Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing

  title={Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing},
  author={Ju-Yong Jeong and Hee-Deung Park and Kyong-Hee Lee and Hang-Yeon Weon and Jong-Ok Ka},
  journal={The Journal of Microbiology},
It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1–V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample… 
Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water
It is shown that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river, and recommended using bacterial community analysis (where possible) along with PCR detection or quantification of host- associated molecular markers to provide information on the sources of feces in waterways.
Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan
Whether nearshore and adjacent beach bacterial contamination originated from the Grand Calumet River and to determine if there were correlations between pathogens/feces associated bacteria in any of the samples to counts of the pathogen indicator species Escherichia coli.
12 DNA extracted from feces (human and bovine) and water samples was used for the massive 13 pyrosequencing of the hypervariable V3 region of the 16S rRNA gene, revealing 4296 operational 14
Bacteroidetes and/ or Prevotella were detected in most samples from the WWTP validating at some extent their usefulness as biomarker to predict environmental contamination by swine wastewaters, thus presenting a potential threat to public health.
Methods of Targeting Animal Sources of Fecal Pollution in Water
The determination of fecal pollution sources in waters is essential in the management of catchments. Although traditional microbial water analyses using indicator microorganisms have been used for
Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines
Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes.
Multiple approaches to microbial source tracking in tropical northern Australia
Generally, connectivity between the sites was observed within distinct geographical locations and it appeared that most of the bacterial contamination on Darwin beaches was confined to local sources.
A Meta-analysis of Bacterial Diversity in the Feces of Cattle
A small number of OTUs shared among datasets indicate that fecal bacterial communities of cattle are greatly affected by various factors, specifically diet.


Identification of Nonpoint Sources of Fecal Pollution in Coastal Waters by Using Host-Specific 16S Ribosomal DNA Genetic Markers from Fecal Anaerobes
A new PCR-based method for distinguishing human and cow fecal contamination in coastal waters without culturing indicator organisms is described and it is shown that the method can be used to track bacterial marker sequences in complex environments.
Quantification of host-specific Bacteroides–Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater
This work identified one human, three cow-, and two pig-specific Bacteroides–Prevotella group-specific 16S rRNA gene markers, designed host-specific real-time polymerase chain reaction (real-time PCR) primer sets, and successfully developed real- time PCR assay to quantify the fecal contamination derived from human, cow, and pig in natural river samples.
Molecular identification of fecal pollution sources in water supplies by host-specific fecal DNA markers and Terminal Restriction Fragment Length Polymorphism profiles of 16S rRNA gene
The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources, which could be used to identify and control the fecals pollution source in the bodies of water in Korea.
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.
Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition, and microbial sewage communities represent a combination of inputs from human faecal microbes and enrichment of specific microbes from the environment to form a unique population structure.
Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers
The results of this study highlight that pig fecal contamination was not as frequent as human or bovine FECal contamination and that fecal pollution generally came from multiple origins.
Development of Bacteroides 16S rRNA Gene TaqMan-Based Real-Time PCR Assays for Estimation of Total, Human, and Bovine Fecal Pollution in Water
Results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds.
Host Distributions of Uncultivated Fecal Bacteroidales Bacteria Reveal Genetic Markers for Fecal Source Identification
Examination of host distribution patterns among fecal bacteria in the order Bacteroidales revealed both endemic and cosmopolitan distributions among the eight hosts, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments.
Quantitative analysis of human and cow-specific 16S rRNA gene markers for assessment of fecal pollution in river waters by real-time PCR.
Real-time PCR assay with human and cow-specific 16S rRNA gene markers identified in the T-RFLP analysis could reliably identify and quantify the fecal pollution sources, enabling effective measures in the watersheds and facilitating water quality management.
Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution.
  • C. Kreader
  • Medicine, Biology
    Applied and environmental microbiology
  • 1995
Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human