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Bacteriophages: an underestimated role in human and animal health?

De Paepe M, Leclerc M, Tinsley CR, Petit MA - Front Cell Infect Microbiol (2014)

Bottom Line: In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages.Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present.This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.

View Article: PubMed Central - PubMed

Affiliation: Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France.

ABSTRACT
Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.

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Related in: MedlinePlus

Phage richness in various viromes. Scores estimated with PHACCS in five environments are shown (blue, open environments, orange, human samples). PHACCS is a program estimating species richness from contig spectra (Angly et al., 2005). Ocean: mix of four oceans samples (Angly et al., 2006). Hot springs: Yellowstone (Schoenfeld et al., 2008), saliva: average of 5 subjects (Pride et al., 2012), lung: non-cystic fibrosis samples (Willner et al., 2009), feces: median value of 12 samples (Reyes et al., 2010).
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Figure 2: Phage richness in various viromes. Scores estimated with PHACCS in five environments are shown (blue, open environments, orange, human samples). PHACCS is a program estimating species richness from contig spectra (Angly et al., 2005). Ocean: mix of four oceans samples (Angly et al., 2006). Hot springs: Yellowstone (Schoenfeld et al., 2008), saliva: average of 5 subjects (Pride et al., 2012), lung: non-cystic fibrosis samples (Willner et al., 2009), feces: median value of 12 samples (Reyes et al., 2010).

Mentions: Virome studies allow for the first time to apprehend the overall phage genomic diversity, which is even greater than bacterial genomic diversity (Kristensen et al., 2013). It should be noted however, that phage genomic diversity is lower in fecal samples compared to that observed in open environments, as has already been observed for bacterial diversity (Ley et al., 2006). Diversity estimations computed with the same index in five environments are shown in Figure 2. The ratio of virotypes to bacterial phylotypes in the fecal microbiota was estimated to be close to 1 (Reyes et al., 2010). Still, phage genomic diversity is huge in the gut microbiota, and since most metagenomic phage sequences do not map to known phage genes, the functional analysis of viromes remains particularly difficult at present. Further advance in this new field of science will certainly allow refining the picture in the coming years. The analysis of the virome of twins and their mothers has shown that each individual has his own complement of phages, regardless of genetic proximity (Reyes et al., 2010). However, the viral fraction of a given individual remains stable over time in a 1 year study (Reyes et al., 2010). Interestingly, each individual virome is often dominated by one or a few phages (Reyes et al., 2010; Minot et al., 2011).


Bacteriophages: an underestimated role in human and animal health?

De Paepe M, Leclerc M, Tinsley CR, Petit MA - Front Cell Infect Microbiol (2014)

Phage richness in various viromes. Scores estimated with PHACCS in five environments are shown (blue, open environments, orange, human samples). PHACCS is a program estimating species richness from contig spectra (Angly et al., 2005). Ocean: mix of four oceans samples (Angly et al., 2006). Hot springs: Yellowstone (Schoenfeld et al., 2008), saliva: average of 5 subjects (Pride et al., 2012), lung: non-cystic fibrosis samples (Willner et al., 2009), feces: median value of 12 samples (Reyes et al., 2010).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3975094&req=5

Figure 2: Phage richness in various viromes. Scores estimated with PHACCS in five environments are shown (blue, open environments, orange, human samples). PHACCS is a program estimating species richness from contig spectra (Angly et al., 2005). Ocean: mix of four oceans samples (Angly et al., 2006). Hot springs: Yellowstone (Schoenfeld et al., 2008), saliva: average of 5 subjects (Pride et al., 2012), lung: non-cystic fibrosis samples (Willner et al., 2009), feces: median value of 12 samples (Reyes et al., 2010).
Mentions: Virome studies allow for the first time to apprehend the overall phage genomic diversity, which is even greater than bacterial genomic diversity (Kristensen et al., 2013). It should be noted however, that phage genomic diversity is lower in fecal samples compared to that observed in open environments, as has already been observed for bacterial diversity (Ley et al., 2006). Diversity estimations computed with the same index in five environments are shown in Figure 2. The ratio of virotypes to bacterial phylotypes in the fecal microbiota was estimated to be close to 1 (Reyes et al., 2010). Still, phage genomic diversity is huge in the gut microbiota, and since most metagenomic phage sequences do not map to known phage genes, the functional analysis of viromes remains particularly difficult at present. Further advance in this new field of science will certainly allow refining the picture in the coming years. The analysis of the virome of twins and their mothers has shown that each individual has his own complement of phages, regardless of genetic proximity (Reyes et al., 2010). However, the viral fraction of a given individual remains stable over time in a 1 year study (Reyes et al., 2010). Interestingly, each individual virome is often dominated by one or a few phages (Reyes et al., 2010; Minot et al., 2011).

Bottom Line: In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages.Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present.This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.

View Article: PubMed Central - PubMed

Affiliation: Institut National de la Recherche Agronomique, Micalis, UMR 1319 Jouy en Josas, France ; Agroparistech, Micalis, UMR 1319 Jouy en Josas, France.

ABSTRACT
Metagenomic approaches applied to viruses have highlighted their prevalence in almost all microbial ecosystems investigated. In all ecosystems, notably those associated with humans or animals, the viral fraction is dominated by bacteriophages. Whether they contribute to dysbiosis, i.e., the departure from microbiota composition in symbiosis at equilibrium and entry into a state favoring human or animal disease is unknown at present. This review summarizes what has been learnt on phages associated with human and animal microbiota, and focuses on examples illustrating the several ways by which phages may contribute to a shift to pathogenesis, either by modifying population equilibrium, by horizontal transfer, or by modulating immunity.

Show MeSH
Related in: MedlinePlus