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Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
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Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
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2
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Cain JL, Norris JK, Swan MP, Nielsen MK. A diverse microbial community and common core microbiota associated with the gonad of female Parascaris spp. Parasitol Res 2023; 123:56. [PMID: 38105374 DOI: 10.1007/s00436-023-08086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
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.
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Affiliation(s)
- Jennifer L Cain
- Maxwell H. Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Road, Lexington, KY, 40503, USA.
| | - Jamie K Norris
- Maxwell H. Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Road, Lexington, KY, 40503, USA
| | - Melissa P Swan
- University of Kentucky Veterinary Diagnostic Laboratory, 1490 Bull Lea Road, Lexington, KY, 40511, USA
| | - Martin K Nielsen
- Maxwell H. Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Road, Lexington, KY, 40503, USA
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3
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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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4
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Shankregowda AM, Siriyappagouder P, Kuizenga M, Bal TMP, Abdelhafiz Y, Eizaguirre C, Fernandes JMO, Kiron V, Raeymaekers JAM. Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species. Front Microbiol 2023; 14:1232358. [PMID: 37901806 PMCID: PMC10601471 DOI: 10.3389/fmicb.2023.1232358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.
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Affiliation(s)
| | | | - Marijn Kuizenga
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | | | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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5
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Salloum PM, Jorge F, Poulin R. Different trematode parasites in the same snail host: Species-specific or shared microbiota? Mol Ecol 2023; 32:5414-5428. [PMID: 37615348 DOI: 10.1111/mec.17111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such as imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals of the same population. Here, we tested several predictions regarding the microbiota of four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. and Maritrema novaezealandense) that parasitize the same snail host population. We predicted that each parasite species would harbour a distinct microbiota, with microbial composition similarity decreasing with increasing phylogenetic distance among parasite species. We also predicted that trematode species co-infecting the same individual host would influence each other's microbiota. We detected significant differences in alpha and beta diversity, as well as differential abundance, in the microbiota of the four trematode species. We found no evidence that phylogenetically closely related trematodes had more similar microbiota. We also uncovered indicator bacterial taxa that were significantly associated with each trematode species. Trematode species sharing the same snail host showed evidence of mostly one-sided bacterial exchanges, with the microbial community of one species approaching that of the other. We hypothesize that natural selection acting on specific microbial lineages may be important to maintain differences in horizontally acquired microbes, with vertical transmission also playing a role. In particular, one trematode species had a more consistent and diverse bacteriota than the others, potentially a result of stronger stabilizing pressures. We conclude that species-specific processes shape microbial community assembly in different trematodes exploiting the same host population.
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Affiliation(s)
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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6
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Salloum PM, Jorge F, Dheilly NM, Poulin R. Adoption of alternative life cycles in a parasitic trematode is linked to microbiome differences. Biol Lett 2023; 19:20230091. [PMID: 37282491 PMCID: PMC10244958 DOI: 10.1098/rsbl.2023.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
For parasites with complex multi-host life cycles, the facultative truncation of the cycle represents an adaptation to challenging conditions for transmission. However, why certain individuals are capable of abbreviating their life cycle while other conspecifics are not remains poorly understood. Here, we test whether conspecific trematodes that either follow the normal three-host life cycle or skip their final host by reproducing precociously (via progenesis) in an intermediate host differ in the composition of their microbiomes. Characterization of bacterial communities based on sequencing of the V4 hypervariable region of the 16S SSU rRNA gene revealed that the same bacterial taxa occur in both normal and progenetic individuals, independent of host identity and temporal variation. However, all bacterial phyla recorded in our study, and two-thirds of bacterial families, differed in abundance between the two morphs, with some achieving higher abundance in the normal morph and others in the progenetic morph. Although the evidence is purely correlative, our results reveal a weak association between microbiome differences and intraspecific plasticity in life cycle pathways. Advances in functional genomics and experimental microbiome manipulation will allow future tests of the significance of these findings.
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Affiliation(s)
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin 9016, New Zealand
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, 22440, Ploufragan, France
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin 9016, New Zealand
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Kashinskaya EN, Simonov EP, Poddubnaya LG, Vlasenko PG, Shokurova AV, Parshukov AN, Andree KB, Solovyev MM. Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of whitefish. Front Microbiol 2023; 14:1090899. [PMID: 36998403 PMCID: PMC10043260 DOI: 10.3389/fmicb.2023.1090899] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/07/2023] [Indexed: 03/15/2023] Open
Abstract
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.
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Affiliation(s)
- Elena N. Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeniy P. Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Larisa G. Poddubnaya
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Russia
| | - Pavel G. Vlasenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V. Shokurova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Aleksey N. Parshukov
- Institute of Biology of the Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Karl B. Andree
- Institut de Recerca i Tecnologìa Agroalimentaries (IRTA), Sant Carles de la Ràpita, Spain
| | - Mikhail M. Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
- Tomsk State University, Biological Institute, Tomsk, Russia
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8
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Sheehy L, MacDonald‐Howard K, Williams CD, Weedall GD, Jones H, Rae R. A parasitic nematode induces dysbiosis in susceptible but not resistant gastropod hosts. Microbiologyopen 2023; 12:e1346. [PMID: 37186232 PMCID: PMC9999464 DOI: 10.1002/mbo3.1346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 03/12/2023] Open
Abstract
Animals’ gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to infection by parasites is still largely unknown, as is how the microbiome changes in hosts that differ in their susceptibility to parasites. To investigate this, we exposed two slug species of differing susceptibility to the parasitic nematode Phasmarhabditis hermaphrodita (Deroceras reticulatum is highly susceptible and Ambigolimax valentianus resistant to the nematode) and profiled the gut microbiota after 7 and 14 days. Before infection, both slug species’ microbiota was dominated by similar bacterial genera: Pseudomonas (by far the most abundant), Sphingobacterium, Pedobacter, Chryseobacterium, and Flavobacterium. In the resistant host A. valentianus, there was no significant change in the bacterial genera after infection, but in D. reticulatum, the bacterial profile changed, with a decrease in the abundance of Pseudomonadaceae and an increase in the abundance of Flavobacteriaceae and Sphingobacteriaceae after 7 days postinfection. This suggests nematode infection causes dysbiosis in hosts that are susceptible to infection, but the microbiome of resistant species remains unaltered. In summary, the regulation of the immune system is tightly linked with host survival, and nematode infection can alter the microbiome structure.
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Affiliation(s)
- Laura Sheehy
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Kerry MacDonald‐Howard
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Chris D. Williams
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Gareth D. Weedall
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Hayley Jones
- Royal Horticultural Society GardenWisley, WokingSurreyUK
| | - Robbie Rae
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
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9
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Eco-evolutionary implications of helminth microbiomes. J Helminthol 2023; 97:e22. [PMID: 36790127 DOI: 10.1017/s0022149x23000056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
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.
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10
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Hodžić A, Dheilly NM, Cabezas-Cruz A, Berry D. The helminth holobiont: a multidimensional host-parasite-microbiota interaction. Trends Parasitol 2023; 39:91-100. [PMID: 36503639 DOI: 10.1016/j.pt.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Adnan Hodžić
- Centre for Microbiology and Environmental Systems Science (CMESS), Department of Microbiology and Ecosystem Science, Division of Microbial Ecology (DoME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Nolwenn M Dheilly
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR VIROLOGIE, Laboratoire de Santé Animale, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - David Berry
- Centre for Microbiology and Environmental Systems Science (CMESS), Department of Microbiology and Ecosystem Science, Division of Microbial Ecology (DoME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
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11
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Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK, Hartmann S. Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host. MICROBIOME 2022; 10:229. [PMID: 36527132 PMCID: PMC9756626 DOI: 10.1186/s40168-022-01399-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. These pathogens live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. Knowledge of the bacterial host microbiome at the site of infection is limited, and data on the parasite microbiome is, to the best of our knowledge, non-existent. RESULTS The intestinal microbiome of the natural parasite and zoonotic macropathogen, Ascaris suum was analyzed in contrast to the diversity and composition of the infected host gut. 16S sequencing of the parasite intestine and host intestinal compartments showed that the parasite gut has a significantly less diverse microbiome than its host, and the host gut exhibits a reduced microbiome diversity at the site of parasite infection in the jejunum. While the host's microbiome composition at the site of infection significantly determines the microbiome composition of its parasite, microbial signatures differentiate the nematodes from their hosts as the Ascaris intestine supports the growth of microbes that are otherwise under-represented in the host gut. CONCLUSION Our data clearly indicate that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut. Video Abstract.
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Affiliation(s)
- Ankur Midha
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Molecular Parasitology, Institute for Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Friederike Ebner
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rima Hayani
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Arkadi Kundik
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Alessio Cardilli
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Institute for Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Sofia Kirke Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Susanne Hartmann
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
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12
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The microbial community associated with Parascaris spp. infecting juvenile horses. Parasit Vectors 2022; 15:408. [PMID: 36333754 PMCID: PMC9636743 DOI: 10.1186/s13071-022-05533-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
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.
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Rajarajan A, Wolinska J, Walser JC, Mäder M, Spaak P. Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community. FEMS Microbiol Ecol 2022; 98:6677393. [PMID: 36026529 PMCID: PMC9869925 DOI: 10.1093/femsec/fiac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 01/26/2023] Open
Abstract
Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.
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Affiliation(s)
- Amruta Rajarajan
- Corresponding author: Office BU-G09, Überlandstrasse 133, 8600 Dübendorf, Zürich, Switzerland. E-mail: and
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany,Department of Biology, Chemistry, Pharmacy, Institut für Biologie, Freie Universität Berlin (FU), 14195 Berlin, Germany
| | - Jean-Claude Walser
- Department of Environmental systems science (D-USYS), Genetic Diversity Centre (GDC), Federal Institute of Technology (ETH) Zürich, 8092, Zürich, Switzerland
| | - Minea Mäder
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
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14
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Poulin R, Jorge F, Salloum PM. Inter-individual variation in parasite manipulation of host phenotype: A role for parasite microbiomes? J Anim Ecol 2022; 92:807-812. [PMID: 35748637 DOI: 10.1111/1365-2656.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
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Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022; 13:e0067922. [PMID: 35502903 PMCID: PMC9239044 DOI: 10.1128/mbio.00679-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections.
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