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Discovering new indicators of fecal pollution - PubMed

Review

Discovering new indicators of fecal pollution

Sandra L McLellan et al. Trends Microbiol. 2014 Dec.

Abstract

Fecal pollution indicators are essential to identify and remediate contamination sources and protect public health. Historically, easily cultured facultative anaerobes such as fecal coliforms, Escherichia coli, or enterococci have been used but these indicators generally provide no information as to their source. More recently, molecular methods have targeted fecal anaerobes, which are much more abundant in humans and other mammals, and some strains appear to be associated with particular host sources. Next-generation sequencing and microbiome studies have created an unprecedented inventory of microbial communities associated with fecal sources, allowing reexamination of which taxonomic groups are best suited as informative indicators. The use of new computational methods, such as oligotyping coupled with well-established machine learning approaches, is providing new insights into patterns of host association. In this review we examine the basis for host-specificity and the rationale for using 16S rRNA gene targets for alternative indicators and highlight two taxonomic groups, Bacteroidales and Lachnospiraceae, which are rich in host-specific bacterial organisms. Finally, we discuss considerations for using alternative indicators for water quality assessments with a particular focus on detecting human sewage sources of contamination.

Keywords: alternative indicators; fecal indicators; microbial communities; next-generation sequencing; oligotyping; sewage; water quality.

Copyright © 2014 Elsevier Ltd. All rights reserved.

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Figures

Figure I
Figure I

Traditional indicators and Prevotella and Lachnospiraceae oligotypes demonstrating human fecal pollution inputs. River sampling transect in the Jiquiriçá River and increasing human Prevotella and Lachnospiraceae oligotypes with increasing residential density. Map shows residential structures along the river transect. Colored circles in the table are proportional to the relative abundance of human Prevotella or Lachnospiraceae oligotypes (red) or the relative abundance of sequences classified as E. coli or Enterococci sp. as a measure of overall fecal pollution (purple). Data were originally reported in Koskey et al. [111].

Figure 1
Figure 1

Resolution of three Bacteroides OTUs using oligotyping to discern differences in human populations across a wide geographic distance. The top panel shows the entropy analysis of 30,637,709 101 nt long V4 reads that are identified as Bacteroides in a publicly available dataset by Yatsunenko et al. [49]. Red dots on entropy bars indicate the nucleotide positions used for oligotyping analysis. Lower panel exemplifies three OTUs that could be further resolved with oligotyping. Colored bars represent the prevalence of a given oligotype in gut samples, where a full bar indicates that the oligotype was found in all individuals from the given region. Each group has two oligotypes that show remarkable differential distribution patterns among human populations that is missed by taxonomical analysis and OTU clustering at 97%. These results were originally reported by Eren et al. [65].

Figure 2
Figure 2

Possible differential abundance patterns of organisms in host species. We propose terminology to describe different abundance patterns of members in the microbial community of host species, as originally reported in [70]. Cosmopolitan refers to organisms prevalent in all host species with no distinguishing patterns of abundance. Organisms that highly abundance in one host species and have low abundance or are absent in other hosts are designated as ‘host-preferred’. Organisms that are in only one host species but not detected in all individuals are designated ‘host-associated’. When describing occurrence patterns, the term host-specific is reserved for organisms that are present in all individuals of a host and absent in other host species. Many other patterns are possible; these terms are working definitions that can be used to assess candidate alternative indicators.

Figure 3
Figure 3

Blautia populations in sewage, humans and animals display host preference and specificity. Heatmap analysis of Blautia oligotypes. The dendrogram (top) shows the hierarchical clustering of samples based on Morisita-Horn dissimilarity index. The samples are ordered based on clustering according to their oligotype profiles, and the oligotypes were ordered based on their occurrence patterns in samples. Blue color identifies oligotypes that are absent or represented by a very small number of reads in a sample. Data are originally presented in McLellan et al. [12].

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