Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.

Shivani, Y.; Yadav, Subhash; Sasikala, Ch.; Ramana, Ch. V.

doi:10.1099/ijsem.0.001574

Cited by 54 publications

(20 citation statements)

References 26 publications

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“…Consistent with our 16S rRNA comparison, the closest relative of QI0027 T was D. legallii, and these bacteria grouped within the 'sensu-stricto' Desulfovibrio based on a well-supported phylogenomic tree reconstructed using 30 marker genes (17) (Figure 1). The family Desulfovibrionaceae has eight described genera: Desulfovibrio, Bilophila, Lawsonia, Halodesulfovibrio, Pseudodesulfovibrio, Desulfocurvus, and Desulfobaculum, although no representative genomes have been sequenced for the former two genera.…”

Section: Genome Sequencing and Phylogenomicssupporting

confidence: 76%

Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation

Sayavedra

Batista

et al. 2020

Preprint

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AbstractSulphate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, genome sequencing, and physiological characterisation of a novel SRB species belonging to the class Deltaproteobacteria (QI0027T). Phylogenomic analysis revealed that the QI0027T strain belongs to the genus Desulfovibrio with its closest relative being Desulfovibrio legallii. Metagenomic sequencing of stool samples from 45 individuals, as well as comparison with 1690 Desulfovibrionaceae metagenome-assembled genomes, revealed the presence of QI0027T in at least 22 further individuals. QI0027T encoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027T overexpressed 45 genes in nitrogen limiting conditions as compared to cultures supplemented with ammonia, including nitrogenases, an urea uptake system and the urease enzyme complex. To the best of our knowledge, this is the first Desulfovibrio human isolate for which nitrogen fixation has been demonstrated. This isolate was named Desulfovibrio diazotrophica sp. nov., referring to its ability to fix nitrogen (‘diazotroph’).ImportanceAnimals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen. These strategies range from amino acid transporters to stable associations with beneficial microbes that can provide fixed nitrogen. Although frequently thought as a nutrient-rich environment, nitrogen fixation can occur in the human gut of some populations, but so far it has been attributed mainly to Clostridia and Klebsiella based on sequencing. We have cultivated a novel Desulfovibrio from human gut origin which encoded, expressed and actively used nitrogen fixation genes, suggesting that some sulphate reducing bacteria could also play a role in the availability of nitrogen in the gut.

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Section: Genome Sequencing and Phylogenomicssupporting

confidence: 76%

Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation

Sayavedra

Batista

et al. 2020

Preprint

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“…Each bacterial genus consists of many species, and different species have different biological functions. For example, in the genus Desulfovibrio, there are at least 62 species and eight subspecies [47], which are usually present in the animal GIT, microbial mats, marshes, soda lakes, anoxic mud and marine sediments, and they are highly divergent on the basis of their phylogenetic and phenotypic characteristics [48].…”

Section: Plos Onementioning

confidence: 99%

Relationship between true digestibility of dietary phosphorus and gastrointestinal bacteria of goats

et al. 2020

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The present research was conducted to evaluate the connection between the true digestibility of Phosphorus (TDP) in diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. Twenty-eight Nubian goats were chosen and metabolic experiment was conducted to analyze TDP of research animals. Eight goats were grouped into the high digestibility of phosphorus (HP) phenotype, and another 8 were grouped into the low digestibility of phosphorus (LP) phenotype. And from the rumen, abomasum, jejunim, cecum and colon content of the goats, bacterial 16S rRNA gene amplicons were sequenced. In the rumen 239 genera belonging to 23 phyla, in abomasum 319 genera belonging to 30 phyla, in jejunum 248 genera belonging to 36 phyla, in colon 248 genera belonging to 25 phyla and in cecum 246 genera belonging to 23 phyla were noticed. In addition, there was a significant correlation between the TDP and the abundance of Ruminococcaceae_UCG-010, Rumino-coccus_2, Ruminococcaceae_UCG-014, Selenomonas_1 and Prevotella in the rumen, Lachnospiraceae_ND3007_group, Saccharofermentans, Ruminococcus_1, Ruminococca-ceae_UCG-014, Lachnospiraceae_XPB1014_group and Desulfovibrio in the abomasum, Prevotella, Clostridium_sensu_stricto_1, Fibrobacter, Desulfovibrio and Ruminococcus_2 in the jejunum, Ruminococcaceae_UCG-014 in the colon, and Desulfovibrio in the cecum. Present research trial recommended that the community of gastrointestinal microbiota is a factor affecting TDP in goats.

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“…africanus DSM 2603 T and strain L21-Syr-AB T contained in addition MK-6 in amounts of 9.3% and 1.5%, respectively. In contrast, the predominating menaquinone in the type species of the genus Desulfovibrio , D. desulfuricans , and several closely related species is MK-6 (Collins and Widdel, 1986; Shivani et al, 2017). The major polar lipids in all three analyzed strains were phosphatidylethanolamine and phosphatidylglycerol, which is a typical feature of most species within the Desulfovibrionaceae (Makula and Finnerty, 1974; Shivani et al, 2017).…”

Section: Resultsmentioning

confidence: 94%

“…In contrast, the predominating menaquinone in the type species of the genus Desulfovibrio , D. desulfuricans , and several closely related species is MK-6 (Collins and Widdel, 1986; Shivani et al, 2017). The major polar lipids in all three analyzed strains were phosphatidylethanolamine and phosphatidylglycerol, which is a typical feature of most species within the Desulfovibrionaceae (Makula and Finnerty, 1974; Shivani et al, 2017). However, strain L21-Syr-AB T could be distinguished from related type strains by the presence of unidentified aminoglycolipids and an aminophospholipid, while the characteristic feature of D. africanus subsp.…”

Section: Resultsmentioning

confidence: 94%

“…Likewise, the cellular fatty acid compositions of these strains were readily distinguishable as illustrated in Supplementary Table S3. The pattern of strain L21-Syr-AB T was unusual due to the complete lack of unsaturated fatty acids, which are present in most species of the Desulfovibrionaceae (Vainshtein et al, 1992; Shivani et al, 2017). It was further characterized by the major fatty acids anteiso -C 15:0 , C 16:0 and iso -C 16:0 , so that it could be easily differentiated from the pattern of D. desulfuricans and related species which usually contain significant amounts of the fatty acid iso -C 17:1 cis 7.…”

Section: Resultsmentioning

confidence: 99%

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Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat

et al. 2019

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Calcifying microbial mats in hypersaline environments are important model systems for the study of the earliest ecosystems on Earth that started to appear more than three billion years ago and have been preserved in the fossil record as laminated lithified structures known as stromatolites. It is believed that sulfate-reducing bacteria play a pivotal role in the lithification process by increasing the saturation index of calcium minerals within the mat. Strain L21-Syr-AB T was isolated from anoxic samples of a several centimeters-thick microbialite-forming cyanobacterial mat of a hypersaline lake on the Kiritimati Atoll (Kiribati, Central Pacific). The novel isolate was assigned to the family Desulfovibrionaceae within the Deltaproteobacteria . Available 16S rRNA-based population surveys obtained from discrete layers of the mat indicate that the occurrence of a species-level clade represented by strain L21-Syr-AB T is restricted to a specific layer of the suboxic zone, which is characterized by the presence of aragonitic spherulites. To elucidate a possible function of this sulfate-reducing bacterium in the mineral formation within the mat a comprehensive phenotypic characterization was combined with the results of a comparative genome analysis. Among the determined traits of strain L21-Syr-AB T , several features were identified that could play a role in the precipitation of calcium carbonate: (i) the potential deacetylation of polysaccharides and consumption of substrates such as lactate and sulfate could mobilize free calcium; (ii) under conditions that favor the utilization of formate and hydrogen, the alkalinity engine within the mat is stimulated, thereby increasing the availability of carbonate; (iii) the production of extracellular polysaccharides could provide nucleation sites for calcium mineralization. In addition, our data suggest the proposal of the novel species and genus Desulfohalovibrio reitneri represented by the type strain L21-Syr-AB T (=DSM 26903 T = JCM 18662 T ).

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Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.

Cited by 54 publications

References 26 publications

Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation

Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation

Relationship between true digestibility of dietary phosphorus and gastrointestinal bacteria of goats

Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat

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