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

Background Chronic 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. Results In 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. Conclusions Contrary 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

The Effects of Antibiotics on the Microbiota Through a Cross-Generational Study of D. magna

The community of bacteria derived from the environment and found in the gut of every animal, comprising the majority of the microbiota, plays a significant role in the animal’s health. Thus, understanding how the microbiota respond to disruption is important in analyzing the interaction between host and bacteria. Common environmental stressors that disrupt the gut microbiota of a host are antibiotics, which are found in aquatic environments due to runoff from agriculture and human use. Past experiments manipulate the gut microbiota using antibiotics and are focused largely on the immediate effects of community disruption on host health by examining individual hosts over a single generation, but my goal was to understand the cross-generational implications of disrupting the gut bacteria of a host organism. Based on previous findings, my interests were two-fold: examining the effects of antibiotic exposure across multiple generations on host life history traits (growth, reproduction, survivorship), and examining the ability of the microbiota and host to recover when removed from an antibiotic environment. I implemented a novel split-brood experimental design utilizing Daphnia magna as the host organism. The animals were originally divided between control and constant antibiotic groups, but at the time of their third brood, the babies were redistributed into new environments: the babies from the control mothers were transferred to a new control environment, half the babies from the antibiotic mothers were transferred to a new antibiotic environment, and the other half of the babies from the antibiotic mothers were transferred to a new control environment. This allowed me to study how host health and the microbiome recover from antibiotic exposure. This pattern was repeated for five generations to allow for comparison of life history traits and microbiota composition/diversity across treatments and generations, which allowed me to study whether recovery depends on the history of antibiotic exposure. The results showed no consistent effect of antibiotic treatment on either host growth or reproductive output, but a strong effect of generation over time – the animals in the later generations were larger and more fecund than those in the early generations. In contrast, the history of antibiotic exposure was the most significant predictor of survivorship: the risk of death was increased when the animal was in an antibiotic treatment or had multiple previous generations exposed to antibiotics. The 16S rRNA sequence results showed that the antibiotic treatment had a distinct microbiome as compared to control and removal treatments because it lost many of the core genera, while removal treatments were more similar to control than antibiotics in terms of diversity. These results show how antibiotic exposure changes a host and its microbial community, which can be further scaled to more complex host-microbiota systems

The Effects of Antibiotics on the Microbiota Through a Cross-Generational Study of D. magna

The community of bacteria derived from the environment and found in the gut of every animal, comprising the majority of the microbiota, plays a significant role in the animal’s health. Thus, understanding how the microbiota respond to disruption is important in analyzing the interaction between host and bacteria. Common environmental stressors that disrupt the gut microbiota of a host are antibiotics, which are found in aquatic environments due to runoff from agriculture and human use. Past experiments manipulate the gut microbiota using antibiotics and are focused largely on the immediate effects of community disruption on host health by examining individual hosts over a single generation, but my goal was to understand the cross-generational implications of disrupting the gut bacteria of a host organism. Based on previous findings, my interests were two-fold: examining the effects of antibiotic exposure across multiple generations on host life history traits (growth, reproduction, survivorship), and examining the ability of the microbiota and host to recover when removed from an antibiotic environment. I implemented a novel split-brood experimental design utilizing Daphnia magna as the host organism. The animals were originally divided between control and constant antibiotic groups, but at the time of their third brood, the babies were redistributed into new environments: the babies from the control mothers were transferred to a new control environment, half the babies from the antibiotic mothers were transferred to a new antibiotic environment, and the other half of the babies from the antibiotic mothers were transferred to a new control environment. This allowed me to study how host health and the microbiome recover from antibiotic exposure. This pattern was repeated for five generations to allow for comparison of life history traits and microbiota composition/diversity across treatments and generations, which allowed me to study whether recovery depends on the history of antibiotic exposure. The results showed no consistent effect of antibiotic treatment on either host growth or reproductive output, but a strong effect of generation over time – the animals in the later generations were larger and more fecund than those in the early generations. In contrast, the history of antibiotic exposure was the most significant predictor of survivorship: the risk of death was increased when the animal was in an antibiotic treatment or had multiple previous generations exposed to antibiotics. The 16S rRNA sequence results showed that the antibiotic treatment had a distinct microbiome as compared to control and removal treatments because it lost many of the core genera, while removal treatments were more similar to control than antibiotics in terms of diversity. These results show how antibiotic exposure changes a host and its microbial community, which can be further scaled to more complex host-microbiota systems