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Sumithra TG, Sharma SRK, Suresh G, Gop AP, Surya S, Gomathi P, Anil MK, Sajina KA, Reshma KJ, Ebeneezar S, Narasimapallavan I, Gopalakrishnan A. Mechanistic insights into the early life stage microbiota of silver pompano ( Trachinotus blochii). Front Microbiol 2024; 15:1356828. [PMID: 38694807 PMCID: PMC11061439 DOI: 10.3389/fmicb.2024.1356828] [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: 12/16/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii. Methods The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed. Results A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, ≤10 DPH (days post-hatching) and > 10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations. Conclusion The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.
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Affiliation(s)
- T. G. Sumithra
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - S. R. Krupesha Sharma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Gayathri Suresh
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
- Cochin University of Science and Technology, Kochi, Kerala, India
| | - Ambarish P. Gop
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - S. Surya
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - P. Gomathi
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - M. K. Anil
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, Kerala, India
| | - K. A. Sajina
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - K. J. Reshma
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Sanal Ebeneezar
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Iyyapparaja Narasimapallavan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - A. Gopalakrishnan
- Marine Biotechnology, Fish Nutrition, and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
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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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3
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Rinaldi G, Paz Meseguer C, Cantacessi C, Cortés A. Form and Function in the Digenea, with an Emphasis on Host-Parasite and Parasite-Bacteria Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1454:3-45. [PMID: 39008262 DOI: 10.1007/978-3-031-60121-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
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.
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Affiliation(s)
- Gabriel Rinaldi
- Department of Life Sciences, Edward Llwyd Building, Aberystwyth University, Aberystwyth, UK
| | - Carla Paz Meseguer
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, School of Pharmacy and Food Sciences, Universitat de València, Valencia, Spain
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alba Cortés
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, School of Pharmacy and Food Sciences, Universitat de València, Valencia, Spain.
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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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5
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Swanson K, Blakeslee AMH, Fowler AE, Roozbehi S, Field EK. Microbial communities are indicators of parasite infection status. Environ Microbiol 2023; 25:3423-3434. [PMID: 37918974 DOI: 10.1111/1462-2920.16533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Growing evidence suggests that microbiomes have been shaping the evolutionary pathways of macroorganisms for millennia and that these tiny symbionts can influence, and possibly even control, species interactions like host-parasite relationships. Yet, while studies have investigated host-parasites and microbiomes separately, little has been done to understand all three groups synergistically. Here, we collected infected and uninfected Eurypanopeus depressus crab hosts from a coastal North Carolina oyster reef three times over 4 months. Infected crabs demonstrated an external stage of the rhizocephalan parasite, Loxothylacus panopaei. Community analyses revealed that microbial richness and diversity were significantly different among tissue types (uninfected crab, infected crab, parasite externae and parasite larvae) and over time (summer and fall). Specifically, the microbial communities from parasite externae and larvae had similar microbiomes that were consistent through time. Infected crabs demonstrated microbial communities spanning those of their host and parasite, while uninfected crabs showed more distinctive communities with greater variability over time. Microbial communities were also found to be indicators of early-stage infections. Resolving the microbial community composition of a host and its parasite is an important step in understanding the microbiome's role in the host-parasite relationship and determining how this tripartite relationship impacts coevolutionary processes.
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Affiliation(s)
- Kyle Swanson
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - April M H Blakeslee
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Amy E Fowler
- Environmental Science & Policy Department, George Mason University, Fairfax, Virginia, USA
| | - Sara Roozbehi
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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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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7
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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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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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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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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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Jorge F, Dheilly NM, Froissard C, Poulin R. Association between parasite microbiomes and caste development and colony structure in a social trematode. Mol Ecol 2022; 31:5608-5617. [PMID: 36004565 PMCID: PMC9826137 DOI: 10.1111/mec.16671] [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: 06/27/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 01/11/2023]
Abstract
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.
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Affiliation(s)
- Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy UnitUniversity of OtagoDunedinNew Zealand
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric SciencesStony Brook UniversityStony BrookNew YorkUSA,Unité Génétique Virale de Biosécurité, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail ‐ Laboratoire de Ploufragan‐PlouzanéANSESPloufraganFrance
| | | | - Robert Poulin
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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13
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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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14
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Abdelhafiz Y, Fernandes JMO, Donati C, Pindo M, Kiron V. Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia. Front Microbiol 2022; 13:879990. [PMID: 35655994 PMCID: PMC9152445 DOI: 10.3389/fmicb.2022.879990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.
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Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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15
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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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16
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Jorge F, Dheilly NM, Froissard C, Wainwright E, Poulin R. Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space. MICROBIAL ECOLOGY 2022; 83:724-738. [PMID: 34136952 DOI: 10.1007/s00248-021-01774-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Nolwenn M Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 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, Ploufragan, France
| | - Céline Froissard
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Eleanor Wainwright
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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17
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Jorge F, Brealey JC, Brindley PJ, Buysse M, Cantacessi C, Duron O, Fichorova R, Fitzpatrick CR, Hahn M, Hunter C, Hervé V, Knoll LJ, Kohl KD, Lalle M, Lukeš J, Martínez JM, Perkins SL, Poulin R, Rosario K, Schneider AC, Schriml LM, Thompson LR, Walls RL, Dheilly NM. MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms. ISME COMMUNICATIONS 2022; 2:9. [PMID: 37938691 PMCID: PMC9723553 DOI: 10.1038/s43705-022-00092-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/26/2021] [Accepted: 01/10/2022] [Indexed: 05/04/2023]
Abstract
The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, Dunedin, New Zealand.
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, D.C, 20037, USA
| | - Marie Buysse
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS)-Institut pour la Recherche et le Développement (IRD) - Université de Montpellier (UM), Montpellier, France
- CREES (Centre de Recherche en Écologie et Évolution de la Santé), Montpellier, France
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Olivier Duron
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS)-Institut pour la Recherche et le Développement (IRD) - Université de Montpellier (UM), Montpellier, France
- CREES (Centre de Recherche en Écologie et Évolution de la Santé), Montpellier, France
| | - Raina Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Connor R Fitzpatrick
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan Hahn
- New York City Department of Health and Mental Hygiene, Long Island City, NY, USA
| | | | - Vincent Hervé
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS-Université de Tours, Avenue Monge, Parc Grandmont, 37200, Tours, France
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Marco Lalle
- Department of Infectious Diseases, Foodborne and Neglected Parasitic Diseases; European Union Reference Laboratory for Parasite, Istituto Superiore di Sanità, Rome, Italy
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), České Budějovice, Czech Republic
| | | | - Susan L Perkins
- Department of Biology, The City College of New York, New York, NY, 10031, USA
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Adam C Schneider
- Biology and Health Sciences Department, Hendrix College, Conway, AR, USA
| | - Lynn M Schriml
- Institute for Genome Sciences, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS, 39762, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, 33149, USA
| | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ, USA
| | - Nolwenn M Dheilly
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, Ploufragan, France.
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR VIROLOGIE, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
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18
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Hahn MA, Piecyk A, Jorge F, Cerrato R, Kalbe M, Dheilly NM. Host phenotype and microbiome vary with infection status, parasite genotype, and parasite microbiome composition. Mol Ecol 2022; 31:1577-1594. [PMID: 35000227 DOI: 10.1111/mec.16344] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/09/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022]
Abstract
A growing literature demonstrates the impact of helminths on their host gut microbiome. We investigated whether the stickleback host microbiome depends on eco-evolutionary variables by testing the impact of exposure to the cestode parasite Schistocephalus solidus with respect to infection success, host genotype, parasite genotype, and parasite microbiome composition. We observed constitutive differences in the microbiome of sticklebacks of different origin, and those differences increased when sticklebacks exposed to the parasite resisted infection. In contrast, the microbiome of successfully infected sticklebacks varied with parasite genotype. More specifically, we revealed that the association between microbiome and immune gene expression increased in infected individuals and varied with parasite genotype. In addition, we showed that S. solidus hosts a complex endo- microbiome and that bacterial abundance in the parasite correlates with expression of host immune genes. Within this comprehensive analysis we demonstrated that (i) parasites contribute to modulating the host microbiome through both successful and unsuccessful infection, (ii) when infection is successful, the host microbiome varies with parasite genotype due to genotype-dependent variation in parasite immunomodulation, and (iii) the parasite-associated microbiome is distinct from its host's and impacts the host immune response to infection.
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Affiliation(s)
- Megan A Hahn
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Agnes Piecyk
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz, Centre for Ocean Research Kiel, Germany
| | - Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Robert Cerrato
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Martin Kalbe
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz, Centre for Ocean Research Kiel, Germany
| | - Nolwenn M Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 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, Ploufragan, France.,UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
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19
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Abstract
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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20
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Jorge F, Froissard C, Dheilly NM, Poulin R. Bacterial community dynamics following antibiotic exposure in a trematode parasite. Int J Parasitol 2021; 52:265-274. [PMID: 34863802 DOI: 10.1016/j.ijpara.2021.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023]
Abstract
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.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Céline Froissard
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Nolwenn M Dheilly
- ANSES, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, Ploufragan, France; UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704 Maisons-Alfort, France
| | - Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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21
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The rise of ecological parasitology: twelve landmark advances that changed its history. Int J Parasitol 2021; 51:1073-1084. [PMID: 34390744 DOI: 10.1016/j.ijpara.2021.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
Abstract
In the five decades since the first publication of the International Journal for Parasitology, ecological parasitology has grown from modest beginnings to become a modern discipline with a strong theoretical foundation, a diverse toolkit, and a multidisciplinary approach. In this review, I highlight 12 advances in the field that have spurred its growth over the past 50 years. Where relevant, I identify pivotal contributions that have altered the course of research, as well as the influence of developments in other fields such as mainstream ecology and molecular biology. The 12 key advances discussed are in areas including parasite population dynamics and community assembly, the regulation of host population abundance and food web structure, parasites as agents of natural selection, the impacts of biodiversity and anthropogenic changes on host-parasite interactions, the biogeography of parasite diversity, and the evolutionary genetics of parasites. I conclude by identifying some challenges and opportunities lying ahead, which need to be met for the future growth of ecological research on host-parasite interactions.
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22
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Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining. Methods Mol Biol 2021; 2369:263-298. [PMID: 34313994 DOI: 10.1007/978-1-0716-1681-9_15] [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: 12/24/2022]
Abstract
Symbiont microbial communities play important roles in animal biology and are thus considered integral components of metazoan organisms, including parasitic worms (helminths). Nevertheless, the study of helminth microbiomes has thus far been largely overlooked, and symbiotic relationships between helminths and their microbiomes have been only investigated in selected parasitic worms. Over the past decade, advances in next-generation sequencing technologies, coupled with their increased affordability, have spurred investigations of helminth-associated microbial communities aiming at enhancing current understanding of their fundamental biology and physiology, as well as of host-microbe interactions. Using the blood fluke Schistosoma mansoni as a key example of parasitic worms with complex life cycles involving multiple hosts, in this chapter we (1) provide an overview of protocols for sample collection and (2) outline an example workflow to characterize worm-associated microbial communities using high-throughput sequencing technologies and bioinformatics analyses of large-scale sequence data.
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