Genome Sequence of the Pigment-Producing Bacterium
            <i>Pseudogulbenkiania ferrooxidans</i>
            , Isolated from Loktak Lake

Puranik, Sampada; Talkal, Reshma; Qureshi, Asifa; Khardenavis, Anshuman A.; Kapley, Atya; Purohit, Hemant J.

doi:10.1128/genomea.01115-13

Cited by 10 publications

(6 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Being a gut commensal present in the flora of healthy individuals, virtually avirulent enterococci have been used as probiotics to benefit health. Therefore we investigated whether a probiotic E. faecalis strain Symbioflor 1 [ 19 ] can be transduced by phages released from E. faecalis V583ΔABC. As expected, induction of prophages in E. faecalis Symbioflor 1 with 100 μM AI-2 did not lead to plaque formation, confirming that Symbioflor 1 does not contain lytic prophages [ 19 ] ( Fig.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing

et al. 2015

View full text Add to dashboard Cite

The microbiome and the phage meta-genome within the human gut are influenced by antibiotic treatments. Identifying a novel mechanism, here we demonstrate that bacteria use the universal communication molecule AI-2 to induce virulence genes and transfer them via phage release. High concentrations (i.e. 100 μM) of AI-2 promote dispersal of bacteria from already established biofilms, and is associated with release of phages capable of infecting other bacteria. Enterococcus faecalis V583ΔABC harbours 7 prophages in its genome, and a mutant deficient in one of these prophages (i.e. prophage 5) showed a greatly reduced dispersal of biofilm. Infection of a probiotic E. faecalis strain without lytic prophages with prophage 5 resulted in increased biofilm formation and also in biofilm dispersal upon induction with AI-2. Infection of the probiotic E. faecalis strain with phage-containing supernatants released through AI-2 from E. faecalis V583ΔABC resulted in a strong increase in pathogenicity of this strain. The polylysogenic probiotic strain was also more virulent in a mouse sepsis model and a rat endocarditis model. Both AI-2 and ciprofloxacin lead to phage release, indicating that conditions in the gastrointestinal tract of hospitalized patients treated with antibiotics might lead to distribution of virulence genes to apathogenic enterococci and possibly also to other commensals or even to beneficial probiotic strains.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Thereby, we could confirm that the polylysogenic transfected E. faecalis Symbioflor 1 harbored prophages 1, 5 and 7 ( Table 1 ). As described previously, all Symbioflor 1 strains contain also pp2 as part of the core genome [ 19 ].…”

Section: Resultsmentioning

confidence: 99%

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing

et al. 2015

View full text Add to dashboard Cite

show abstract

“…This search and subsequent analysis using IMG-ABC tools took less than an hour, and has led to the identification of putative DAPG biosynthesis clusters in four betaproteobacteria: a bacterium identified as Pseudogulbenkiania ferrooxidans EGD-HP2 (19) and three members of Chromobacterium genus, Chromobacterium vaccinii MWU205 (20), C. vaccinii MWU328 (20) and Chromobacterium piscinae ND17 (21). The IMG tools for analysis of biogeography and habitat specificity of these isolates indicate that all of them were collected from freshwater environments across the globe (Northeastern India, Northeastern United States of America and Malaysia).…”

Section: New Features and Updatesmentioning

confidence: 99%

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

et al. 2016

View full text Add to dashboard Cite

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.

show abstract

“…This draft genome has been deposited at DDBJ/EMBL/ GenBank under the accession no. AVPH00000000 [13].…”

Section: Ncbi Database Submissionmentioning

confidence: 99%

“…1, 2). For example, prior studies reported violacein production in chromobacterium species but [13] reported the same in Pseudogulbenkiania ferroxidans EGD-HP2 (EGD-HP2) via genome annotation in which they reported key genes of enzymes for pigment production and further 3D structure prediction. Violacein pigment producing Chromobacterium species was reported for a various biological activity like Anti-bacterial, Anti-cancerous [14], and Anti-leishmania [15].…”

Section: Introductionmentioning

confidence: 99%

An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools

2018

Self Cite

View full text Add to dashboard Cite

All the genetic potential and the intelligence a bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with the relevant set of in silico tools using a novel bacteria as an example. This study presents a multi-dimensional approach from genome annotation to tracing genes and their network of metabolism operating in an organism. It also shows how the sequence can be used to mine the enzymes and construction of its 3-dimensional structure so that its functional behavior can be predicted and compared. The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted altered physiology can be understood through the presence of secondary metabolite, antibiotic resistance genes, and viral genes; and it helps in the valorization of genetic information for developing new biological application/processes. This study provides an in silico work plan and necessary steps for genome analysis of novel bacteria without any rigorous wet lab experiments.

show abstract

Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans , Isolated from Loktak Lake

Cited by 10 publications

References 10 publications

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools

Contact Info

Product

Resources

About