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Bansept, F.

Publications and source records attributed to Bansept, F..

9 recordsLinked to original sources

Weakest link epistasis and the geometry of genetic load

Because natural selection must optimise multiple traits at once, previous work has suggested that phenotypic dimensionality can substantially worsen the equilibrium fitness defect of a population relative to the phenotypic optimum. However, it remains unclear how conclusions drawn from classical theoretical phenotype-fitness maps extend to models grounded in explicit biological mechanisms. Here we introduce weakest-link epistasis (WLE), a framework in which fitness is determined by the least-fit phenotypic component, an extreme form of diminishing returns epistasis. We show that in this framework, increasing dimensionality amplifies the load in a manner comparable to, but surprisingly not more than, Fishers geometric model (FGM). Building on this similarity, we demonstrate why genetic load is often invariant across different rules for combining trait-specific fitness components into an overall organismal fitness. We explore these ideas by considering the family of models where the organismal fitness is determined based on the{ell} p-norm of the vector of trait-specific fitness defects, a framework that includes both FGM and WLE, but also captures a continuum of genetic architectures, ranging from generalist to specialist regimes. Altogether, our approach proposes a new perspective on the geometry of adaptive landscapes, and may help provide quantitative insight into the cost of complexity.

evolutionary biology↗

Optimizing microbial intake helps to maintain the gut microbiome diversity

The animal gut holds a myriad of microbes with demonstrated importance for the hosts health. Properties of this microbiome have been studied in different host conditions in search of the best biomarkers for practical medical interventions. One well-studied quantity is the -diversity, which usually correlates with lower values and pathological status. Diet plays an important part in the gut microbiome assembly. While its nutritional content has been extensively investigated, we ask instead how can the microbial content of food impact the gut -diversity, taking into account the intermittent nature of feeding. We design a simple model that isolates the effect of intermittent microbial migration, for which we are able to develop an analytical treatment. Specifically, we find that there is a set of feeding parameters (feeding interval and food microbial content) that maximizes the time-averaged observed Shannon diversity, which we call the Optimal Feeding Strategy. Using a combination of numerical and analytical techniques, we show that, in the optimal scenario, diversity converges to that of the food, and that the optimal feeding rate converges to the average clearance rate. As probiotics become more and more widely used, we hope this work can help assess how quantitative ecological control can be used to improve intake protocols of live biotherapeutic products.

ecology↗

Inferring interactions from microbiome data

Parameter inference of high-dimensional data is challenging and microbiome time series data is no exception. Methods aimed at predicting from point estimates exist, but often even fail to recover the true parameters from simulated data. Computational methods to robustly infer and quantify the uncertainty in model parameters are needed. Here, we propose a computational workflow addressing such challenges - allowing us to compare mechanistic models and identify the values and the certainty of inferred parameters. This approach allows us to infer which kind of interactions occur in the microbial community. In contrast to point-estimate inference, the distribution for the parameters, our outcome, reflects their uncertainty. To achieve this, we consider as many equations for the statistical moments of the microbiome as parameters. Our inference workflow, which builds upon a mechanistic foundation of microscopic processes, can take into account that commonly metagenomic datasets only provide information on relative abundances and hosts ensembles. With our framework, we move from qualitative prediction to quantifying the likelihood of certain interaction types in microbiomes.

ecology↗

Bacterial c-di-GMP plays a key role in the evolution of host-association

Most microbes evolve faster than their hosts and should therefore drive evolution of host-microbe interactions1-3. However, relatively little is known about the characteristics that define the adaptive path of microbes to host-association. In this study we have identified microbial traits that mediate adaptation to hosts by experimentally evolving the bacterium Pseudomonas lurida with the nematode Caenorhabditis elegans. We repeatedly observed the evolution of beneficial host-specialist bacteria with improved persistence in the nematode, achieved by mutations that uniformly upregulate the universal second messenger c-di-GMP. We subsequently upregulated c-di-GMP in different Pseudomonas species, consistently causing increased host-association. Comparison of Pseudomonad genomes from various environments revealed that c-di-GMP underlies adaptation to a variety of hosts, from plants to humans, suggesting that it is fundamental for establishing host-association.

evolutionary biology↗

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.

microbiology↗

On the effect of inheritance of microbes in commensal microbiomes

BackgroundOur current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally. ResultsWe have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes. ConclusionBy modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories.

ecology↗

Modeling host-associating microbes under selection

The concept of fitness is often reduced to a single component, such as the replication rate in a given habitat. For species with complex life cycles, this can be an unjustified oversimplification, as every step of the life cycle can contribute to reproductive success in a specific way. In particular, this applies to microbes that spend part of their life cycles associated to a host, i.e. in a microbiota. In this case, there is a selection pressure not only on the replication rates, but also on the phenotypic traits associated to migrating from the external environment to the host and vice-versa. Here, we investigate a simple model of a microbial population living, replicating, migrating and competing in and between two compartments: a host and its environment. We perform a sensitivity analysis on the global growth rate to determine the selection gradient experienced by the microbial population. We focus on the direction of selection at each point of the phenotypic space, defining an optimal way for the microbial population to increase its fitness. We show that microbes can adapt to the two-compartment life cycle through either changes in replication or migration rates, depending on the initial values of the traits, the initial distribution of the population across the compartments, the intensity of competition, and the time scales involved in the life cycle versus the time scale of adaptation (which determines the adequate probing time to measure fitness). Overall, our model provides a conceptual framework to study the selection on microbes experiencing a host-associated life cycle.

evolutionary biology↗

Antibody-mediated cross-linking of gut bacteria hinders the spread of antibiotic resistance

The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within-host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity-driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance pre-exists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within-host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine-based strategies to combat antibiotic resistance.

evolutionary biology↗

Enchained growth and cluster dislocation: a possible mechanism for microbiota homeostasis

Immunoglobulin A is a class of antibodies produced by the adaptive immune system and secreted into the gut lumen to fight pathogenic bacteria. We recently demonstrated that the main physical effect of these antibodies is to enchain daughter bacteria, i.e. to cross-link bacteria into clusters as they divide, preventing them from interacting with epithelial cells. These links between bacteria may break over time. Using analytical and numerical calculations on several models to check the results robustness, we study the rate of increase in the number of free bacteria as a function of the replication rate of bacteria, and the resulting distribution of chain sizes. At higher replication rates, the bacteria replicate before the link between daughter bacteria breaks, leading to growing cluster sizes. However at low growth rates two daughter cells have a high probability to break apart. Thus the gut could produce IgA against all the bacteria it has encountered, but the most affected bacteria would be the fast replicating ones, which could destabilize the microbiota.

biophysics↗