New insights into intestinal phages

Sausset, Romain; Petit, Marie-Agnès; Gaboriau-Routhiau, Valérie; Paepe, Marianne De

doi:10.1038/s41385-019-0250-5

Cited by 166 publications

(173 citation statements)

References 128 publications

Supporting

Mentioning

167

Contrasting

Unclassified

Order By: Relevance

“…In addition, environmental stress (e.g. inflammation) is known to influence the rate of HGT events [20,21]. Thus, we tested for this evolutionary mechanism by enquiring if clones sampled from mice where coexistence was seen, had acquired two known active prophages.…”

Section: Resultsmentioning

confidence: 99%

Mutation accumulation and horizontal gene transfer inEscherichia colicolonizing the gut of old mice

Barreto

Frazão

Sousa

et al. 2020

Communicative & Integrative Biology

View full text Add to dashboard Cite

The ecology and environment of the microbes that inhabit the mammalian intestine undergoes several changes as the host ages. Here, we ask if the selection pressure experienced by a new strain colonizing the aging gut differs from that in the gut of young adults. Using experimental evolution in mice after a short antibiotic treatment, as a model for a common clinical situation, we show that a new colonizing E. coli strain rapidly adapts to the aging gut via both mutation accumulation and bacteriophage-mediated horizontal gene transfer (HGT). The pattern of evolution of E. coli in aging mice is characterized by a larger number of transposable element insertions and intergenic mutations compared to that in young mice, which is consistent with the gut of aging hosts harboring a stressful and iron limiting environment.

show abstract

Section: Resultsmentioning

confidence: 99%

Mutation accumulation and horizontal gene transfer inEscherichia colicolonizing the gut of old mice

Barreto

Frazão

Sousa

et al. 2020

Communicative & Integrative Biology

View full text Add to dashboard Cite

show abstract

“…An estimated 10 31 phages exist in nature. And the human gastrointestinal tract contains a large diversity consisting of >10 10 phages many of which are just beginning to be discovered (Shkoporov and Hill, 2019;Sausset et al, 2020). Reasoning that human sewage or the feces of animals may contain phage that have evolved to target their host in high mucin environments, such as the intestinal tract, we screened our phage library (Gibson et al, 2019) and other phages (Table 1) recently isolated from these environments for enhanced activity in LB containing 1.5% mucin ( Figure 2C).…”

Section: Discovery Of a Mucin-enhanced Phagementioning

confidence: 99%

Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

Green

Liu

et al. 2020

Preprint

View full text Add to dashboard Cite

The human mucosal surface is a complex ecosystem comprised of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. A less characterized, third entity, that of bacteriophage (phage), parasitizes prokaryotes but generally do not interact with eukaryotic cells. In the gastrointestinal tract, the interaction of these two domains of life influences the health status of the host, especially if there is colonization with invasive pathobionts. If the pathobiont causes a symptomatic infection, treatment with antibiotics is necessary. However, antibiotics act broadly thereby killing many protective commensals and they lack the physio-chemical properties to be optimally active in the mucosa, and may have associated adverse effects, including toxicities. Here, we report a novel C3 type phage of the genus Kuravirus whose lytic cycle is enhanced in intestinal environments. The enhanced activity is encoded in the viral tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, thereby positioning it near the location of its bacterial host. This finding offers the prospect of developing epithelial-targeting phage to selectively remove invasive pathobiont species from mucosal surfaces.

show abstract

“…The relative frequency of temperate and virulent phages vary across bacterial taxa and environments. In the mammalian gut, for instance, temperate phages seem to be more prevalent (5), while most intracellular and many environmental bacteria lack prophages (6), and are thus presumably rarely infected by temperate phages. Phages also drive horizontal gene transfer among bacteria by transduction (3), which may disseminate virulence factors (7) and antibiotic resistance (8).…”

Section: Introductionmentioning

confidence: 99%

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Sousa

Pfeifer

Touchon

et al. 2020

Preprint

View full text Add to dashboard Cite

11 12Bacteriophages (henceforth phages) evolve by mutation and recombination. Temperate 13 phages are known to evolve rapidly by genetic exchanges. In contrast, recombination events 14 between virulent and between temperate and virulent phages have rarely been reported. A 15 gene flow barrier between these two large distinct groups of phages could affect the ability of 16 phages to acquire novel functions. Here, we show that genomes of temperate and virulent 17 phages are very distinct but often have a few almost identical genes. These cases are due to 18 recent genetic exchanges of both phage-like and bacterial-like genes. These exchanges were 19 probably mediated by phage recombinases with low homology requirements and mechanisms 20 of non-homologous end joining, since both were over-represented in recombinant phages and 21 their hosts. When assessing the impact of gene flow across the two populations of phages we 22 realized that temperate phages have narrower host ranges than virulent phages. This 23 suggests, and we find some evidence, that gene flow between temperate phages infecting 24 distant bacterial hosts might be mediated by recombination with the broader host virulent 25 phages. Hence, gene flow across phages with distinct lifestyles could drastically increase the 26 gene repertoire available for phage evolution, including the transfer of functional innovations 27 across taxa. These results also have implications for bacterial evolution because of the impact 28 of phage predation in bacterial population dynamics and the contribution of temperate phages 29 to the evolution of bacterial gene repertoires. 31 SIGNIFICANCE STATEMENT 33Many microbial communities are intensely predated by temperate and virulent 34 bacteriophages. The former also contribute to bacterial gene repertoires. Gene transfers 35 between bacteriophages favor their rapid adaptation, but are thought to occur rarely between 36 virulent and temperate bacteriophages because their genomes are very different in terms of 37 gene repertoires and genetic organization. We found that genetic exchanges occur frequently 38 3 between these types of bacteriophages, involve different phage and bacterial functions, and 39 are likely due to multiple DNA repair processes. Since we show that virulent bacteriophages 40 have broader host ranges, they can shuttle genes between temperate bacteriophages present 41 in taxa that are beyond the typical range of the latter. This enhances phages diversification 42 and has multiple impacts on bacterial evolution. 43 65 accretion in virulent phages, even if some families of virulent phages have remarkable 66 diversity in their genomes' size, suggesting the existence of mechanisms of gene exchange 67 (12). The genomic plasticity of temperate lambdoid phages has been much more extensively 68 studied (9, 13, 14). Their analyses reveal that pairs of phages tend to have patches of regions 69 of very similar sequences within genomes that are often very dissimilar. This genome 70 mosaicism is facilitated by the modular or...

show abstract

New insights into intestinal phages

Cited by 166 publications

References 128 publications

Mutation accumulation and horizontal gene transfer inEscherichia colicolonizing the gut of old mice

Mutation accumulation and horizontal gene transfer inEscherichia colicolonizing the gut of old mice

Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Contact Info

Product

Resources

About