Biology subjects

Rousseau, G. M.

Publications and source records attributed to Rousseau, G. M..

4 recordsLinked to original sources

bioRxiv2026

Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus

Bacteria encode diverse antiviral defense systems, yet the evolutionary reservoirs that generate this immune innovation remain poorly defined. Although genomic context has been instrumental in discovering defense systems, genomic islands (GIs), variable chromosomal regions enriched in defense genes and proteins of unknown function, have not been systematically explored as sources of new bacterial immunity. Here, using comparative genomics of Streptococcus thermophilus, we identified 30 defense-associated GIs displaying extensive accessory gene diversity. Investigation of candidate loci from three GIs uncovered 15 previously uncharacterized antiviral systems, including 10 with novel architectures or features, revealing the potential within even a small subset of GIs. Several systems were not located near known defense genes, highlighting that GI-based discovery complements the traditional guilt-by-association approach, revealing systems that would otherwise remain undetected. Together, our findings establish GIs as reservoirs of antiviral innovation and provide a framework for uncovering the diversity of bacterial immune systems.

microbiology↗

bioRxiv2024

Strengthening Phage Resistance of Streptococcus thermophilus by Leveraging Complementary Defense Systems

CRISPR-Cas and restriction-modification systems represent the core defense arsenal in Streptococcus thermophilus to block lytic phages, but their effectiveness is compromised by phages encoding anti-CRISPR proteins (ACRs) and other counter-defense strategies. Here, we explored the resistome of 263 S. thermophilus strains to uncover other anti-phage systems. The defense landscape of S. thermophilus was enriched by 21 accessory defense systems, 13 of which had not been previously investigated in this species. Experimental validation of 17 systems with 14 phages showed varying anti-phage levels, uncovering intra-genus specificities among the five viral genera infecting S. thermophilus. Interestingly, the resistance levels were even higher when some defense systems (Dodola and PD-Lambda-1) were expressed from a low-copy plasmid or when integrated into the chromosome. We also observed a synergistic effect when combining Gabija with CRISPR-Cas, underscoring the potential of these additional defense systems for developing more robust industrial S. thermophilus strains, particularly against ACR-encoding phages.

microbiology↗

bioRxiv2022

CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice

Many prokaryotes harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, very few of these systems have been experimentally confirmed to be active in gut bacteria. Here, we experimentally demonstrate that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage-assays in vitro but also in vivo using gnotobiotic (GB) mice. An increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Interestingly, much less new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.

microbiology↗

bioRxiv2021

Competition and coevolution drive the evolution and the diversification of CRISPR immunity

The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations [1-3]. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition among host genotypes and coevolution with pathogens. Here we study experimentally the effect of coevolving phage populations on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host-pathogen coevolution.

microbiology↗