypoth

etic

al

pilin li

ke h

ypoth

etic

al

aroK

aroC

pilDpilin li

ke h

ypoth

etic

al

pilO

Di-G

MP c

ycla

se

Ferrit

in

Hyp

othet

ical

Pro

tein

Hyp

othet

ical

Pro

tein

galE

pilQ Sulfate

bin

ding p

rote

in

Hyp

othet

ical

Pro

tein

uup

GAMMA-PROTEOBACTERIA(Pseudomonas aeruginosa PA01)

pilB pilC

pilApilD

Hyp

othet

ical

Pro

tein

coaE

nadC

Hyp

othet

ical

Pro

tein

pilM pilN pilO pilQpilP aroK

aroB

ponA

HALANAEROBIALES(Halothermothrix orenii H 168)

NATRANAEROBIALES(Natranaerobius thermophilus JW/NM-WN-LF)

pilin li

ke h

ypoth

etic

al

NEGATIVICUTES(Pelonsinus fermentans DSM 17108)

pilin li

ke h

ypoth

etic

al


pilin li

ke h

ypoth

etic

al

pilin li

ke h

ypoth

etic

al

pilA pilA

HALANAEROBIALES(Acetohalobium arabaticum DSM 5501)

pilin li

ke h

ypoth

etic

al

NEGATIVICUTES(Veillonella parvula DSM 2008)

Figure 5—figure supplement 3. Structure of the main Type IV pilus cluster in Negativicutes and Halanaerobiales. Structure of the region coding for

components of the type IV pilus in representative members of Negativicutes and Halanaerobiales, in comparison with their closely related monoderm

relatives Therminicola potens, and Natranaerobius thermophiles, respectively. The genomic structure in Pseudomonas aeruginosa is also shown as the

most studied model for diderm type IV pili. Colors are only meant to highlight synteny.

DOI: 10.7554/eLife.14589.014





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