Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments

Casale, Antonio Del; Flanagan, Paul; Larkin, Michael J.; Allen, Christopher C. R.; Kulakov, Leonid

doi:10.1128/aem.00457-11

Cited by 11 publications

(5 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, the high proportion of unassigned sequences and relatively low number of 16S rRNA matching sequences (Supplementary Table 3) supported a viral origin for the bacterially annotated reads. Because bacterial genes can be packaged into generalized transducing phage particles (Beumer and Robinson, 2005; Ghosh et al , 2008; Del Casale et al , 2011), the bacterial-like sequences in the guelta metagenomes might come from excised prophages mistakenly annotated as bacterial and/or from genes of bacterial origins that were transferred to their phages.…”

Section: Discussionmentioning

confidence: 99%

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

et al. 2012

View full text Add to dashboard Cite

Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in the central Sahara (Mauritania). Three of the four gueltas (Ilij, Molomhar and Hamdoun) are located at the source of three different wadis belonging to the same hydrologic basin, whereas the fourth (El Berbera) belongs to a different basin. Overall, sequences belonging to tailed bacteriophages were the most abundant in all four metagenomes although electron microscopy and sequencing confirmed the presence of other viral groups, such as large DNA viruses. We observed a decrease in the local viral biodiversity in El Berbera, a guelta with sustained human activities, compared with the pristine Ilij and Molomhar, and sequences related to viruses infecting crop pests were also detected as a probable consequence of the agricultural use of the soil. However, the structure of the El Berbera viral community shared the common global characteristics of the pristine gueltas, that is, it was dominated by Myoviridae and, more particularly, by virulent phages infecting photosynthetic cyanobacteria, such as Prochlorococcus and Synechococcus spp. In contrast, the Hamdoun viral community was characterized by a larger proportion of phages with the potential for a temperate lifestyle and by dominant species related to phages infecting heterotrophic bacteria commonly found in terrestrial environments. We hypothesized that the differences observed in the structural and functional composition of the Hamdoun viral community resulted from the critically low water level experienced by the guelta.

show abstract

Section: Discussionmentioning

confidence: 99%

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Ribosomal 16S are highly conserved bacterial DNA segments and many bacteria have multiple copies, thereby making this a gene that has a high chance of transduction compared to other genes. [34][35][36] Therefore, testing for bacteriophages having 16S in their virion heads indirectly evaluates the generalized transduction potential for a bacteriophage. This testing includes denaturing the bacteriophage therapeutic capsid to release the phage DNA and then using 16S polymerase chain reaction to amplify 16S genes if these are present.…”

Section: Testing For Transduction Of Ribosomal 16smentioning

confidence: 99%

“…This testing includes denaturing the bacteriophage therapeutic capsid to release the phage DNA and then using 16S polymerase chain reaction to amplify 16S genes if these are present. [34][35][36] While not a perfect testing platform, this is an indirect way of assessing the potential for generalized transduction.…”

Section: Testing For Transduction Of Ribosomal 16smentioning

confidence: 99%

Risk of Bacteriophage Therapeutics to Transfer Genetic Material and Contain Contaminants Beyond Endotoxins with Clinically Relevant Mitigation Strategies

Doub¹

2021

IDR

View full text Add to dashboard Cite

Bacteriophage therapy is a promising adjuvant therapeutic in the treatment of multidrug-resistant infections and chronic biofilm infections. However, there is limited knowledge about how to best utilize these agents in vivo, leading to a wide range of treatment protocols. Moreover, while bacteriophages are similar to antibiotics in their antimicrobial effects, these are active viruses and are very different from conventional antibiotics. One main difference that clinicians should be cognizant about is the potential ability of these therapeutics to horizontally transfer genetic material, and the clinical ramifications of such events. In addition, while bacteriophage therapeutics are readily tested for sterility and endotoxins, clinicians should also be aware of other contaminants, such as exotoxins, pathogenicity islands and prophages, that can contaminate bacteriophage therapeutics, and their clinical ramifications. While the perception may be that these are only theoretical issues, regulatory agencies are starting to recommend their evaluation when using bacteriophage therapy and subsequently these topics are discussed herein, as are ways to test for and mitigate the adverse effects of these issues.

show abstract

“…Cloning of 16S rRNA genes was carried out as described previously [11] at depths of 2.1 m and 5.9 m as these depths were found on either side of the sulphate boundary [8]. Operational taxonomic units (OTUs) were grouped by restriction analysis using Fastdigest RSaI and HaeIII (Fermentas) restriction enzymes.…”

Section: Cloning and Sequence Analysismentioning

confidence: 99%

“…Amplification efficiency ranged from 91% to 105% with samples analyzed in triplicate. Samples of qPCR products were chosen at random, cloned, as described previously [11] and sequenced to confirm product identity.…”

Section: Qpcrmentioning

confidence: 99%

A Depth Resolved Insight into Benzoyl CoA Reductase and Benzoate Dioxygenase Gene Copy Numbers within a Marine Sediment Associated with Methane Seepage

Flanagan¹,

Kelleher²,

O’Reilly³

et al. 2013

OJMS

Self Cite

View full text Add to dashboard Cite

A marine sediment core obtained from a methane seepage site off the northern coast of Ireland was analysed, at 3 depths, for catabolic genes associated with the aerobic and anaerobic degradation of aromatic compounds. Catabolic gene copy numbers varied through the core peaking at 2.1 meters below sediment surface (mbsf)-just above the sulphate boundary. Beyond the sulphate boundary gene copy numbers fell considerably, suggesting the boundary may be a critical factor in the degradation of aromatic compounds within marine sediments. At the 2.1 mbsf depth our data also suggest that known benzoyl CoA reductase utilizing bacteria are readily detectable.

show abstract

Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments

Cited by 11 publications

References 15 publications

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

Risk of Bacteriophage Therapeutics to Transfer Genetic Material and Contain Contaminants Beyond Endotoxins with Clinically Relevant Mitigation Strategies

A Depth Resolved Insight into Benzoyl CoA Reductase and Benzoate Dioxygenase Gene Copy Numbers within a Marine Sediment Associated with Methane Seepage

Contact Info

Product

Resources

About