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Sun H, Chen F, Zheng W, Huang Y, Peng H, Hao H, Wang KJ. Impact of captivity and natural habitats on gut microbiome in Epinephelus akaara across seasons. BMC Microbiol 2024; 24:239. [PMID: 38961321 PMCID: PMC11221007 DOI: 10.1186/s12866-024-03398-y] [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: 01/10/2024] [Accepted: 06/23/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND The gut microbiota significantly influences the health and growth of red-spotted grouper (Epinephelus akaara), a well-known commercial marine fish from Fujian Province in southern China. However, variations in survival strategies and seasons can impact the stability of gut microbiota data, rendering it inaccurate in reflecting the state of gut microbiota. Which impedes the effective enhancement of aquaculture health through a nuanced understanding of gut microbiota. Inspired by this, we conducted a comprehensive analysis of the gut microbiota of wild and captive E. akaara in four seasons. RESULTS Seventy-two E. akaara samples were collected from wild and captive populations in Dongshan city, during four different seasons. Four sections of the gut were collected to obtain comprehensive information on the gut microbial composition and sequenced using 16S rRNA next-generation Illumina MiSeq. We observed the highest gut microbial diversity in both captive and wild E. akaara during the winter season, and identified strong correlations with water temperature using Mantel analysis. Compared to wild E. akaara, we found a more complex microbial network in captive E. akaara, as evidenced by increased abundance of Bacillaceae, Moraxellaceae and Enterobacteriaceae. In contrast, Vibrionaceae, Clostridiaceae, Flavobacteriaceae and Rhodobacteraceae were found to be more active in wild E. akaara. However, some core microorganisms, such as Firmicutes and Photobacterium, showed similar distribution patterns in both wild and captive groups. Moreover, we found the common community composition and distribution characteristics of top 10 core microbes from foregut to hindgut in E. akaara. CONCLUSIONS Collectively, the study provides relatively more comprehensive description of the gut microbiota in E. akaara, taking into account survival strategies and temporal dimensions, which yields valuable insights into the gut microbiota of E. akaara and provides a valuable reference to its aquaculture.
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Affiliation(s)
- Hang Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Fujian Innovation Research Institute for Marine Biological Antimicrobial Peptide Industrial Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wenbin Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yixin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hui Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Fujian Innovation Research Institute for Marine Biological Antimicrobial Peptide Industrial Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hua Hao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Fujian Innovation Research Institute for Marine Biological Antimicrobial Peptide Industrial Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
- Fujian Innovation Research Institute for Marine Biological Antimicrobial Peptide Industrial Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
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Li JD, Gao YY, Stevens EJ, King KC. Dual stressors of infection and warming can destabilize host microbiomes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230069. [PMID: 38497264 PMCID: PMC10945407 DOI: 10.1098/rstb.2023.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/02/2024] [Indexed: 03/19/2024] Open
Abstract
Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- J. D. Li
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - Y. Y. Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
- School of Ecology and Nature Conservation, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, People's Republic of China
| | - E. J. Stevens
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - K. C. King
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
- Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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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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Sharpton TJ, Alexiev A, Tanguay RL. Defining the environmental determinants of dysbiosis at scale with zebrafish. CURRENT OPINION IN TOXICOLOGY 2023; 36:100430. [PMID: 38486798 PMCID: PMC10938905 DOI: 10.1016/j.cotox.2023.100430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The gut microbiome, critical to maintaining vertebrate homeostasis, is susceptible to a various exposures. In some cases, these exposures induce dysbiosis, wherein the microbiome changes into a state conducive to disease progression. To better prevent, manage, and treat health disorders, we need to define which exposures induce dysbiosis. Contemporary methods face challenges due to the immense diversity of the exposome and the restricted throughput of conventional experimental tools used for dysbiosis evaluation. We propose integrating high-throughput model systems as an augment to traditional techniques for rapid identification of dysbiosis-inducing agents. Although high-throughput screening tools revolutionized areas such as pharmacology and toxicology, their incorporation in gut microbiome research remains limited. One particularly powerful high-throughput model system is the zebrafish, which affords access to scalable in vivo experimentation involving a complex gut microbiome. Numerous studies have employed this model to identify potential dysbiosis triggers. However, its potential could be further harnessed via innovative study designs, such as evaluation of synergistic effects from combined exposures, expansions to the methodological toolkit to discern causal effects of microbiota, and efforts to assess and improve the translational relevance of the model. Ultimately, this burgeoning experimental resource can accelerate the discovery of agents that underlie dysbiotic disorders.
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Affiliation(s)
- Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR
- Department of Statistics, Oregon State University, Corvallis, OR
| | | | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR
- Sinnhuber Aquatic Research Center, Oregon State University, Corvallis, OR
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5
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Scheifler M, Magnanou E, Sanchez-Brosseau S, Desdevises Y. Host-microbiota-parasite interactions in two wild sparid fish species, Diplodus annularis and Oblada melanura (Teleostei, Sparidae) over a year: a pilot study. BMC Microbiol 2023; 23:340. [PMID: 37974095 PMCID: PMC10652623 DOI: 10.1186/s12866-023-03086-3] [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: 06/14/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The microbiota in fish external mucus is mainly known for having a role in homeostasis and protection against pathogens, but recent evidence suggests it is also involved in the host-specificity of some ectoparasites. In this study, we investigated the influence of seasonality and environmental factors on both fish external microbiota and monogenean gill ectoparasites abundance and diversity and assessed the level of covariations between monogenean and bacterial communities across seasons. To do so, we assessed skin and gill microbiota of two sparid species, Oblada melanura and Diplodus annularis, over a year and collected their specific monogenean ectoparasites belonging to the Lamellodiscus genus. RESULTS Our results revealed that diversity and structure of skin and gill mucus microbiota were strongly affected by seasonality, mainly by the variations of temperature, with specific fish-associated bacterial taxa for each season. The diversity and abundance of parasites were also influenced by seasonality, with the abundance of some Lamellodiscus species significantly correlated to temperature. Numerous positive and negative correlations between the abundance of given bacterial genera and Lamellodiscus species were observed throughout the year, suggesting their differential interaction across seasons. CONCLUSIONS The present study is one of the first to demonstrate the influence of seasonality and related abiotic factors on fish external microbiota over a year. We further identified potential interactions between gill microbiota and parasite occurrence in wild fish populations, improving current knowledge and understanding of the establishment of host-specificity.
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Affiliation(s)
- Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France.
| | - Elodie Magnanou
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
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6
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Leroux N, Sylvain FE, Holland A, Luis Val A, Derome N. Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections. Microbiol Spectr 2023; 11:e0275522. [PMID: 37724869 PMCID: PMC10581195 DOI: 10.1128/spectrum.02755-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.
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Affiliation(s)
- Nicolas Leroux
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
| | - Francois-Etienne Sylvain
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
| | - Aleicia Holland
- Department of Environment and Genetics, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Adalberto Luis Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, Manaus, Brazil
| | - Nicolas Derome
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Quebec City, Quebec, Canada
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7
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Sieler MJ, Al-Samarrie CE, Kasschau KD, Varga ZM, Kent ML, Sharpton TJ. Disentangling the link between zebrafish diet, gut microbiome succession, and Mycobacterium chelonae infection. Anim Microbiome 2023; 5:38. [PMID: 37563644 PMCID: PMC10413624 DOI: 10.1186/s42523-023-00254-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/21/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome's important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (129- and 214-day-old) zebrafish fed each diet throughout their lifespan. RESULTS Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated how 214-day-old fish microbiome compositions respond to exposure of a common laboratory pathogen, Mycobacterium chelonae, and whether these responses differ as a function of diet. Our analysis finds that diet determines the manner in which the zebrafish gut microbiome responds to M. chelonae exposure, especially for moderate and low abundance taxa. Moreover, histopathological analysis finds that male fish fed different diets are differentially infected by M. chelonae. CONCLUSIONS Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.
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Affiliation(s)
- Michael J Sieler
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
| | | | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
| | - Zoltan M Varga
- Zebrafish International Resource Center, University of Oregon, Eugene, OR, 97330, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, 97330, USA
- Zebrafish International Resource Center, University of Oregon, Eugene, OR, 97330, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97330, USA.
- Department of Statistics, Oregon State University, Corvallis, OR, 97330, USA.
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8
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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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9
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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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10
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Tian C, Jiang D, Hammer A, Sharpton T, Jiang Y. Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model. J Am Stat Assoc 2023; 118:1500-1514. [PMID: 38143789 PMCID: PMC10746147 DOI: 10.1080/01621459.2022.2164287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called "compositional graphical lasso" upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study, which aims to gain insight into how the gut microbiome and parasite burden covary during infection, thus uncovering novel putative methods of disrupting parasite success. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.
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Affiliation(s)
- Chuan Tian
- Department of Statistics, Oregon State University, Corvallis, OR
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR
| | - Austin Hammer
- Department of Microbiology, Oregon State University, Corvallis, OR
| | - Thomas Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR
- Department of Microbiology, Oregon State University, Corvallis, OR
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR
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11
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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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12
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Sieler M, Al-Samarrie C, Kasschau K, Varga Z, Kent M, Sharpton T. Common laboratory diets differentially influence zebrafish gut microbiome's successional development and sensitivity to pathogen exposure. RESEARCH SQUARE 2023:rs.3.rs-2530939. [PMID: 36778316 PMCID: PMC9915791 DOI: 10.21203/rs.3.rs-2530939/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome's important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (4- and 7-month-old) zebrafish fed each diet throughout their lifespan. Results Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated whether the 7-month-old fish microbiome compositions that result from dietary variation are differentially sensitive to infection by a common laboratory pathogen, Mycobacterium chelonae. Our analysis finds that the gut microbiome's sensitivity to M. chelonae infection varies as a function of diet, especially for moderate and low abundance taxa. Conclusions Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.
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13
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Boisseau M, Dhorne-Pollet S, Bars-Cortina D, Courtot É, Serreau D, Annonay G, Lluch J, Gesbert A, Reigner F, Sallé G, Mach N. Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses. iScience 2023; 26:106044. [PMID: 36818309 PMCID: PMC9929684 DOI: 10.1016/j.isci.2023.106044] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/16/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The nature and strength of interactions entertained among helminths and their host gut microbiota remain largely unexplored. Using 40 naturally infected Welsh ponies, we tracked the gut microbiota-cyathostomin temporal dynamics and stability before and following anthelmintic treatment and the associated host blood transcriptomic response. High shedders harbored 14 species of cyathostomins, dominated by Cylicocyclus nassatus. They exhibited a highly diverse and temporal dynamic gut microbiota, with butyrate-producing Clostridia likely driving the ecosystem steadiness and host tolerance toward cyathostomins infection. However, anthelmintic administration sharply bent the microbial community. It disrupted the ecosystem stability and the time-dependent network of interactions, affecting longer term microbial resilience. These observations highlight how anthelmintic treatments alter the triangular relationship of parasite, host, and gut microbiota and open new perspectives for adding nutritional intervention to current parasite management strategies.
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Affiliation(s)
- Michel Boisseau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France
| | - Sophie Dhorne-Pollet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - David Bars-Cortina
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Élise Courtot
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Delphine Serreau
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| | - Gwenolah Annonay
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Jérôme Lluch
- INRAE, US UMR 1426, Genomic platform, 31326 Castanet-Tolosan, France
| | - Amandine Gesbert
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Fabrice Reigner
- INRAE, UE Physiologie Animale de l’Orfrasière, 37380 Nouzilly, France
| | - Guillaume Sallé
- , Université de Tours, INRAE, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France,Corresponding author
| | - Núria Mach
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France,IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France,Corresponding author
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14
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Xia H, Chen H, Cheng X, Yin M, Yao X, Ma J, Huang M, Chen G, Liu H. Zebrafish: an efficient vertebrate model for understanding role of gut microbiota. Mol Med 2022; 28:161. [PMID: 36564702 PMCID: PMC9789649 DOI: 10.1186/s10020-022-00579-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Gut microbiota plays a critical role in the maintenance of host health. As a low-cost and genetically tractable vertebrate model, zebrafish have been widely used for biological research. Zebrafish and humans share some similarities in intestinal physiology and function, and this allows zebrafish to be a surrogate model for investigating the crosstalk between the gut microbiota and host. Especially, zebrafish have features such as high fecundity, external fertilization, and early optical transparency. These enable the researchers to employ the fish to address questions not easily addressed in other animal models. In this review, we described the intestine structure of zebrafish. Also, we summarized the methods of generating a gnotobiotic zebrafish model, the factors affecting its intestinal flora, and the study progress of gut microbiota functions in zebrafish. Finally, we discussed the limitations and challenges of the zebrafish model for gut microbiota studies. In summary, this review established that zebrafish is an attractive research tool to understand mechanistic insights into host-microbe interaction.
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Affiliation(s)
- Hui Xia
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Huimin Chen
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Xue Cheng
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Mingzhu Yin
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Xiaowei Yao
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Jun Ma
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Mengzhen Huang
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Gang Chen
- grid.477392.cHubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061 China
| | - Hongtao Liu
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
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15
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Fulham M, Power M, Gray R. Gut microbiota of endangered Australian sea lion pups is unchanged by topical ivermectin treatment for endemic hookworm infection. Front Microbiol 2022; 13:1048013. [PMID: 36601397 PMCID: PMC9806137 DOI: 10.3389/fmicb.2022.1048013] [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: 09/19/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
The gut microbiota is essential for the development and maintenance of the hosts' immune system. Disturbances to the gut microbiota in early life stages can result in long-lasting impacts on host health. This study aimed to determine if topical ivermectin treatment for endemic hookworm (Uncinaria sanguinis) infection in endangered Australian sea lion (Neophoca cinerea) pups resulted in gut microbial changes. The gut microbiota was characterised for untreated (control) (n = 23) and treated (n = 23) Australian sea lion pups sampled during the 2019 and 2020/21 breeding seasons at Seal Bay, Kangaroo Island. Samples were collected pre- and post-treatment on up to four occasions over a four-to-five-month period. The gut microbiota of untreated (control) and treated pups in both seasons was dominated by five bacterial phyla, Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A significant difference in alpha diversity between treatment groups was seen in pups sampled during the 2020/21 breeding season (p = 0.008), with higher richness and diversity in treated pups. Modelling the impact of individual pup identification (ID), capture, pup weight (kg), standard length (cm), age and sex on beta diversity revealed that pup ID accounted for most of the variation (35% in 2019 and 42% in 2020/21), with pup ID, capture, and age being the only significant contributors to microbial variation (p < 0.05). There were no statistically significant differences in the composition of the microbiota between treatment groups in both the 2019 and 2020/21 breeding seasons, indicating that topical ivermectin treatment did not alter the composition of the gut microbiota. To our knowledge, this is the first study to characterise the gut microbiota of free-ranging Australian pinniped pups, compare the composition across multiple time points, and to consider the impact of parasitic treatment on overall diversity and microbial composition of the gut microbiota. Importantly, the lack of compositional changes in the gut microbiota with treatment support the utility of topical ivermectin as a safe and minimally invasive management strategy to enhance pup survival in this endangered species.
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Affiliation(s)
- Mariel Fulham
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Michelle Power
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Rachael Gray
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia,*Correspondence: Rachael Gray,
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16
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Zhou Q, Zhu X, Li Y, Yang P, Wang S, Ning K, Chen S. Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis. MICROBIOME 2022; 10:153. [PMID: 36138436 PMCID: PMC9503257 DOI: 10.1186/s40168-022-01346-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/10/2022] [Indexed: 06/06/2023]
Abstract
BACKGROUND Infectious diseases have caused huge economic loss and food security issues in fish aquaculture. Current management and breeding strategies heavily rely on the knowledge of regulative mechanisms underlying disease resistance. Though the intestinal microbial community was linked with disease infection, there is little knowledge about the roles of intestinal microbes in fish disease resistance. Cynoglossus semilaevis is an economically important and widely cultivated flatfish species in China. However, it suffers from outbreaks of vibriosis, which results in huge mortalities and economic loss. RESULTS Here, we used C. semilaevis as a research model to investigate the host-microbiome interactions in regulating vibriosis resistance. The resistance to vibriosis was reflected in intestinal microbiome on both taxonomic and functional levels. Such differences also influenced the host gene expressions in the resistant family. Moreover, the intestinal microbiome might control the host immunological homeostasis and inflammation to enhance vibriosis resistance through the microbe-intestine-immunity axis. For example, Phaeobacter regulated its hdhA gene and host cyp27a1 gene up-expressed in bile acid biosynthesis pathways, but regulated its trxA gene and host akt gene down-expressed in proinflammatory cytokines biosynthesis pathways, to reduce inflammation and resist disease infection in the resistant family. Furthermore, the combination of intestinal microbes and host genes as biomarkers could accurately differentiate resistant family from susceptible family. CONCLUSION Our study uncovered the regulatory patterns of the microbe-intestine-immunity axis that may contribute to vibriosis resistance in C. semilaevis. These findings could facilitate the disease control and selective breeding of superior germplasm with high disease resistance in fish aquaculture. Video Abstract.
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Affiliation(s)
- Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Shengpeng Wang
- Dezhou Key Laboratory for Applied Bile Acid Research, Shandong Longchang Animal Health Product Co., Ltd., Qihe, Shandong Lachance Co., Ltd., Jinan, 251100, Shandong, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China.
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17
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Kayani MUR, Yu K, Qiu Y, Yu X, Chen L, Huang L. Longitudinal analysis of exposure to a low concentration of oxytetracycline on the zebrafish gut microbiome. Front Microbiol 2022; 13:985065. [PMID: 36212820 PMCID: PMC9536460 DOI: 10.3389/fmicb.2022.985065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Oxytetracycline, a widely produced and administered antibiotic, is uncontrollably released in low concentrations in various types of environments. However, the impact of exposure to such low concentrations of antibiotics on the host remains poorly understood. In this study, we exposed zebrafish to a low concentration (5,000 ng/L) of oxytetracycline for 1 month, collected samples longitudinally (Baseline, and Days 3, 6, 9, 12, 24, and 30), and elucidated the impact of exposure on microbial composition, antibiotic resistance genes, mobile genetic elements, and phospholipid metabolism pathway through comparison of the sequenced data with respective sequence databases. We identified Pseudomonas aeruginosa, a well-known pathogen, to be significantly positively associated with the duration of oxytetracycline exposure (Adjusted P = 5.829e-03). Several tetracycline resistance genes (e.g., tetE) not only showed significantly higher abundance in the exposed samples but were also positively associated with the duration of exposure (Adjusted P = 1.114e-02). Furthermore, in the exposed group, the relative abundance of genes involved in phospholipid metabolism had also decreased. Lastly, we characterized the impact of exposure on zebrafish intestinal structure and found that the goblet cell counts were decreased (~82%) after exposure. Overall, our results show that a low concentration of oxytetracycline can increase the abundance of pathogenic bacteria and lower the abundance of key metabolic pathways in the zebrafish gut microbiome that can render them prone to bacterial infections and health-associated complications.
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Affiliation(s)
- Masood ur Rehman Kayani
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kan Yu
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yushu Qiu
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaogang Yu
- Ministry of Education and Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Chen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lisu Huang
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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18
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Matthewman C, Narin A, Huston H, Hopkins CE. Systems to model the personalized aspects of microbiome health and gut dysbiosis. Mol Aspects Med 2022; 91:101115. [PMID: 36104261 DOI: 10.1016/j.mam.2022.101115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023]
Abstract
The human gut microbiome is a complex and dynamic microbial entity that interacts with the environment and other parts of the body including the brain, heart, liver, and immune system. These multisystem interactions are highly conserved from invertebrates to humans, however the complexity and diversity of human microbiota compositions often yield a context that is unique to each individual. Yet commonalities remain across species, where a healthy gut microbiome will be rich in symbiotic commensal biota while an unhealthy gut microbiota will be experiencing abnormal blooms of pathobiont bacteria. In this review we discuss how omics technologies can be applied in a personalized approach to understand the microbial crosstalk and microbial-host interactions that affect the delicate balance between eubiosis and dysbiosis in an individual gut microbiome. We further highlight the strengths of model organisms in identifying and characterizing these conserved synergistic and/or pathogenic host-microbe interactions. And finally, we touch upon the growing area of personalized therapeutic interventions targeting gut microbiome.
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19
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Stagaman K, Kasschau KD, Tanguay RL, Sharpton TJ. Experimental methods modestly impact interpretation of the effect of environmental exposures on the larval zebrafish gut microbiome. Sci Rep 2022; 12:14538. [PMID: 36008504 PMCID: PMC9411601 DOI: 10.1038/s41598-022-18532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Rapidly growing fields, such as microbiome science, often lack standardization of procedures across research groups. This is especially the case for microbiome investigations in the zebrafish (Danio rerio) model system, which is quickly becoming a workhorse system for understanding the exposure-microbiome-physiology axis. To guide future investigations using this model system, we defined how various experimental decisions affect the outcomes of studies on the effects of exogenous exposure on the zebrafish gut microbiome. Using a model toxicant, benzo[a]pyrene (BaP), we assessed how each of two dissection methods (gut dissection vs. whole fish), three DNA extraction kits (Qiagen Blood & Tissue, Macherey-Nagel NucleoSpin, and Qiagen PowerSoil), and inclusion of PCR replicates (single vs. pooled triplicate reactions) affected our interpretation of how exposure influences the diversity and composition of the gut microbiome, as well as our ability to identify microbiome biomarkers of exposure. We found that inclusion of PCR replicates had the smallest effect on our final interpretations, and the effects of dissection method and DNA extraction kit had significant effects in specific contexts, primarily in the cases of identifying microbial biomarkers.
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Affiliation(s)
- Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.
| | | | - Robyn L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental Toxicology, Oregon State University, Corvallis, OR, USA
| | - Thomas J Sharpton
- Department of Microbiology & Department of Statistics, Oregon State University, Corvallis, OR, USA
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20
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Colin Y, Molbert N, Berthe T, Agostini S, Alliot F, Decencière B, Millot A, Goutte A, Petit F. Dysbiosis of fish gut microbiota is associated with helminths parasitism rather than exposure to PAHs at environmentally relevant concentrations. Sci Rep 2022; 12:11084. [PMID: 35773378 PMCID: PMC9246949 DOI: 10.1038/s41598-022-15010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Although parasite infection and pollution are common threats facing wild populations, the response of the gut microbiota to the joint impact of these stressors remains largely understudied. Here, we experimentally investigated the effects of exposure to Polycyclic Aromatic Hydrocarbons (PAHs) and infection by a common acanthocephalan intestinal parasite (Pomphorhynchus sp.) on the gut microbial flora of a freshwater fish, the European chub (Squalius cephalus). Naturally infected or uninfected individuals were exposed to PAHs at environmentally realistic concentrations over a five-week period. Characterization of the gut bacterial community through 16S rRNA gene amplicon sequencing revealed that parasitic infection was a more structuring factor of bacterial diversity and composition than PAH exposure. Specifically, chub infected by Pomphorhynchus sp. harbored significantly less evenly represented gut bacterial communities than the uninfected ones. In addition, substantial changes in sequence abundance were observed within the main bacterial phyla, including the Firmicutes, Fusobacteriota, Actinobacteriota, and Proteobacteria. Again, these compositional changes correlated with host infection with Pomphorhynchus sp., confirming its pivotal role in gut microbial assemblage. Overall, these results highlight the importance of defining the parasitic status of individuals when conducting microbial ecotoxicological analyses at the digestive tract level, as this should lead to better understanding of microbiota modulations and help to identify microbial markers specifically associated with chemicals.
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Affiliation(s)
- Yannick Colin
- CNRS, M2C, UNICAEN, UNIROUEN, Normandie University, 76821, Rouen, France. .,CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France.
| | - Noëlie Molbert
- CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France
| | - Thierry Berthe
- CNRS, M2C, UNICAEN, UNIROUEN, Normandie University, 76821, Rouen, France.,CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France
| | - Simon Agostini
- Département de biologie, Centre de recherche en ecologie expérimentale et prédictive (CEREEP-Ecotron IleDeFrance), Ecole normale supérieure, CNRS, PSL University, 77140, Saint-Pierre-lès-Nemours, France
| | - Fabrice Alliot
- CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France.,EPHE, UMR 7619, PSL Research University, Sorbonne University, 4 place Jussieu, 75005, Paris, France
| | - Beatriz Decencière
- Département de biologie, Centre de recherche en ecologie expérimentale et prédictive (CEREEP-Ecotron IleDeFrance), Ecole normale supérieure, CNRS, PSL University, 77140, Saint-Pierre-lès-Nemours, France
| | - Alexis Millot
- Département de biologie, Centre de recherche en ecologie expérimentale et prédictive (CEREEP-Ecotron IleDeFrance), Ecole normale supérieure, CNRS, PSL University, 77140, Saint-Pierre-lès-Nemours, France
| | - Aurélie Goutte
- CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France.,EPHE, UMR 7619, PSL Research University, Sorbonne University, 4 place Jussieu, 75005, Paris, France
| | - Fabienne Petit
- CNRS, M2C, UNICAEN, UNIROUEN, Normandie University, 76821, Rouen, France.,CNRS, EPHE, UMR METIS, Sorbonne Université, 75005, Paris, France
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21
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The Adhesion and Spoilage of Shewanella putrefaciens in Tilapia. Foods 2022; 11:foods11131913. [PMID: 35804729 PMCID: PMC9266031 DOI: 10.3390/foods11131913] [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: 05/16/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023] Open
Abstract
Shewanella putrefaciens is a typical spoilage bacteria organism in seafood. The adhesion ability of three S. putrefaciens strains (HR-15, JR-18, HC-71) isolated from putrefied tilapia were evaluated by mucus adhesion in vitro and intestinal adhesion in vivo. The results of the spoilage of the inoculated fish fillets and spoilage of the refrigerated fish both showed that the adhesion ability of S. putrefaciens was positively correlated with the spoilage ability. High-throughput sequencing and GC-MS results showed that S. putrefaciens with high adhesion ability also significantly changed the intestinal flora of fish, causing an increase in the intestinal bacteria such as Plesionomas, Macellibacteroides, Acinetobacter, and Legionella, which then led to the increase in volatile substances such as low-grade aldehydes, alcohols, and ketones in the fish, serious fatty acid oxidation, and excitement of the fishy smell.
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22
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Li P, Zhang J, Liu X, Gan L, Xie Y, Zhang H, Si J. The Function and the Affecting Factors of the Zebrafish Gut Microbiota. Front Microbiol 2022; 13:903471. [PMID: 35722341 PMCID: PMC9201518 DOI: 10.3389/fmicb.2022.903471] [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: 03/24/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota has become a topical issue in unraveling the research mechanisms underlying disease onset and progression. As an important and potential “organ,” gut microbiota plays an important role in regulating intestinal epithelial cell differentiation, proliferation, metabolic function and immune response, angiogenesis and host growth. More recently, zebrafish models have been used to study the interactions between gut microbiota and hosts. It has several advantages, such as short reproductive cycle, low rearing cost, transparent larvae, high genomic similarity to humans, and easy construction of germ-free (GF) and transgenic zebrafish. In our review, we reviewed a large amount of data focusing on the close relationship between gut microbiota and host health. Moreover, we outlined the functions of gut microbiota in regulating intestinal epithelial cell differentiation, intestinal epithelial cell proliferation, metabolic function, and immune response. More, we summarized major factors that can influence the composition, abundance, and diversity of gut microbiota, which will help us to understand the significance of gut microbiota in regulating host biological functions and provide options for maintaining the balance of host health.
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Affiliation(s)
- Pingping Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinhua Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Liu
- College of Life Science, Lanzhou University, Lanzhou, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
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23
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Kayani MUR, Zaidi SSA, Feng R, Yu K, Qiu Y, Yu X, Chen L, Huang L. Genome-Resolved Characterization of Structure and Potential Functions of the Zebrafish Stool Microbiome. Front Cell Infect Microbiol 2022; 12:910766. [PMID: 35782152 PMCID: PMC9240224 DOI: 10.3389/fcimb.2022.910766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Zebrafish have been used as a model organism for more than 50 years and are considered an excellent model for studying host-microbiome interactions. However, this largely depends on our understanding of the zebrafish gut microbiome itself. Despite advances in sequencing and data analysis methods, the zebrafish gut microbiome remains highly understudied. This study performed the de novo metagenome assembly and recovery of the metagenome-assembled genomes (MAGs) through genome binning (and refinement) of the contigs assembled from the zebrafish stool. The results indicate that majority of the MAGs had excellent quality i.e. high completeness (≥90%) and low contamination levels (≤5%). MAGs mainly belong to the taxa that are known to be members of the core zebrafish stool microbiome, including the phylum Proteobacteria, Fusobacteriota, and Actinobacteriota. However, most of the MAGs remained unclassified at the species level and reflected previously unexplored microbial taxa and their potential novelty. These MAGs also contained genes with predicted functions associated with diverse metabolic pathways that included carbohydrate, amino acid, and lipid metabolism pathways. Lastly, we performed a comparative analysis of Paucibacter MAGs and reference genomes that highlighted the presence of novel Paucibacter species and enriched metabolic potential in the recovered MAGs.
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Affiliation(s)
- Masood ur Rehman Kayani
- Department of Infectious Diseases, Xinhua Children’s Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Ru Feng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kan Yu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yushu Qiu
- Department of Infectious Diseases, Xinhua Children’s Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaogang Yu
- Ministry of Education and Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Chen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Lei Chen, ; Lisu Huang,
| | - Lisu Huang
- Department of Infectious Diseases, Xinhua Children’s Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Lei Chen, ; Lisu Huang,
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24
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Mocho JP, Collymore C, Farmer SC, Leguay E, Murray KN, Pereira N. FELASA-AALAS Recommendations for Biosecurity in an Aquatic Facility, Including Prevention of Zoonosis, Introduction of New Fish Colonies, and Quarantine. Comp Med 2022; 72:149-168. [PMID: 35688609 PMCID: PMC9334003 DOI: 10.30802/aalas-cm-22-000042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 12/12/2022]
Abstract
FELASA and AALAS established a joint working group to advise on good practices for the exchange of fish for research. In a first manuscript, the working group made recommendations for health monitoring and reporting of monitoring results. The focus of this second related manuscript is biosecurity in fish facilities. First, we define the risk of contamination of personnel by zoonotic pathogens from fish or from system water, including human mycobacteriosis. Preventive measures are recommended, such as wearing task-specific personal protective equipment. Then we discuss biosecurity, highlighting the establishment of biosecurity barriers to preserve the health status of a facility. A functional biosecurity program relies on integration of the entire animal facility organization, including the flow of staff and animals, water treatments, and equipment sanitation. Finally, we propose 4 steps for introducing new fish colonies: consideration of international trade and national restrictions; assessing risk according to fish source and developmental stage; establishing quarantine barriers; and the triage, screening, and treatment of newly imported fish. We then provide 3 realistic sample scenarios to illustrate practical biosecurity risk assessments and mitigation measures based on considerations of health status and quarantine conditions.
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Affiliation(s)
| | - Chereen Collymore
- Veterinary Care and Services, Charles River Laboratories, Senneville, Quebec, Canada
| | - Susan C Farmer
- Zebrafish Research Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Katrina N Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon, USA
| | - Nuno Pereira
- Chronic Diseases Research Center (CEDOC), Nova Medical School, Lisbon; Faculty of Veterinary Medicine, Lusophone University of Humanities and Technologies, Lisbon, Portugal; Gulbenkian Institute of Science, Oeiras, Portugal; ISPA - University Institute of Psychological, Social and Life Sciences, Lisbon, Portugal; Lisbon Oceanarium, Lisbon, Portugal
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25
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Mocho JP, Collymore C, Farmer SC, Leguay E, Murray KN, Pereira N. FELASA-AALAS Recommendations for Monitoring and Reporting of Laboratory Fish Diseases and Health Status, with an Emphasis on Zebrafish ( Danio Rerio). Comp Med 2022; 72:127-148. [PMID: 35513000 PMCID: PMC9334007 DOI: 10.30802/aalas-cm-22-000034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 11/05/2022]
Abstract
The exchange of fish for research may expose an aquatic laboratory to pathogen contamination as incoming fish can introduce bacteria, fungi, parasites, and viruses capable of affecting both experimental results and fish and personnel health and welfare. To develop risk mitigation strategies, FELASA and AALAS established a joint working group to recommend good practices for health monitoring of laboratory fish. The recommendations address all fish species used for research, with a particular focus on zebrafish (Danio rerio). First, the background of the working group and key definitions are provided. Next, fish diseases of high impact are described. Third, recommendations are made for health monitoring of laboratory fishes. The recommendations emphasize the importance of daily observation of the fish and strategies to determine fish colony health status. Finally, report templates are proposed for historical screening data and aquatic facility description to facilitate biohazard risk assessment when exchanging fish.
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Affiliation(s)
| | - Chereen Collymore
- Veterinary Care and Services, Charles River Laboratories, Senneville, Quebec, Canada
| | - Susan C Farmer
- Zebrafish Research Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Katrina N Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon, USA
| | - Nuno Pereira
- Chronic Diseases Research Center (CEDOC), Nova Medical School, Lisbon; Faculty of Veterinary Medicine, Lusophone University of Humanities and Technologies, Lisbon, Portugal; Gulbenkian Institute of Science, Oeiras. Portugal; ISPA - University Institute of Psychological, Social and Life Sciences, Lisbon, Portugal; Lisbon Oceanarium, Lisbon, Portugal
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26
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Draft Genome Sequence of Plesiomonas shigelloides Strain zfcc0051 (Phylum
Proteobacteria
). Microbiol Resour Announc 2022; 11:e0007422. [PMID: 35639031 PMCID: PMC9302144 DOI: 10.1128/mra.00074-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report a draft genome sequence of
Plesiomonas shigelloides
strain zfcc0051, an isolate derived from zebrafish (
Danio rerio
) feces. The genome consists of 115 contigs (>500 bp) and has a total assembly length of 4,041,537 bases.
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27
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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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28
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Scheifler M, Sanchez-Brosseau S, Magnanou E, Desdevises Y. Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites. Anim Microbiome 2022; 4:27. [PMID: 35418308 PMCID: PMC9009028 DOI: 10.1186/s42523-022-00180-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/03/2022] [Indexed: 12/31/2022] Open
Abstract
Background Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species. Results Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection. Conclusions This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00180-1.
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Affiliation(s)
- Mathilde Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France.
| | - Sophie Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Elodie Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Yves Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
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29
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Cheng Y, Zhang J, Gao F, Xu Y, Wang C. Protective effects of 5-aminolevulinic acid against toxicity induced by alpha-cypermethrin to the liver-gut-microbiota axis in zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113422. [PMID: 35305352 DOI: 10.1016/j.ecoenv.2022.113422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/24/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
To explore whether and how 5-aminolevulinic acid (ALA) can relieve the toxicity to the liver-gut-microbiota axis caused by alpha-cypermethrin (α-CP), adult zebrafish were exposed to α-CP (1.0 µg L-1) with or without 5.0 mg L-1 ALA supplementation. In the present work, the calculated LC50 of α-CP+ALA was 1.15 μg L-1, increasing about 1.16-fold compared with that of α-CP group (0.99 μg L-1), which indicated that ALA can alleviate the toxicity of α-CP. ALA also alleviated the histopathological lesions in the liver and gut induced by α-CP. Transcriptome sequencing of the liver showed that ALA rescues the differential expression of genes involved in the oxidation-reduction, heme metabolism, and complement activation pathways associated with dysfunctions induced by α-CP, and these findings were verified by RT-qPCR analysis and detection of the activities of enzymes in the liver-gut axis. The gut microbiota 16S rRNA sequencing results showed that α-CP alone induced gut microbial dysbiosis, which was efficiently antagonized by ALA due to decreasing the relative abundances of Cetobacterium and 3 major pathogens, and increasing the relative abundances of beneficial genera. Taken together, the results indicate that ALA might be a promising candidate for attenuating the adverse effects caused by pesticide-induced environmental pollution.
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Affiliation(s)
- Yi Cheng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China.
| | - Jie Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China.
| | - Fei Gao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China.
| | - Yong Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China.
| | - Chengju Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China.
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30
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Marana MH, Poulsen R, Thormar EA, Clausen CG, Thit A, Mathiessen H, Jaafar R, Korbut R, Hansen AMB, Hansen M, Limborg MT, Syberg K, von Gersdorff Jørgensen L. Plastic nanoparticles cause mild inflammation, disrupt metabolic pathways, change the gut microbiota and affect reproduction in zebrafish: A full generation multi-omics study. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127705. [PMID: 34802818 DOI: 10.1016/j.jhazmat.2021.127705] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Plastic pollution has become a major concern on a global scale. The plastic is broken down into minuscule particles, which have an impact on the biosystems, however long-term impacts through an entire generation is largely unknown. Here, we present the first whole generation study exposing fish to a 500 nm polystyrene plastic particle at environmentally relevant concentrations. Short- and long-term adverse effects were investigated in the zebrafish model organism using a holistic multi-omics approach. The particles accumulated in the yolk sac of young larvae and short-term biological impacts included immune-relevant gene regulation related to inflammation and tolerance as well as disruption of metabolic processes, such as the fatty acid and lipid pathways. The long-term effects comprised gene regulations pointing towards skin and/or gill inflammation, dysbiosis of the gut microbiota, a tendency towards decreased condition factor in adult males as well as a lowered reproductive capability. From this study, it can be concluded that exposures to plastic nanoparticles have an impact on population as well as ecosystem level in fish and likely also in other vertebrates.
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Affiliation(s)
- Moonika Haahr Marana
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C., Denmark
| | - Rikke Poulsen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Eiríkur Andri Thormar
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Cecilie Grønlund Clausen
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Amalie Thit
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Heidi Mathiessen
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C., Denmark
| | - Rzgar Jaafar
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C., Denmark
| | - Rozalia Korbut
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C., Denmark
| | - Anna Magdalene Brun Hansen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Martin Hansen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Morten Tønsberg Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Kristian Syberg
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Louise von Gersdorff Jørgensen
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C., Denmark.
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31
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Mondal HK, Maji UJ, Mohanty S, Sahoo PK, Maiti NK. Alteration of gut microbiota composition and function of Indian major carp, rohu (Labeo rohita) infected with Argulus siamensis. Microb Pathog 2022; 164:105420. [DOI: 10.1016/j.micpath.2022.105420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 01/16/2023]
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32
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Shu Y, Xie Y, Li S, Cai L, Liu Y, Feng Y, He J, Zhang H, Ran M, Jia Q, Wu H, Lu L. Risk and protection strategies of Amolops wuyiensis intestine against gastrointestinal nematode (Cosmocercoides wuyiensis n. sp.) infection. Environ Microbiol 2021; 24:1454-1466. [PMID: 34967095 DOI: 10.1111/1462-2920.15881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/18/2021] [Indexed: 12/13/2022]
Abstract
Anuran amphibians are susceptible to infection by intestinal nematodes, but the damage and response mechanisms that occur in their intestines after infection are only partially understood. In this study, the intestinal disruption and response mechanisms in Amolops wuyiensis frogs infected with Cosmocercoides wuyiensis n. sp. were revealed through analysis of the intestinal histopathology, digestive enzyme activity, transcriptome and intestinal microbiota. Tissue section analysis showed histological damage and inflammation in the infected intestine, and the digestive enzyme activity indicated a decrease in digestion and absorption of some nutrients. We found that infection led to differences in the intestinal microbiota composition, including lower diversity and symbiotic relationships. The greater relative abundance of the genera Burkholderia and Rhodococcus may enhance intestinal immunity to resist pathogenic infections. A comparison of the transcriptomes of infected and uninfected intestines revealed 1055 differentially expressed genes. GO enrichment and KEGG pathways analyses suggested that the guts of infected C. wuyiensis n. sp. show enhanced complement activation, cell adhesion molecule function, NOD-like receptor signalling pathway activity and other innate immunity responses. Among the adaptive immune responses, the intestinal immune network for IgA production was significantly enriched, and the expression of IL-17D and transforming growth factor beta-1 genes were upregulated in the infected intestine. These results imply that C. wuyiensis n. sp. infection of A. wuyiensis intestine may trigger innate and adaptive immune responses, which reduce the post-infection burden. Furthermore, the intestine of A. wuyiensis may also respond to C. wuyiensis n. sp. infection by increasing metallocarboxypeptidase activity and accelerating smooth muscle contraction.
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Affiliation(s)
- Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Yunyun Xie
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Shikun Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Liming Cai
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Ying Liu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China.,School of Basic Medicine, Wannan Medical College, Wuhu, Anhui, 241000, China
| | - Yalin Feng
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Jun He
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Menglong Ran
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, 100034, China
| | - Qina Jia
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, 241002, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, Anhui, 241002, China
| | - Linming Lu
- Department of Pathology, Wannan Medical College, Wuhu, Anhui, 241002, China
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Wu L, Hu X, Dai H, Chen K, Liu B. Identification of an m6A Regulators-Mediated Prognosis Signature For Survival Prediction and Its Relevance to Immune Infiltration in Melanoma. Front Cell Dev Biol 2021; 9:718912. [PMID: 34900983 PMCID: PMC8656227 DOI: 10.3389/fcell.2021.718912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Despite robust evidence for the role of m6A in cancer development and progression, its association with immune infiltration and survival outcomes in melanoma remains obscure. Here, we aimed to develop an m6A-related risk signature to improve prognostic and immunotherapy responder prediction performance in the context of melanoma. We comprehensively analyzed the m6A cluster and immune infiltration phenotypes of public datasets. The TCGA (n = 457) and eleven independent melanoma cohorts (n = 758) were used as the training and validation datasets, respectively. We identified two m6A clusters (m6A-clusterA and m6A-clusterB) based on the expression pattern of m6A regulators via unsupervised consensus clustering. IGF2BP1 (7.49%), KIAA1429 (7.06%), and YTHDC1 (4.28%) were the three most frequently mutated genes. There was a correlation between driver genes mutation statuses and the expression of m6A regulators. A significant difference in tumor-associated immune infiltration between two m6A clusters was detected. Compared with m6A-clusterA, the m6A-clusterB was characterized by a lower immune score and immune cell infiltration but higher mRNA expression-based stemness index (mRNAsi). An m6A-related risk signature consisting of 12 genes was determined via Cox regression analysis and divided the patients into low- and high-risk groups (IL6ST, MBNL1, NXT2, EIF2A, CSGALNACT1, C11orf58, CD14, SPI1, NCCRP1, BOK, CD74, PAEP). A nomogram was developed for the prediction of the survival rate. Compared with the high-risk group, the low-risk group was characterized by high expression of immune checkpoints and immunophenoscore (IPS), activation of immune-related pathways, and more enriched in immune cell infiltrations. The low-risk group had a favorable prognosis and contained the potential beneficiaries of the immune checkpoint blockade therapy and verified by the IMvigor210 cohort (n = 298). The m6A-related signature we have determined in melanoma highlights the relationships between m6A regulators and immune cell infiltration. The established risk signature was identified as a promising clinical biomarker of melanoma.
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Affiliation(s)
- Liuxing Wu
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Liu C, Zhao LP, Shen YQ. A systematic review of advances in intestinal microflora of fish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:2041-2053. [PMID: 34750711 DOI: 10.1007/s10695-021-01027-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 10/13/2021] [Indexed: 05/26/2023]
Abstract
Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.
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Affiliation(s)
- Chang Liu
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Li-Ping Zhao
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Yan-Qin Shen
- Wuxi Medical School of Jiangnan University, Wuxi, China.
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35
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Vargas O, Gutiérrez MS, Caruffo M, Valderrama B, Medina DA, García K, Reyes-Jara A, Toro M, Feijóo CG, Navarrete P. Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae. Front Microbiol 2021; 12:647977. [PMID: 34248866 PMCID: PMC8260990 DOI: 10.3389/fmicb.2021.647977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.
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Affiliation(s)
- Orlando Vargas
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Mario Caruffo
- Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Benjamín Valderrama
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Daniel A Medina
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
| | - Katherine García
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Carmen G Feijóo
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
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Kayani MUR, Yu K, Qiu Y, Shen Y, Gao C, Feng R, Zeng X, Wang W, Chen L, Su HL. Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116760. [PMID: 33725532 DOI: 10.1016/j.envpol.2021.116760] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/31/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
A paradoxical impact of high rates of production and consumption of antibiotics is their widespread release in the environment. Consequently, low concentrations of antibiotics and their byproducts have been routinely identified from various environmental settings especially from aquatic environments. However, the impact of such low concentrations of antibiotics on the exposed host especially in early life remains poorly understood. We exposed zebrafish to two different environmental concentrations of oxytetracycline and sulfamethoxazole, from larval stage to adulthood (∼120 days) and characterized their impact on the taxonomic diversity, antibiotic resistance genes, and metabolic pathways of the gut microbiome using metagenomic shotgun sequencing and analysis. Long term exposure of environmental concentrations of oxytetracycline and sulfamethoxazole significantly impacted the taxonomic composition and metabolic pathways of zebrafish gut microbiome. The antibiotic exposed samples exhibited significant enrichment of multiple flavobacterial species, including Flavobacterium sp. F52, Flavobacterium johnsoniae and Flavobacterium sp. Fl, which are well known pathogenic bacteria. The relative abundance of antibiotic resistance genes, especially several tetratcycline and sulfonamide resistance genes were significantly higher in the exposed samples and showed a linear correlation with the antibiotic concentrations. Furthermore, several metabolic pathways, including folate biosynthesis, oxidative phosphorylation, and biotin metabolism pathways, showed significant enrichment in the antibiotic exposed samples. Collectively, our results suggest that early life exposure of the environmental concentrations of antibiotics can increase the abundance of unfavorable bacteria, antibiotic resistance genes and associated pathways in the gut microbiome of zebrafish.
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Affiliation(s)
- Masood Ur Rehman Kayani
- Department of Pediatrics Infectious Diseases, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China; Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, China
| | - Kan Yu
- Department of Pediatrics Infectious Diseases, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China; School of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yushu Qiu
- Department of Pediatrics Infectious Diseases, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Yao Shen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, China
| | - Caixia Gao
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, China
| | - Ru Feng
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, China
| | - Xinxin Zeng
- Department of Pediatrics Infectious Diseases, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Weiye Wang
- Municipal Key Lab of Environment and Children's Health, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai, 2000025, China
| | - Huang Li Su
- Department of Pediatrics Infectious Diseases, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China.
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Kent ML, Wall ES, Sichel S, Watral V, Stagaman K, Sharpton TJ, Guillemin K. Pseudocapillaria tomentosa, Mycoplasma spp., and Intestinal Lesions in Experimentally Infected Zebrafish Danio rerio. Zebrafish 2021; 18:207-220. [PMID: 33999743 DOI: 10.1089/zeb.2020.1955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intestinal neoplasms and preneoplastic lesions are common in zebrafish research facilities. Previous studies have demonstrated that these neoplasms are caused by a transmissible agent, and two candidate agents have been implicated: a Mycoplasma sp. related to Mycoplasma penetrans and the intestinal parasitic nematode, Pseudocapillaria tomentosa, and both agents are common in zebrafish facilities. To elucidate the role of these two agents in the occurrence and severity of neoplasia and other intestinal lesions, we conducted two experimental inoculation studies. Exposed fish were examined at various time points over an 8-month period for intestinal histopathologic changes and the burden of Mycoplasma and nematodes. Fish exposed to Mycoplasma sp. isolated from zebrafish were associated with preneoplastic lesions. Fish exposed to the nematode alone or with the Mycoplasma isolate developed severe lesions and neoplasms. Both inflammation and neoplasm scores were associated with an increase in Mycoplasma burden. These results support the conclusions that P. tomentosa is a strong promoter of intestinal neoplasms in zebrafish and that Mycoplasma alone can also cause intestinal lesions and accelerate cancer development in the context of nematode infection.
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Affiliation(s)
- Michael L Kent
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA.,Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Elena S Wall
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA
| | - Sophie Sichel
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA
| | - Virginia Watral
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA
| | - Keaton Stagaman
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA
| | - Thomas J Sharpton
- Department of Microbiology and Oregon State University, Corvallis, Oregon, USA.,Department of Statistics, Oregon State University, Corvallis, Oregon, USA
| | - Karen Guillemin
- Department of Biology and Institute of Molecular Biology, Eugene, University of Oregon, Eugene, Oregon, USA.,Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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38
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Émie AG, François-Étienne S, Sidki B, Nicolas D. Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact. MICROBIOME 2021; 9:109. [PMID: 34001275 PMCID: PMC8130386 DOI: 10.1186/s40168-021-01058-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocysts' discharge. Resident bacteria are known as key drivers of epithelial mucus chemical signature in vertebrates. A recent study has proposed a restructuration of the skin microbiota in a generalist clown fish when first contacting its symbiotic anemone. We explored a novel hypothesis by testing the effect of remote interaction on epithelial microbiota restructuration in both partners. METHODS With metataxonomics, we investigated the epithelial microbiota dynamic of 18 pairs of percula clownfish (Amphiprion percula) and their symbiotic anemone Heteractis magnifica in remote interaction, physical interaction and control groups for both partners during a 4-week trial. RESULTS The Physical and Remote Interaction groups' results evidence gradual epithelial microbiota convergence between both partners when fish and anemone were placed in the same water system. This convergence occurred preceding any physical contact between partners, and was maintained during the 2-week interaction period in both contact groups. After the interaction period, community structure of both fish and anemone's epthelial community structures maintained the interaction signature 2 weeks after fish-anemone pairs' separation. Furthermore, the interaction signature persistence was observed both in the Physical and Remote Interaction groups, thus suggesting that water-mediated chemical communication between symbiotic partners was strong enough to shift the skin microbiota durably, even after the separation of fish-anemone pairs. Finally, our results suggest that fish-anemone convergent microbiota restructuration was increasingly associated with the parallel recruitment of three Flavobacteriaceae strains closely related to a tyrosinase-producing Cellulophaga tyrosinoxydans. CONCLUSIONS Our study shows that bacterial community restructuration, in the acclimation process, does not only rely on direct physical contact. Furthermore, our results challenge, for the first time, the traditional unidirectional chemical camouflage hypothesis, as we argue that convergence of the epithelial microbiota of both partners may play essential roles in establishing mutual acceptance. Video abstract Fish-anemone symbiotic relationship.
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Affiliation(s)
- Audet-Gilbert Émie
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - Sylvain François-Étienne
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - Bouslama Sidki
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - Derome Nicolas
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
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39
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Bozzi D, Rasmussen JA, Carøe C, Sveier H, Nordøy K, Gilbert MTP, Limborg MT. Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals. Anim Microbiome 2021; 3:30. [PMID: 33879261 PMCID: PMC8056536 DOI: 10.1186/s42523-021-00096-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment. RESULTS We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones. CONCLUSIONS We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.
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Affiliation(s)
- Davide Bozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | | | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark.
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Weitekamp CA, Kvasnicka A, Keely SP, Brinkman NE, Howey XM, Gaballah S, Phelps D, Catron T, Zurlinden T, Wheaton E, Tal T. Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish. Anim Microbiome 2021; 3:12. [PMID: 33499997 PMCID: PMC7818562 DOI: 10.1186/s42523-020-00069-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Background Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivity. The mechanism through which bacteria interact with host cells to trigger normal neurobehavioral development in larval zebrafish is not well understood. Here, we monoassociated zebrafish with either one of six different zebrafish-associated bacteria, mixtures of these host-associates, or with an environmental bacterial isolate. Results As predicted, the axenic cohort was hyperactive. Monoassociation with three different host-associated bacterial species, as well as with the mixtures, resulted in control-like locomotor behavior. Monoassociation with one host-associate and the environmental isolate resulted in the hyperactive phenotype characteristic of axenic larvae, while monoassociation with two other host-associated bacteria partially blocked this phenotype. Furthermore, we found an inverse relationship between the total concentration of bacteria per larvae and locomotor behavior. Lastly, in the axenic and associated cohorts, but not in the larvae with complex communities, we detected unexpected bacteria, some of which may be present as facultative predators. Conclusions These data support a growing body of evidence that individual species of bacteria can have different effects on host behavior, potentially related to their success at intestinal colonization. Specific to the zebrafish model, our results suggest that differences in the composition of microbes in fish facilities could affect the results of behavioral assays within pharmacological and toxicological studies. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00069-x.
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Affiliation(s)
| | - Allison Kvasnicka
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Scott P Keely
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Nichole E Brinkman
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Xia Meng Howey
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Shaza Gaballah
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Drake Phelps
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Tara Catron
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Todd Zurlinden
- , Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Emily Wheaton
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Tamara Tal
- , Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA. .,Bioanalytical Ecotoxicology Department, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany. .,Present Address: Bioanalytical Ecotoxicology Department, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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41
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Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures. TOXICS 2021; 9:toxics9010010. [PMID: 33467528 PMCID: PMC7829988 DOI: 10.3390/toxics9010010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/19/2022]
Abstract
Zebrafish are increasingly used to study how environmental exposures impact vertebrate gut microbes. However, we understand little about which microbial taxa are common to the zebrafish gut across studies and facilities. Here, we define the zebrafish core gut microbiome to resolve microbiota that are both relatively robust to study or facility effects and likely to drive proper microbiome assembly and functioning due to their conservation. To do so, we integrated publicly available gut microbiome 16S gene sequence data from eight studies into a phylogeny and identified monophyletic clades of gut bacteria that are unexpectedly prevalent across individuals. Doing so revealed 585 core clades of bacteria in the zebrafish gut, including clades within Aeromonas, Pseudomonas, Cetobacterium, Shewanella, Chitinibacter, Fluviicola, Flectobacillus, and Paucibacter. We then applied linear regression to discern which of these core clades are sensitive to an array of different environmental exposures. We found that 200 core clades were insensitive to any exposure we assessed, while 134 core clades were sensitive to more than two exposures. Overall, our analysis defines the zebrafish core gut microbiome and its sensitivity to exposure, which helps future studies to assess the robustness of their results and prioritize taxa for empirical assessments of how gut microbiota mediate the effects of exposure on the zebrafish host.
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Bulteel L, Houwenhuyse S, Declerck SAJ, Decaestecker E. The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure. Genes (Basel) 2021; 12:70. [PMID: 33430247 PMCID: PMC7825712 DOI: 10.3390/genes12010070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.
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Affiliation(s)
- Lore Bulteel
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Shira Houwenhuyse
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Steven A. J. Declerck
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6700 AB Wageningen, The Netherlands;
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KULeuven, 3000 Leuven, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
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Hu D, Cui L, Qi Y, Jia X, Chen J, Niu W, Miller MR, Loh M, Zhou H, Deng F, Liu J, Guo X. Identification of potential markers for internal exposure to ambient ozone in oral cavity of healthy adults. ENVIRONMENTAL RESEARCH 2020; 190:109907. [PMID: 32758550 DOI: 10.1016/j.envres.2020.109907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/16/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Ozone is a highly oxidative gaseous pollutant associated with adverse health outcomes, but markers for internal exposure to ambient ozone are not well-established. METHODS We aimed to evaluate the feasibility and suitability of the markers in oral microbiome for ambient ozone exposure. Between March and May in 2018, 97 healthy adults were examined on 2 or 3 occasions for oral swab sampling. Hourly concentrations of ambient ozone 1-7 days preceding sampling were collected. Mixed-effect models were fitted to examine the associations between ambient ozone and the diversity and taxon abundances of oral microbiome. Receiver operating characteristic (ROC) curves estimated the accuracies of markers to delineate between samples exposed to different concentrations of ambient ozone. The associations between the makers and lung function were further examined by linear mixed effect models. RESULTS The averages of daily mean concentrations of ambient ozone (O3-daily), maximum 8-h means (O3-8hmax) and 1-h maximums (O3-1hmax) were respectively 72 μg/m³, 123 μg/m³ and 144 μg/m³. O3-daily was positively associated with α-diversity of oral microbiome, but the exposure-response curves only yielded positive associations in the range of O3-daily from 60 μg/m³ to 75 μg/m³. Results of O3-8hmax and O3-1hmax were consistent with these of O3-daily. With an interquartile range increase in O3-daily at lag04, the abundance of Proteobacteria decreased by 3.1% (95% CI: -4.0%, -2.2%) and Firmicutes increased by 3.3% (95% CI: 2.3%, 4.3%), whilst the Proteobacteria:Firmicutes ratio (P/F) decreased by 0.9 (95% CI: -1.5, -0.4). The areas under ROC curves for Proteobacteria, Firmicutes and P/F were 0.8535, 0.7569 and 0.8929, respectively. Proteobacteria and P/F were associated with forced expiratory volume in the first second and fractional exhaled nitric oxide significantly. CONCLUSION Ambient ozone disturbs oral microbial homeostasis. Proteobacteria, Firmicutes and their ratio may be potential markers for short-term ambient ozone exposure, and indicators of airway inflammation or lung function decline.
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Affiliation(s)
- Dayu Hu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, 100191, China
| | - Yuze Qi
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Xu Jia
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Jiahui Chen
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Wei Niu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Mark R Miller
- University/BHF Centre for Cardiovascular Science, Queens Medical Research Institute, The University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Miranda Loh
- Institute of Occupational Medicine, Research Avenue North Riccarton, Edinburgh, EH144AP, UK
| | - Hui Zhou
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China.
| | - Junxiu Liu
- Department of Otolaryngology Head and Neck Surgery, Peking University Third Hospital, Beijing, 100191, China.
| | - Xinbiao Guo
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, 100191, China
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Schaaf RM, Sharpton TJ, Murray KN, Kent AD, Kent ML. Retrospective analysis of the Zebrafish International Resource Center diagnostic data links Pseudocapillaria tomentosa to intestinal neoplasms in zebrafish Danio rerio (Hamilton 1822). JOURNAL OF FISH DISEASES 2020; 43:1459-1462. [PMID: 32892418 PMCID: PMC7924165 DOI: 10.1111/jfd.13233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 05/02/2023]
Affiliation(s)
- Russel M. Schaaf
- Department of Microbiology, Oregon State University, Corvallis, Oregon
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon
- Department of Statistics, Oregon State University, Corvallis, Oregon
| | - Katrina N. Murray
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon
| | | | - Michael L. Kent
- Department of Microbiology, Oregon State University, Corvallis, Oregon
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon
- Zebrafish International Resource Center, Eugene, Oregon
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Norris L, Lawler N, Hunkapiller A, Mulrooney DM, Kent ML, Sanders JL. Detection of the parasitic nematode, Pseudocapillaria tomentosa, in zebrafish tissues and environmental DNA in research aquaria. JOURNAL OF FISH DISEASES 2020; 43:1087-1095. [PMID: 32720361 DOI: 10.1111/jfd.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Although zebrafish continue to increase in popularity as a vertebrate animal model for biomedical research, chronic infectious diseases in laboratory populations remain prevalent. The presence of pathogens such as Pseudocapillaria tomentosa, a parasitic nematode found in the intestine of infected zebrafish, can significantly influence experimental endpoints and negatively impact reproducibility of research findings. Thus, there is a need for screening tests for zebrafish with the sensitivity to detect even low levels of pathogens present in tissues. Assays based on the detection of DNA are commonly used for such screening tests. Newer technologies such as digital PCR provide an opportunity to improve the sensitivity and precision of these assays, so they can be reliably used to detect pathogen DNA in water, reducing the need for lethal testing. We have designed a qPCR-based assay with the sensitivity to detect less than 5 copies of the P. tomentosa SSU-rDNA gene in tissues of infected zebrafish and environmental DNA from aquarium water housing infected fish. In addition, we adapted this test to a dPCR platform to provide a precise quantification of P. tomentosa DNA and demonstrate the resistance of this assay to inhibitors commonly found in freshwater aquaria.
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Affiliation(s)
- Lauren Norris
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Noah Lawler
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Andree Hunkapiller
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Donna M Mulrooney
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Michael L Kent
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Justin L Sanders
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
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Investigating Both Mucosal Immunity and Microbiota in Response to Gut Enteritis in Yellowtail Kingfish. Microorganisms 2020; 8:microorganisms8091267. [PMID: 32825417 PMCID: PMC7565911 DOI: 10.3390/microorganisms8091267] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/03/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
The mucosal surfaces of fish play numerous roles including, but not limited to, protection against pathogens, nutrient digestion and absorption, excretion of nitrogenous wastes and osmotic regulation. During infection or disease, these surfaces act as the first line of defense, where the mucosal immune system interacts closely with the associated microbiota to maintain homeostasis. This study evaluated microbial changes across the gut and skin mucosal surfaces in yellowtail kingfish displaying signs of gut inflammation, as well as explored the host gene expression in these tissues in order to improve our understanding of the underlying mechanisms that contribute to the emergence of these conditions. For this, we obtained and analyzed 16S rDNA and transcriptomic (RNA-Seq) sequence data from the gut and skin mucosa of fish exhibiting different health states (i.e., healthy fish and fish at the early and late stages of enteritis). Both the gut and skin microbiota were perturbed by the disease. More specifically, the gastrointestinal microbiota of diseased fish was dominated by an uncultured Mycoplasmataceae sp., and fish at the early stage of the disease showed a significant loss of diversity in the skin. Using transcriptomics, we found that only a few genes were significantly differentially expressed in the gut. In contrast, gene expression in the skin differed widely between health states, in particular in the fish at the late stage of the disease. These changes were associated with several metabolic pathways that were differentially expressed and reflected a weakened host. Altogether, this study highlights the sensitivity of the skin mucosal surface in response to gut inflammation.
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Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota. Anim Microbiome 2020; 2:26. [PMID: 33499964 PMCID: PMC7807502 DOI: 10.1186/s42523-020-00046-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. RESULTS Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. CONCLUSION As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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Stagaman K, Sharpton TJ, Guillemin K. Zebrafish microbiome studies make waves. Lab Anim (NY) 2020; 49:201-207. [PMID: 32541907 DOI: 10.1038/s41684-020-0573-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/18/2020] [Indexed: 12/16/2022]
Abstract
Zebrafish have a 50-year history as a model organism for studying vertebrate developmental biology and more recently have emerged as a powerful model system for studying vertebrate microbiome assembly, dynamics and function. In this Review, we discuss the strengths of the zebrafish model for both observational and manipulative microbiome studies, and we highlight some of the important insights gleaned from zebrafish gut microbiome research.
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Affiliation(s)
- Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.,Department of Statistics, Oregon State University, Corvallis, OR, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA. .,Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada.
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Kent M, Sanders J, Spagnoli S, Al-Samarrie C, Murray K. Review of diseases and health management in zebrafish Danio rerio (Hamilton 1822) in research facilities. JOURNAL OF FISH DISEASES 2020; 43:637-650. [PMID: 32291793 PMCID: PMC7253333 DOI: 10.1111/jfd.13165] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 05/09/2023]
Abstract
The use of zebrafish (Danio rerio) in biomedical research has expanded at a tremendous rate over the last two decades. Along with increases in laboratories using this model, we are discovering new and important diseases. We review here the important pathogens and diseases based on some 20 years of research and findings from our diagnostic service at the NIH-funded Zebrafish International Resource Center. Descriptions of the present status of biosecurity programmes and diagnostic and treatment approaches are included. The most common and important diseases and pathogens are two parasites, Pseudoloma neurophilia and Pseudocapillaria tomentosa, and mycobacteriosis caused by Mycobacterium chelonae, M. marinum and M. haemophilum. Less common but deadly diseases are caused by Edwardsiella ictaluri and infectious spleen and kidney necrosis virus (ISKNV). Hepatic megalocytosis and egg-associated inflammation and fibroplasia are common, apparently non-infectious, in zebrafish laboratories. Water quality diseases include supersaturation and nephrocalcinosis. Common neoplasms are spindle cell sarcomas, ultimobranchial tumours, spermatocytic seminomas and a small-cell carcinoma that is caused by a transmissible agent. Despite the clear biosecurity risk, researchers continue to use fish from pet stores, and here, we document two novel coccidia associated with significant lesions in zebrafish from one of these stores.
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Affiliation(s)
- M.L Kent
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - J.L. Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - S. Spagnoli
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - C.E. Al-Samarrie
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331
| | - K.N. Murray
- Zebrafish International Resource Center, Eugene, Oregon 97403
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