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Chapter 1 : Genome Diversity of Spore-Forming

Author: Michael Y. Galperin1
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Affiliations: 1: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
Content Type: Monograph
Publication Year: 2016

Category: Bacterial Pathogenesis

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Abstract:

The taxonomy of spore-forming Gram-positive bacteria has a long and colorful history. In 1872, 35 years after Christian Ehrenberg provided the initial description of (and also ), Ferdinand Cohn assigned it to the genus and family , specifically noting the existence of heat-sensitive vegetative cells and heat-resistant endospores (see reference ). Soon after that, Robert Koch identified as the causative agent of anthrax in cattle and the endospores as a means of the propagation of this organism among its hosts. In subsequent studies, the ability to form endospores, the specific purple staining by crystal violet-iodine (Gram-positive staining, reflecting the presence of a thick peptidoglycan layer and the absence of an outer membrane), and the relatively low (typically less than 50%) molar fraction of guanine and cytosine in the genomic DNA have been used as diagnostic characteristics of the phylum (low-G+C Gram-positive bacteria).

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
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References

/content/book/10.1128/9781555819323.chap1
1. Drews G . 1999. Ferdinand Cohn, a founder of modern microbiology. ASM News 65 : 547.
2. Olsen GJ,, Woese CR,, Overbeek R . 1994. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176 : 1– 6.[PubMed]
3. Woese CR,, Stackebrandt E,, Macke TJ,, Fox GE . 1985. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 6 : 143– 151.[PubMed]
4. Woese CR . 1987. Bacterial evolution. Microbiol Rev 51 : 221– 271.
5. Woese CR,, Kandler O,, Wheelis ML . 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87 : 4576– 4579.[PubMed]
6. Ludwig W,, Schleifer KH . 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15 : 155– 173.[PubMed]
7. Ludwig W,, Strunk O,, Klugbauer S,, Klugbauer N,, Weizenegger M,, Neumaier J,, Bachleitner M,, Schleifer KH . 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 : 554– 568.[PubMed] [CrossRef]
8. Wolf YI,, Rogozin IB,, Grishin NV,, Tatusov RL,, Koonin EV . 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1 : 8. doi:10.1186/1471-2148-1-8. [PubMed]
9. Yutin N,, Puigbo P,, Koonin EV,, Wolf YI . 2012. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7 : e36972. doi:10.1371/journal.pone.0036972. [PubMed] [CrossRef]
10. Wagner M,, Horn M . 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17 : 241– 249.[PubMed] [CrossRef]
11. Gupta RS . 2000. The natural evolutionary relationships among prokaryotes. Crit Rev Microbiol 26 : 111– 131.[PubMed] [CrossRef]
12. Lake JA,, Skophammer RG,, Herbold CW,, Servin JA . 2009. Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci 364 : 2177– 2185.[PubMed] [CrossRef]
13. Mira A,, Pushker R,, Legault BA,, Moreira D,, Rodriguez-Valera F . 2004. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol 4 : 50. doi:10.1186/1471-2148-4-50. [PubMed] [CrossRef]
14. Zhaxybayeva O,, Swithers KS,, Lapierre P,, Fournier GP,, Bickhart DM,, DeBoy RT,, Nelson KE,, Nesbo CL,, Doolittle WF,, Gogarten JP,, Noll KM . 2009. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales . Proc Natl Acad Sci USA 106 : 5865– 5870.[PubMed] [CrossRef]
15. Ciccarelli FD,, Doerks T,, von Mering C,, Creevey CJ,, Snel B,, Bork P . 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311 : 1283– 1287.[PubMed] [CrossRef]
16. Beiko RG . 2011. Telling the whole story in a 10,000-genome world. Biol Direct 6 : 34. doi:10.1186/1745-6150-6-34. [PubMed]
17. Saw JH,, Mountain BW,, Feng L,, Omelchenko MV,, Hou S,, Saito JA,, Stott MB,, Li D,, Zhao G,, Wu J,, Galperin MY,, Koonin EV,, Makarova KS,, Wolf YI,, Rigden DJ,, Dunfield PF,, Wang L,, Alam M . 2008. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol 9 : R161. [PubMed] [CrossRef]
18. Yutin N,, Galperin MY . 9 July 2013. An genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. Environ Microbiol 15 : 2631– 2641.[PubMed] [CrossRef]
19. Gupta RS . 1998. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62 : 1435– 1491.[PubMed]
20. Karlin S,, Mrazek J,, Campbell AM . 1997. Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179 : 3899– 3913.[PubMed]
21. Mrazek J,, Guo X,, Shah A . 2007. Simple sequence repeats in prokaryotic genomes. Proc Natl Acad Sci USA 104 : 8472– 8477.[PubMed]
22. Karlin S,, Campbell AM,, Mrazek J . 1998. Comparative DNA analysis across diverse genomes. Annu Rev Genet 32 : 185– 225.[PubMed] [CrossRef]
23. Sutcliffe IC . 2010. A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18 : 464– 470.[PubMed] [CrossRef]
24. Cavalier-Smith T . 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52 : 7– 76.[PubMed]
25. Cavalier-Smith T . 2006. Rooting the tree of life by transition analyses. Biol Direct 1 : 19. doi:10.1186/1745-6150-1-19. [PubMed] [CrossRef]
26. Woese CR . 1998. Default taxonomy: Ernst Mayr’s view of the microbial world. Proc Natl Acad Sci USA 95 : 11043– 11046.[PubMed]
27. Falah M,, Gupta RS . 1997. Phylogenetic analysis of mycoplasmas based on Hsp70 sequences: cloning of the dnaK ( hsp70) gene region of Mycoplasma capricolum . Int J Syst Bacteriol 47 : 38– 45.[PubMed]
28. Wolf M,, Muller T,, Dandekar T,, Pollack JD . 2004. Phylogeny of Firmicutes with special reference to Mycoplasma ( Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol 54 : 871– 875.[PubMed]
29. Ogawa Y,, Ooka T,, Shi F,, Ogura Y,, Nakayama K,, Hayashi T,, Shimoji Y . 2011. The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of firmicutes and the organism’s intracellular adaptations. J Bacteriol 193 : 2959– 2971.[PubMed] [CrossRef]
30. Zhao Y,, Davis RE,, Lee IM . 2005. Phylogenetic positions of ‘ Candidatus Phytoplasma asteris’ and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. Int J Syst Evol Microbiol 55 : 2131– 2141.[PubMed] [CrossRef]
31. Garrity GM,, Lilburn TG,, Cole JR,, Harrison SH,, Euzeby J,, Tindall BJ, . 2007. The Bacteria: phylum Firmicutes: class Mollicutes , p 317– 332. In Garrity GM (ed), The Taxonomic Outline of Bacteria and Archaea, release 7.7, http://www.taxonomicoutline.org/.
32. Ludwig W,, Schleifer K-H,, Whitman WB, . 2009. Revised road map to the phylum Firmicutes , p 1– 8. In De Vos P,, Garrity GM,, Jones D,, Krieg NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman WB (ed), Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol 3. The Firmicutes. Springer, New York, NY.
33. Verbarg S,, Rheims H,, Emus S,, Fruhling A,, Kroppenstedt RM,, Stackebrandt E,, Schumann P . 2004. Erysipelothrix inopinata sp. nov., isolated in the course of sterile filtration of vegetable peptone broth, and description of Erysipelotrichaceae fam. nov. Int J Syst Evol Microbiol 54 : 221– 225.[PubMed]
34. Sokolova T,, Hanel J,, Onyenwoke RU,, Reysenbach AL,, Banta A,, Geyer R,, Gonzalez JM,, Whitman WB,, Wiegel J . 2007. Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov. Extremophiles 11 : 145– 157.[PubMed] [CrossRef]
35. Marchandin H,, Teyssier C,, Campos J,, Jean-Pierre H,, Roger F,, Gay B,, Carlier JP,, Jumas-Bilak E . 2010. Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes . Int J Syst Evol Microbiol 60 : 1271– 1279.[PubMed] [CrossRef]
36. Tocheva EI,, Matson EG,, Morris DM,, Moussavi F,, Leadbetter JR,, Jensen GJ . 2011. Peptidoglycan remodeling and conversion of an inner membrane into an outer membrane during sporulation. Cell 146 : 799– 812.[PubMed] [CrossRef]
37. Izquierdo JA,, Goodwin L,, Davenport KW,, Teshima H,, Bruce D,, Detter C,, Tapia R,, Han S,, Land M,, Hauser L,, Jeffries CD,, Han J,, Pitluck S,, Nolan M,, Chen A,, Huntemann M,, Mavromatis K,, Mikhailova N,, Liolios K,, Woyke T,, Lynd LR . 2012. Complete genome sequence of Clostridium clariflavum DSM 19732. Stand Genomic Sci 6 : 104– 115.[PubMed] [CrossRef]
38. Möller B,, Ossmer R,, Howard BH,, Gottschalk G,, Hippe H . 1984. Sporomusa, a new genus of gram-negative anaerobic bacteria including Sporomusa sphaeroides spec. nov. and Sporomusa ovata spec. nov. Arch Microbiol 139 : 388– 396.
39. Kane MD,, Breznak JA . 1991. Acetonema longum gen. nov. sp. nov., an H 2/CO 2 acetogenic bacterium from the termite, Pterotermes occidentis . Arch Microbiol 156 : 91– 98.[PubMed]
40. Collins MD,, Lawson PA,, Willems A,, Cordoba JJ,, Fernandez-Garayzabal J,, Garcia P,, Cai J,, Hippe H,, Farrow JA . 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44 : 812– 826.[PubMed]
41. Federhen S . 2012. The NCBI Taxonomy database. Nucleic Acids Res 40 : D136– D143.[PubMed] [CrossRef]
42. Munoz R,, Yarza P,, Ludwig W,, Euzéby J,, Amann R,, Schleifer KH,, Glockner FO,, Rossello-Mora R . 2011. Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 34 : 169– 170.[PubMed] [CrossRef]
43. Onyenwoke RU,, Brill JA,, Farahi K,, Wiegel J . 2004. Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes). Arch Microbiol 182 : 182– 192.[PubMed] [CrossRef]
44. Galperin MY,, Mekhedov SL,, Puigbo P,, Smirnov S,, Wolf YI,, Rigden DJ . 2012. Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 14 : 2870– 2890.[PubMed] [CrossRef]
45. Wu D,, Hugenholtz P,, Mavromatis K,, Pukall R,, Dalin E,, Ivanova NN,, Kunin V,, Goodwin L,, Wu M,, Tindall BJ,, Hooper SD,, Pati A,, Lykidis A,, Spring S,, Anderson IJ,, D’Haeseleer P,, Zemla A,, Singer M,, Lapidus A,, Nolan M,, Copeland A,, Han C,, Chen F,, Cheng JF,, Lucas S,, Kerfeld C,, Lang E,, Gronow S,, Chain P,, Bruce D,, Rubin EM,, Kyrpides NC,, Klenk HP,, Eisen JA . 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462 : 1056– 1060.
46. de Hoon MJ,, Eichenberger P,, Vitkup D . 2010. Hierarchical evolution of the bacterial sporulation network. Curr Biol 20 : R735– R745.[PubMed] [CrossRef]
47. Stragier P, . 2002. A gene odyssey: Exploring the genomes of endospore-forming bacteria, p 519– 526. In Sonenshein AL,, Hoch JA,, Losick R (ed), Bacillus subtilis and Its Closest Relatives: From Genes to Cells. ASM Press, Washington, DC.
48. Zavarzina DG,, Sokolova TG,, Tourova TP,, Chernyh NA,, Kostrikina NA,, Bonch-Osmolovskaya EA . 2007. Thermincola ferriacetica sp. nov., a new anaerobic, thermophilic, facultatively chemolithoautotrophic bacterium capable of dissimilatory Fe(III) reduction. Extremophiles 11 : 1– 7.[PubMed] [CrossRef]
49. Sokolova TG,, Kostrikina NA,, Chernyh NA,, Kolganova TV,, Tourova TP,, Bonch-Osmolovskaya EA . 2005. Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic, hydrogenogenic bacterium from a hot spring of the Lake Baikal area. Int J Syst Evol Microbiol 55 : 2069– 2073.[PubMed] [CrossRef]
50. Byrne-Bailey KG,, Wrighton KC,, Melnyk RA,, Agbo P,, Hazen TC,, Coates JD . 2010. Complete genome sequence of the electricity-producing ‘ Thermincola potens’ strain JR. J Bacteriol 192 : 4078– 4079.[PubMed] [CrossRef]
51. Wrighton KC,, Thrash JC,, Melnyk RA,, Bigi JP,, Byrne-Bailey KG,, Remis JP,, Schichnes D,, Auer M,, Chang CJ,, Coates JD . 2011. Evidence for direct electron transfer by a gram-positive bacterium isolated from a microbial fuel cell. Appl Environ Microbiol 77 : 7633– 7639.[PubMed] [CrossRef]
52. Carlson HK,, Iavarone AT,, Gorur A,, Yeo BS,, Tran R,, Melnyk RA,, Mathies RA,, Auer M,, Coates JD . 2012. Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc Natl Acad Sci USA 109 : 1702– 1707.[PubMed] [CrossRef]
53. Strompl C,, Tindall BJ,, Jarvis GN,, Lunsdorf H,, Moore ER,, Hippe H . 1999. A re-evaluation of the taxonomy of the genus Anaerovibrio, with the reclassification of Anaerovibrio glycerini as Anaerosinus glycerini gen. nov., comb. nov., and Anaerovibrio burkinabensis as Anaeroarcus burkinensis [corrig.] gen. nov., comb. nov. Int J Syst Bacteriol 49( Pt 4) : 1861– 1872.
54. Hermann M,, Popoff M-R,, Senbald M . 1987. Sporomusa paucivorans sp. nov., a methylotrophic bacterium that forms acetic acid from hydrogen and carbon dioxide. Int J Syst Evol Microbiol 37 : 93– 101.
55. Pagani I,, Liolios K,, Jansson J,, Chen IM,, Smirnova T,, Nosrat B,, Markowitz VM,, Kyrpides NC . 2012. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40 : D571– D579.[PubMed] [CrossRef]
56. Pruitt KD,, Tatusova T,, Brown GR,, Maglott DR . 2012. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40 : D130– D135.[PubMed] [CrossRef]
57. Bowen De León K,, Young ML,, Camilleri LB,, Brown SD,, Skerker JM,, Deutschbauer AM,, Arkin AP,, Fields MW . 2012. Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. J Bacteriol 194 : 5456– 5457.[PubMed] [CrossRef]
58. Brown SD,, Podar M,, Klingeman DM,, Johnson CM,, Yang ZK,, Utturkar SM,, Land ML,, Mosher JJ,, Hurt RA Jr,, Phelps TJ,, Palumbo AV,, Arkin AP,, Hazen TC,, Elias DA . 2012. Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. J Bacteriol 194 : 5147– 5148.[PubMed] [CrossRef]
59. Sokolova TG,, Gonzalez JM,, Kostrikina NA,, Chernyh NA,, Slepova TV,, Bonch-Osmolovskaya EA,, Robb FT . 2004. Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park. Int J Syst Evol Microbiol 54 : 2353– 2359.[PubMed] [CrossRef]
60. Rasko DA,, Altherr MR,, Han CS,, Ravel J . 2005. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev 29 : 303– 329.[PubMed] [CrossRef]
61. Makarova KS,, Koonin EV . 2007. Evolutionary genomics of lactic acid bacteria. J Bacteriol 189 : 1199– 1208.[PubMed] [CrossRef]
62. Rigden DJ,, Galperin MY . 2008. Sequence analysis of GerM and SpoVS, uncharacterized bacterial ‘sporulation’ proteins with widespread phylogenetic distribution. Bioinformatics 24 : 1793– 1797.[PubMed] [CrossRef]
63. Horneck G,, Klaus DM,, Mancinelli RL . 2010. Space microbiology. Microbiol Mol Biol Rev 74 : 121– 156.[PubMed] [CrossRef]
64. Setlow P . 2007. I will survive: DNA protection in bacterial spores. Trends Microbiol 15 : 172– 180.[PubMed] [CrossRef]
65. Klobutcher LA,, Ragkousi K,, Setlow P . 2006. The Bacillus subtilis spore coat provides ‘eat resistance’ during phagocytic predation by the protozoan Tetrahymena thermophila . Proc Natl Acad Sci USA 103 : 165– 170.[PubMed] [CrossRef]
66. Lu J,, Nogi Y,, Takami H . 2001. Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol Lett 205 : 291– 297.[PubMed]
67. Takami H,, Takaki Y,, Uchiyama I . 2002. Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30 : 3927– 3935.[PubMed]
68. Takami H,, Takaki Y,, Chee GJ,, Nishi S,, Shimamura S,, Suzuki H,, Matsui S,, Uchiyama I . 2004. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res 32 : 6292– 6303.[PubMed] [CrossRef]
69. Chivian D,, Brodie EL,, Alm EJ,, Culley DE,, Dehal PS,, DeSantis TZ,, Gihring TM,, Lapidus A,, Lin LH,, Lowry SR,, Moser DP,, Richardson PM,, Southam G,, Wanger G,, Pratt LM,, Andersen GL,, Hazen TC,, Brockman FJ,, Arkin AP,, Onstott TC . 2008. Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322 : 275– 278.[PubMed] [CrossRef]
70. Takami H,, Nakasone K,, Takaki Y,, Maeno G,, Sasaki R,, Masui N,, Fuji F,, Hirama C,, Nakamura Y,, Ogasawara N,, Kuhara S,, Horikoshi K . 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis . Nucleic Acids Res 28 : 4317– 4331.[PubMed]
71. Abd El-Rahman HA,, Fritze D,, Sproer C,, Claus D . 2002. Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls. Int J Syst Evol Microbiol 52 : 2127– 2133.[PubMed]
72. Krishnamurthi S,, Ruckmani A,, Pukall R,, Chakrabarti T . 2010. Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillusinsolitus comb. nov., Psychrobacilluspsychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov. Syst Appl Microbiol 33 : 367– 373.[PubMed] [CrossRef]
73. Mesbah NM,, Hedrick DB,, Peacock AD,, Rohde M,, Wiegel J . 2007. Natranaerobius thermophilus gen. nov., sp. nov., a halophilic, alkalithermophilic bacterium from soda lakes of the Wadi An Natrun, Egypt, and proposal of Natranaerobiaceae fam. nov. and Natranaerobiales ord. nov. Int J Syst Evol Microbiol 57 : 2507– 2512.[PubMed] [CrossRef]
74. Zhao B,, Mesbah NM,, Dalin E,, Goodwin L,, Nolan M,, Pitluck S,, Chertkov O,, Brettin TS,, Han J,, Larimer FW,, Land ML,, Hauser L,, Kyrpides N,, Wiegel J . 2011. Complete genome sequence of the anaerobic, halophilic alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF. J Bacteriol 193 : 4023– 4024.[PubMed] [CrossRef]
75. Orsburn BC,, Melville SB,, Popham DL . 2010. EtfA catalyses the formation of dipicolinic acid in Clostridium perfringens . Mol Microbiol 75 : 178– 186.[PubMed] [CrossRef]
76. Huber R,, Rossnagel P,, Woese CR,, Rachel R,, Langworthy TA,, Stetter KO . 1996. Formation of ammonium from nitrate during chemolithoautotrophic growth of the extremely thermophilic bacterium Ammonifex degensii gen. nov. sp. nov. Syst Appl Microbiol 19 : 40– 49.[PubMed] [CrossRef]
77. Rainey FA,, Donnison AM,, Janssen PH,, Saul D,, Rodrigo A,, Bergquist PL,, Daniel RM,, Stackebrandt E,, Morgan HW . 1994. Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium. FEMS Microbiol Lett 120 : 263– 266.[PubMed]
78. Bredholt S,, Sonne-Hansen J,, Nielsen P,, Mathrani IM,, Ahring BK . 1999. Caldicellulosiruptor kristjanssonii sp. nov., a cellulolytic, extremely thermophilic, anaerobic bacterium. Int J Syst Bacteriol 49 : 991– 996.[PubMed]
79. Miroshnichenko ML,, Kublanov IV,, Kostrikina NA,, Tourova TP,, Kolganova TV,, Birkeland NK,, Bonch-Osmolovskaya EA . 2008. Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs. Int J Syst Evol Microbiol 58 : 1492– 1496.[PubMed] [CrossRef]
80. Blumer-Schuette SE,, Ozdemir I,, Mistry D,, Lucas S,, Lapidus A,, Cheng JF,, Goodwin LA,, Pitluck S,, Land ML,, Hauser LJ,, Woyke T,, Mikhailova N,, Pati A,, Kyrpides NC,, Ivanova N,, Detter JC,, Walston-Davenport K,, Han S,, Adams MW,, Kelly RM . 2011. Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus . J Bacteriol 193 : 1483– 1484.[PubMed] [CrossRef]
81. Demain AL,, Newcomb M,, Wu JH . 2005. Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev 69 : 124– 154.[PubMed] [CrossRef]
82. Klenk H-P,, Lapidus A,, Chertkov O,, Copeland A,, Glavina del Rio T,, Nolan M,, Lucas S,, Chen F,, Tice H,, Cheng JF,, Han C,, Bruce D,, Goodwin L,, Pitluck S,, Pati A,, Ivanova N,, Mavromatis K,, Daum C,, Chen A,, Palaniappan K,, Chang YJ,, Land ML,, Hauser LJ,, Jeffries CD,, Detter JC,, Rohde M,, Abt B,, Pukall R,, Göker M,, Bristow J,, Markowitz V,, Hugenholtz P,, Eisen JA . 2011. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2 T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci 5 : 121– 134.[PubMed] [CrossRef]
83. Li B,, Chen Y,, Liu Q,, Hu S,, Chen X . 2011. Complete genome analysis of Sulfobacillus acidophilus strain TPY, isolated from a hydrothermal vent in the Pacific Ocean. J Bacteriol 193 : 5555– 5556.[PubMed] [CrossRef]
84. Wu M,, Ren Q,, Durkin AS,, Daugherty SC,, Brinkac LM,, Dodson RJ,, Madupu R,, Sullivan SA,, Kolonay JF,, Haft DH,, Nelson WC,, Tallon LJ,, Jones KM,, Ulrich LE,, Gonzalez JM,, Zhulin IB,, Robb FT,, Eisen JA . 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet 1 : e65. doi:10.1371/journal.pgen.0010065.
85. Kopke M,, Held C,, Hujer S,, Liesegang H,, Wiezer A,, Wollherr A,, Ehrenreich A,, Liebl W,, Gottschalk G,, Durre P . 2010. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci USA 107 : 13087– 13092.[PubMed] [CrossRef]
86. Asao M,, Madigan MT . 2010. Taxonomy, phylogeny, and ecology of the heliobacteria. Photosynth Res 104 : 103– 111.[PubMed] [CrossRef]
87. Sattley WM,, Madigan MT,, Swingley WD,, Cheung PC,, Clocksin KM,, Conrad AL,, Dejesa LC,, Honchak BM,, Jung DO,, Karbach LE,, Kurdoglu A,, Lahiri S,, Mastrian SD,, Page LE,, Taylor HL,, Wang ZT,, Raymond J,, Chen M,, Blankenship RE,, Touchman JW . 2008. The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol 190 : 4687– 4696.[PubMed] [CrossRef]
88. Tang KH,, Yue H,, Blankenship RE . 2010. Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth. BMC Microbiol 10 : 150. doi:10.1186/1471-2180-10-150. [PubMed] [CrossRef]
89. Heggeset TM,, Krog A,, Balzer S,, Wentzel A,, Ellingsen TE,, Brautaset T . 2012. Genome sequence of thermotolerant Bacillus methanolicus: features and regulation related to methylotrophy and production of L-lysine and L-glutamate from methanol. Appl Environ Microbiol 78 : 5170– 5181.[PubMed] [CrossRef]
90. Paredes CJ,, Alsaker KV,, Papoutsakis ET . 2005. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol 3 : 969– 978.[PubMed] [CrossRef]
91. Abecasis AB,, Serrano M,, Alves R,, Quintais L,, Pereira-Leal JB,, Henriques AO . 2013. A genomic signature and the identification of new sporulation genes. J Bacteriol 195 : 2101– 2115.[PubMed] [CrossRef]
92. Galperin MY . 2006. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 188 : 4169– 4182.[PubMed] [CrossRef]
93. Farrow JA,, Wallbanks S,, Collins MD . 1994. Phylogenetic interrelationships of round-spore-forming bacilli containing cell walls based on lysine and the non-spore-forming genera Caryophanon, Exiguobacterium, Kurthia, and Planococcus . Int J Syst Bacteriol 44 : 74– 82.[PubMed]
94. Kloos WE,, Ballard DN,, George CG,, Webster JA,, Hubner RJ,, Ludwig W,, Schleifer KH,, Fiedler F,, Schubert K . 1998. Delimiting the genus Staphylococcus through description of Macrococcus caseolyticus gen. nov., comb. nov. and Macrococcus equipercicus sp. nov., and Macrococcus bovicus sp. no. and Macrococcus carouselicus sp. nov. Int J Syst Bacteriol 48 : 859– 877.[PubMed]
95. Snel J,, Heinen PP,, Blok HJ,, Carman RJ,, Duncan AJ,, Allen PC,, Collins MD . 1995. Comparison of 16S rRNA sequences of segmented filamentous bacteria isolated from mice, rats, and chickens and proposal of ‘Candidatus Arthromitus’. Int J Syst Bacteriol 45 : 780– 782.[PubMed]
96. Kuwahara T,, Ogura Y,, Oshima K,, Kurokawa K,, Ooka T,, Hirakawa H,, Itoh T,, Nakayama-Imaohji H,, Ichimura M,, Itoh K,, Ishifune C,, Maekawa Y,, Yasutomo K,, Hattori M,, Hayashi T . 2011. The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. DNA Res 18 : 291– 303.[PubMed] [CrossRef]
97. Klaasen HL,, Koopman JP,, Poelma FG,, Beynen AC . 1992. Intestinal, segmented, filamentous bacteria. FEMS Microbiol Rev 8 : 165– 180.[PubMed]
98. Klaasen HL,, Koopman JP,, Van den Brink ME,, Bakker MH,, Poelma FG,, Beynen AC . 1993. Intestinal, segmented, filamentous bacteria in a wide range of vertebrate species. Lab Anim 27 : 141– 150.[PubMed]
99. Chase DG,, Erlandsen SL . 1976. Evidence for a complex life cycle and endospore formation in the attached, filamentous, segmented bacterium from murine ileum. J Bacteriol 127 : 572– 583.[PubMed]
100. Prakash T,, Oshima K,, Morita H,, Fukuda S,, Imaoka A,, Kumar N,, Sharma VK,, Kim SW,, Takahashi M,, Saitou N,, Taylor TD,, Ohno H,, Umesaki Y,, Hattori M . 2011. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation. Cell Host Microbe 10 : 273– 284.[PubMed] [CrossRef]
101. Sczesnak A,, Segata N,, Qin X,, Gevers D,, Petrosino JF,, Huttenhower C,, Littman DR,, Ivanov II . 2011. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe 10 : 260– 272.[PubMed] [CrossRef]
102. Makarova K,, Slesarev A,, Wolf Y,, Sorokin A,, Mirkin B,, Koonin E,, Pavlov A,, Pavlova N,, Karamychev V,, Polouchine N,, Shakhova V,, Grigoriev I,, Lou Y,, Rohksar D,, Lucas S,, Huang K,, Goodstein DM,, Hawkins T,, Plengvidhya V,, Welker D,, Hughes J,, Goh Y,, Benson A,, Baldwin K,, Lee JH,, Diaz-Muniz I,, Dosti B,, Smeianov V,, Wechter W,, Barabote R,, Lorca G,, Altermann E,, Barrangou R,, Ganesan B,, Xie Y,, Rawsthorne H,, Tamir D,, Parker C,, Breidt F,, Broadbent J,, Hutkins R,, O’Sullivan D,, Steele J,, Unlu G,, Saier M,, Klaenhammer T,, Richardson P,, Kozyavkin S,, Weimer B,, Mills D . 2006. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103 : 15611– 15616.[PubMed] [CrossRef]
103. Skerman VBD,, McGowan V,, Sneath PHA . 1980. Approved lists of bacterial names. Int J Syst Bacteriol 30 : 225– 420.
104. Bisby FA,, Roskov YR,, Orrell TM,, Nicolson D,, Paglinawan LE,, Bailly N,, Kirk PM,, Bourgoin T,, Baillargeon G (ed) . 2009. Species 2000 & ITIS Catalogue of Life: 2009 Annual Checklist Taxonomic Classification. Species 2000, Reading, UK.
105. Ludwig W,, Schleifer K-H,, Whitman WB, . 2009. Taxonomic outline of the phylum Firmicutes, p 15– 17. In De Vos P,, Garrity GM,, Jones D,, Krieg NR,, Ludwig W,, Rainey FA,, Schleifer K-H,, Whitman WB (ed), Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol 3. The Firmicutes. Springer, New York, NY.
106. Quast C,, Pruesse E,, Yilmaz P,, Gerken J,, Schweer T,, Yarza P,, Peplies J,, Glöckner FO . 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41 : D590– D596.
107. DeSantis TZ,, Hugenholtz P,, Larsen N,, Rojas M,, Brodie EL,, Keller K,, Huber T,, Dalevi D,, Hu P,, Andersen GL . 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72 : 5069– 5072.[PubMed] [CrossRef]
108. McDonald D,, Price MN,, Goodrich J,, Nawrocki EP,, DeSantis TZ,, Probst A,, Andersen GL,, Knight R,, Hugenholtz P . 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6 : 610– 618.[PubMed] [CrossRef]
109. Cole JR,, Wang Q,, Cardenas E,, Fish J,, Chai B,, Farris RJ,, Kulam-Syed-Mohideen AS,, McGarrell DM,, Marsh T,, Garrity GM,, Tiedje JM . 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37 : D141– D145.[PubMed] [CrossRef]
110. Starr MP,, Sayre RM . 1988. Pasteuria thornei sp. nov. and Pasteuria penetrans sensu stricto emend., mycelial and endospore-forming bacteria parasitic, respectively, on plant-parasitic nematodes of the genera Pratylenchus and Meloidogyne . Ann Inst Pasteur Microbiol 139 : 11– 31.[PubMed]
111. Yassin AF,, Hupfer H,, Klenk HP,, Siering C . 2009. Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006. Int J Syst Evol Microbiol 59 : 454– 459.[PubMed]
112. Hatayama K,, Shoun H,, Ueda Y,, Nakamura A . 2006. Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov. Int J Syst Evol Microbiol 56 : 2545– 2551.[PubMed] [CrossRef]
113. Yokoyama H,, Wagner ID,, Wiegel J . 2010. Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov. Int J Syst Evol Microbiol 60 : 67– 71.[PubMed] [CrossRef]
114. Jabari L,, Gannoun H,, Cayol JL,, Hamdi M,, Fauque G,, Ollivier B,, Fardeau ML . 2012. Characterization of Defluviitalea saccharophila gen. nov., sp. nov., a thermophilic bacterium isolated from an upflow anaerobic filter treating abattoir wastewaters, and proposal of Defluviitaleaceae fam. nov. Int J Syst Evol Microbiol 62 : 550– 555.[PubMed] [CrossRef]
115. Eeckhaut V,, Van Immerseel F,, Pasmans F,, De Brandt E,, Haesebrouck F,, Ducatelle R,, Vandamme P . 2010. Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes . Int J Syst Evol Microbiol 60 : 1108– 1112.[PubMed] [CrossRef]
116. Grech-Mora I,, Fardeau M-L,, Patel BKC,, Ollivier B,, Rimbault A,, Prensier G,, Garcia JL,, Garnier-Sillam E . 1996. Isolation and characterization of Sporobacter termitidis gen. nov., sp. nov., from the digestive tract of the wood-feeding termite Nasutitermes lujae . Int J Syst Evol Microbiol 46 : 512– 518.
117. Matthies C,, Springer N,, Ludwig W,, Schink B . 2000. Pelospora glutarica gen. nov., sp. nov., a glutarate-fermenting, strictly anaerobic, spore-forming bacterium. Int J Syst Evol Microbiol 50 : 645– 648.[PubMed]
118. Wisotzkey JD,, Jurtshuk P Jr,, Fox GE,, Deinhard G,, Poralla K . 1992. Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int J Syst Bacteriol 42 : 263– 269.[PubMed]
119. Darland G,, Brock TD . 1971. Bacillus acidocaldarius sp.nov., an acidophilic thermophilic spore-forming bacterium. J Gen Microbiol 67 : 9– 15.
120. Qi H,, Chen H,, Ao J,, Zhou H,, Chen X . 2009. Isolation and identification of a strain of moderate thermophilic and acidophilic bacterium from deep sea. Acta Oceanol Sin 31 : 152– 158.
121. Anderson I,, Chertkov O,, Chen A,, Saunders E,, Lapidus A,, Nolan M,, Lucas S,, Hammon N,, Deshpande S,, Cheng J-F,, Han C,, Tapia R,, Goodwin LA,, Pitluck S,, Liolios K,, Pagani I,, Ivanova N,, Mikhailova N,, Pati A,, Palaniappan K,, Land M,, Pan C,, Rohde M,, Pukall R,, Göker M,, Detter JC,, Woyke T,, Bristow J,, Eisen JA,, Markowitz V,, Hugenholtz P,, Kyrpides NC,, Klenk H-P,, Mavromatis K . 2012. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL T). Stand Genomic Sci 6 : 293– 303.[PubMed] [CrossRef]
122. Watling HR,, Perrot FA,, Shiers DW . 2008. Comparison of selected characteristics of Sulfobacillus species and review of their occurrence in acidic and bioleaching environments. Hydrometallurgy 93 : 57– 65.
123. Ye Q,, Roh Y,, Carroll SL,, Blair B,, Zhou J,, Zhang CL,, Fields MW . 2004. Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl Environ Microbiol 70 : 5595– 5602.[PubMed] [CrossRef]
124. Nielsen P,, Fritze D,, Priest FG . 1995. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141 : 1745– 1761.
125. Sturr MG,, Guffanti AA,, Krulwich TA . 1994. Growth and bioenergetics of alkaliphilic Bacillus firmus OF4 in continuous culture at high pH. J Bacteriol 176 : 3111– 3116.[PubMed]
126. Janto B,, Ahmed A,, Ito M,, Liu J,, Hicks DB,, Pagni S,, Fackelmayer OJ,, Smith TA,, Earl J,, Elbourne LD,, Hassan K,, Paulsen IT,, Kolsto AB,, Tourasse NJ,, Ehrlich GD,, Boissy R,, Ivey DM,, Li G,, Xue Y,, Ma Y,, Hu FZ,, Krulwich TA . 2011. Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4. Environ Microbiol 13 : 3289– 3309.[PubMed] [CrossRef]
127. Yoon JH,, Oh TK,, Park YH . 2004. Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov. Int J Syst Evol Microbiol 54 : 2163– 2167.[PubMed] [CrossRef]
128. Lee SJ,, Lee YJ,, Jeong H,, Lee HS,, Pan JG,, Kim BC,, Lee DW . 2012. Draft genome sequence of Virgibacillus halodenitrificans 1806. J Bacteriol 194 : 6332– 6333.[PubMed]
129. Larsen L,, Nielsen P,, Ahring BK . 1997. Thermoanaerobacter mathranii sp. nov., an ethanol-producing, extremely thermophilic anaerobic bacterium from a hot spring in Iceland. Arch Microbiol 168 : 114– 119.[PubMed]
130. Lechner S,, Mayr R,, Francis KP,, Pruss BM,, Kaplan T,, Wiessner-Gunkel E,, Stewart GS,, Scherer S . 1998. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 48 : 1373– 1382.[PubMed]
131. Gioia J,, Yerrapragada S,, Qin X,, Jiang H,, Igboeli OC,, Muzny D,, Dugan-Rocha S,, Ding Y,, Hawes A,, Liu W,, Perez L,, Kovar C,, Dinh H,, Lee S,, Nazareth L,, Blyth P,, Holder M,, Buhay C,, Tirumalai MR,, Liu Y,, Dasgupta I,, Bokhetache L,, Fujita M,, Karouia F,, Eswara Moorthy P,, Siefert J,, Uzman A,, Buzumbo P,, Verma A,, Zwiya H,, McWilliams BD,, Olowu A,, Clinkenbeard KD,, Newcombe D,, Golebiewski L,, Petrosino JF,, Nicholson WL,, Fox GE,, Venkateswaran K,, Highlander SK,, Weinstock GM . 2007. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One 2 : e928. doi:10.1371/journal.pone.0000928. [PubMed] [CrossRef]
132. Link L,, Sawyer J,, Venkateswaran K,, Nicholson W . 2004. Extreme spore UV resistance of Bacillus pumilus isolates obtained from an ultraclean spacecraft assembly facility. Microb Ecol 47 : 159– 163.[PubMed] [CrossRef]
133. Poehlein A,, Gottschalk G,, Daniel R . 2013. First insights into the genome of the Gram-negative, endospore-forming organism Sporomusa ovata strain H1 DSM 2662. Genome Announc 1( 5) doi:10.1128/genomeA.00734-13. [PubMed] [CrossRef]
134. Wunderlin T,, Junier T,, Roussel-Delif L,, Jeanneret N,, Junier P . 2013. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. Environ Microbiol Rep. doi:10.1111/1758-2229.12094. [PubMed] [CrossRef]
135. Alauzet C,, Marchandin H,, Courtin P,, Mory F,, Lemee L,, Pons JL,, Chapot-Chartier MP,, Lozniewski A,, Jumas-Bilak E . 2014. Multilocus analysis reveals diversity in the genus Tissierella: description of Tissierella carlieri sp. nov. in the new class Tissierellia classis nov. Syst Appl Microbiol 37 : 23– 34.
136. Watanabe M,, Kojima H,, Fukui M . 2015. Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes . Int J Syst Evol Microbiol 65 : 2378– 2384.
137. Watanabe M,, Kojima H,, Fukui M . 2016. Complete genome sequence and cell structure of Limnochorda pilosa, a Gram-negative spore former within the phylum Firmicutes. Int J Syst Evol Microbiol doi:10.1099/ijsem.0.000881.
138. Rinke C,, Schwientek P,, Sczyrba A,, Ivanova NN,, Anderson IJ,, Cheng JF,, Darling A,, Malfatti S,, Swan BK,, Gies EA,, Dodsworth JA,, Hedlund BP,, Tsiamis G,, Sievert SM,, Liu WT,, Eisen JA,, Hallam SJ,, Kyrpides NC,, Stepanauskas R,, Rubin EM,, Hugenholtz P,, Woyke T . 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499 : 431– 437.
139. Sankar SA,, Lagier JC,, Pontarotti P,, Raoult D,, Fournier PE . 2015. The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 38 : 276– 286

Tables

Genome Diversity of Spore-Forming Firmicutes
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Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
/content/10.1128/9781555819323.chap1.tab1-1
Table 1

Principal data sources on bacterial () taxonomy

Generic image for table
Table 1

Principal data sources on bacterial () taxonomy

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
/content/10.1128/9781555819323.chap1.tab1-2
Table 2

Distribution of spore-forming bacteria among

Generic image for table
Table 2

Distribution of spore-forming bacteria among

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
/content/10.1128/9781555819323.chap1.tab1-3
Table 3

Recent renaming of some well-known sporeformers

Generic image for table
Table 3

Recent renaming of some well-known sporeformers

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
/content/10.1128/9781555819323.chap1.tab1-4
Table 4

Genome sequencing of extremophilic sporeformers

Generic image for table
Table 4

Genome sequencing of extremophilic sporeformers

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012
/content/10.1128/9781555819323.chap1.tab1-5
Table 5

Distribution of sporulation genes in some non-spore-forming bacteria

Generic image for table
Table 5

Distribution of sporulation genes in some non-spore-forming bacteria

Citation: Galperin M. 2016. Genome Diversity of Spore-Forming , p 3-19. In Driks A, Eichenberger P (ed), The Bacterial Spore: from Molecules to Systems. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.TBS-0015-2012

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