Biology subjects

Ravantti, J.

Publications and source records attributed to Ravantti, J..

6 recordsLinked to original sources

bioRxiv2025

ssDNA phage FLiP resides in dsDNA form in resistant Flavobacterium host

Most of the environmental flavobacteria decompose organic matter, playing a crucial role in ecosystem balance. Phages infecting these bacteria regulate the host populations and thereby the ecosystem functions, however, bacterial resistance against phage may cause changes in bacterial phenotypic characteristics. ssDNA phage Finnlakevirus FLiP infects three known environmental Flavobacterium sp. isolates: B330, B167, and B114. Building on our previous FLiP-host interaction studies, we aimed to broaden our understanding of the host perspective by exploring phage resistance mechanisms against FLiP and similar phages. We compared growth dynamics of ancestral and resistant variants to detect the effect of resistance on host fitness. Genomic comparison between the variants was used to identify resistance-related mutations. Additionally, we analysed genomic differences among the three host strains, screening for anti-phage systems. Sequence analyses, PCR, and nuclease treatments of resistant host genomes and plasmids were used to assess the possibility of lysogeny and superinfection immunity. No single mutation or anti-phage system consistently explained FLiP resistance, as these varied across hosts. Resistant B114 contained FLiP genome in circular extrachromosomal dsDNA form, suggesting possible lysogeny. Surprisingly, we found that low quantities of FLiP sequences exist in bacterial populations not exposed to FLiP in the laboratory. This suggests that residing as extrachromosomal dsDNA elements in a small percentage of host cells may be a natural strategy for FLiP type phages to endure unfavourable conditions.

microbiology↗

bioRxiv2025

New Finnlakevirus isolate FLiP-2 provides insight into the ecology of ssDNA phages in Flavobacterium hosts

Life cycle details or ecological impact are well characterized only for a few ssDNA phages. The Finnlakeviridae family includes one species, Finnlakevirus FLiP. Here, using the same Flavobacterium host and sampling location, we isolated a new strain designated FLiP-2, with 96,7 % genetic identity to the original isolate FLiP. To understand the ecology of this Flavobacterium-infecting phage species, we explored the host interactions of the two FLiP strains and a dsDNA Flavobacterium phage MaF61 under various conditions representing those encountered in their natural habitats in boreal lakes including different temperatures, anoxic conditions, and in the presence of different nutrients and antibiotics. While FLiP and FLiP-2 had similar virion stability outside the host, they exhibited significant differences in plaque morphology and infectivity. FLiP-2 could not replicate in the presence of ampicillin, whereas FLiP thrived even at high concentrations. Both strains of Finnlakevirus FLiP propagated better under or after stress exposure compared to MaF61. Additionally, Finnlakevirus FLiP plaques appeared far from the original infection site, particularly in response to stress, suggesting latent presence within a motile or filamentous bacterium. In conclusion, Finnlakevirus FLiP showed remarkable flexibility in host-interactions being well adapted to fluctuating conditions in boreal freshwaters.

microbiology↗

bioRxiv2025

Longitudinal dynamics of gut plasmidome and antibiotic resistance during antibiotic therapy: a case report

The human gut microbiome is composed of diverse microbes, and its association with human health is well-recognized. Antibiotic therapies for treating infectious diseases often mediate adverse influences on gut microbial ecosystems. Further, ESBL (extended-spectrum beta-lactamase)-producing bacteria potentially residing in the gut benefit from antibiotic-induced environmental changes via positive selection for resistance traits. As antimicrobial resistance (AMR) genes are often harbored by mobile plasmids, the importance of these extrachromosomal mobile genetic elements during antibiotic exposure is evident. However, there is still a knowledge gap in how microbiomes respond to antibiotic treatment especially in terms of plasmid carriage and how gut plasmid populations evolve following and revive after antibiotic therapy. To address these questions, in this case report we investigated the changes in plasmid population in the gut microbiome of a single ESBL-carrying patient during antibiotic therapy for uncomplicated acute appendicitis. Employing longitudinal sampling, we collected E. coli strains and performed metagenomic analysis before, during, and after the treatment. Our findings indicate that the antibiotic treatment is associated with a transient alteration in the microbial composition, AMR profile, and plasmid population. An extensive but temporary domination of ESBL-E. coli within the gut microbiome was observed parallel to the ongoing antibiotic treatment. However, this was not sustained in the follow-up period, indicating a slight restoration of both the microbial composition and the plasmid population. The research underscores the temporary impact of antibiotic therapy on the dynamics of the gut plasmidome which essentially mediate the spread of AMR within the gut microbiome.

microbiology↗

bioRxiv2022

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability

Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. Following the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. The cryo-EM reconstructions of ten capsids solved to resolutions between 2.2 and 4 [A]ngstroms revealed that eight of them exhibit major capsid proteins that are linked by a covalent cross-linking (isopeptide bond) between subunits that was first described in the HK97 phage. Those covalent interactions ultimately lead to the formation of mutually interlinked capsomers that has been compared to the structure of chain mail. However, three of the closely related phages do not exhibit such an isopeptide bond as demonstrated by both our cryo-EM maps and the lack of the required residue. This work raises questions about the importance of previously described capsid stabilization mechanisms.

biochemistry↗

bioRxiv2022

New Vista into Origins of Viruses from a Prototypic ssDNA Phage

Viruses play a central role in all ecological niches; the origin of viruses, however, remains an open question. While phylogenetic analysis of distantly related viruses is hampered by a lack of detectable sequence similarity, structural biology can reveal conserved capsid protein structures that facilitate the study of distant evolutionary relationships. Here, we characterize the lipid-containing ssDNA temperate bacteriophage {Phi}CjT23, which is infecting Flavobacterium sp. (Bacteroidetes). We further detected {Phi}CjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy revealed similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses. Common to these viruses, infecting hosts from all domains of life, is a major capsid protein composed of two upright {beta}-sandwiches. The minimalistic structure of {Phi}CjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both {Phi}CjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.

microbiology↗

bioRxiv2017

Long-term genomic coevolution of host-parasite interaction in natural environment

The antagonistic coevolution of parasite infectivity and host resistance alters the biological functionality of species, with effects spanning to communities and ecosystems. Still, studies describing long-term host-parasite coevolutionary dynamics in nature are largely missing. Furthermore, the role of host resistance mechanisms for parasite evolution is poorly understood, necessitating for the molecular and phenotypic characterization of both coevolving parasites and their hosts. We combined long-term field sampling (2007-2014), in vitro cross-infections and time-shift experiments with bacteriophage whole genome sequencing and bacterial (Flavobacterium columnare) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) profiling to show the molecular details of the phage-bacterium arms race in the environment. Bacteria were generally resistant to phages from the past and susceptible to phages in the future. The bacterial resistance selected for increased phage infectivity and host range, correlating directly with the expansion of phage genome size by 2656 bp. In the bacterial host, two CRISPR loci were identified: a type II-C locus and an RNA-targeting type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appeared in the variable end of both CRISPR loci over time. The appearance of these CRISPR spacers in the bacterial host often corresponded with arms race -manner molecular changes in the protospacers of the coevolving phage population. However, the phenotypic data indicated that the relative role of constitutive defence may be more important in high phage pressure, highlighting the importance of our findings for understanding microbial community ecology and in the development of phage therapy applications.

microbiology↗