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Hansen SB, Bozzi D, Mak SST, Clausen CG, Nielsen TK, Kodama M, Hansen LH, Gilbert MTP, Limborg MT. Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics 2023; 115:110629. [PMID: 37100093 DOI: 10.1016/j.ygeno.2023.110629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/22/2023] [Indexed: 04/28/2023]
Abstract
It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value off considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.
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Affiliation(s)
- Søren B Hansen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Davide Bozzi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie G Clausen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Denmark
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
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Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S, Delaneau O, Rasmussen S, Malaspinas AS. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics 2023; 39:6986969. [PMID: 36637197 PMCID: PMC9901408 DOI: 10.1093/bioinformatics/btad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023] Open
Abstract
SUMMARY We introduce mapache, a flexible, robust and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large datasets-such as reference panels and multiple extracts and libraries per sample - to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools. AVAILABILITY AND IMPLEMENTATION Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Vital-IT, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Davide Bozzi
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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Scheuring I, Rasmussen JA, Bozzi D, Limborg MT. A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis. Front Microbiol 2022; 13:912806. [PMID: 35992720 PMCID: PMC9386248 DOI: 10.3389/fmicb.2022.912806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host–microbe–microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the spread of pathogenic strains, such as Aliivibrio sp. Even after a skin infection, the Mycoplasma does not recover; Aliivibrio sp. often remains the dominant species, or Mycoplasma–Aliivibrio coexistence was occasionally observed. We devised a model involving interactions among the host immune system, Mycoplasma sp. plus a toxin-producing pathogen. Our model embraces a complete microbiota community and is in harmony with experimental results that host–Mycoplasma mutualism prevents the spread of pathogens. Contrary, stress suppresses the host immune system allowing dominance of pathogens, and Mycoplasma does not recover after stress disappears.
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Affiliation(s)
- István Scheuring
- Centre for Ecological Research, Institute of Evolution, Budapest, Hungary
- MTA-ELTE, Research Group of Theoretical Biology and Evolutionary Ecology, Eötvõs University, Budapest, Hungary
| | - Jacob A. Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Davide Bozzi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Morten T. Limborg
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Agostinetto G, Bozzi D, Porro D, Casiraghi M, Labra M, Bruno A. SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. Database (Oxford) 2022; 2022:6586378. [PMID: 35576001 PMCID: PMC9216470 DOI: 10.1093/database/baac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/25/2022] [Accepted: 05/09/2022] [Indexed: 04/07/2023]
Abstract
Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and it is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, it urges the need for data accessibility and reusability, according to findable, accessible, interoperable and reusable (FAIR) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon-sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analyses, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field. Database URL: https://github.com/giuliaago/SKIOMEMetadataRetrieval.
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Affiliation(s)
- Giulia Agostinetto
- *Corresponding author: Giulia Agostinetto. E-mail: and Antonia Bruno. Tel: +0039 0264483413; E-mail:
| | | | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, Milan 20126, Italy
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), via Fratelli Cervi, 93, Segrate (MI) 20054, Italy
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, Milan 20126, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, Milan 20126, Italy
| | - Antonia Bruno
- *Corresponding author: Giulia Agostinetto. E-mail: and Antonia Bruno. Tel: +0039 0264483413; E-mail:
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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: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Twenty-five patients with advanced breast cancer were treated with 4-demethoxydaunorubicin (4-DMDR), a new antitumor analogue of daunorubicin, at the dose of 15-20 mg/m2/day X 3 days by oral route every 3-4 weeks. All patients were previously treated with chemotherapy and/or hormone therapy but none with anfhracyclines. Of 23 evaluable patients, 1 complete and 5 partial remissions (26%) were observed for a median duration of 4+ months. Leukopenia and nausea occurred in 61% of the patients, vomiting in 30%, diarrhea in 17% and alopecia in 43%. There were 2 cases with minimal and transient EKG variations. 4-DMDR, administered orally in advanced breast cancer, was found to be generally well tolerated. Nevertheless, randomized trials with adriamycin or epirubicin are necessary to compare and to define the therapeutic activity and the toxicity of 4-DMDR.
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