Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space

Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites

Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.

Does the host matter? Testing the impact of host identity on the microbiome of a trematode parasite

Animal microbiomes have been recognized to have significant impact on animal behaviour, development, and health. For parasites, one of the sources of their associated microbes is likely their hosts, making host identity a potential factor explaining variation of microbial communities among conspecific parasites. Using the host-parasite system including the amphipod Paracalliope fluviatilis, and isopod Austridotea annectens, and their common trematode parasite Maritrema poulini, we hypothesized that host identity has an impact on the diversity and community composition of the microbiomes of M. poulini parasites. We focused on the bacterial component of the trematodes' microbiomes. We investigated the effect of host identity under both intraspecific (among individual isopods) and interspecific (between amphipods and isopods) host levels and predicted that the effect of host identity can be detected under both host hierarchical levels. We found an effect of host identity on both the diversity and community composition of parasite microbiomes between conspecific isopod hosts, while host identity only had an impact on microbiome community composition when comparing parasites infecting amphipod versus isopod hosts. Our study results show that host identity impacts both parasite microbiome composition and taxonomic diversity, providing indirect evidence that the assembly of parasite microbiomes is not merely random, and that horizontal transmission from the host to the parasite might play a key role in shaping parasite microbiomes.

Microbial artists: the role of parasite microbiomes in explaining colour polymorphism among amphipods and potential link to host manipulation

Parasite infections are increasingly reported to change the microbiome of the parasitized hosts, while parasites bring their own microbes to what can be a multi-dimensional interaction. For instance, a recent hypothesis suggests that the microbial communities harboured by parasites may play a role in the well-documented ability of many parasites to manipulate host phenotype, and explain why the degree to which host phenotype is altered varies among conspecific parasites. Here, we explored whether the microbiomes of both hosts and parasites are associated with variation in host manipulation by parasites. Using colour quantification methods applied to digital images, we investigated colour variation among uninfected Transorchestia serrulata amphipods, as well as amphipods infected with Plagiorhynchus allisonae acanthocephalans and with a dilepidid cestode. We then characterized the bacteriota of amphipod hosts and of their parasites, looking for correlations between host phenotype and the bacterial taxa associated with hosts and parasites. We found large variation in amphipod colours, and weak support for a direct impact of parasites on the colour of their hosts. Conversely, and most interestingly, the parasite's bacteriota was more strongly correlated with colour variation among their amphipod hosts, with potential impact of amphipod-associated bacteria as well. Some bacterial taxa found associated with amphipods and parasites may have the ability to synthesize pigments, and we propose they may interact with colour determination in the amphipods. This study provides correlational support for an association between the parasite's microbiome and the evolution of host manipulation by parasites and host-parasite interactions more generally.

Form and Function in the Digenea, with an Emphasis on Host-Parasite and Parasite-Bacteria Interactions

This review covers the general aspects of the anatomy and physiology of the major body systems in digenetic trematodes, with an emphasis on new knowledge of the area acquired since the publication of the second edition of this book in 2019. In addition to reporting on key recent advances in the morphology and physiology of tegumentary, sensory, neuromuscular, digestive, excretory, and reproductive systems, and their roles in host-parasite interactions, this edition includes a section discussing the known and putative roles of bacteria in digenean biology and physiology. Furthermore, a brief discussion of current trends in the development of novel treatment and control strategies based on a better understanding of the trematode body systems and associated bacteria is provided.

A diverse microbial community and common core microbiota associated with the gonad of female Parascaris spp

The microbiome plays an important role in health, where changes in microbiota composition can have significant downstream effects within the host, and host-microbiota relationships can be exploited to affect health outcomes. Parasitic helminths affect animals globally, but an exploration of their microbiota has been limited, despite the development of anti-Wolbachia drugs to help control infections with some filarial nematodes. The equine ascarids, Parascaris spp., are considered the most pathogenic nematodes affecting juvenile horses and are also the only ascarid parasite to have developed widespread anthelmintic resistance. The aim of this study was to characterize the microbiota of this helminth, focusing on the female gonad, determine a core microbiota for this organ, identify bacterial species, and show bacterial localization to the female gonad via in situ hybridization (ISH). A total of 22 gonads were isolated from female Parascaris spp. collected from three foals, and 9 female parasites were formalin-fixed and paraffin-embedded for ISH. Next-generation sequencing was performed using V3-V4 primers as well as the Swift Amplicon™ 16S+ ITS Panel. Overall, ten genera were identified as members of the Parascaris spp. female gonad and twelve bacterial species were identified. The most prevalent genus was Mycoplasma, followed by Reyranella, and there were no differences in alpha diversity between parasites from different horses. Specific eubacteria staining was identified in both the intestine and within the gonad using ISH. Overall, this study provided in-depth information regarding the female Parascaris spp. microbiota and was the first to identify the core microbiota within a specific parasite organ.

Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of whitefish

Introduction

The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. This study has focused on the influence that trophic behavior and resulting parasitism has on the structure of the microbiome.

Methods

Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode's surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the washout procedure from the mucosa to understand the real structure of the fish gut microbiota.

Results and discussion

Our results demonstrate that additional microbial community in the intestine are formed by the parasitic helminths that caused the restructuring of the microbiota in infected fish compared to those uninfected. Using the desorption method in Ringer's solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from "surface" bacteria, and bacteria which are weakly and strongly associated with the tegument, bacteria obtained after treatment of the tegument with detergent, and bacteria obtained after removal of the tegument from the cestodes.

Eco-evolutionary implications of helminth microbiomes

The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.

The helminth holobiont: a multidimensional host-parasite-microbiota interaction

Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.

The microbial community associated with Parascaris spp. infecting juvenile horses

Background

Parasitic nematodes, including large roundworms colloquially known as ascarids, affect the health and well-being of livestock animals worldwide. The equine ascarids, Parascaris spp., are important parasites of juvenile horses and the first ascarids to develop widespread anthelmintic resistance. The microbiota has been shown to be an important factor in the fitness of many organisms, including parasitic nematodes, where endosymbiotic Wolbachia have been exploited for treatment of filariasis in humans.

Methods

This study used short-read 16S rRNA sequences and Illumina sequencing to characterize and compare microbiota of whole worm small intestinal stages and microbiota of male and female intestines and gonads. Diversity metrics including alpha and beta diversity, and the differential abundance analyses DESeq2, ANCOM-BC, corncob, and metagenomeSeq were used for comparisons.

Results

Alpha and beta diversity of whole worm microbiota did not differ significantly between groups, but Simpson alpha diversity was significantly different between female intestine (FI) and male gonad (MG) (P= 0.0018), and Shannon alpha diversity was significantly different between female and male gonads (P = 0.0130), FI and horse jejunum (HJ) (P = 0.0383), and FI and MG (P= 0.0001). Beta diversity (Fig. 2B) was significantly different between female and male gonads (P = 0.0006), male intestine (MI) and FG (P = 0.0093), and MG and FI (P = 0.0041). When comparing organs, Veillonella was differentially abundant for DESeq2 and ANCOM-BC (p < 0.0001), corncob (P = 0.0008), and metagenomeSeq (P = 0.0118), and Sarcina was differentially abundant across four methods (P < 0.0001). Finally, the microbiota of all individual Parascaris spp. specimens were compared to establish shared microbiota between groups.

Conclusions

Overall, this study provided important information regarding the Parascaris spp. microbiota and provides a first step towards determining whether the microbiota may be a viable target for future parasite control options.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05533-y.

Association between parasite microbiomes and caste development and colony structure in a social trematode

Division of labour through the formation of morphologically and functionally distinct castes is a recurring theme in the evolution of animal sociality. The mechanisms driving the differentiation of individuals into distinct castes remain poorly understood, especially for animals forming clonal colonies. We test the association between microbiomes and caste formation within the social trematode Philophthalmus attenuatus, using a metabarcoding approach targeting the bacterial 16S SSU rRNA gene. Clonal colonies of this trematode within snail hosts comprise large reproductive individuals which produce dispersal stages, and small, non-reproducing soldiers which defend the colony against invaders. In colonies extracted directly from field-collected snails, reproductives harboured more diverse bacterial communities than soldiers, and reproductives and soldiers harboured distinct bacterial communities, at all taxonomic levels considered. No single bacterial taxon showed high enough prevalence in either soldiers or reproductives to be singled out as a key driver, indicating that the whole microbial community contributes to these differences. Other colonies were experimentally exposed to antibiotics to alter their bacterial communities, and sampled shortly after treatment and weeks later after allowing for turnover of colony members. At those time points, bacterial communities of the two castes still differed across all antibiotic treatments; however, the caste ratio within colonies changed: after antibiotic disruption and turnover of individuals, new individuals were more likely to become reproductives than in undisturbed control colonies. Our results reveal that each caste has a distinct microbiome; whether the social context affects the microbiota, or whether microbes contribute to modulating the phenotype of individuals, remains to be determined.

Inter-individual variation in parasite manipulation of host phenotype: A role for parasite microbiomes?

Alterations in host phenotype induced by metazoan parasites are widespread in nature, yet the underlying mechanisms and the sources of intraspecific variation in the extent of those alterations remain poorly understood. In light of the microbiome revolution sweeping through ecology and evolutionary biology, we hypothesise that the composition of symbiotic microbial communities living within individual parasites influences the nature and extent of their effect on host phenotype. The interests of both the parasite and its symbionts are aligned through the latter's vertical transmission, favouring joint contributions to the manipulation of host phenotype. Our hypothesis can explain the variation in the extent to which parasites alter host phenotype, as microbiome composition varies among individual parasites. We propose two non-exclusive approaches to test the hypothesis, furthering the integration of microbiomes into studies of host-parasite interactions.

Bacterial community dynamics following antibiotic exposure in a trematode parasite

Parasites harbour rich microbial communities that may play a role in host-parasite interactions, from influencing the parasite's infectivity to modulating its virulence. Experimental manipulation of a parasite's microbes would be essential, however, in order to establish their causal role. Here, we tested whether indirect exposure of a trematode parasite within its snail intermediate host to a variety of antibiotics could alter its bacterial community. Based on sequencing the prokaryotic 16S ssrRNA gene, we characterised and compared the bacterial community of the trematode Philophthalmus attenuatus before, shortly after, and weeks after exposure to different antibiotics (penicillin, colistin, gentamicin) with distinct activity spectra. Our findings revealed that indirectly treating the parasites by exposing their snail host to antibiotics resulted in changes to their bacterial communities, measured as their diversity, taxonomic composition, and/or the relative abundance of certain taxa. However, alterations to the parasite's bacterial community were not always as predicted from the activity spectrum of the antibiotic used. Furthermore, the bacterial communities of the parasites followed significantly divergent trajectories in the days post-exposure to antibiotics, but later converged toward a new state, i.e. a new bacterial community structure different from that pre-exposure. Our results confirm that a trematode's microbial community can be experimentally altered by antibiotic exposure while within its snail host, with the dynamic nature of the bacterial assemblage driving it to a new state over time after the perturbation. This research opens new possibilities for future experimental investigations of the functional roles of microbes in host-parasite interactions.