Abstract
Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
Highlights
The faecal contamination of environmental waters used for drinking and recreational purposes poses a major potential risk to public health
To evaluate the relative representation of genes with similarity to those encoded by ɸB124-14 in viral metagenomes, we calculated the cumulative relative abundance of sequences similar to translated ɸB124-14 open reading frames (ORFs) in each metagenome (Fig. 1)
Sequences generating valid hits to at least one ɸB124-14 ORF were identified in all data sets evaluated, but a significantly greater mean relative abundance of ɸB124-14-encoded ORFs was evident in human gut viromes, compared with environmental data sets (Fig. 1a)
Summary
The faecal contamination of environmental waters used for drinking and recreational purposes poses a major potential risk to public health. The detection and enumeration of FIB have long been useful in strategies to improve and maintain water quality, they are subject to a range of limitations that impair their overall utility. Limitations include their lack of specificity to human faeces, poor persistence or potential regrowth in certain environments, and long turnaround times associated with culturebased detection [5,6,7,8]
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