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

AbstractBackgroundChronic 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.

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

mSystems ◽

10.1128/msystems.00916-20 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

Reilly O. Cooper ◽

Janna M. Vavra ◽

Clayton E. Cressler

Keyword(s):

Life History ◽

Microbial Community ◽

Daphnia Magna ◽

Community Composition ◽

Microbial Community Composition ◽

Community Members ◽

Host Fitness ◽

Rare Taxa ◽

Host Life ◽

Context Shapes

ABSTRACT 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.

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Targeted manipulation of abundant and rare taxa in the Daphnia magna microbiota with antibiotics impacts host fitness differentially

10.1101/2020.09.07.286427 ◽

2020 ◽

Author(s):

Reilly O. Cooper ◽

Janna M. Vavra ◽

Clayton E. Cressler

Keyword(s):

Life History ◽

Microbial Community ◽

Daphnia Magna ◽

Community Composition ◽

Microbial Community Composition ◽

Community Members ◽

Host Fitness ◽

Rare Taxa ◽

Host Life ◽

Context Shapes

AbstractHost-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.

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Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa022 ◽

2020 ◽

Vol 96 (3) ◽

Cited By ~ 2

Author(s):

Gavin J Fenske ◽

Sudeep Ghimire ◽

Linto Antony ◽

Jane Christopher-Hennings ◽

Joy Scaria

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Culture Techniques ◽

Microbiome Composition ◽

Culture Independent ◽

Health And Disease ◽

The Media ◽

And Function ◽

Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

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Multigenerational effects of carbendazim in Daphnia magna : From a subcellular to a population level

Environmental Toxicology and Chemistry ◽

10.1002/etc.4307 ◽

2019 ◽

Vol 38 (2) ◽

pp. 412-422 ◽

Cited By ~ 5

Author(s):

Ana Rita R. Silva ◽

Cátia S.A. Santos ◽

Nuno G.C. Ferreira ◽

Rui Morgado ◽

Diogo N. Cardoso ◽

...

Keyword(s):

Daphnia Magna ◽

Population Level ◽

Multigenerational Effects

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Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

10.1101/736843 ◽

2019 ◽

Cited By ~ 2

Author(s):

Diana J. Rennison ◽

Seth M. Rudman ◽

Dolph Schluter

Keyword(s):

Microbial Communities ◽

Local Adaptation ◽

Biotic Interactions ◽

Ecological Speciation ◽

Microbiome Composition ◽

Interacting Species ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

And Function ◽

Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

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Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

10.1101/2020.08.03.234146 ◽

2020 ◽

Author(s):

Jeffrey Marlow ◽

Rachel Spietz ◽

Keun-Young Kim ◽

Mark Ellisman ◽

Peter Girguis ◽

...

Keyword(s):

Salt Marsh ◽

Microbial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Community Members ◽

Marsh Sediment ◽

Anabolic Activity ◽

Salt Marsh Sediment ◽

Rrna Gene Sequencing ◽

And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

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Abstract 15705: Chronic Inhaled Acrolein Depresses Circulating Endothelial Progenitor Cells and Promotes Atherosclerosis

Circulation ◽

10.1161/circ.132.suppl_3.15705 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Daniel J Conklin ◽

Abhinav Agarwal ◽

Srinivas Sithu ◽

Iris Zeller ◽

Petra Haberzettl ◽

...

Keyword(s):

Blood Flow ◽

Hind Limb ◽

Disease Risk ◽

Cardiovascular Disease Risk ◽

Limb Ischemia ◽

Tobacco Product ◽

Acute Exposure ◽

Circulating Angiogenic Cells ◽

New Policies ◽

And Function

We have previously shown that acute exposure to air pollutants including particulate matter or the volatile acrolein leads to reversible suppression of circulating angiogenic cells in humans and mice. Exposure to tobacco smoke, which contains both particles and aldehydes such as acrolein, also suppresses EPC number and function in association with an increase in cardiovascular disease risk. To assess whether acrolein alone worsened vascular pathogenesis, we exposed mice to acrolein (1 ppm * 6h/day) in a murine model of hind limb ischemia. Mice were exposed to acrolein for 4 days prior to permanent right femoral artery and vein ligation and bisection (distal to inguinal ligament) with continued exposure to filtered air (control) or acrolein for another 2 weeks. Blood flow recovery in the ischemic hind limb was measured via Laser Doppler Perfusion Imaging (LDPI) and normalized as a percentage of flow in the non-ischemic limb. Although acute exposure to acrolein reduced the number of circulating angiogenic cells it had only a modest effect blood flow recovery after 7 days (% Recovery: air, 86.2±21.4; acrolein, 68.3±21.6, n=8,8, p=0.12). Hence to determine whether chronic acrolein exposure worsened chronic vascular injury, we exposed C57BL/6J mice to 1 ppm acrolein for 12 weeks. This long-term exposure significantly depressed (by 51%) circulating levels of Flk-1+/Sca-1+ cells (as % of lymphocytic counts: air 0.15±0.09; acrolein 0.07±0.05; p<0.02). To tested if cell changes were associated with changes in atherogenesis, apoE-null mice on normal chow or high-fat diet were exposed to chronic acrolein (1 ppm; 12 week). Acrolein accelerated aortic atherosclerosis by 1.6-fold (p<0.001) but it did not affect coincident dyslipidemia (total cholesterol: air, 1224±189; acrolein, 1076±195 mg/dL) compared with air-exposed, HFD-fed mice. These results suggest that that chronic low level acrolein exposure suppresses circulating angiogenic cells and accelerates atherogenesis; hence the atherogenic effect of exposure to traffic pollutants, indoor smoke or cigarette smoke may be in part attributable to acrolein. These findings could inform exposure risk assessments and the development of new policies for regulating pollutant exposure and tobacco product use.

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Virtual Hate Communities in the 21st Century

Handbook of Research on Practices and Outcomes in Virtual Worlds and Environments ◽

10.4018/978-1-60960-762-3.ch003 ◽

2011 ◽

pp. 34-53

Author(s):

Glenn T. Tsunokai ◽

Allison R. McGrath

Keyword(s):

Virtual Communities ◽

Hate Speech ◽

Computer Mediated Communication ◽

Interactive Media ◽

Virtual Community ◽

Community Members ◽

Mediated Communication ◽

Computer Mediated ◽

Using Data ◽

And Function

Technological innovations in computer-mediated communication have helped hate groups to transform themselves into virtual communities. Likeminded individuals are now able to unite from all parts of the globe to promote hatred against visible minorities and other out-groups. Through their online interactions, a sense of place is often created. In this chapter, we explore the content and function of online hate communities. Since bigotry tends to be the cornerstone of virtual hate communities, we highlight the legal debate surrounding the regulation of Internet hate speech; in particular, we address the question: Does the First Amendment protect virtual community members who use the Internet to advocate hate? Next, using data collected from the largest hate website, Stormfront.org, we also investigate how Stormfront members utilize interactive media features to foster a sense of community. Finally, we direct our attention to the future of online hate communities by outlining the issues that need to be further investigated.

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Links between metabolic syndrome and the microbiome

Evolution Medicine and Public Health ◽

10.1093/emph/eoaa007 ◽

2020 ◽

Vol 2020 (1) ◽

pp. 45-46 ◽

Cited By ~ 1

Author(s):

Theresa E Gildner

Keyword(s):

Metabolic Syndrome ◽

Disease Risk ◽

Activity Patterns ◽

Human Populations ◽

Microbiome Composition ◽

Diet Patterns ◽

Metabolic Disease Risk ◽

Disease Rates ◽

Microbiome Diversity ◽

Human Intestinal Tract

Abstract Metabolic syndrome (MetS) is a cluster of harmful conditions which occur together, such as insulin resistance, abdominal obesity, and hypertension. The global prevalence of MetS is growing rapidly, with some estimates suggesting over one billion people worldwide experience increased morality and disease rates linked with this syndrome. One possible factor contributing to MetS risk is changes in microbiome composition. Approximately 100 trillion bacteria and other microbes reside in the human intestinal tract, collectively termed the gut microbiome. Humans and microbes share a long evolutionary history, with many of these microbes influencing human health outcomes. However, environmental conditions have changed dramatically with human technological innovations; many of these changes (e.g., diets high in processed foods and sedentary lifestyles) appear to impact human-microbe relationships. In general, recent changes in diet and activity patterns have been linked to decreased microbiome diversity, elevating inflammation and metabolic disease risk and likely promoting the development of MetS. Targeting patient diet or exercise patterns may therefore help doctors better treat patients suffering from MetS. Still, additional work is needed to determine how the microbiome responds to changes in patient activity and diet patterns across culturally and biologically diverse human populations.

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