Screening and characterization of prophages in Desulfovibrio genomes

Crispim, Josicelli Souza; Dias, Roberto Sousa; Vidigal, Pedro Marcus Pereira; Sousa, Maíra Paula de; Silva, Cynthia Canêdo da; Santana, Mateus Ferreira; Paula, Sérgio Oliveira de

doi:10.1038/s41598-018-27423-z

Cited by 36 publications

(31 citation statements)

References 48 publications

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“…3 & Table S9), while no virus sequences were detected in the four deltaproteobacterial genome bins. Seven and three viruses were found in D. vulgaris and D. multivorans respectively, which seemed to be not in complete agreement with previous ndings that eight and no viruses were identi ed in the two model SRMs correspondingly [47,61]. This discrepancy likely resulted from the utilization of different viral prediction methods.…”

Section: Viruses Of Srmscontrasting

confidence: 77%

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

Li¹,

Jia²,

Wang³

et al. 2020

Preprint

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BackgroundThe widespread occurrence of sulfate-reducing microorganisms (SRMs, which are typically considered anaerobic organisms) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in continuously oxic/hypoxic terrestrial environments rich in sulfate. However, little attention has been paid to such a possibility, leading to an incomplete understanding of microorganisms driving terrestrial part of the global sulphur cycle.ResultsIn this study, genome-centric metagenomics was employed to explore SRMs in a revegetated acidic mine wasteland under continuously oxic/hypoxic conditions. We reconstructed 12 Acidobacteria and four Deltaproteobacteria genomes encoding reductive DsrAB, of which five represented three new SRM genera. Our results showed that Acidobacteria-related SRMs differed considerably from Deltaproteobacteria-related SRMs in metabolic potentials. Genomes of Acidobacteria-related SRMs harbored more glycoside hydrolase (GH) genes than those of previously known SRMs. They also tended to encode more oxygen-tolerant hydrogenases and cytochrome c oxidases, but less methyl-accepting chemotaxis proteins (MCPs) than genomes of Deltaproteobacteria-related SRMs. More importantly, we discovered that SRM-infecting viruses can contribute to glycoside hydrolysis, chemotaxis and antioxidation of their hosts. Remarkably, one GH encoded by a SRM-infecting virus is responsible for the liberation of rhamnose (a monosaccharide that is accessible directly to SRMs for dissimilatory sulfate reduction) from plant cell-wall-derived oligosaccharides.ConclusionsTaken together, our results do not only improve our understanding of microorganisms driving dissimilatory sulfate reduction in terrestrial environments under continuously oxic/hypoxic conditions but also provides the first evidence for putative roles of viruses in S biogeochemical cycle in terrestrial ecosystems.

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Section: Viruses Of Srmscontrasting

confidence: 77%

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

Li¹,

Jia²,

Wang³

et al. 2020

Preprint

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“…The G4P1-like prophages were common in the genomes of B. vietnamiensis being found in 17% of the strain collection. Although phage genomes are renowned for being mosaic in nature [7], recent studies have used genomics to discover the presence of syntenous prophages across different species [77,78], and across different strains of the same species [79][80][81][82]. The present study is the first to report the population genomics of B. vietnamiensis and map prophage carriage onto the population.…”

Section: Discussionmentioning

confidence: 91%

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Weiser

Yap

Otter

et al. 2020

Viruses

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Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.

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“…The genus Desulfovibrio, a dominant group of Sulfate Reducing Bacteria (SRB), is a class of anaerobic bacteria which can reduce sulfate to produce H 2 S. Endogenous H 2 S can inhibit the oxidation of acid salts, affect the respiration of cells and induce apoptosis and chronic inflammation. It has been reported that Desulfovibrio is related to the occurrence and development of colon cancer, irritable bowel syndrome, metabolic syndrome and other diseases (Crispim et al, 2018). Hence, Isoflavones are essential in the diet.…”

Section: Discussionmentioning

confidence: 99%

Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota

et al. 2018

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Isoflavones, presenting in leguminous plants and the normal chow diet, are known to alter intestinal microbiota, yet their deficiency has not been widely studied for its effect on constipation in biochemical state of rats. Our previous study discovered the differences in pharmacokinetic traits of isoflavones from Semen sojae praeparatum fed with normal chow diet (ISO) and non-isoflavones diet (NISO). To gain insight into the key role of intestinal microbiota in constipation and metabolic differences caused by isoflavones deficiency, we observed a significant decrease in fecal pellet numbers, fecal water content, intestinal transit rate together with the serum concentrations of substance P (SP) and vasoactive intestinal peptide (VIP) in NISO group, compared with those in the ISO group. Following 16S rRNA compositional sequencing, results excluded the changes in intestinal microbiota over time and highlighted that a total of 5 phyla and 21 genera changed significantly, among which Firmicutes, Bacteroidetes, Blautia, Prevotella, Lactobacillus and Bifidobacterium were closely related to constipation. In addition, Lactobacillus, produceing β-glucosidase which contribute to biotransform glycosides into aglycons and exert the bioactivities consequently, was decreased after non-isoflavones diet intake. Meanwhile, predicted metagenomics indicated that the pathway of glycan biosynthesis and metabolism was markedly down-regulated after non-isoflavones diet intake. Taken together, the findings suggested that the changes in the dietary components could alter the biochemical state of rats, which may be triggered by the abnormal modifications facilitated by β-glucosidase-producing bacteria. Our study shed a new strategy to explore the relationship among disease phenotypes (D), intestinal microbiota (I), enzymes (E) and traits of metabolism (T) named as “DIET,” which can provide a reference for further study of the mechanism in regulation of intestinal bacteria-mediated diet on diseases.

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Screening and characterization of prophages in Desulfovibrio genomes

Cited by 36 publications

References 48 publications

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota

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