TABLE 3-2 Metagenomic Characterization of Pathogens and Microbial Populations in Biosolids, Wastewater, Rivers, and Lakes

Environment Sampled Target and Approach Findings Reference
Wastewater biosolids Bacterial 16S rRNA genes; PCR, pyrosequencing (454 GS-FLX sequencer) Most of the pathogenic sequences belonged to the genera Clostridium and Mycobacterium Bibby et al. 2010
Wastewater (activated sludge, influent, and effluent) Bacterial 16S rRNA gene (hypervariable V4 region); PCR, pyrosequencing (454 GS-FLX sequencer) Most of the pathogenic sequences belonged to the genera Aeromonas and Clostridium Ye and Zhang 2011
River sediment Bacterial antibiotic-resistance genes; MDA, pyrosequencing (454 GS-FLX sequencer) Large amounts of several classes of resistance genes in bacterial communities exposed to antibiotic were identified Kristiansson et al. 2011
Reclaimed and potable water Viral DNA and RNA; tangential flow filtration, DNase treatment, MDA, pyrosequencing (454 GS-FLX and GS20 sequencer) Over 50% of the viral sequences had no significant similarity to proteins in GenBank; bacteriophages dominated the DNA viral community; the RNA metagenomes contained sequences related to plant viruses and invertebrate picornaviruses Rosario et al. 2009
Wastewater biosolids Viral DNA and RNA; DNase and RNase treatment, reverse transcription for RNA, pyrosequencing (454 GS-FLX sequencer), optimal annotation approach specific for viral pathogen identification is described Parechovirus, coronavirus, adenovirus, aichi virus, and herpesvirus were identified Bibby et al. 2011
Lake water Viral RNA; tangential flow filtration, DNase and RNase treatment, random amplification (klenow DNA polymerase), pyrosequencing (454GS-FLX sequencer) 66% of the sequences had no significant similarity to known sequences; presence of viral sequences (30 viral families) with significant homology to insect, human, and plant pathogens Djikeng et al. 2009

Abbreviations: DNase, deoxyribonuclase; MDA, multiple displacement amplification; PCR, polymerase chain reaction; RNase, ribonuclease; rRNA, ribosomal RNA.

Source: Aw and Rose 2012. Reprinted with permission; copyright 2012, Current Opinion in Biotechnology.



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