Biology subjects

Wendling, C. C.

Publications and source records attributed to Wendling, C. C..

10 recordsLinked to original sources

bioRxiv2026

A humanized Galleria mellonella model reveals prophage-mediated breakdown of colonization resistance against Salmonella

BackgroundColonisation resistance provided by the gut microbiota is a critical barrier to pathogen invasion, yet its study in vivo is constrained by the complexity and cost of vertebrate models. Here, we developed a humanised Galleria mellonella infection model by inoculating wax moth larvae with complex human faecal microbiota. 16S rRNA gene sequencing confirmed stable, reproducible establishment of a diverse human-associated community across larvae over four days. ResultsHumanised larvae exhibited colonisation resistance against Salmonella enterica serovar Typhimurium, with mortality reduced to 20% compared to 90% in non-colonised controls. To test whether prophages could overcome this barrier, we infected larvae with isogenic S. Tm strains differing in the presence of prophage P22. Infection with the P22-carrying strain resulted in a threefold higher larval mortality (60% vs. 20%), increased pathogen load, and a significant reduction in the abundance of resident E. coli. Free P22 virions were detected early after infection, indicating extensive prophage activity. Notably, P22 can neither adsorb nor lyse resident E. coli, indicating that prophage-mediated invasion success did not rely on direct lysis. Instead, using high-throughput metabolic profiling paired with whole genome sequencing of three replicate lineages, we found that phage activation intensified resource-partitioning, accelerating functional metabolic adaptations in E. coli that significantly reduced the niche-overlap between the invading pathogen and the commensal E. coli. ConclusionOur findings establish the first humanised G. mellonella model supporting complex human microbiota and provide a novel non-lytic mechanism by which prophages influence species interactions. This scalable, low-cost model offers a new platform to dissect pathogen-phage-microbiota interactions relevant to human gut ecology.

microbiology↗

bioRxiv2023

COMPLETE GENOME SEQUENCE OF VIBRIO SYNGNATHI SP. NOV., A FISH PATHOGEN, ISOLATED FROM THE KIEL FJORD

A new Vibrio strain K08M4T was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. Infection experiments revealed that K08M4T is highly virulent for juvenile pipefish. Cells of strain K08M4T are Gram-stain-negative, curved rod-shaped and motile by means of a single polar flagellum. The strain can grow aerobically at 9 to 40{degrees}C, at pH 4 to 10.5 and tolerates up to 12% (w/v) NaCl. The most prevalent (> 10%) cellular fatty acids of K08M4T were C16:1{omega} 7c and C16:0. Whole-genome comparisons revealed that K08M4T represents a separate evolutionary lineage which is distinct from other Vibrio species and falls within the Vibrio Splendidus clade. The genome is 4,886,292 bp in size, consists of two circular chromosomes (3,298,328 bp, 1,587,964 bp), and comprises 4,178 protein-coding genes and 175 RNA genes. In this study, we describe the phenotypic features of the new isolate and present the annotation and analysis of its complete genome sequence. Based on these data, the new isolate represents a new species for which we propose the name Vibrio syngnathi. The type strain is K08M4T (=DSM 109818T). Supplementary materialOne supplementary figure and six supplementary table are available with the online version of the Manuscript.

microbiology↗

bioRxiv2023

Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability

Prophages, viral sequences integrated into bacterial genomes, can be beneficial and costly. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding of the selective forces that maintain prophages in bacterial populations is limited. Combining experimental evolution with stochastic modelling, we show that prophage maintenance and loss are primarily determined by environmental conditions that alter the net fitness effect of a prophage. When prophages are too costly, they are rapidly lost through environment-specific sequences of selective sweeps. Conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can maintain prophages. The dynamics of prophage maintenance additionally depends on the sociality of this accessory gene. Non-cooperative genes maintain prophages at higher frequencies than cooperative genes, which can protect phage-free cheaters that may emerge if prophage costs outweigh their benefits. Our simulations suggest that environmental variation plays a larger role than mutation rates in determining prophage maintenance. These findings highlight the complexity of selection pressures that act on mobile genetic elements and challenge our understanding of the role of environmental factors relative to random chance events in shaping the evolutionary trajectory of bacterial populations.

evolutionary biology↗

bioRxiv2022

SUB-OPTIMAL ENVIRONMENTAL CONDITIONS PROLONG PHAGE EPIDEMICS IN BACTERIAL POPULATIONS

Infections by filamentous phages influence bacterial fitness in various ways. While phage-encoded accessory genes, e.g., virulence genes, can be highly beneficial, the production of viral particles is energetically costly and often reduces bacterial growth. Consequently, if costs outweigh benefits, bacteria evolve resistance which can shorten phage epidemics. Abiotic conditions are known to influence the net-fitness effect for infected bacteria. Their impact on the dynamics and trajectories of host resistance evolution, however, remains yet unknown. To address this, we experimentally evolved the bacterium Vibrio alginolyticus in the presence of a filamentous phage at three different salinity levels, i.e., (1) ambient (2) 50% reduction, and (3) fluctuations between reduced and ambient. In all three salinities, bacteria rapidly acquired resistance through super infection exclusion (SIE), whereby phage-infected cells acquired immunity at the cost of reduced growth. Over time, SIE was gradually replaced by evolutionary fitter surface receptor mutants (SRM). This replacement was significantly faster at ambient and fluctuating conditions compared to the low saline environment. Our experimentally parameterized mathematical model explains that suboptimal environmental conditions, in which bacterial growth is slower, slow down phage resistance evolution ultimately prolonging phage epidemics. Our results imply that, if filamentous phages encode virulence genes, these may persist longer in bacterial populations at sub-optimal environmental conditions, which, in times of climate change, are becoming more frequent. Thus, our future ocean may favour the emergence of phage-born pathogenic bacteria, and impose a greater risk for disease outbreaks, impacting not only marine animals but also humans.

evolutionary biology↗

bioRxiv2022

Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages

Lambdoid (or Lambda-like) phages, are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure which served as basis for the "modular genome hypothesis". Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into twelve groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26% of homologous protein clusters in the four known operons (i.e., the early left, early right, immunity, and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be in close proximity to one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the CI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, plays an important role in the evolution of the modular structure of these genomes. Data summaryThe genomes used in this research are publicly available (Table S1). All supporting data is available in supplementary tables. Source code and documentation to calculate GRR is available under GPLv2 (https://github.com/annecmg/GRRpair). Impact statementTemperate phages, viruses that can integrate their own genetic material into bacterial genomes, are pervasive mobile genetic elements that can influence bacterial fitness in manifold ways. The E. coli phage lambda has been a model phage of molecular biology for decades. Lambdoid phages are highly prevalent in Enterobacteria such as E. coli and Salmonella, have a mosaic-like genome, the same genome architecture as lambda, and can recombine with phage lambda. Nevertheless, these phages can be very distinct, and no lambdoid core genome exits. Although lambdoid phage genomes have been studied for decades, we know relatively little about how they evolve. Early observations led to the modular genome hypothesis, according to which, phages are assemblages of genetic modules. But what determines the structure of these modules and which genes do preferentially occur together in modules? In this study, we provide answers to these questions using a novel computational approach that allows to infer gene transfer events between distantly related phages despite the absence of a core genome. We find that co-transfer of functionally related genes is frequent during the evolution of lambdoid phages. This suggests epistatic interactions among these genes, i.e., the co-transferred genes likely need to function together to ensure a viable phage. A prime example is the co-transfer of structural genes, such as genes encoding for the phage capsid or the phage tail. Additionally, we also find co-transfer of known interacting regulatory genes and co-transfer between functionally related genes that have so far been unknown to interact. Together, our analysis provides novel insights into the evolution of temperate phages. Moreover, our approach, which allows to identify gene transfer in the absence of a core phylogeny might be valuable for studying the evolution of other fast-evolving genomes, including viruses of other hosts.

microbiology↗

bioRxiv2021

Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates

Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. Using E. coli, prophage{lambda} and the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.

evolutionary biology↗

bioRxiv2021

HIGH VIRULENCE SELECTS FOR FAST HOST RESISTANCE EVOLUTION

Parasites and pathogens vary strikingly in their virulence and the resulting selection they impose on their hosts. While the evolution of different virulence levels is well studied, the evolution of host resistance in response to different virulence levels is less understood and as of now mainly based on observations and theoretical predictions with few experimental tests. Increased virulence can increase selection for host resistance evolution if resistance costs are outweighed by the benefits of avoiding infection. To test this, we experimentally evolved the bacterium Vibrio alginolyticus in the presence of two variants of the filamentous phage, VALG{Phi}8, that differ in their virulence. The bacterial host exhibited two alternative defence strategies against future phage infection: (1) super infection exclusion (SIE) whereby phage-infected cells were immune to subsequent infection at a cost of reduced growth, and (2) surface receptor mutations (SRM) in genes encoding the MSHA type-IV pilus providing resistance to infection by preventing phage attachment. While SIE emerged rapidly against both phages, SRM evolved faster against the high virulence compared to the low virulence phage. Using a mathematical model of our system we show that increasing virulence strengthens selection for SRM due to the higher costs of infection suffered by SIE immune hosts. In both the experiments and the model, higher levels of SRM in the host population drove more rapid phage extinction. Thus, by accelerating the evolution of host resistance, more virulent phages caused shorter epidemics.

evolutionary biology↗

bioRxiv2020

Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels.

Genetic adaptation and phenotypic plasticity facilitate the invasion of new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high or low saline environments. We hypothesized that wild S. typhle populations are locally adapted to the salinity and prevailing pathogens of their native environment, and that short-term acclimation of parents to a novel salinity may aid in buffering offspring phenotypes in a matching environment. To test these hypotheses, we exposed all wild caught animals, to either high or low salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life history traits of fathers (offspring survival, offspring size) and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenging conditions of low salinity. Genetic adaptation increased survival rates of juveniles from parents in lower salinity (in contrast to those from high salinity). Juvenile gene expression indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. The results of our study suggest that pipefish locally adapted to low salinity retain phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.

evolutionary biology↗

bioRxiv2020

FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENTS

Bacteria can acquire antibiotic resistance genes (ARGs) via prophages, phage genomes integrated into bacterial chromosomes. Such prophages may influence bacterial fitness via increased antibiotic resistance, protection from further phage infection, or by switching to a lytic lifecycle that releases free phages which can infect phage-susceptible competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, our understanding of how costs and benefits of prophage-encoded ARGs vary across environments remains limited. Here, by studying prophages with and without ARGs in Escherichia coli, we distinguished between effects of prophages alone and ARGs they carry. In competition with prophage-free strains, fitness benefits from prophages and ARGs peaked in different environments. Prophage carriage was most beneficial in conditions where induction of the lytic lifecycle was common, whereas ARGs were more beneficial in the presence of antibiotics and when prophage induction was lower. Acquisition of prophage-encoded ARGs by competing phage-susceptible strains was most common when prophage induction, and therefore the amount of free phages, was high. Thus, selection on prophages and ARGs varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in antibiotic resistance evolution.

evolutionary biology↗

bioRxiv2019

Closely related Vibrio alginolyticus strains encode an identical repertoire of prophages and filamentous phages

Filamentous vibriophages represent a massive repertoire of virulence factors which can be transferred across species boundaries, leading to the emergence of deadly pathogens. All filamentous vibriophages that were characterized until today were isolated from human pathogens. Considering frequent horizontal gene transfer among vibrios, we predict that other environmental isolates, including non-human pathogens also carry filamentous phages, of which some may encode virulence factors. The aim of this study was to characterize the phage repertoire, consisting of prophages and filamentous phages, of a marine pathogen, Vibrio alginolyticus. To do so, we sequenced eight different V. alginolyticus strains, isolated from different pipefish and characterised their phage repertoire using a combination of morphological analyses and comparative genomics. We were able to identify a total of five novel phage regions (three different Caudovirales and two different Inoviridae), whereby only those two loci predicted to correspond to filamentous phages (family Inoviridae) represent actively replicating phages. Unique for this study was that all eight host strains, which were isolated from different eukaryotic hosts have identical bacteriophages, suggesting a clonal expansion of this strain after the phages had been acquired by a common ancestor. We further found that co-occurrence of two different filamentous phages leads to within-host competition resulting in reduced phage replication by one of the two phages. One of the two filamentous phages encoded two virulence genes (Ace and Zot), homologous to those encoded on the V. cholerae phage CTX{Phi}. The coverage of these zot-encoding phages correlated positively with virulence (measured in controlled infection experiments on the eukaryotic host), suggesting that this phages is an important virulence determinant. Impact statementMany bacteria of the genus Vibrio, such as V. cholerae or V. parahaemolyticus impose a strong threat to human health. Often, small viruses, known as filamentous phages encode virulence genes. Upon infecting a bacterial cell, these phages can transform a previously harmless bacterium into a deadly pathogen. While filamentous phages and their virulence factors are well-characterized for human pathogenic vibrios, filamentous phages of marine vibrios, pathogenic for a wide range of marine organisms, are predicted to carry virulence factors, but have so far not been characterized in depth. Using whole genome sequencing and comparative genomics of phages isolated from a marine fish pathogen V. alginolyticus, we show that also environmental strains harbour filamentous phages that carry virulence genes. These phages were most likely acquired from other vibrios by a process known as horizontal gene transfer. We found that these phages are identical across eight different pathogenic V. alginolyticus strains, suggesting that they have been acquired by a common ancestor before a clonal expansion of this ecotype took place. The phages characterized in this study have not been described before and are unique for the Kiel V. alginolyticus ecotype. Data SummaryO_LIThe GenBank accession numbers for all genomic sequence data analysed in the present study can be found in Table S1. C_LIO_LIAll phage regions identified by PHASTER analysis of each chromosome and the respective coverage of active phage loci are listed in Table S2. C_LIO_LIGenBank files were deposited at NCBI for the two actively replicating filamentous phages VALG{Phi}6 (Accession number: MN719123) and VALG{Phi}8 (Accession number: MN690600) C_LIO_LIThe virulence data from the infection experiments have been deposited at PANGAEA: Accession number will be provided upon acceptance of the manuscript. C_LI Data statementAll supporting data have been provided within the article or through supplementary data files. Four supplementary tables and six supplementary figures are available with the online version of this article.

microbiology↗