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Wang Y, Wang Q, Chen L, Li B. The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108864. [PMID: 37277051 DOI: 10.1016/j.fsi.2023.108864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/20/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0 h, 20 h, 60 h and 100 h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.
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Affiliation(s)
- Yanxia Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; University of Chinese Academy of Science, Beijing, 10049, China
| | - Quanchao Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linlin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Baoquan Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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2
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Zhang Y, Liu Y, Ma H, Sun M, Wang X, Jin S, Yuan X. Insufficient or excessive dietary carbohydrates affect gut health through change in gut microbiota and regulation of gene expression of gut epithelial cells in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2023; 132:108442. [PMID: 36410648 DOI: 10.1016/j.fsi.2022.11.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Dietary carbohydrate levels can affect gut health, but the roles played by gut microbiota and gut epithelial cells, and their interactions remain unclear. In this experiment, we investigated gut health, gut microbiota, and the gene expression profiles of gut epithelial cells in grass carp consuming diets with different carbohydrate levels. Compared to the moderate-carbohydrate diet, low-carbohydrate diet significantly increased the relative abundance of pathogenic bacteria (Ralstonia and Elizabethkingia) and decreased the abundance of metabolism in cofactors and vitamins, implying a dysregulated gut microbiota and compromised metabolic function. Moreover, low-carbohydrate diet inhibited the expression levels of key genes in autophagy-related pathways in gut epithelial cells, which might directly lead to reduced clearance of defective organelles and pathogenic microorganisms. These aforementioned factors may be responsible for the imperfect organization of the intestinal tract. High-carbohydrate diet also significantly increased the abundance of pathogenic bacteria (Flavobacterium), which directly contributed to a decrease in the abundance of immune system of the microbiota. Furthermore, the active pathways of staphylococcus aureus infection and complement and coagulation cascades, as well as the inhibition of the glutathione metabolism pathway were observed. Above results implied that high-carbohydrate diet might ultimately cause severe gut damage by affecting immune function of microbiota, mentioned immune-related pathways, and the antioxidant capacity. Finally, the correlation network diagram revealed strong correlations of the differentially immune-related gene major histocompatibility complex class I antigen (MR1) with Enhydrobacter and Ruminococcus_gnavus_group in low-carbohydrate diet group, and Arenimonas in high-carbohydrate diet group, respectively, suggesting that MR1 might be a central target for immune responses in gut epithelial cells induced by gut microbiota at different levels of dietary carbohydrate. All these results provided insight in the development of antagonistic probiotics and target genes to improve the utilization of carbohydrate.
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Affiliation(s)
- Yanpeng Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yucheng Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Huan Ma
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Manjie Sun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Xin Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Shengzhen Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Xiaochen Yuan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China.
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3
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The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection. Life (Basel) 2021; 11:life11020099. [PMID: 33525589 PMCID: PMC7912457 DOI: 10.3390/life11020099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
Epinephelus coioides, or grouper, is a high economic value fish species that plays an important role in the aquaculture industry in Asia. However, both viral and bacterial diseases have threatened grouper for many years, especially nervous necrosis virus, grouper iridovirus and Vibrio harveyi, which have caused a bottleneck in the grouper industry. Currently, intestinal microbiota can provide novel insights into the pathogenesis-related factors involved in pathogen infection. Hence, we investigated the comparison of intestinal microbiota communities in control group and pathogen-infected grouper through high-throughput sequencing of the 16S rRNA gene. Our results showed that microbial diversity was decreased, whereas microbial richness was increased during pathogen infection. The individuals in each group were distributed distinctly on the PLSDA diagram, especially the GIV group. Proteobacteria and Firmicutes were the most abundant bacterial phyla in all groups. Interestingly, beneficial genera, Faecalibacterium and Bifidobacterium, predominated in the intestines of the control group. In contrast, the intestines of pathogen-infected grouper had higher levels of harmful genera such as Sphingomonas, Atopostipes, Staphylococcus and Acinetobacter. Additionally, we investigated the expression levels of innate and adaptive immune-related genes after viral and bacterial infection. The results revealed that immunoglobulin T and proinflammatory cytokine levels in the intestine increased after pathogen infection. Through these unique bacterial compositions in diseased and uninfected fish, we could establish a novel therapeutic approach and bacterial marker for preventing and controlling these diseases.
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4
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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Borges N, Keller-Costa T, Sanches-Fernandes GMM, Louvado A, Gomes NCM, Costa R. Bacteriome Structure, Function, and Probiotics in Fish Larviculture: The Good, the Bad, and the Gaps. Annu Rev Anim Biosci 2020; 9:423-452. [PMID: 33256435 DOI: 10.1146/annurev-animal-062920-113114] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aquaculture is the fastest-growing sector in food production worldwide. For decades, research on animal physiology, nutrition, and behavior established the foundations of best practices in land-based fish rearing and disease control. Current DNA sequencing, bioinformatics, and data science technologies now allow deep investigations of host-associated microbiomes in a tractable fashion. Adequate use of these technologies can illuminate microbiome dynamics and aid the engineering of microbiome-based solutions to disease prevention in an unprecedented manner. This review examines molecular studies of bacterial diversity, function, and host immunitymodulation at early stages of fish development, where microbial infections cause important economic losses. We uncover host colonization and virulence factors within a synthetic assemblage of fish pathogens using high-end comparative genomics and address the use of probiotics and paraprobiotics as applicable disease-prevention strategies in fish larval and juvenile rearing. We finally propose guidelines for future microbiome research of presumed relevance to fish larviculture.
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Affiliation(s)
- Nuno Borges
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - Gracinda M M Sanches-Fernandes
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , ,
| | - António Louvado
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; ,
| | - Newton C M Gomes
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; ,
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; , , , .,Centre of Marine Sciences, Algarve University, 8005-139 Faro, Portugal.,Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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6
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Zhang X, Zhao Q, Wu C, Xie Z, Ci X, Li H, Lin W, Zhang H, Xie Q. Nitrate Is Crucial for the Proliferation of Gut Escherichia coli Caused by H9N2 AIV Infection and Effective Regulation by Chinese Herbal Medicine Ageratum-Liquid. Front Microbiol 2020; 11:555739. [PMID: 33193136 PMCID: PMC7662154 DOI: 10.3389/fmicb.2020.555739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
H9N2 avian influenza virus (AIV) infection in chickens is often accompanied by secondary bacterial infection, but the mechanism is unclear. The aim of the present study was to reveal that mechanism and explore non-antibiotic treatment. 16s rRNA sequencing and metabonomics were performed in the intestinal contents of chickens infected with H9N2 AIV or H9N2 AIV and fed with ageratum-liquid (AL) to reveal the metabolite that promote intestinal Escherichia coli (E. coli) proliferation caused by H9N2 AIV, as well as to determine the regulatory effect of AL. It was found that H9N2 AIV infection led E. coli to become the dominant gut microbe and promoted E. coli translocation from the intestinal tract to the visceral tissue through the damaged intestinal barrier. H9N2 AIV infection induces inflammation in the intestinal mucosa and promotes the secretion and release of nitrate from the host intestinal epithelium. In addition, nitrate promoted E. coli proliferation in the inflamed intestinal tract following H9N2 AIV infection. Furthermore, Chinese herbal medicine AL can restore intestinal homeostasis, inhibit the production of nitrate in the intestinal epithelium and effectively prevent the proliferation and translocation of E. coli in the intestines. This is the first report on the mechanism of E. coli secondary infection induced by H9N2 AIV, where herbal medicine AL was shown to have a good preventive effect on the secondary infection.
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Affiliation(s)
- Xinheng Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Qiqi Zhao
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Che Wu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Zi Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Xiaotong Ci
- College of Animal Science, South China Agricultural University, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Hongxin Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Wencheng Lin
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
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7
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Nhu TQ, Bich Hang BT, Cornet V, Oger M, Bach LT, Anh Dao NL, Thanh Huong DT, Quetin-Leclercq J, Scippo ML, Phuong NT, Kestemont P. Single or Combined Dietary Supply of Psidium guajava and Phyllanthus amarus Extracts Differentially Modulate Immune Responses and Liver Proteome in Striped Catfish ( Pangasianodon hyphophthalmus). Front Immunol 2020; 11:797. [PMID: 32431710 PMCID: PMC7214933 DOI: 10.3389/fimmu.2020.00797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/07/2020] [Indexed: 01/16/2023] Open
Abstract
Guava Psidium guajava L (Pg) and bhumi amla Phyllanthus amarus Schum. et Thonn (Pa) are well-known plants in traditional medicine. However, the capacity of these plants for improving the immune system of aquatic species has received less attention so far. This study aimed to investigate the effects of single supply or mixture of Pg and Pa extracts on immune responses, disease resistance and liver proteome profiles in striped catfish Pangasianodon hypophthalmus. Fish were fed diets including basal diet 0% or one of three doses of each plant extract, either alone or in mixture, 0.08, 0.2, or 0.5% Pg, Pa or mixture (Pg:Pa, v/v) for 6 weeks. The immune parameters (respiratory burst activity (RBA); nitric oxide synthase (NOS), total immunoglobulin, lysozyme, and complement activities) were examined at W3, W6 post-feeding, and after challenge test. The growth parameters and the challenge test with Edwardsiella ictaluri were done at W6. The liver proteome profiles were analyzed in W6 at 0.08 and 0.5% of each extract. The results showed that extract-based diets significantly improved growth parameters in the Pg0.2 group compared to control. The cellular immune responses in spleen and the humoral immune responses in plasma were significantly improved in a dose and time-dependent manner. Diets supplemented with single Pg and Pa extracts, and to lesser extent to combined extracts, could significantly decrease the mortality of striped catfish following bacterial infection compared to control. The proteomic results indicated that some pathways related to immune responses, antioxidant and lipid metabolism were enriched in liver at W6. Several proteins (i.e., CD8B, HSP90AA1, HSP90AB1, PDIA3, CASP8, TUBA1C, CCKAR, GNAS, GRIN2D, PLCG1, PRKCA, SLC25A5, VDAC2, ACTN4, GNAI2, LCK, CARD9, NLRP12, and NLRP3) were synergistically upregulated in mixture of Pg and Pa-based diets compared to control and single dietary treatments. Taken together, the results revealed that single Pg and Pa extracts at 0.2 and 0.5% and their mixture at 0.08 and 0.5% have the potential to modulate the immune mechanisms and disease resistance of striped catfish. Moreover, the combination of Pg and Pa in diets suggested positive synergistic effects liver proteome profile related to immune system processes.
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Affiliation(s)
- Truong Quynh Nhu
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment, University of Namur, Namur, Belgium.,College of Aquaculture and Fisheries, Cantho University, Cantho City, Vietnam
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Cantho University, Cantho City, Vietnam
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Mathilde Oger
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Le Thi Bach
- College of Natural Sciences, Cantho University, Cantho City, Vietnam
| | - Nguyen Le Anh Dao
- College of Aquaculture and Fisheries, Cantho University, Cantho City, Vietnam
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Cantho University, Cantho City, Vietnam
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Marie-Louise Scippo
- Laboratory of Food Analysis, Department of Food Sciences, Faculty of Veterinary Medicine, Fundamental and Applied Research for Animals & Health, Veterinary Public Health, University of Liège, Liège, Belgium
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Cantho University, Cantho City, Vietnam
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
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8
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Woodhams DC, Bletz MC, Becker CG, Bender HA, Buitrago-Rosas D, Diebboll H, Huynh R, Kearns PJ, Kueneman J, Kurosawa E, LaBumbard BC, Lyons C, McNally K, Schliep K, Shankar N, Tokash-Peters AG, Vences M, Whetstone R. Host-associated microbiomes are predicted by immune system complexity and climate. Genome Biol 2020; 21:23. [PMID: 32014020 PMCID: PMC6996194 DOI: 10.1186/s13059-019-1908-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. RESULTS Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. CONCLUSIONS Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
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Affiliation(s)
- Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - C. Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Hayden A. Bender
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Daniel Buitrago-Rosas
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Hannah Diebboll
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Roger Huynh
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Patrick J. Kearns
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Jordan Kueneman
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Emmi Kurosawa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | | | - Casandra Lyons
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Kerry McNally
- School for the Environment, University of Massachusetts, Boston, MA 02125 USA
- Animal Health Department, New England Aquarium, Boston, MA 02110 USA
| | - Klaus Schliep
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nachiket Shankar
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Amanda G. Tokash-Peters
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, RN1, Butare, Rwanda
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
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