Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'

Jumas‐Bilak, Estelle; Roudière, Laurent; Marchandin, Hélène

doi:10.1099/ijs.0.006718-0

“…A small number of isolates were shown to be present in human infections, including soft tissue infections, abscesses, blood, peritoneal fluid, and dental infections (5)(6)(7)(8)(9)(10)(11). However, the lack of identification of Synergistetes isolates at the genus level led to the generic grouping under the Synergistes group of organisms (SGO) (3,7,(11)(12)(13). With the initial description of the genus Cloacibacillus in 2008, 16S rRNA gene sequencing and phylogenetic analysis are now available for the proper identification of Cloacibacillus species (1, 2).…”

mentioning

confidence: 99%

“…The phylum contains 12 genera, Aminiphilus, Aminobacterium, Aminomonas, Anaerobaculum, Cloacibacillus, Dethiosulfovibrio, Fretibacterium, Jonquetella, Pyramidobacter, Synergistes, Thermanaerovibrio, and Thermovirga (4). Previously, most of the 16S rRNA gene sequences available from this phylum were obtained from culture-independent studies (3,(5)(6)(7)(8)(9)(10)(11). A small number of isolates were shown to be present in human infections, including soft tissue infections, abscesses, blood, peritoneal fluid, and dental infections (5)(6)(7)(8)(9)(10)(11).…”

mentioning

confidence: 99%

Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick

Domingo

¹

,

Yansouni

²

,

Gaudreau

³

et al. 2015

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“…Members of this group have been isolated from a variety of environments including anaerobic digesters (LaPara et al, 2000;Wu et al, 2001), the termite hindgut (Ohkuma & Kudo, 1996), subgingival plaque (Munson et al, 2004) and petroleum reservoirs (Orphan et al, 2000;van der Kraan et al, 2010;Voordouw et al, 1996). The species in this group with validly published names display diverse physiological properties, but all currently cultivated strains catabolize amino acids (Jumas-Bilak et al, 2009;Vartoukian et al, 2007). It has been noted that these organisms, although underrepresented amongst cultivated taxa, are not uncultivable but are present at low cell numbers in microbial communities (Godon et al, 2005).…”

mentioning

confidence: 99%

“…The bacterial phylum Synergistetes is an under-represented phylogenetic cluster of Gram-negative, anaerobic, rodshaped bacteria that are related to Synergistes jonesii (Jumas-Bilak et al, 2009). Members of this group have been isolated from a variety of environments including anaerobic digesters (LaPara et al, 2000;Wu et al, 2001), the termite hindgut (Ohkuma & Kudo, 1996), subgingival plaque (Munson et al, 2004) and petroleum reservoirs (Orphan et al, 2000;van der Kraan et al, 2010;Voordouw et al, 1996).…”

mentioning

confidence: 99%

Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum

Maune

¹

,

Tanner

²

2012

International Journal of Systematic and Evolutionary Microbiology

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A novel anaerobic, moderately thermophilic, NaCl-requiring fermentative bacterium, strain OS1T, was isolated from oil production water collected from Alaska, USA. Cells were Gram-negative, non-motile, non-spore-forming rods (1.7–2.7 × 0.4–0.5 µm). The G+C content of the genomic DNA of strain OS1T was 46.6 mol%. The optimum temperature, pH and NaCl concentration for growth of strain OS1T were 55 °C, pH 7 and 10 g l−1, respectively. The bacterium fermented d-fructose, d-glucose, maltose, d-mannose, α-ketoglutarate, l-glutamate, malonate, pyruvate, l-tartrate, l-asparagine, Casamino acids, l-cysteine, l-histidine, l-leucine, l-phenylalanine, l-serine, l-threonine, l-valine, inositol, inulin, tryptone and yeast extract. When grown on d-glucose, 3.86 mol hydrogen and 1.4 mol acetate were produced per mol substrate. Thiosulfate, sulfur and l-cystine were reduced to sulfide, and crotonate was reduced to butyrate with glucose as the electron donor. 16S rRNA gene sequence analysis indicated that strain OS1T was related to Anaerobaculum thermoterrenum (99.7 % similarity to the type strain), a member of the phylum Synergistetes . DNA–DNA hybridization between strain OS1T and A. thermoterrenum DSM 13490T yielded 68 % relatedness. Unlike A. thermoterrenum , strain OS1T fermented malonate, maltose, tryptone, l-leucine and l-phenylalanine, but not citrate, fumarate, lactate, l-malate, glycerol, pectin or starch. The major cellular fatty acid of strain OS1T was iso-C15 : 0 (91 % of the total). Strain OS1T also contained iso-C13 : 0 3-OH (3 %), which was absent from A. thermoterrenum , and iso-C13 : 0 (2 %), which was absent from Anaerobaculum mobile . On the basis of these results, strain OS1T represents a novel species of the genus Anaerobaculum , for which the name Anaerobaculum hydrogeniformans sp. nov. is proposed. The type strain is OS1T ( = DSM 22491T = ATCC BAA-1850T). An emended description of the genus Anaerobaculum is also given.

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“…An analysis of environmental 16S rRNA gene sequences revealed that Synergistes-group bacteria were present in 90 % of 93 anaerobic ecosystems, in spite of their low abundance (less than 1 % of total bacteria in each environment investigated) (Godon et al, 2005). Based on phylogenetic analysis of 16S rRNA gene sequences, Jumas-Bilak et al (2009) proposed the phylum Synergistetes containing one class (Synergistia), one order (Synergistales), one family (Synergistaceae) and nine recognized genera: Aminobacterium, Aminomonas, Aminiphilus, Anaerobaculum, Dethiosulfovibrio, Jonquetella, Synergistes, Thermovirga and Thermanaerovibrio. Synergistes is the type genus of the family Synergistaceae and the order Synergistales.…”

mentioning

confidence: 99%

Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field

Honda

¹

,

Fujita

²

,

Tonouchi

³

2013

International Journal of Systematic and Evolutionary Microbiology

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A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6ET, were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0–2.5 µm) with two or three lateral flagella. Growth occurred at 20–42 °C (optimum at 37–40 °C), at pH 6.4–8.4 (optimum at pH 7.3) and at 0–1.5 % (w/v) NaCl (optimum at 0–0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, l-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen Methanobacterium formicicum JCM 10132T, strain 4F6ET oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of Fretibacterium fastidiosum , Aminobacterium colombiense and Aminobacterium mobile , members of the family Synergistaceae , were the closest relatives of strain 4F6ET, with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6ET contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of F. fastidiosum , Aminobacterium colombiense and Aminobacterium mobile . On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6ET and the type strains of F. fastidiosum and Aminobacterium species, we propose that strain 4F6ET represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6ET ( = JCM 18417T = DSM 25964T).

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Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'

Cited by 183 publications

References 38 publications

Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick

Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick

Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum

Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field

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