Evidence for a Causal Role for Escherichia coli Strains Identified as Adherent-Invasive (AIEC) in Intestinal Inflammation.

Enrichment of adherent-invasive Escherichia coli (AIEC) has been consistently detected in subsets of inflammatory bowel disease (IBD) patients. Although some AIEC strains cause colitis in animal models, these studies did not systematically compare AIEC with non-AIEC strains, and causal links between AIEC and disease are still disputed. Specifically, it remains unclear whether AIEC shows enhanced pathogenicity compared to that of commensal E. coli found in the same ecological microhabitat and if the in vitro phenotypes used to classify strains as AIEC are pathologically relevant. Here, we utilized in vitro phenotyping and a murine model of intestinal inflammation to systematically compare strains identified as AIEC with those identified as non-AIEC and relate AIEC phenotypes to pathogenicity. Strains identified as AIEC caused, on average, more severe intestinal inflammation. Intracellular survival/replication phenotypes routinely used to classify AIEC positively correlated with disease, while adherence to epithelial cells and tumor necrosis factor alpha production by macrophages did not. This knowledge was then applied to design and test a strategy to prevent inflammation by selecting E. coli strains that adhered to epithelial cells but poorly survived/replicated intracellularly. Two E. coli strains that ameliorated AIEC-mediated disease were subsequently identified. In summary, our results show a relationship between intracellular survival/replication in E. coli and pathology in murine colitis, suggesting that strains possessing these phenotypes might not only become enriched in human IBD but also contribute to disease. We provide new evidence that specific AIEC phenotypes are pathologically relevant and proof of principle that such mechanistic information can be therapeutically exploited to alleviate intestinal inflammation. IMPORTANCE Inflammatory bowel disease (IBD) is associated with an altered gut microbiota composition, including expansion of Proteobacteria. Many species in this phylum are thought to contribute to disease under certain conditions, including adherent-invasive Escherichia coli (AIEC) strains, which are enriched in some patients. However, whether this bloom contributes to disease or is just a response to IBD-associated physiological changes is unknown. Although assigning causality is challenging, appropriate animal models can test the hypothesis that AIEC strains have an enhanced ability to cause colitis in comparison to other gut commensal E. coli strains and to identify bacterial traits contributing to virulence. We observed that AIEC strains are generally more pathogenic than commensal E. coli and that bacterial intracellular survival/replication phenotypes contributed to disease. We also found that E. coli strains lacking primary virulence traits can prevent inflammation. Our findings provide critical information on E. coli pathogenicity that may inform development of IBD diagnostic tools and therapies.

Stochasticity directs adaptive evolution toward nonequilibrium evolutionary attractors.

Stochastic processes such as genetic drift may hinder adaptation, but the effect of such stochasticity on evolution via its effect on ecological dynamics is poorly understood. Here we evaluate patterns of adaptation in a population subject to variation in demographic stochasticity. We show that stochasticity can alter population dynamics and lead to evolutionary outcomes that are not predicted by classic eco-evolutionary modeling approaches. We also show, however, that these outcomes are governed by nonequilibrium evolutionary attractors-these are maxima in lifetime reproductive success when stochasticity keeps the ecological system away from the deterministic equilibrium. These NEEAs alter the path of evolution but are not visible through the equilibrium lens that underlies much evolutionary theory. Our results reveal that considering population processes during transient periods can greatly improve our understanding of the path and pace of evolution.

Circadian rhythms mediate infection risk in Daphnia dentifera.

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera-Metschnikowia bicuspidata host-pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit a circadian rhythm in phenoloxidase activity. We found that the time of day when individuals are exposed to pathogens affects the probability of infection with higher infection prevalence at night, indicating that infection risk is driven by a host's circadian rhythm in feeding behavior. These results suggest that the natural circadian rhythm of the host should be considered when addressing epidemiological dynamics.

Predation shifts coevolution toward higher host contact rate and parasite virulence.

Hosts can avoid parasites (and pathogens) by reducing social contact, but such isolation may carry costs, e.g. increased vulnerability to predators. Thus, many predator-host-parasite systems confront hosts with a trade-off between predation and parasitism. Parasites, meanwhile, evolve higher virulence in response to increased host sociality and consequently, increased multiple infections. How does predation shift coevolution of host behaviour and parasite virulence? What if predators are selective, i.e. predators disproportionately capture the sickest hosts? We answer these questions with an eco-coevolutionary model parametrized for a Trinidadian guppy-Gyrodactylus spp. system. Here, increased predation drives host coevolution of higher grouping, which selects for higher virulence. Additionally, higher predator selectivity drives the contact rate higher and virulence lower. Finally, we show how predation and selectivity can have very different impacts on host density and prevalence depending on whether hosts or parasites evolve, or both. For example, higher predator selectivity led to lower prevalence with no evolution or only parasite evolution but higher prevalence with host evolution or coevolution. These findings inform our understanding of diverse systems in which host behavioural responses to predation may lead to increased prevalence and virulence of parasites.

Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species.

Chronic antibiotic exposure impacts host health through changes to the microbiome. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied, but less is understood about multigenerational effects of antibiotic exposure and subsequent recovery. In this study, we examined microbiome composition and host fitness across five generations of exposure to antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we examined recovery and resilience of the microbiome. Unexpectedly, we discovered that isolation of single host individuals across generations exerted a strong effect on microbiome composition, with microbiome diversity decreasing over generations regardless of treatment, while host body size and cumulative reproduction increased across generations. Though antibiotics did cause substantial changes to microbiome composition within a generation, recovery generally occurred in one generation regardless of the number of prior generations spent in antibiotics. Our results demonstrate that isolation of individual hosts leads to stochastic extinction of less abundant taxa in the microbiome, suggesting that these taxa are likely maintained via transmission in host populations.

Shoaling guppies evade predation but have deadlier parasites.

Parasites exploit hosts to replicate and transmit, but overexploitation kills both host and parasite. Predators may shift this cost-benefit balance by consuming infected hosts or changing host behaviour, but the strength of these effects remains unclear. Here we use field and lab data on Trinidadian guppies and their Gyrodactylus spp. parasites to show how differential predation pressure influences parasite virulence and transmission. We use an experimentally demonstrated virulence-transmission trade-off to parametrize a mathematical model in which host shoaling (as a means of anti-predator defence), increases contact rates and selects for higher virulence. Then we validate model predictions by collecting parasites from wild, Trinidadian populations; parasites from high-predation populations were more virulent in common gardens than those from low-predation populations. Broadly, our results indicate that reduced social contact selects against parasite virulence.

Daily feeding rhythm linked to microbiome composition in two zooplankton species.

Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host's active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.

Circadian Rhythm in Feeding Behavior of Daphnia dentifera.

Circadian rhythms enable organisms to mediate their molecular and physiological processes with changes in their environment. Although feeding behavior directly affects within-organism processes, there are few examples of a circadian rhythm in this key behavior. Here, we show that Daphnia have a nocturnal circadian rhythm in feeding behavior that corresponds with their diel vertical migration (DVM), an important life history strategy for predator and UV avoidance. In addition, this feeding rhythm appears to be temperature compensated, which suggests that feeding behavior is robust to seasonal changes in water temperature. A circadian rhythm in feeding behavior can impact energetically demanding processes like metabolism and immunity, which may have drastic effects on susceptibility to disease, starvation risk, and ultimately, fitness.

Identifying co-phylogenetic hotspots for zoonotic disease.

The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host-parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host-parasite association data with host and parasite phylogenies. Here, we use host-parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host-parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

The ghost of hosts past: impacts of host extinction on parasite specificity.

A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may impact the host specificity of parasites, and offer examples from historical extinctions, present-day endangerment, and future projections of biodiversity loss. We suggest that an improved understanding of the impact of host extinction on contemporary host-parasite interactions may shed light on core aspects of disease ecology, including comparative studies of host specificity, virulence evolution in multi-host parasite systems, and future trajectories for host and parasite biodiversity. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially.

Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness.IMPORTANCE Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.

A high-throughput method to quantify feeding rates in aquatic organisms: A case study with Daphnia.

Food ingestion is one of the most basic features of all organisms. However, obtaining precise-and high-throughput-estimates of feeding rates remains challenging, particularly for small, aquatic herbivores such as zooplankton, snails, and tadpoles. These animals typically consume low volumes of food that are time-consuming to accurately measure.We extend a standard high-throughput fluorometry technique, which uses a microplate reader and 96-well plates, as a practical tool for studies in ecology, evolution, and disease biology. We outline technical and methodological details to optimize quantification of individual feeding rates, improve accuracy, and minimize sampling error.This high-throughput assay offers several advantages over previous methods, including i) substantially reduced time allotments per sample to facilitate larger, more efficient experiments; ii) technical replicates; and iii) conversion of in vivo measurements to units (mL-1 hr-1 ind-1) which enables broad-scale comparisons across an array of taxa and studies.To evaluate the accuracy and feasibility of our approach, we use the zooplankton, Daphnia dentifera, as a case study. Our results indicate that this procedure accurately quantifies feeding rates and highlights differences among seven genotypes.The method detailed here has broad applicability to a diverse array of aquatic taxa, their resources, environmental contaminants (e.g., plastics), and infectious agents. We discuss simple extensions to quantify epidemiologically relevant traits, such as pathogen exposure and transmission rates, for infectious agents with oral or trophic transmission.

Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics.

The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.

Starving the Enemy? Feeding Behavior Shapes Host-Parasite Interactions.

The loss of appetite that typically accompanies infection or mere exposure to parasites is traditionally considered a negative byproduct of infection, benefitting neither the host nor the parasite. Numerous medical and veterinary practices directly or indirectly subvert this 'illness-mediated anorexia'. However, the ecological factors that influence it, its effects on disease outcomes, and why it evolved remain poorly resolved. We explore how hosts use anorexia to defend against infection and how parasites manipulate anorexia to enhance transmission. Then, we use a coevolutionary model to illustrate how shifts in the magnitude of anorexia (e.g., via drugs) affect disease dynamics and virulence evolution. Anorexia could be exploited to improve disease management; we propose an interdisciplinary approach to minimize unintended consequences.

Phenotypically plastic responses to predation risk are temperature dependent.

Predicting how organisms respond to climate change requires that we understand the temperature dependence of fitness in relevant ecological contexts (e.g., with or without predation risk). Predation risk often induces changes to life history traits that are themselves temperature dependent. We explore how perceived predation risk and temperature interact to determine fitness (indicated by the intrinsic rate of increase, r) through changes to its underlying components (net reproductive rate, generation time, and survival) in Daphnia magna. We exposed Daphnia to predation cues from dragonfly naiads early, late, or throughout their ontogeny. Predation risk increased r differentially across temperatures and depending on the timing of exposure to predation cues. The timing of predation risk likewise altered the temperature-dependent response of T and R0. Daphnia at hotter temperatures responded to predation risk by increasing r through a combination of increased R0 and decreased T that together countered an increase in mortality rate. However, only D. magna that experienced predation cues early in ontogeny showed elevated r at colder temperatures. These results highlight the fact that phenotypically plastic responses of life history traits to predation risk can be strongly temperature dependent.

Parasite-Mediated Anorexia and Nutrition Modulate Virulence Evolution.

Temporary but substantial reductions in voluntary food intake routinely accompany parasite infection in hosts ranging from insects to humans. This "parasite-mediated anorexia" drives dynamic nutrient-dependent feedbacks within and among hosts, which should alter the fitness of both hosts and parasites. Yet, few studies have examined the evolutionary and epidemiological consequences of this ubiquitous but overlooked component of infection. Moreover, numerous biomedical, veterinary, and farming practices (e.g., rapid biomass production via high-calorie or high-fat diets, low-level antibiotics to promote growth, nutritional supplementation, nonsteroidal anti-inflammatory drugs like Ibuprofen) directly or indirectly alter the magnitude of host anorexia-while also controlling host diet and therefore the nutrients available to hosts and parasites. Here, we show that anorexia can enhance or diminish disease severity, depending on whether the current dietary context provides nutrients that bolster or inhibit immune function. Feedbacks driven by nutrition-mediated competition between host immune function and parasite production can create a unimodal relationship between anorexia and parasite fitness. Subsequently, depending on the host's diet, medical or husbandry practices that suppress anorexia could backfire, and inadvertently select for more virulent parasites and larger epidemics. These findings carry implications for the development of integrated treatment programs that consider links between host feeding behavior, nutrition, and disease severity.

Parasite resource manipulation drives bimodal variation in infection duration.

Over a billion people on earth are infected with helminth parasites and show remarkable variation in parasite burden and chronicity. These parasite distributions are captured well by classic statistics, such as the negative binomial distribution. But the within-host processes underlying this variation are not well understood. In this study, we explain variation in macroparasite infection outcomes on the basis of resource flows within hosts. Resource flows realize the interactions between parasites and host immunity and metabolism. When host metabolism is modulated by parasites, we find a positive feedback of parasites on their own resources. While this positive feedback results in parasites improving their resource availability at high burdens, giving rise to chronic infections, it also results in a threshold biomass required for parasites to establish in the host, giving rise to acute infections when biomass fails to clear the threshold. Our finding of chronic and acute outcomes in bistability contrasts with classic theory, yet is congruent with the variation in helminth burdens observed in human and wildlife populations.

Fueling Defense: Effects of Resources on the Ecology and Evolution of Tolerance to Parasite Infection.

Resource availability is a key environmental constraint affecting the ecology and evolution of species. Resources have strong effects on disease resistance, but they can also affect the other main parasite defense strategy, tolerance. A small but growing number of animal studies are beginning to investigate the effects of resources on tolerance phenotypes. Here, we review how resources affect tolerance strategies across animal taxa ranging from fruit flies to frogs to mice. Surprisingly, resources (quality and quantity) can increase or reduce tolerance, dependent upon the particular host-parasite system. To explore this seeming contradiction, we recast predictions of models of sterility tolerance and mortality tolerance in a resource-dependent context. Doing so reveals that resources can have very different epidemiological and evolutionary effects, depending on what aspects of the tolerance phenotype are affected. Thus, it is critical to consider both sterility and mortality in future empirical studies of how behavioral and environmental resource availability affect tolerance to infection.

Predators modify the temperature dependence of life-history trade-offs.

Although life histories are shaped by temperature and predation, their joint influence on the interdependence of life-history traits is poorly understood. Shifts in one life-history trait often necessitate shifts in another-structured in some cases by trade-offs-leading to differing life-history strategies among environments. The offspring size-number trade-off connects three traits whereby a constant reproductive allocation (R) constrains how the number (O) and size (S) of offspring change. Increasing temperature and size-independent predation decrease size at and time to reproduction which can lower R through reduced time for resource accrual or size-constrained fecundity. We investigated how O, S, and R in a clonal population of Daphnia magna change across their first three clutches with temperature and size-independent predation risk. Early in ontogeny, increased temperature moved O and S along a trade-off curve (constant R) toward fewer larger offspring. Later in ontogeny, increased temperature reduced R in the no-predator treatment through disproportionate decreases in O relative to S. In the predation treatment, R likewise decreased at warmer temperatures but to a lesser degree and more readily traded off S for O whereby the third clutch showed a constant allocation strategy of O versus S with decreasing R. Ontogenetic shifts in S and O rotated in a counterclockwise fashion as temperature increased and more drastically under risk of predation. These results show that predation risk can alter the temperature dependence of traits and their interactions through trade-offs.

Resource-driven changes to host population stability alter the evolution of virulence and transmission.

What drives the evolution of parasite life-history traits? Recent studies suggest that linking within- and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to pinpoint the critical factors connecting these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions. First, we dynamically link resources and between-host processes (host density, stability, transmission) to virulence evolution, using a 'non-nested' model. Then, we consider a 'nested' model where population-level processes (transmission and virulence) depend on resource-driven changes to individual-level (within-host) processes (energetics, immune function, parasite production). Contrary to 'non-nested' model predictions, the 'nested' model reveals complex effects of host population dynamics on parasite evolution, including regions of evolutionary bistability; evolution can push parasites towards strongly or weakly stabilizing strategies. This bistability results from dynamic feedbacks between resource-driven changes to host density, host immune function and parasite production. Together, these results highlight how cross-scale feedbacks can provide key insights into the structuring role of parasites and parasite evolution.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.