Biology subjects

Cooper, R. O.

Publications and source records attributed to Cooper, R. O..

3 recordsLinked to original sources

bioRxiv2021

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

BackgroundChronic antibiotic exposure impacts host health through changes to the microbiome, increasing disease risk and reducing the functional repertoire of community members. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied. However, much less is understood about the multigenerational effects of antibiotic exposure and how the microbiome may recover across host generations. ResultsIn this study, we examined microbiome composition and host fitness across five generations of exposure to a suite of three 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 aimed to examine recovery and resilience of the microbiome. Unexpectedly, we discovered that experimental isolation of single host individuals across generations also exerted a strong effect on microbiome composition, with composition becoming less diverse over generations regardless of treatment. Simultaneously, Daphnia magna body size and cumulative reproduction increased across generations while survival decreased. Though antibiotics did cause substantial changes to microbiome composition, the microbiome generally became similar to the no antibiotic control treatment within one generation of recovery no matter how many prior generations were spent in antibiotics. ConclusionsContrary to results found in vertebrate systems, Daphnia magna microbiome composition recovers quickly after antibiotic exposure. However, our results suggest that the isolation of individual hosts leads to the stochastic extinction of rare taxa in the microbiome, indicating that these taxa are likely maintained via transmission in host populations rather than intrinsic mechanisms. This may explain the intriguing result that microbiome diversity loss increased host fitness.

ecology↗

bioRxiv2020

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, 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 non-target taxa were impacted by antibiotic treatment, suggesting no rare keystone taxa exist in the Daphnia magna microbiota but 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 ecological context shapes within-host microbial responses and effects on host fitness. ImportanceUnderstanding 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 on 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 on host fitness.

ecology↗

bioRxiv2019

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

BackgroundThe 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.\n\nResultsFive metagenome-assembled genomes (MAGs) were assembled from the Daphnia magna microbiota. Phylogenetic placement of these MAGs indicated that two belong to the Limnohabitans genus, one to Polaromonas, one to Pedobacter, and one unclassifiable below the Burkholderiaceae family. Average nucleotide identity of these MAGs to their closest sequenced relative was <95%, suggesting these may be new species in known genera. 16S rRNA community profiling shows that the Daphnia magna microbiota is distinct from its culture environment. 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. Threonine and arginine exporters were encoded by the Limnohabitans and Burkholderiaceae MAGs, and pathways for key vitamin biosynthesis and export were identified across MAGs.\n\nConclusionsIn this study, we characterize five metagenome-assembled bacterial genomes within the Daphnia magna microbiota. Our examination of functions associated with these genomes 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.

genomics↗