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The Info List - Synergistetes


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The Synergistetes is a recently recognized phylum of anaerobic bacteria that show Gram-negative
Gram-negative
staining and have rod/vibrioid cell shape.[1][2] Although Synergistetes have a diderm cell envelope,[3][4] the genes for various proteins involved in lipopolysaccharides biosynthesis have not yet been detected in Synergistetes, indicating that they may have an atypical outer cell envelope.[3][4] The Synergistetes inhabit a majority of anaerobic environments including animal gastrointestinal tracts, soil, oil wells, and wastewater treatment plants and they are also present in sites of human diseases such as cysts, abscesses, and areas of periodontal disease.[5][6] Due to their presence at illness related sites, the Synergistetes are suggested to be opportunistic pathogens but they can also be found in healthy individuals in the microbiome of the umbilicus and in normal vaginal flora.[6][7] Species within this phylum have also been implicated in periodontal disease,[8] gastrointestinal infections and soft tissue infections.[6] Other species from this phylum have been identified as significant contributors in the degradation of sludge for production of biogas in anaerobic digesters and are potential candidates for use in renewable energy production through their production of hydrogen gas.[9] All of the known Synergistetes species and genera are presently part of a single class (Synergistia), order (Synergistiales) and family (Synergistaceae).[2]

Contents

1 Comparative genomics and molecular signatures 2 Phylogeny 3 Taxonomy 4 References

Comparative genomics and molecular signatures[edit] Recent comparative analyses of sequenced Synergistetes genomes have led to identification of large numbers of conserved signature indels (CSIs) in protein sequences that are specific for either all sequenced Synergistetes species or some of their sub-clades that are observed in phylogenetic trees.[10] Of the CSIs that were identified, 32 in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert in the RpoC protein, are present in various Synergistetes species, but except for isolated bacteria, these CSIs are not found in the protein homologues from all other organisms. These CSIs provide novel molecular markers for distinguishing Synergistetes species from all other bacteria.[10] Seven other CSIs in important proteins including a 13 aa in RpoB were found to be uniquely present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a close and specific relationship among these bacteria, which is also strongly supported by phylogenetic trees. Fifteen addition CSIs that were only present in Jonquetella and Pyramidobacter indicate a close association between these two species.[10] Lastly, a close relationship between the Aminomonas and Thermanaerovibrio species is also supported by 9 identified CSIs. The identified molecular markers provide reliable means for the division of species from the phylum Synergistetes into intermediate taxonomic ranks such as families and orders.[10] Phylogeny[edit] See also: Bacterial taxonomy The phylogeny based on the work of the All-Species Living Tree Project.[11]

Acetomicrobium flavidum (type sp.) [was Bacteroideaceae]

Anaerobaculum

A. hydrogeniformans

A. thermoterrenum

Thermovirga lienii

Aminiphilus circumscriptus

Thermanaerovibrio

T. acidaminovorans (type sp.)

T. velox

Synergistes jonesii

Cloacibacillus

C. evryensis

C. porcorum

Lactivibrio alcoholicus

Aminivibrio pyruvatiphilus

Fretibacterium fastidiosum

Aminobacterium

A. thunnarium

A. colombiense (type sp.)

A. mobile

Jonquetella anthropi

Pyramidobacter piscolens

Dethiosulfovibrio

D. salsuginis

D. peptidovorans (type sp.)

D. acidaminovorans

D. marinus

D. russensis

Taxonomy[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[12] and the National Center for Biotechnology Information (NCBI).[13]

Phylum Synergistetes Jumas-Bilak et al. 2009 [Synergistaeota Oren et al. 2015 [Aminanaerobia Hugenholtz]

Class Synergistia Jumas-Bilak et al. 2009

Order Synergistales Jumas-Bilak et al. 2009

Family Synergistaceae Jumas-Bilak et al. 2009 [ Clostridiales
Clostridiales
Family XV]

Genus Acetomicrobium Soutschek et al. 1985

Species Acetomicrobium flavidum Soutschek et al. 1985

Genus Aminiphilus Díaz et al. 2007

Species Aminiphilus circumscriptus Díaz et al. 2007

Genus Aminivibrio Honda et al. 2013

Species Aminivibrio pyruvatiphilus Honda et al. 2013

Genus Aminobacterium Baena et al. 1999

Species A. colombiense Baena et al. 1999 (type sp.) Species A. mobile Baena et al. 2000 Species A. thunnarium Hamdi et al. 2015

Genus Aminomonas Baena et al. 1999

Species Aminomonas paucivorans Baena et al. 1999

Genus Anaerobaculum Rees et al. 1997 emend. Maune & Tanner 2012

Species A. hydrogeniformans Maune & Tanner 2012 Species A. mobile Menes & Muxí 2002 Species A. thermoterrenum Rees et al. 1997 (type sp.)

Genus Candidatus Tammella Hongoh et al. 2007

Species Candidatus Tammella caduceiae Hongoh et al. 2007

Genus Cloacibacillus Ganesan et al. 2008 emend. Looft et al. 2013

Species Cloacibacillus evryensis Ganesan et al. 2008 Species Cloacibacillus porcorum Looft et al. 2013

Genus Dethiosulfovibrio Magot et al. 1997

Species D. salsuginis Díaz-Cárdenas et al. 2010 Species D. peptidovorans Magot et al. 1997 (type sp.) Species D. acidaminovorans Surkov et al. 2001 Species D. marinus Surkov et al. 2001 Species D. russensis Surkov et al. 2001

Genus Fretibacterium Vartoukian et al. 2013

Species Fretibacterium fastidiosum Vartoukian et al. 2013

Genus Jonquetella Jumas-Bilak et al. 2007

Species Jonquetella anthropi Jumas-Bilak et al. 2007

Genus Lactivibrio Qiu et al. 2014

Species Lactivibrio alcoholicus Qiu et al. 2014

Genus Pyramidobacter Downes et al. 2009

Species Pyramidobacter piscolens Downes et al. 2009

Genus Synergistes Allison et al. 1993

Species Synergistes jonesii Allison et al. 1993

Genus Thermanaerovibrio Baena et al. 1999 emend. Palaniappan et al. 2013

Species T. acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 [Selenomonas acidaminovorans Guangsheng et al. 1997](type sp.) Species T. velox Zavarzina et al. 2000

Genus Thermovirga Dahle and Birkeland 2006

Species Thermovirga lienii Dahle and Birkeland 2006

Notes: ♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN) References[edit]

^ Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329. ^ a b Jumas-Bilak, E.; Roudiere, L.; Marchandin, H. (2009). "Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'". Int. J. Syst. Evol. Microbiol. 59: 1028–1035. doi:10.1099/ijs.0.006718-0.  ^ a b Gupta, R. S. (2011) Origin of Diderm (Gram-negative) Bacteria: Antibiotic Selection Pressure Rather than Endosymbiosis Likely led to the Evolution of Bacterial Cells with Two Membranes. Antonie Van Leeuwenhoek. 100: 171–182 ^ a b Sutcliffe, I.C. (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18: 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.  ^ Jumas-Bilak, E.; Carlier, J.P.; Jean-Pierre, H.; Citron, D.; Bernard, K.; Damay, A.; Gay, B.; Teyssier, C.; Campos, J.; Marchandin, H. (2007). "Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man". Int. J. Syst. Evol. Microbiol. 57: 2743–2748. doi:10.1099/ijs.0.65213-0.  ^ a b c Vartoukian, S.R., Palmer, R.M., and Wade, W.G. (2007). The division "Synergistes". Anaerobe. 13, 99–106. ^ Marchandin, H., Damay, A., Roudiere, L., Teyssier, C., Zorgniotti, I., Dechaud, H., Jean-Pierre, H., and Jumas-Bilak, E. (2010). Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin. Res. Microbiol. 161, 91–100. ^ Horz, H.P.; D.M. Citron; Y.A. Warren; E.J. Goldstein; G. Conrads (August 2006). " Synergistes Group Organisms of Human Origin". Journal of Clinical Microbiology. 44 (8): 2914–2920. doi:10.1128/JCM.00568-06. PMC 1594628 . PMID 16891512.  ^ Riviere, D., Desvignes, V., Pelletier, E., Chaussonnerie, S., Guermazi, S., Weissenbach, J., Li, T., Camacho, P., and Sghir, A. (2009). Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME. J. 3, 700–714. ^ a b c d Bhandari, V.; Gupta, R. S. (2012). "Molecular signatures for the phylum Synergistetes and some of its subclades". Antonie Van Leeuwenhoek. 102: 517–40. doi:10.1007/s10482-012-9759-2. PMID 22711299.  ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.  ^ J.P. Euzéby. "Synergistetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.  ^ Sayers; et al. "Synergistetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20. 

v t e

Prokaryotes: Bacteria
Bacteria
classification (phyla and orders)

Domain Archaea Bacteria Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta

Animal Fungi)

G-/ OM

Terra-/ Glidobacteria (BV1)

Eobacteria

Deinococcus–Thermus

Deinococcales Thermales

Chloroflexi

Anaerolineales Caldilineales Chloroflexales Herpetosiphonales Dehalococcoidales Ktedonobacterales Thermogemmatisporales Thermomicrobiales Sphaerobacterales

other glidobacteria

Thermodesulfobacteria thermophiles

Aquificae Thermotogae

Cyanobacteria

Proteobacteria (BV2)

Alpha

Caulobacterales Kiloniellales Kordiimonadales Magnetococcales Parvularculales Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sneathiellales Sphingomonadales

Beta

Burkholderiales Hydrogenophilales Methylophilales Neisseriales Nitrosomonadales Procabacteriales Rhodocyclales

Gamma

Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromatiales Enterobacteriales Legionellales Methylococcales Oceanospirillales Orbales Pasteurellales Pseudomonadales Salinisphaerales Thiotrichales Vibrionales Xanthomonadales

Delta

Bdellovibrionales Desulfarculales Desulfobacterales Desulfovibrionales Desulfurellales Desulfuromonadales Myxococcales Syntrophobacterales Syntrophorhabdales

Epsilon

Campylobacterales Nautiliales

Zeta

Mariprofundales

BV4

Spirochaetes

Spirochaetes

Sphingobacteria (FCB group)

Fibrobacteres Chlorobi

Chlorobiales Ignavibacteriales

Bacteroidetes

Bacteroidales Cytophagales Flavobacteriales Sphingobacteriales

Planctobacteria/ (PVC group)

Chlamydiae Lentisphaerae

Lentisphaerales Oligosphaerales Victivallales

Planctomycetes

Phycisphaerales Planctomycetales

Verrucomicrobia

Puniceicoccales Opitutales Chthoniobacterales Verrucomicrobiales

"Poribacteria"

Other GN

Acidobacteria

Acidobacteriales Acanthopleuribacterales Holophagales Solibacterales

Armatimonadetes

Armatimonadales Chthonomonadales Fimbriimonadales

Caldiserica Chrysiogenetes Deferribacteres Dictyoglomi Elusimicrobia Fusobacteria Gemmatimonadetes Nitrospirae Synergistetes

G+/ no OM

Firmicutes (BV3)

Bacilli

Bacillales Lactobacillales

Clostridia

Clostridiales Halanaerobiales Thermoanaerobacteriales Natranaerobiales

Erysipelotrichia

Erysipelotrichiales

Thermolithobacteria

Thermolithobacterales

Tenericutes/ Mollicutes

Mycoplasmatales Entomoplasmatales Anaeroplasmatales Acholeplasmatales Haloplasmatales

Negativicutes

Selenomonadales

Actinobacteria (BV5)

Actinobacteria

Actinomycetales Bifidobacteriales

Acidimicrobiia

Acidimicrobiales

Coriobacteriidae

Coriobacteriales

Nitriliruptoria

Euzebyales Nitriliruptorales

Rubrobacteria

Gaiellales Rubrobacterales Thermoleophilales Solirubrobacterales

Incertae sedis

†Archaeosphaeroides †Eobacterium †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

Taxon identifiers

Wd: Q1318124 EoL: 10648033 ITIS: 9

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