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The SYNERGISTETES is a recently recognized phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape. Although Synergistetes have a diderm cell envelope, 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. 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 . 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 . Species within this phylum have also been implicated in periodontal disease , gastrointestinal infections and soft tissue infections. 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. All of the known Synergistetes species and genera are presently part of a single class (Synergistia), order (Synergistiales) and family (Synergistaceae).

CONTENTS

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

COMPARATIVE GENOMICS AND MOLECULAR SIGNATURES

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 . 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. 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. 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.

PHYLOGENY

See also: Bacterial taxonomy
Bacterial taxonomy

The phylogeny based on the work of the All-Species Living Tree Project .

Acetomicrobium flavidum (type sp.)

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

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

* Phylum SYNERGISTETES Jumas-Bilak et al. 2009

* Class SYNERGISTIA Jumas-Bilak et al. 2009

* Order SYNERGISTALES Jumas-Bilak et al. 2009

* Family SYNERGISTACEAE Jumas-Bilak et al. 2009

* 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 ">

* ^ 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
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
Cyanobacteria

Proteobacteria (BV2 )

ALPHA

* Caulobacterales * Kiloniellales * Kordiimonadales * Magnetococcales * Parvularculales * Rhizobiales
Rhizobiales
* Rhodobacterales * Rhodospirillales * Rickettsiales * Sneathiellales * Sphingomonadales

BETA

* Burkholderiales * Hydrogenophilales * Methylophilales * Neisseriales * Nitrosomonadales * Procabacteriales * Rhodocyclales

GAMMA

* Acidithiobacillales * Aeromonadales * Alteromonadales * Cardiobacteriales * Chromatiales * Enterobacteriales * Legionellales * Methylococcales
Methylococcales
* Oceanospirillales * Orbales * Pasteurellales * Pseudomonadales
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
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
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.

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