GPAC GNAR GNAR. Firmicutes Clostridia Clostridiales GPAC Clostridiaceae Lachnospiracheae Peptococcaceae Peptostreptococcaceae Ruminococcaceae

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1 Clinical evaluation of total amount of Urinary cytokeratin 8 and cytokeratin 18 measurement for detection of transitional cell carcinoma of the bladder. Kunitomo WATANABE Takatsugu GOTO Kaori TANAKA GPAC GNAR GNAR GPAC GPAC Finegoldia magna Peptostreptococcus magnus GPAC Firmicutes Clostridia 1 GPAC GPAC S rrna GPAC 16S rrna GPAC Low GC Firmicutes Clostridia Clostridiales Family GPAC ClostridiaceaeLachnospiracheaePeptococcaceaePeptostreptococcaceae Ruminococcaceae 5 Family Incertae sedis Peptococcaceae Peptococcus Peptostreptococcaceae Peptostreptococcus Family Incertae Sedis Family XI Peptoniphilus Anaerococcus Finegoldia Parvimonas Gallicola Peptoniphilus Anaerococcus Finegoldia Parvimonas Peptostreptococcus Firmicutes Clostridia Clostridiales Clostridiaceae SarcinaLachnospiracheae Coprococcus Ruminococcaceae Ruminococcus GPAC Ruminococcus Clostridium coccoides Blautia Murdochiella M. asaccharolytica Fastidiosipila F. sanguinis Division of Anaerobe Research, Life Science Research Center, Gifu University (1-1 Yanagido, Gifu)

2 Ruminococcaceae Streptococcus 3 Streptococcus parvulus Streptococcus heliortinreducens 2 High GC Actinobacteria Actinobacteria Coriobacteriales Atopobium Slackia 2 Firmicutes Streptococcus morbillorum Firmicutes Bacilli Bacillales Family Incertae Sedis Gemella Bacilli Bacillales StaphylococcaceaeStaphylococcus saccharolyticus Peptococcus saccharolyticus GPAC GPAC Actinobacteria Propionibacterium Corynebacterium Firmicutes Bacilli Staphylococcus Finegoldia Peptostreptococcus Peptoniphilus Anaerococcus GPAC 8 GPAC Firmicutes Clostridia Clostridiales Ruminococcus Coprococcus Blautia Finegoldia Parvimonas Peptostreptococcus Peptoniphilus Anaerococcus GPAC 9 Firmicutes Bacilli Lactobacillus Actinobacteria Atopobium Fir- GPAC Firmicutes Clostridia Clostridiales GPAC 1 Peptococcaceae Genus Peptococcus P. niger Peptococcus niger 2Peptostreptococcaceae Genus Peptostreptococcus P. anaerobius Peptostreptococcus anaerobius P. stomatis 3 Family XI. Incertae sedis Genus Peptoniphilus P. asaccharolyticus Peptostreptococcus asaccharolyticus Peptococcus asaccharolyticus P. harei Peptostreptococcus harei P. indolicus Peptostreptococcus indolicus Peptococcus indolicus P. ivorii Peptostreptococcus ivorii P. lacrimalis Peptostreptococcus lacrimalis P. gorbachii P. olsenii Genus Anaerococcus A. prevotii Peptostreptococcus prevotii Peptococcus prevotii A. tetradius Peptostreptococcus tetradius A. lactolyticus A. octavius A. hydrogenalis A. vaginalis Peptostreptococcus vaginalis A. murdochii Genus Finegoldia F. magna Peptostreptococcus magnus Peptococcus magnus Genus Parvimonas P. micra Micromonas micros Peptostreptococcus micros Peptococcus glycinophilus 2 Genus Gallicola G. barnesae Peptostreptococcus barnesae 4 3 Genus Murdochiella M. asaccharolytica 1 Peptostreptococcus P. stomatis 3 Peptoniphilus P. gorbachii P. olsenii 2 Anaerococcus A. murdochii 2 Gallicola G. barnesae 3 Murdochiella 2010

3 GPAC Firmicutes Clostridia Clostridiales 1 Clostridiaceae Genus Sarcina S. ventriculi 2Lachnospiracheae Genus Coprococcus C. catus C. comes C. eutactus 3Ruminococcaceae Genus Ruminococcus R. albus R. bromii Peptostreptococcus bromii R. gnavus R. lactaris R. obeum R. torques R. callidus R. flavefaciens 5 Genus Fastidiosipila F. sanguinis Family Incertae sedis 2 Genus Blautia B. producta Ruminococcus productus Peptostreptococcus productus B. hansenii Ruminococcus hansenii Streptococcus hansenii B. coccoides Clostridium coccoides B. hydrogenotrophica* Ruminococcus hydrogenotrophicus B. shinkii B. luti 5 Family Incertae sedis 3 Genus Anaerosphaera 1 Fastidiosipila F. sanguinis 26 2 Blautia Ruminococcus Clostridium coccoides 3 Anaerosphaera A. aminiphila Peptoniphilus16S rrna 89 GPAC Firmicutes Clostridia Clostridiales 1. Firmicutes Bacilli Bacillales 1Staphylococcaceae Genus Staphylococcus S. saccharolyticus Peptococcus saccharolyticus 2 Family incertae sedis Genus Gemella G. morbillorum Streptococcus morbillorum Peptostreptococcus morbillorum 2. Firmicutes Bacilli Lactobacillales 1 Streptococcaceae Genus Streptococcus S. intermedius Peptostreptococcus intermedius S. constellatus Peptococcus constellatus 3. Actinobacteria Actinobacteria Coriobacteriales 1 Coriobacteriaceae Genus Atopobium Aparvulum Streptococcus parvulus Peptostreptococcus parvulus Genus Slackia S. heliotrinreducens Peptostreptococcus heliortinreducens Peptococcus heliotrinreducens

4 micutes Clostridia Veillonella GPAC 10 Finegoldia Parvimonas Peptostreptococcus Peptoniphilus Anaerococcus Firmicutes Clostridia GPAC GPAC Bacteroides fragilis group Prevotella GNAR , 11 GPAC 5 Finegoldia magna Parvimonas micra Peptostreptococcus anaerobius Peptoniphilus asaccharolyticus Anaerococcus prevotii GPAC Staphylococcus aureus Streptococcus anginosus group GPAC GPAC P. asaccharolyticus P. anaerobius P. micra GPAC GPAC GPAC GNAR 1 GPAC 1 Finegoldia F. magna Peptostreptococcus magnus 12, 13 F. magna 2 Parvimonas Parvimonas micra Micromonas micros Peptostreptococcus micros GPAC Peptoniphilus Peptoniphilus GPAC Peptoniphilus asaccharolyticus Peptostreptococcus asaccharolyticus 4 Peptoniphilus 1 4 Anaerococcus Anaerococcus GPAC Anaerococcus prevotii Peptostreptococcus prevotii 4 5 Peptostreptococcus Peptostreptococcus Peptostreptococcus anaerobius 2006 Peptostreptococcus stomatis 3 P. anaerobius GPAC

5 P. anaerobius P. anaerobius P. stomatis P. anaerobius GPAC GPAC GPAC F. magna , 15 P. anaerobius F. magna P. micra GPAC GPAC - P. asacharolyticus F. magna A. prevotii MIC90 8 g ml GPAC GPAC GPAC GPAC F. magna F. magna ProteinL 16 Peptostreptococcal albumin-binding protein Protein PAB 17 Subtilisin-like serine proteinase SufA 18 Finegoldia Adehesion factor Protein FAF 19 ProteinL F. magna F. magna erm Finegoldia magnapeptostreptococcus magnus

6 10 LPXTG 16 - L C S100A8 A9 cathelicidin LL-37 IFN- MIG CXCL9 albumin Protein PAB albumin 17 albumin 20 SufA α - helical cathelicidin C-X-C fibrinogen fibrin network 18 Protein FAF F. magna Basement membrane Protein BM40 LL37 19 F. magna ATCC ,797,577 bp, GC ,163 bp, GC 29.7 DDBJ EMBL GeneBank AP AP low-gc ORF 84 leading transposase 1 1, ORF 0 (Mb) ori C rrn D (kb) 1.5 ppep1 189,163 bp 50 rrn A rrn B 1.0 F. magna ATCC ,797,577 bp : sortase : sortase 0.5 rrn C J : Translation, ribosomal structure and biogenesis K : Transcription L : DNA replication, recombination and repair D : Cell division and chromosome partitioning O : Posttranslational modification, protein turnover, chaperones M : Cell envelope biogenesis, outer membrane N : Cell motility and secretion P : Inorganic ion transport and metabolism T : Signal transduction mechanisms C : Energy production and conversion G : Carbohydrate transport and metabolism E : Amino acid transport and metabolism F : Nucleotide transport and metabolism H : Coenzyme metabolism I : Lipid metabolism Q : Secondary metabolites biosynthesis, transport and catabolism R,S : General function prediction only, Function unknown F. magna ATCC Sortase G C GC skew G C G C trna rrna ORF COG

7 F. magna Clostridium ortholog plots Sortase protease transpeptidase C LPXTG Protein PAB ProteinL Sortase F. magna Sortase 21 F. magna ORF Pfam, SignalP Protein PAB Protein FAF Clostridium difficile Cwp66 Staphylococcus aureus 21 Kb G C Anaerococcus hydrogenalis Anaerococcus lactolyticus Anaerococcus octavius Anaerococcus prevotii Anaerococcus tetradius Anaerococcus vaginalis Anaerococcus sp. DSM 7454 ATCC ATCC 9321 ATCC Oral Taxon 788 F0127 ATCC ,889 2,139 1, ,100 1, Finishing Finishing Published Ref.22 Finishing Draft Seq. WashU JGI MBRI Peptoniphilus asaccharolyticus Peptoniphilus duerdenii Peptoniphilus harei Peptoniphilus indolicus Peptoniphilus ivorii Peptoniphilus lacrimalis Peptoniphilus sp. DSM Onderdonk ACS-315-V-Sch6 ATCC BAA-1640 ACS-146-V-Sch2b ACS-024-V-Col5 ATCC B ACS-171-V-Sch10b Oral Taxon 836 F0141 ACS-146-V-Sch6a Oral Taxon 375 F0436 Oral Taxon 386 F0131 1, Draft Seq. JGI BROAD MBRI MBRI BROAD BROAD Peptostreptococcus anaerobius Peptostreptococcus stomatis Peptostreptococcus sp. Finegoldia magna Parvimonas micra Parvimonas sp Hillier 653-L DSM ACS-065-V-Col13 ATCC ATCC ACS -171-V-Col3 BVS033A4 SY403409CC ATCC Hillier Oral Taxon 110 F0139 Oral Taxon 393 F0440 2,083 1, ,889 1, Draft Seq. Published Ref.21 Draft Seq. Finishing GOLD Genomes Online Database WashU, Washington University ; BCM HGSC, Human Genome Sequencing Center at the Baylor College of Medicine ; MBRI, Medical Biofilm Research Institute ; BROAD, The Broad Institute ; JGI, Department of Energy Joint Genome Institute ;, The J. Craig Venter Institute ; WakaU, Wakayama Medical University, ;, MBRI WakaU MBRI WashU

8 F. magna fructose fructose F. magna 5 Gly, Ser, Thr, Asp, Asn X-Pro aminopeptidase 21 F. magna ATCC A. prevotii ATCC Anaerococcus 6 10 Peptoniphilus 6 16 Peptostreptococcus 2 6 F. magna 5 P. micra , 24 GPAC GPAC 1 Murdoch DA: Gram-positive anaerobic cocci. Clin. Microbiol. Rev. : , Murdoch DA, Shah HN: Reclassification of Peptostreptococcus magnus Prevot 1933 Holdeman and Moore 1972 as Finegoldia magna comb. nov. and Peptostreptococcus micros Prevot 1933 Smith 1957 as Micromonas micros comb. nov. Anaerobe. : , Downes J, Wade WG: Peptostreptococcus stomatis sp. nov., isolated from the human oral cavity. Int. J. Syst. Evol. Microbiol. : , Song Y, Liu C, Finegold SM: Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin. J. Clin. Microbiol. : , Tindall BJ, Euzéby JP: Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002, respectively. Int. J. Syst. Evol. Microbiol. : , Ezaki T, Kawamura Y, Li N, et al.: Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus. Int. J. Syst. Evol. Microbiol. : , Ludwig W, Schleifer KH, Whitman WB: Revised road map to the phylum Firmicutes in Bergey s Manual of Systematic bacteriology. 2nd ed. Vol.3 The Firmicutes, De Vos P, Garrity D, Jones NR et al. eds, Springer-Verlag, New York, Gao Z, Tseng CH, Pei Z, et al.: Molecular analysis of human forearm superficial skin bacterial flora. Proc. Natl. Acad. Sci. U S A. : , : , Zouh X, Bent SJ, Schneider MG, et al.: Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology. : , : p8, Levy PY, Fenollar F, Stein A, et al.: Finegoldia magna: a forgotten pathogen in prosthetic joint infection rediscovered by molecular biology. Clin. Infect. Dis. : , Kerneis S, Matta M, Hoi AB, et al.: Postoperative mediastinitis due to Finegoldia magna with negative blood cultures. J. Clin. Microbiol. : , Hawser SP: Activity of tigecycline and comparators against recent clinical isolates of Finegoldia magna from Europe. Eur. J. Clin. Microbiol. Infect. Dis. : , Brazier J, Chmelar D, Dubreuil L, et al.: European surveillance study on antimicrobial susceptibility of Gram-positive anaerobic cocci. Int. J. Antimicrob. Agents. : , Smith D, D Argy R, Nilsson M, et al.: Whole-body autoradiography reveals that the Peptostreptococcus magnus immunoglobulin-binding domains of protein L preferentially target B lymphocytes in the spleen and lymph nodes in vivo. Cell Microbiol. : , Lejon S, Frick IM, Björck L, et al.: Crystal structure and biological implications of abacterial albumin binding module in complex with human serum albumin. J. Biol. Chem. : , Karlsson C, Andersson ML, Collin M, et al.: SufA a bacterial enzyme that cleaves fibrinogen and blocks fibrin network formation. Microbiology. : , 2009.

9 19 Frick IM, Karlsson C, Mörgelin M, et al.: Identification of a novel protein promoting the colonization and survival of Finegoldia magna, a bacterial commensal and opportunistic pathogen. Mol. Microbiol. : , de Chateau M, Holst E, Bjorck L: Protein PAB, an albumin-binding bacterial surface protein promoting growth and virulence. J. Biol. Chem. : , Goto T, Yamashita A, Hirakawa H, et al.: Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen. DNA Res. : 39-47, LaButti K, Pukall R, Steenblock K, et al.: Complete genome sequence of Anaerococcus prevotii type strain PC1 T. Stand. Genomic Sci. : ISSN , GOLD Genomes Online Database v nline.org index2.htm 24 NCBI Entrez Genome sites entrez db=genome

10 1.5 0 (Mb) ori C rrn D (kb) ppep1 189,163 bp 50 rrn A rrn B 1.0 F. magna ATCC ,797,577 bp : sortase : sortase 0.5 rrn C J : K : L : D : O : M : N : P : T : C : G : E : F : H : I : Q : R,S : Translation, ribosomal structure and biogenesis Transcription DNA replication, recombination and repair Cell division and chromosome partitioning Posttranslational modification, protein turnover, chaperones Cell envelope biogenesis, outer membrane Cell motility and secretion Inorganic ion transport and metabolism Signal transduction mechanisms Energy production and conversion Carbohydrate transport and metabolism Amino acid transport and metabolism Nucleotide transport and metabolism Coenzyme metabolism Lipid metabolism Secondary metabolites biosynthesis, transport and catabolism General function prediction only, Function unknown F. magna ATCC Sortase G C GC skew G CG C trna rrna ORF COG