Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

Henry, Rebekah; Schang, Christelle; Coutts, Scott; Kolotelo, Peter; Prosser, Toby; Crosbie, Nicholas D.; Grant, Trish; Cottam, Darren; O’Brien, Peter; Deletić, Ana; McCarthy, David Thomas

doi:10.1016/j.watres.2016.02.029

Cited by 113 publications

(102 citation statements)

References 34 publications

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“…However, both of these methods are subject to loss of information by binning OTUs into taxa and may be subjected to biases associated with taxonomic databases (37). SourceTracker has previously been used in environmental and clinical studies to effectively determine sources of contamination using a Bayesian approach without taxonomic binning (28, 39, 40). This methodology was employed here to assess donor engraftment as the percentage of patient samples attributable to donor communities.…”

Section: Discussionmentioning

confidence: 99%

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

Staley

Kelly

Brandt

et al. 2016

mBio

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Bacterial communities from subjects treated for recurrent Clostridium difficile infection (rCDI) by fecal microbiota transplantation (FMT), using either heterologous donor stool samples or autologous stool samples, were characterized by Illumina next-generation sequencing. As previously reported, the success of heterologous FMT (90%) was superior to that of autologous FMT (43%) (P = 0.019), and post-FMT intestinal bacterial communities differed significantly between treatment arms (P < 0.001). Subjects cured by autologous FMT typically had greater abundances of the Clostridium XIVa clade and Holdemania bacteria prior to treatment, and the relative abundances of these groups increased significantly after FMT compared to heterologous FMT and pre-FMT samples. The typical shift to post-FMT, donor-like assemblages, featuring high relative abundances of genera within the Bacteroidetes and Firmicutes phyla, was not observed in the autologous FMT subjects. Autologous FMT patient bacterial communities were significantly different in composition than those for heterologous FMT patients and donors (P < 0.001). The SourceTracker program, which employs a Bayesian algorithm to determine source contributions to sink communities, showed that patients initially treated by heterologous FMT had significantly higher percentages of engraftment (i.e., similarity to donor communities, mean value of 74%) compared to those who suffered recurrence following autologous FMT (1%) (P ≤ 0.013). The findings of this study suggest that complete donor engraftment may be not necessary if functionally critical taxa are present in subjects following antibiotic therapy.

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Section: Discussionmentioning

confidence: 99%

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

Staley

Kelly

Brandt

et al. 2016

mBio

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“…For a more comprehensive review of HTS for assessing water quality see Tan et al (2015). Targeted sequencing of 16S rRNA for bacteria and 18S rRNA for eukaryote small sub-unit rRNA permits an estimate of diversity and abundance (Henry et al, 2016), although the resolution of the 18S RNA gene as a phylogenetic marker us variable amongst taxa and is often not suitable for the resolution of FIOs belonging to the enterobacteriaceae for example. However, coupled sequencing and flow cytometry approaches can be used for more accurate taxon quantification (Props et al, 2016), although a different quantitative technology would be required for sediments.…”

Section: Discussionmentioning

confidence: 99%

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

et al. 2016

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The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

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“…SourceTracker has recently been used to determine sources of fecal and environmental contamination in coral reefs off the Florida coast, in a Lake Superior estuary and in potable rainwater and recreational beaches in Australia (Ahmed et al, 2015;Brown et al, 2017;Henry et al, 2016;Neave et al, 2014). In these studies, FTLs were prepared by characterising fecal communities in source samples using NGS of hypervariable regions of the 16S rRNA gene.…”

Section: Sourcetrackermentioning

confidence: 99%

“…These libraries were then compared against bacterial communities characterized from surface waters. Both computational and in vitro experiments were performed to test the accuracy of the qualitative and quantitative predictions generated by SourceTracker, and a previous study found that source predictions for fecal pollution from sources present at high abundance were relatively accurate (Henry et al, 2016). The calculation of the relative standard deviation (RSD) among several runs has been used as a gauge by which to measure confidence (Brown et al, 2017;Henry et al, 2016;McCarthy et al, 2017).…”

Section: Sourcetrackermentioning

confidence: 99%

Fecal pollution: new trends and challenges in microbial source tracking using next‐generation sequencing

Unno

Staley

Brown

et al. 2018

Environmental Microbiology

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In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

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Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

Cited by 113 publications

References 34 publications

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

Fecal pollution: new trends and challenges in microbial source tracking using next‐generation sequencing

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