Symbiosis and host responses to heating

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.

Deleterious effects of Wolbachia on life history and physiological traits of common pill woodlice

Most of eukaryotic organisms live in close interaction with micro-organisms called symbionts. Symbiotic interactions underpin the evolution of biological complexity, the health of organisms and, ultimately, the proper functioning of ecosystems. While some symbionts confer adaptive benefits on their host (mutualistic symbionts) and others clearly induce costs (parasitic symbionts), a number of micro-organisms are difficult to classify because they have been described as conferring both benefits and costs on their host. This is particularly true of the most widespread animal endosymbiont, Wolbachia pipientis. In this study, we investigated the influence of Wolbachia infection on a broad spectrum of ecological and physiological parameters of one of its native hosts, Armadillidium vulgare. The aim was to gain as complete a picture as possible of the influence of this endosymbiont on its host. Our results showed that the presence of Wolbachia resulted in a decrease in individual reproductive success and survival. Host immune cells density decreased and β-galactosidase activity (ageing biomarker) increased with the presence of Wolbachia, suggesting a negative impact of this endosymbiont on woodlice health. While previous studies have shown that Wolbachia can have a positive impact on the immunocompetence of A. vulgare, here we shed more light on the costs of infection. Our results illustrate the complex dynamics that exist between Wolbachia and its arthropod host and therefore offer valuable insights into the intricate interplay of symbiotic relationships in ecological systems.

Nano- and microplastics drive the dynamic equilibrium of amoeba-associated bacteria and antibiotic resistance genes

As emerging pollutants, microplastics have become pervasive on a global scale, inflicting significant harm upon ecosystems. However, the impact of these microplastics on the symbiotic relationship between protists and bacteria remains poorly understood. In this study, we investigated the mechanisms through which nano- and microplastics of varying sizes and concentrations influence the amoeba-bacterial symbiotic system. The findings reveal that nano- and microplastics exert deleterious effects on the adaptability of the amoeba host, with the magnitude of these effects contingent upon particle size and concentration. Furthermore, nano- and microplastics disrupt the initial equilibrium in the symbiotic relationship between amoeba and bacteria, with nano-plastics demonstrating a reduced ability to colonize symbiotic bacteria within the amoeba host when compared to their microplastic counterparts. Moreover, nano- and microplastics enhance the relative abundance of antibiotic resistance genes and heavy metal resistance genes in the bacteria residing within the amoeba host, which undoubtedly increases the potential transmission risk of both human pathogens and resistance genes within the environment. In sum, the results presented herein provide a novel perspective and theoretical foundation for the study of interactions between microplastics and microbial symbiotic systems, along with the establishment of risk assessment systems for ecological environments and human health.

The Impact of High-Temperature Stress on Gut Microbiota and Reproduction in Siberian Hamsters (Phodopus sungorus)

Global warming has induced alterations in the grassland ecosystem, such as elevated temperatures and decreased precipitation, which disturb the equilibrium of these ecosystems and impact various physiological processes of grassland rodents, encompassing growth, development, and reproduction. As global warming intensifies, the repercussions of high-temperature stress on small mammals are garnering increased attention. Recently, research has highlighted that the composition and ratio of gut microbiota are not only shaped by environmental factors and the host itself but also reciprocally influence an array of physiological functions and energy metabolism in animals. In this research, we combined 16S rRNA high-throughput sequencing with conventional physiological assessments, to elucidate the consequences of high-temperature stress on the gut microbiota structure and reproductive capacity of Siberian hamsters (Phodopus sungorus). The results were as follows: 1. The growth and development of male and female hamsters in the high-temperature group were delayed, with lower body weight and reduced food intake. 2. High temperature inhibits the development of reproductive organs in both female and male hamsters. 3. High temperature changes the composition and proportion of gut microbiota, reducing bacteria that promote reproduction, such as Pseudobutyricoccus, Ruminiclostridium-E, Sporofaciens, UMGS1071, and CAG_353. Consequently, our study elucidates the specific impacts of high-temperature stress on the gut microbiota dynamics and reproductive health of Siberian hamsters, thereby furnishing insights for managing rodent populations amidst global climatic shifts. It also offers a valuable framework for understanding seasonal variations in mammalian reproductive strategies, contributing to the broader discourse on conservation and adaptation under changing environmental conditions.

Dual stressors of infection and warming can destabilize host microbiomes

Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

The gut microbiota facilitate their host tolerance to extreme temperatures

BACKGROUND

Exposure to extreme cold or heat temperature is one leading cause of weather-associated mortality and morbidity in animals. Emerging studies demonstrate that the microbiota residing in guts act as an integral factor required to modulate host tolerance to cold or heat exposure, but common and unique patterns of animal-temperature associations between cold and heat have not been simultaneously examined. Therefore, we attempted to investigate the roles of gut microbiota in modulating tolerance to cold or heat exposure in mice.

RESULTS

The results showed that both cold and heat acutely change the body temperature of mice, but mice efficiently maintain their body temperature at conditions of chronic extreme temperatures. Mice adapt to extreme temperatures by adjusting body weight gain, food intake and energy harvest. Fascinatingly, 16 S rRNA sequencing shows that extreme temperatures result in a differential shift in the gut microbiota. Moreover, transplantation of the extreme-temperature microbiota is sufficient to enhance host tolerance to cold and heat, respectively. Metagenomic sequencing shows that the microbiota assists their hosts in resisting extreme temperatures through regulating the host insulin pathway.

CONCLUSIONS

Our findings highlight that the microbiota is a key factor orchestrating the overall energy homeostasis under extreme temperatures, providing an insight into the interaction and coevolution of hosts and gut microbiota.

Wolbachia infection negatively impacts Drosophila simulans heat tolerance in a strain- and trait-specific manner

The susceptibility of insects to rising temperatures has largely been measured by their ability to survive thermal extremes. However, the capacity for maternally inherited endosymbionts to influence insect heat tolerance has been overlooked. Further, while some studies have addressed the impact of heat on traits like fertility, which can decline at temperatures below lethal thermal limits, none have considered the impact of endosymbionts. Here, we assess the impact of three Wolbachia strains (wRi, wAu and wNo) on the survival and fertility of Drosophila simulans exposed to heat stress during development or as adults. The effect of Wolbachia infection on heat tolerance was generally small and trait/strain specific. Only the wNo infection significantly reduced the survival of adult males after a heat shock. When exposed to fluctuating heat stress during development, the wRi and wAu strains reduced egg-to-adult survival but only the wNo infection reduced male fertility. Wolbachia densities of all three strains decreased under developmental heat stress, but reductions occurred at temperatures above those that reduced host fertility. These findings emphasize the necessity to account for endosymbionts and their effect on both survival and fertility when investigating insect responses to heat stress.

Gut microbiota modulation enhances the immune capacity of lizards under climate warming

BACKGROUND

Host-microbial interactions are expected to affect species' adaptability to climate change but have rarely been explored in ectothermic animals. Some studies have shown that short-term warming reduced gut microbial diversity that could hamper host functional performance.

RESULTS

However, our longitudinal experiments in semi-natural conditions demonstrated that warming decreased gut microbiota diversity at 2 months, but increased diversity at 13 and 27 months in a desert lizard (Eremias multiocellata). Simultaneously, long-term warming significantly increased the antibacterial activity of serum, immune responses (higher expression of intestinal immune-related genes), and the concentration of short-chain fatty acids (thereby intestinal barrier and immunity) in the lizard. Fecal microbiota transplant experiments further revealed that increased diversity of gut microbiota significantly enhanced antibacterial activity and the immune response of lizards. More specifically, the enhanced immunity is likely due to the higher relative abundance of Bacteroides in warming lizards, given that the bacteria of Bacteroides fragilis regulated IFN-β expression to increase the immune response of lizards under a warming climate.

CONCLUSIONS

Our study suggests that gut microbiota can help ectotherms cope with climate warming by enhancing host immune response, and highlights the importance of long-term studies on host-microbial interactions and their biological impacts.

Skin microbiome disturbance linked to drought-associated amphibian disease

The onset of global climate change has led to abnormal rainfall patterns, disrupting associations between wildlife and their symbiotic microorganisms. We monitored a population of pumpkin toadlets and their skin bacteria in the Brazilian Atlantic Forest during a drought. Given the recognized ability of some amphibian skin bacteria to inhibit the widespread fungal pathogen Batrachochytrium dendrobatidis (Bd), we investigated links between skin microbiome health, susceptibility to Bd and host mortality during a die-off event. We found that rainfall deficit was an indirect predictor of Bd loads through microbiome disruption, while its direct effect on Bd was weak. The microbiome was characterized by fewer putative Bd-inhibitory bacteria following the drought, which points to a one-month lagged effect of drought on the microbiome that may have increased toadlet susceptibility to Bd. Our study underscores the capacity of rainfall variability to disturb complex host-microbiome interactions and alter wildlife disease dynamics.

Barley Yellow Dwarf Virus Influences Its Vector's Endosymbionts but Not Its Thermotolerance

The barley yellow dwarf virus (BYDV) of cereals is thought to substantially increase the high-temperature tolerance of its aphid vector, Rhopalosiphum padi, which may enhance its transmission efficiency. This is based on experiments with North American strains of BYDV and R. padi. Here, we independently test these by measuring the temperature tolerance, via Critical Thermal Maximum (CTmax) and knockdown time, of Australian R. padi infected with a local BYDV isolate. We further consider the interaction between BYDV transmission, the primary endosymbiont of R. padi (Buchnera aphidicola), and a transinfected secondary endosymbiont (Rickettsiella viridis) which reduces the thermotolerance of other aphid species. We failed to find an increase in tolerance to high temperatures in BYDV-infected aphids or an impact of Rickettsiella on thermotolerance. However, BYDV interacted with R. padi endosymbionts in unexpected ways, suppressing the density of Buchnera and Rickettsiella. BYDV density was also fourfold higher in Rickettsiella-infected aphids. Our findings indicate that BYDV does not necessarily increase the temperature tolerance of the aphid transmission vector to increase its transmission potential, at least for the genotype combinations tested here. The interactions between BYDV and Rickettsiella suggest new ways in which aphid endosymbionts may influence how BYDV spreads, which needs further testing in a field context.

Effects of heat and pesticide stress on life history, physiology and the gut microbiome of two congeneric damselflies that differ in stressor tolerance

The combined impact of toxicants and warming on organisms is getting increased attention in ecotoxicology, but is still hard to predict, especially with regard to heat waves. Recent studies suggested that the gut microbiome may provide mechanistic insights into the single and combined stressor effects on their host. We therefore investigated effects of sequential exposure to a heat spike and a pesticide on both the phenotype (life history and physiology) and the gut microbiome composition of damselfly larvae. We compared the fast-paced Ischnura pumilio, which is more tolerant to both stressors, with the slow-paced I. elegans, to obtain mechanistic insights into species-specific stressor effects. The two species differed in gut microbiome composition, potentially contributing to their pace-of-life differences. Intriguingly, there was a general resemblance between the stressor response patterns in the phenotype and in the gut microbiome, whereby both species responded broadly similar to the single and combined stressors. The heat spike negatively affected the life history of both species (increased mortality, reduced growth rate), which could be explained not only by shared negative effects on physiology (inhibition of acetylcholinesterase, increase of malondialdehyde), but also by shared effects on gut bacterial species' abundances. The pesticide only had negative effects (reduced growth rate, reduced net energy budget) in I. elegans. The pesticide generated shifts in the bacterial community composition (e.g. increased abundance of Sphaerotilus and Enterobacteriaceae in the gut microbiome of I. pumilio), which potentially contributed to the relatively higher pesticide tolerance of I. pumilio. Moreover, in line with the response patterns in the host phenotype, the effects of the heat spike and the pesticide on the gut microbiome were mainly additive. By contrasting two species differing in stress tolerance, our results suggest that response patterns in the gut microbiome may improve our mechanistic understanding of single and combined stressor effects.

Still standing: The heat protection delivered by a facultative symbiont to its aphid host is resilient to repeated thermal stress

Insects have evolved diverse strategies to resist extreme high temperatures (EHT). The adaptive value of such strategies has to be evaluated when organisms experience multiple EHT events during their lifetime, as predicted in a changing climate. This is particularly the case for associations with facultative microbial partners involved in insect heat tolerance, the resilience of which to repeated heat stress has never been studied. We compared two artificial lines of the pea aphid (Acyrthosiphon pisum) differing by the absence or presence of the heat-protective facultative bacterium Serratia symbiotica. We exposed insect nymphs to a varying number of EHT events (between 0 and 3), and recorded fitness parameters. Except survival traits, fitness estimates were affected by the interaction between aphid infection status (absence/presence of S. symbiotica) and thermal treatment (number of heat shocks applied). Costs of bacterial infection were detected in the absence of thermal stress: symbiont-hosting aphids incurred longer development, decreased fecundity and body size. However, symbiotic infection turned neutral, and even beneficial for some traits (development and body size), as the number of heat shocks increased, and compared to the aposymbiotic strain. Conversely, symbiotic infection mediated aphid response to heat shock(s): fitness decreased only in the uninfected group. These findings suggest that (i) the facultative symbiont may alternatively act as a pathogen, commensal or mutualist depending on thermal environment, and (ii) the heat protection it delivered to its host persists under frequent EHT. We discuss eco-evolutionary implications and the role of potentially confounding factors (stage-specific effects, genetic polymorphism displayed by the obligate symbiont).

Infection burdens and virulence under heat stress: ecological and evolutionary considerations

As a result of global change, hosts and parasites (including pathogens) are experiencing shifts in their thermal environment. Despite the importance of heat stress tolerance for host population persistence, infection by parasites can impair a host's ability to cope with heat. Host-parasite eco-evolutionary dynamics will be affected if infection reduces host performance during heating. Theory predicts that within-host parasite burden (replication rate or number of infecting parasites per host), a key component of parasite fitness, should correlate positively with virulence-the harm caused to hosts during infection. Surprisingly, however, the relationship between within-host parasite burden and virulence during heating is often weak. Here, we describe the current evidence for the link between within-host parasite burden and host heat stress tolerance. We consider the biology of host-parasite systems that may explain the weak or absent link between these two important host and parasite traits during hot conditions. The processes that mediate the relationship between parasite burden and host fitness will be fundamental in ecological and evolutionary responses of host and parasites in a warming world. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming

Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that 'depleted' tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than 'colonized' tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compared gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.

Experimental temperatures shape host microbiome diversity and composition

Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.

Fungicides have transgenerational effects on Rhopalosiphum padi but not their endosymbionts

BACKGROUND

While several agricultural fungicides are known to directly affect invertebrate pests, including aphids, the mechanisms involved are often unknown. One hypothesis is that fungicides with antibacterial activity suppress bacterial endosymbionts present in aphids which are important for aphid survival. Endosymbiont-related effects are expected to be transgenerational, given that these bacteria are maternally inherited. Here, we test for these associations using three fungicides (chlorothalonil, pyraclostrobin and trifloxystrobin) against the bird cherry-oat aphid, Rhopalosiphum padi, using a microinjected strain that carried both the primary endosymbiont Buchnera and the secondary endosymbiont Rickettsiella.

RESULTS

We show that the fungicide chlorothalonil did not cause an immediate effect on aphid survival, whereas both strobilurin fungicides (pyraclostrobin and trifloxystrobin) decreased survival after 48 h exposure. However, chlorothalonil substantially reduced the lifespan and fecundity of the F1 generation. Trifloxystrobin also reduced the lifespan and fecundity of F1 offspring, however, pyraclostrobin did not affect these traits. None of the fungicides consistently altered the density of Buchnera or Rickettsiella in whole aphids.

CONCLUSIONS

Our results suggest fungicides have sublethal impacts on R. padi that are not fully realized until the generation after exposure, and these sublethal impacts are not associated with the density of endosymbionts harbored by R. padi. However, we cannot rule out other effects of fungicides on endosymbionts that might influence fitness, like changes in their tissue distribution. We discuss these results within the context of fungicidal effects on aphid suppression across generations and point to potential field applications. © 2022 Society of Chemical Industry.

Metabarcoding approaches in amphibian disease ecology: Disentangling the functional contributions of skin bacteria on disease outcome

Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host-pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I re-analyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.