Article
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.
Great Lakes Water Institute, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA.
Environmental Microbiology (impact factor:
5.84).
10/2009;
12(2):378-92.
DOI:10.1111/j.1462-2920.2009.02075.x
pp.378-92
Source: PubMed
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Article: Accuracy and quality of massively parallel DNA pyrosequencing.
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ABSTRACT: Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls. We performed an empirical study of the per-base error rate for the Roche GS20 system using sequences of the V6 hypervariable region from cloned microbial ribosomal DNA (tag sequencing). We calculated a 99.5% accuracy rate in unassembled sequences, and identified several factors that can be used to remove a small percentage of low-quality reads, improving the accuracy to 99.75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.Genome biology 02/2007; 8(7):R143. · 6.63 Impact Factor -
Article: Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters.
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ABSTRACT: The goal of this study was to develop and test the efficacy of a PCR assay for the environmental detection of the nifH gene of Methanobrevibacter smithii, a methanogen found in human faeces and sewage. PCR primers for the nifH gene of M. smithii were designed, tested and used to detect the presence or absence of this organism in faecal and environmental samples. Specificity analysis showed that the Mnif primers amplified products only in M. smithii pure culture strains (100%), human faeces (29%), human sewage samples (93%) and sewage-contaminated water samples (100%). No amplification was observed when primers were tested against 43 bacterial stock cultures, 204 animal faecal samples, 548 environmental bacterial isolates and water samples from a bovine waste lagoon and adjacent polluted creek. Sequencing of PCR products from sewers demonstrated that a 222-bp product was the nifH gene of M. smithii. The minimal amount of total DNA required for the detection of M. smithii was 10 ng for human faeces, 10 ng for faecally contaminated water and 5 ng for sewage. Recreational water seeded with M. smithii established a lower detection limit of 13 cells ml(-1). The Mnif assay developed during this investigation showed successful detection of M. smithii in individual human faecal samples, sewage and sewage-contaminated water but not in uncontaminated marine water or bovine-contaminated waters. The Mnif assay appears to be a potentially useful method to detect sewage-polluted coastal waters. This study was the first to utilize methanogens as an indicator of sewage pollution. Mnif PCR detection of M. smithii was shown to be a rapid, inexpensive and reliable test for determining the presence or absence of sewage pollution in coastal recreational waters.Journal of Applied Microbiology 08/2006; 101(1):44-52. · 2.34 Impact Factor
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Keywords
discernible human faecal signature
faecal signature
High-abundance sequences
human faecal microbes
human faecal samples
influent flows
massively parallel 454 pyrosequencing
sewage influent
sewage profiles
sewage samples
small fraction
specific microbes
standard indicators species
surface water samples
surface waters
taxa present
taxonomic groups
unique population structure
untreated sewage influent samples
untreated sewage introduces non-indigenous microbial populations