Biology subjects

Deines, P.

Publications and source records attributed to Deines, P..

3 recordsLinked to original sources

bioRxiv2024

Nutrition induced changes in the microbiota can cause dysbiosis and disease development

The increasing global prevalence of inflammatory and autoimmune diseases highlights the need to understand their origins. The overfeeding hypothesis suggests that disturbances in the microbiota due to diet may initiate these diseases. Using the model organism Hydra, we established a causal link between environmental alterations in the microbiota and disease development. Relocating Hydra to natural lakes caused significant microbial shifts due to new colonizers and nutrients. Nutrient manipulation removed the competitive advantage of the well-adapted resident microbiota, disrupted its nutrient-blocking capacity and triggered specific microbiota changes leading to disease. L-arginine supplementation alone transformed Pseudomonas from a commensal microbe into a pathogen, showing pathogenicity as context-dependent. Our findings support the overfeeding hypothesis, highlighting the role of microbial and nutrient dynamics in disease development.

microbiology↗

bioRxiv2019

Microbial traits and the realized niche in a simple metaorganism

Organisms and their resident microbial communities - the microbiome - form a complex and mostly stable ecosystem. It is known that the composition of the microbiome and bacterial species abundances can have a major impact on host health and Darwinian fitness, but the processes that lead to these microbial patterns have not yet been identified. We here apply the niche concept and trait-based approaches as a first step in understanding the patterns underlying microbial community assembly and structure in the simple metaorganism Hydra. We find that the carrying capacities in single associations do not reflect microbiota densities as part of the community, indicating a discrepancy between the fundamental and realized niche. Whereas in most cases, the realized niche is smaller than the fundamental one, as predicted by theory, the opposite is observed for Hydra’s two main bacterial colonizers. Both, Curvibacter sp. and Duganella sp. benefit from association with the other members of the microbiome and reach higher fractions as compared to when they are the only colonizer. This cannot be linked to any particular trait that is relevant for interacting with the host or by the utilization of specific nutrients but is most likely determined by metabolic interactions between the individual microbiome members.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2019

Fitness effects of host-bacterial interactions - the microbial perspective

Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germ free hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial structure of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the fractions of both species on the host do not match the fractions reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that the rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems. ImportanceThis work studies microbial interactions within the microbiome of the simple cnidarian, Hydra, and investigates whether microbial species coexistence and community stability depends on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydras microbiome differs depending on the environment and only results in a stable coexistence in the host context. The interactive ecology between the host, the two most dominant microbes, but also the less abundant members of the microbiome, are critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

ecology↗