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Water 2016, 8(6), 231; doi:10.3390/w8060231

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

1
CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, Queensland 4102, Australia
2
School of Agriculture and Food Science, University of Queensland, St. Lucia, Queensland 4072, Australia
3
Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Yiping Cao
Received: 19 April 2016 / Revised: 24 May 2016 / Accepted: 26 May 2016 / Published: 31 May 2016
(This article belongs to the Special Issue Pathogens in Water)
View Full-Text   |   Download PDF [1365 KB, uploaded 31 May 2016]   |  

Abstract

Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or “markers” of sewage pollution, including known advantages and deficiencies of the many polymerase chain reaction (PCR)-based methods that have been published since 2000. Host specificity is a paramount criterion for confidence that detection of a marker is a true indicator of the target host. Host sensitivity, or the prevalence of the marker in feces/waste from the target host, is necessary for confidence that absence of the marker is indicative of the absence of the pollution source. Each of these parameters can vary widely depending on the type of waste assessed and the geographic location. Differential decay characteristics of bacterial targets and their associated DNA contribute to challenges in interpreting MST results in the context of human health risks. The HF183 marker, derived from the 16S rRNA gene of Bacteroides dorei and closely related taxa, has been used for almost two decades in MST studies, and is well characterized regarding host sensitivity and specificity, and in prevalence and concentration in sewage in many countries. Other markers such as HumM2 and HumM3 show promise, but require further performance testing to demonstrate their widespread utility. An important limitation of the one-marker-one-assay approach commonly used for MST is that given the complexities of microbial persistence in environmental waters, and the methodological challenges of quantitative PCR (qPCR) in such samples, the absence of a given marker does not ensure the absence of fecal pollution in the source water. Approaches under development, such as microarray and community analysis, have the potential to improve MST practices, thereby increasing our ability to protect human and ecosystem health. View Full-Text
Keywords: microbial source tracking; Bacteroides; fecal pollution; fecal indicator bacteria; wastewater; water quality; next-generation sequencing microbial source tracking; Bacteroides; fecal pollution; fecal indicator bacteria; wastewater; water quality; next-generation sequencing
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ahmed, W.; Hughes, B.; Harwood, V.J. Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters. Water 2016, 8, 231.

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