1
|
Muurmann AT, Banovic M, Gilbert MTP, Sogari G, Limborg MT, Sicheritz-Pontén T, Bahrndorff S. Framework for valorizing waste- and by-products through insects and their microbiomes for food and feed. Food Res Int 2024; 187:114358. [PMID: 38763642 DOI: 10.1016/j.foodres.2024.114358] [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: 12/15/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
One third of the food produced for human consumption is currently lost or wasted. Insects have a high potential for converting organic waste- and by-products into food and feed for a growing human population due to symbiosis with microorganisms. These symbioses provide an untapped reservoir of functional microbiomes that can be used to improve industrial insect production but are poorly studied in most insect species. Here we review the most current understanding and challenges of valorizing organic waste- and by-products through insects and their microbiomes for food and feed, and emerging novel food technologies that can be used to investigate and manipulate host(insects)-microbiome interactions. We further construct a holistic framework, by integration of novel food technologies including holo-omics, genome editing, breeding, phage therapy, and administration of prebiotics and probiotics to investigate and manipulate host(insects)-microbiome interactions, and solutions for achieving stakeholder acceptance of novel food technologies for a sustainable food production.
Collapse
Affiliation(s)
- Asmus Toftkær Muurmann
- Aalborg University, Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark.
| | - Marija Banovic
- Aarhus University, Aarhus BSS, Department of Management, MAPP Centre, Fuglsangs Allé 4, 8210 Aarhus V, Denmark.
| | - M Thomas P Gilbert
- University of Copenhagen, GLOBE Institute, Øster Farimagsgade 5, 1014 København K, Denmark; University Museum, NTNU, Erling Skakkes gate 47B, 7012 Trondheim, Norway.
| | - Giovanni Sogari
- University of Parma, Department of Food and Drug, Parco Area delle Scienze, 45, 43124 Parma, Italy.
| | | | - Thomas Sicheritz-Pontén
- University of Copenhagen, GLOBE Institute, Øster Farimagsgade 5, 1014 København K, Denmark; AIMST University, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia.
| | - Simon Bahrndorff
- Aalborg University, Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark.
| |
Collapse
|
2
|
Pepke ML, Hansen SB, Limborg MT. Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. Trends Microbiol 2024:S0966-842X(24)00137-9. [PMID: 38839511 DOI: 10.1016/j.tim.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.
Collapse
Affiliation(s)
- Michael L Pepke
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
| |
Collapse
|
3
|
Hou D, Li H, Wang S, Weng S, He J. Nitrite nitrogen stress disrupts the intestine bacterial community by altering host-community interactions in shrimp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171536. [PMID: 38461992 DOI: 10.1016/j.scitotenv.2024.171536] [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: 01/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Environmental stress can disrupt the intricate interactions between the host and intestine microbiota, thereby impacting the host health. In this study, we aimed to elucidate the dynamic changes in the bacterial community within shrimp intestines under nitrite nitrogen (nitrite-N) stress and investigate potential host-related factors influencing these changes. Our results revealed a significant reduction in community diversity within the intestine exposed to nitrite-N compared to control conditions. Furthermore, distinct differences in community structures were observed between these two groups at 72 h and 120 h post-stress induction. Nitrite-N stress also altered the abundances of some bacterial species in the intestine dramatically. It is noteworthy that, in comparison to the 72 h, intestine bacterial community structure of stressed shrimp exhibited a significantly higher degree of dispersion after 120 h of nitrite-N stress when compared to control shrimp, and the relative abundance of numerous bacterial species experienced a substantial decrease or even reached 0 %. Moreover, it led to a reduction in bacterial community interactions and decreased competitiveness within the intestine microbiota. Notably, the influence of bacterial community assemblies in the shrimp intestine shifted from a stochastic process to a deterministic one after 24 h and 72 h of nitrite-N stress, returning to a stochastic process at 120 h. We further observed a close association between this phenomenon and host's response to nitrite-N stress. Expression levels of differentially expressed genes in the intestinal tissue significantly impact the intestine bacterial diversity and abundance of species. In particular, the significant decline in bacterial diversity and abundances of quite a few species in intestine was attributed to the up-regulation of peritrophin-48-like. Overall, nitrite-N stress indeed disrupted the intestine microbiota and changed the host-microbiota interactions of shrimp. This study offered novel insights into environment-host-microbiota interactions and also provided practical guidance for promoting healthy shrimp cultivation practices.
Collapse
Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haoyang Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| |
Collapse
|
4
|
Mishra A, Kim HS, Kumar R, Srivastava V. Advances in Vibrio-related infection management: an integrated technology approach for aquaculture and human health. Crit Rev Biotechnol 2024:1-28. [PMID: 38705837 DOI: 10.1080/07388551.2024.2336526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/25/2023] [Indexed: 05/07/2024]
Abstract
Vibrio species pose significant threats worldwide, causing mortalities in aquaculture and infections in humans. Global warming and the emergence of worldwide strains of Vibrio diseases are increasing day by day. Control of Vibrio species requires effective monitoring, diagnosis, and treatment strategies at the global scale. Despite current efforts based on chemical, biological, and mechanical means, Vibrio control management faces limitations due to complicated implementation processes. This review explores the intricacies and challenges of Vibrio-related diseases, including accurate and cost-effective diagnosis and effective control. The global burden due to emerging Vibrio species further complicates management strategies. We propose an innovative integrated technology model that harnesses cutting-edge technologies to address these obstacles. The proposed model incorporates advanced tools, such as biosensing technologies, the Internet of Things (IoT), remote sensing devices, cloud computing, and machine learning. This model offers invaluable insights and supports better decision-making by integrating real-time ecological data and biological phenotype signatures. A major advantage of our approach lies in leveraging cloud-based analytics programs, efficiently extracting meaningful information from vast and complex datasets. Collaborating with data and clinical professionals ensures logical and customized solutions tailored to each unique situation. Aquaculture biotechnology that prioritizes sustainability may have a large impact on human health and the seafood industry. Our review underscores the importance of adopting this model, revolutionizing the prognosis and management of Vibrio-related infections, even under complex circumstances. Furthermore, this model has promising implications for aquaculture and public health, addressing the United Nations Sustainable Development Goals and their development agenda.
Collapse
Affiliation(s)
- Anshuman Mishra
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Li M, Liang H, Yang H, Ding Q, Xia R, Chen J, Zhou W, Yang Y, Zhang Z, Yao Y, Ran C, Zhou Z. Deciphering the gut microbiome of grass carp through multi-omics approach. MICROBIOME 2024; 12:2. [PMID: 38167330 PMCID: PMC10763231 DOI: 10.1186/s40168-023-01715-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking. RESULTS We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp. CONCLUSIONS The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.
Collapse
Affiliation(s)
- Ming Li
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Liang
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Yang
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qianwen Ding
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Xia
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Chen
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenhao Zhou
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yalin Yang
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhen Zhang
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Yao
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Ran
- Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhigang Zhou
- China-Norway Joint Lab On Fish Gastrointestinal Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
7
|
Liu S, Lai X, Xie Q, Wang Z, Pan Y, Wang Q, Zhang Z. Holo-omics analysis reveals the influence of gut microbiota on obesity indicators in Jinhua pigs. BMC Microbiol 2023; 23:322. [PMID: 37923989 PMCID: PMC10623862 DOI: 10.1186/s12866-023-03011-8] [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: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The mechanisms behind obesity are complex and multi-faceted, involving the interplay of both host genomics and gut microbiome. In recent years, research has largely focused on these factors separately, but rarely from the viewpoint of holo-omics, which considers the host and microbiome as an integrated entity. To address this gap in knowledge, the present study aimed to investigate the holo-omics basis of obesity in Jinhua pigs, a Chinese indigenous breed known for its high degree of fat deposition and superior meat quality. METHODS Six pigs with extreme obesity phenotype were selected from a larger cohort of eighteen Jinhua pigs, and the contents of the jejunum, cecum, and colon regions were collected after slaughter at 240 days of age. The data obtained was processed, denoised, and annotated using QIIME2, with expression differences being analyzed using edgeR software. RESULTS The results showed significant differences in jejunal microbial diversity and composition between the two groups, with gut transcriptomics also indicating that differentially expressed genes in the jejunum were enriched in lipid metabolism pathways. These findings provide further evidence of the influence of the gut microbiome and host gene expression on fat deposition in Jinhua pigs. CONCLUSIONS This study provides valuable insights into the mechanisms of fat deposition in Jinhua pigs from the viewpoint of holo-omics. The integration of host transcriptomics and microbiome data helps shed light on the complex interactions between the host and gut microbiome, and highlights the importance of considering both factors in our understanding of obesity.
Collapse
Affiliation(s)
- Shuang Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Xueshuang Lai
- School of Agriculture and Biology, Department of Animal Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qinqin Xie
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China.
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China.
| |
Collapse
|
8
|
Venegas L, López P, Derome N, Yáñez JM. Leveraging microbiome information for animal genetic improvement. Trends Genet 2023; 39:721-723. [PMID: 37516623 DOI: 10.1016/j.tig.2023.07.004] [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: 04/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.
Collapse
Affiliation(s)
- Lucas Venegas
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - José M Yáñez
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Millennium Nucleus of Austral Invasive Salmonids, INVASAL, Concepción, Chile.
| |
Collapse
|
9
|
Hou D, Lian T, Guo G, Gong H, Wu C, Han P, Weng S, He J. Integration of microbiome and Koch's postulates to reveal multiple bacterial pathogens of whitish muscle syndrome in mud crab, Scylla paramamosain. MICROBIOME 2023; 11:155. [PMID: 37475003 PMCID: PMC10357871 DOI: 10.1186/s40168-023-01570-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/12/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND For more than a century, the Koch's postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can cause the same disease, the selection of microorganisms that regress infection is hard when Koch's postulates are applied. Microbiome approaches can obtain relatively complete information about disease-related microorganisms and can guide the selection of target microorganisms for regression infection. In the present study, whitish muscle syndrome (WMS) of Scylla paramamosain, which has typical symptoms with whitish muscle and blackened hemolymph was used as an example to establish a new research strategy that integrates microbiome approaches and Koch's postulates to determinate causative agents of multiple pathogens-one disease. RESULTS Microbiome results revealed that Aeromonas, Acinetobacter, Shewanella, Chryseomicrobium, Exiguobacterium, Vibrio and Flavobacterium, and Kurtzmaniella in hemolymph were bacterial and fungal indicators for WMS. A total of 23 bacteria and 14 fungi were isolated from hemolymph and muscle tissues, and among the bacteria, Shewanella chilikensis, S. xiamenensis, Vibrio alginolyticus, S. putrefaciens, V. fluvialis, and V. parahaemolyticus were present in hemolymph and/or muscle tissues in each WMS crab, and the last three species were also present in three Healthy crabs. The target bacteria and fungi were further screened to regression infections based on two criteria: whether they belonged to the indicator genera for WMS, whether they were isolated from both hemolymph and muscle tissues in most WMS crabs. Only S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria. The six bacteria that met both two criteria and six fungi and another bacterium that unmatched any of two criteria were used to perform regression infection experiments based on Koch's postulates. S. chilikensis, S. putrefaciens, S. xiamenensis, V. alginolyticus, V. fluvialis, and V. parahaemolyticus met both two criteria, and the results indicate that they cause WMS in crabs independently. CONCLUSIONS This study fully demonstrated that our research strategy that integrates the microbiome and Koch's postulates can maximize the ability to catch pathogens in one net for the situation of multiple pathogens-one disease. Video Abstract.
Collapse
Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Taixin Lian
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Guangyu Guo
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Han Gong
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chengcheng Wu
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Peiyun Han
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- School of Life Sciences/China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People's Republic of China.
| |
Collapse
|
10
|
Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
Collapse
Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
| |
Collapse
|
11
|
Rasmussen JA, Kiilerich P, Madhun AS, Waagbø R, Lock EJR, Madsen L, Gilbert MTP, Kristiansen K, Limborg MT. Co-diversification of an intestinal Mycoplasma and its salmonid host. THE ISME JOURNAL 2023; 17:682-692. [PMID: 36807409 PMCID: PMC10119124 DOI: 10.1038/s41396-023-01379-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/19/2023]
Abstract
Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.
Collapse
Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Pia Kiilerich
- Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300, Copenhagen, Denmark
| | | | - Rune Waagbø
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
12
|
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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
13
|
Fallet M, Montagnani C, Petton B, Dantan L, de Lorgeril J, Comarmond S, Chaparro C, Toulza E, Boitard S, Escoubas JM, Vergnes A, Le Grand J, Bulla I, Gueguen Y, Vidal-Dupiol J, Grunau C, Mitta G, Cosseau C. Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection. MICROBIOME 2022; 10:85. [PMID: 35659369 PMCID: PMC9167547 DOI: 10.1186/s40168-022-01280-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/14/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation - and, importantly, protection from infectious disease - is still an open question. RESULTS Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS. CONCLUSIONS We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease. tag the videobyte/videoabstract in this section Video Abstract.
Collapse
Affiliation(s)
- Manon Fallet
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Caroline Montagnani
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Bruno Petton
- Ifremer, UBO CNRS IRD, LEMAR UMR 6539, Argenton, France
| | - Luc Dantan
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Julien de Lorgeril
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, ENTROPIE, F-98800, Nouméa, Nouvelle-Calédonie, France
| | - Sébastien Comarmond
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Cristian Chaparro
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Simon Boitard
- CBGP, CIRAD, INRAE, Institut Agro, IRD, Université de Montpellier, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Agnès Vergnes
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | | | - Ingo Bulla
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Yannick Gueguen
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
- MARBEC, CNRS, Ifremer, IRD, Univ Montpellier, Sète, France
| | - Jérémie Vidal-Dupiol
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Christoph Grunau
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Guillaume Mitta
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France.
- Ifremer, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, BP 49, 98725, Tahiti, French Polynesia.
| | - Céline Cosseau
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France.
| |
Collapse
|
14
|
Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
Collapse
Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| |
Collapse
|
15
|
Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
Collapse
Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
16
|
Rasmussen JA, Villumsen KR, Ernst M, Hansen M, Forberg T, Gopalakrishnan S, Gilbert MTP, Bojesen AM, Kristiansen K, Limborg MT. A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). MICROBIOME 2022; 10:21. [PMID: 35094708 PMCID: PMC8802455 DOI: 10.1186/s40168-021-01221-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism. RESULTS Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites. CONCLUSION Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.
Collapse
Affiliation(s)
- Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
- University Museum NTNU, Trondheim, Norway
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Morten Tønsberg Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| |
Collapse
|
17
|
Zhu J, Li H, Jing ZZ, Zheng W, Luo YR, Chen SX, Guo F. Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker. MICROBIOME 2022; 10:18. [PMID: 35081990 PMCID: PMC8790850 DOI: 10.1186/s40168-021-01214-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/12/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Given the lack of genetic background, the source tracking unknown individuals of fish species with both farmed and wild populations often cannot be robustly achieved. The gut microbiome, which is shaped by both deterministic and stochastic processes, can serve as a molecular marker of fish host source tracking, particularly as an alternative to the yet-to-be-established host genetic marker. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea, which is carnivorous and ranks the top mariculture fish in China. Wild resource of this fish was depleted decades ago and might have potential problematic estimation because of escaping of farmed individuals. RESULTS The rectums of wild (n = 212) and farmed (n = 79) croakers from multiple batches were collected for the profiling of their gut bacterial communities. The farmed individuals had a higher alpha diversity and lower bacterial load than the wild individuals. The gut microbiota of the two sources exhibited divergence and high inter-batch variation, as featured by the dominance of Psychrobacter spp. in the wild group. Predicted functional capacity of the gut microbiome and representative isolates showed differences in terms of host source. This difference can be linked to the potential diet divergence between farmed and wild fishes. The non-stochastic distribution pattern of the core gut microbiota of the wild and farmed individuals supports the feasibility of microbiota-based host source tracking via the machine learning algorithm. A random forest classifier based on the divergence and non-stochastic assembly of the gut microbiome was robust in terms of host source tracking the individuals from all batches of croaker, including a newly introduced batch. CONCLUSIONS Our study revealed the divergence of gut microbiota and related functional profiles between wild and farmed croakers. For the first time, with representative datasets and non-stochastic patterns, we have verified that gut microbiota can be robustly applied to the tracking of host source even in carnivorous fish. Video abstract.
Collapse
Affiliation(s)
- Jun Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Hao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ze Zhou Jing
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Wei Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuan Rong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
| | - Shi Xi Chen
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Feng Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| |
Collapse
|
18
|
Rasmussen JA, Villumsen KR, von Gersdorff Jørgensen L, Forberg T, Zuo S, Kania PW, Buchmann K, Kristiansen K, Bojesen AM, Limborg MT. Integrative analyses of probiotics, pathogenic infections, and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 2022; 132:3201-3216. [PMID: 35032344 DOI: 10.1111/jam.15433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022]
Abstract
AIMS Given the pivotal role played by the gut microbiota in regulating the host immune system, interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, the need for a better understanding of the host-microbiota interactions after disease responses to optimise the use of probiotics to strengthen disease resilience and recovery. METHODS AND RESULTS We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric redmouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and on the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses. CONCLUSIONS We discuss the relevance of these results emphasising the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses. SIGNIFICANCE AND IMPACT OF THE STUDY Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota and the resulting host immune response.
Collapse
Affiliation(s)
- Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Denmark
| | | | | | - Shaozhi Zuo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Denmark
| | - Per Walter Kania
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Denmark
| | - Kurt Buchmann
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Metagenomics, BGI- Shenzhen, Shenzhen, China
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Denmark
| | - Morten Tønsberg Limborg
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| |
Collapse
|
19
|
Zhu L, Wang J, Bahrndorff S. Editorial: The Wildlife Gut Microbiome and Its Implication for Conservation Biology. Front Microbiol 2021; 12:697499. [PMID: 34234768 PMCID: PMC8256134 DOI: 10.3389/fmicb.2021.697499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Lifeng Zhu
- Colleges of Life Science, Nanjing Normal University, Nanjing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Simon Bahrndorff
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
20
|
Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, Jørgensen LVG, Præbel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K, Limborg MT. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol 2021; 4:579. [PMID: 33990699 PMCID: PMC8121932 DOI: 10.1038/s42003-021-02105-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
Collapse
Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kasper R Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - David A Duchêne
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara C Puetz
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom O Delmont
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Copenhagen, Denmark
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, China
| | - Morten T Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
21
|
Xu L, Pierroz G, Wipf HML, Gao C, Taylor JW, Lemaux PG, Coleman-Derr D. Holo-omics for deciphering plant-microbiome interactions. MICROBIOME 2021; 9:69. [PMID: 33762001 PMCID: PMC7988928 DOI: 10.1186/s40168-021-01014-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets-referred to here as holo-omics-provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness. Video abstract.
Collapse
Affiliation(s)
- Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Heidi M.-L. Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Cheng Gao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Peggy G. Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA USA
| |
Collapse
|
22
|
Serra CR, Oliva-Teles A, Enes P, Tavares F. Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets. Sci Rep 2021; 11:447. [PMID: 33432059 PMCID: PMC7801451 DOI: 10.1038/s41598-020-80138-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina's MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.
Collapse
Affiliation(s)
- Cláudia R Serra
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Aires Oliva-Teles
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
| | - Paula Enes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, Universidade do Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
| | - Fernando Tavares
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Ed. FC4, 4169-007, Porto, Portugal
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| |
Collapse
|
23
|
Dvergedal H, Sandve SR, Angell IL, Klemetsdal G, Rudi K. Association of gut microbiota with metabolism in juvenile Atlantic salmon. MICROBIOME 2020; 8:160. [PMID: 33198805 PMCID: PMC7670802 DOI: 10.1186/s40168-020-00938-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/13/2020] [Indexed: 05/27/2023]
Abstract
The gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links between gut microbes and fish genetics and production phenotypes are not well understood.In this study, we investigate the associations between gut microbial communities, fish feed conversion, and fish genetics in the domestic Atlantic salmon. Microbial community composition was determined for 230 juvenile fish from 23 full-sib families and was then regressed on growth, carbon and nitrogen metabolism, and feed efficiency. We only found weak associations between host genetics and microbial composition. However, we did identify significant (p < 0.05) associations between the abundance of three microbial operational taxonomical units (OTUs) and fish metabolism phenotypes. Two OTUs were associated with both carbon metabolism in adipose tissue and feed efficiency, while a third OTU was associated with weight gain.In conclusion, this study demonstrates an intriguing association between host lipid metabolism and the gut microbiota composition in Atlantic salmon. Video Abstract.
Collapse
Affiliation(s)
- H Dvergedal
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P. O. Box 5003, NO-1433, Ås, Norway
| | - S R Sandve
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P. O. Box 5003, NO-1433, Ås, Norway.
| | - I L Angell
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, NO-1433, Ås, Norway
| | - G Klemetsdal
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P. O. Box 5003, NO-1433, Ås, Norway
| | - K Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, NO-1433, Ås, Norway
| |
Collapse
|
24
|
Nyholm L, Koziol A, Marcos S, Botnen AB, Aizpurua O, Gopalakrishnan S, Limborg MT, Gilbert MTP, Alberdi A. Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. iScience 2020; 23:101414. [PMID: 32777774 PMCID: PMC7416341 DOI: 10.1016/j.isci.2020.101414] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/18/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.
Collapse
Affiliation(s)
- Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark.
| | - Adam Koziol
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Sofia Marcos
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| |
Collapse
|
25
|
Legrand TPRA, Wynne JW, Weyrich LS, Oxley APA. Investigating Both Mucosal Immunity and Microbiota in Response to Gut Enteritis in Yellowtail Kingfish. Microorganisms 2020; 8:E1267. [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] [Grants] [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.
Collapse
Affiliation(s)
- Thibault P. R. A. Legrand
- Department of Ecology and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia;
- CSIRO, Agriculture and Food, Hobart, TAS 7004, Australia;
- South Australia Research and Development Institute, Aquatic Sciences Centre, West Beach, SA 5024, Australia
| | - James W. Wynne
- CSIRO, Agriculture and Food, Hobart, TAS 7004, Australia;
| | - Laura S. Weyrich
- Department of Ecology and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia;
- Department of Anthropology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA 16801, USA
| | - Andrew P. A. Oxley
- School of Life and Environmental Sciences, Faculty of Sciences Engineering and Built Environment, Deakin University, Waurn Ponds, VIC 3216, Australia
| |
Collapse
|
26
|
Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy DL, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:135906. [PMID: 31926407 DOI: 10.1016/j.scitotenv.2019.135906] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.
Collapse
Affiliation(s)
- Thomas A Edge
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.
| | | | - Nellie Gagné
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Charles Greer
- National Research Council Canada, Montreal, Quebec, Canada
| | - David Konkin
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Glen Newton
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | | | - Lee Beaudette
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Satpal Bilkhu
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Alexander Bush
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wen Chen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jérôme Comte
- Environment and Climate Change Canada, Burlington, Ontario, Canada; Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | | | | | - Erik J S Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Donna-Lee Fancy
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Iyad Kandalaft
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ian King
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - David Kreutzweiser
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John Lawrence
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Lowe
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | | | - Matthew Meier
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nicholas Ogden
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - David Paré
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Lori Phillips
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada; Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada
| | - Joel Sachs
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Zachery Staley
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Royce Steeves
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Teodor Veres
- National Research Council Canada, Ottawa, Ontario, Canada
| | - Cynthia Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Susan Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - James Macklin
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| |
Collapse
|
27
|
Shen Y, Yue G. Current status of research on aquaculture genetics and genomics-information from ISGA 2018. AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Special Issue: Coevolution of Hosts and Their Microbiome. Genes (Basel) 2018; 9:genes9110549. [PMID: 30428546 PMCID: PMC6266481 DOI: 10.3390/genes9110549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
|