Periodic Reporting for period 1 - 3D-omics (Three-dimensional holo’omic landscapes to unveil host-microbiota interactions shaping animal production)
Okres sprawozdawczy: 2021-09-01 do 2023-02-28
The world's population continues to grow - but the Earth's surface does not. This urges us to ensure that the associated need for increased food production is performed in a sustainable fashion, because optimising food production is not only of commercial interest for companies, but also of critical importance for humanity and biodiversity. In this regard, understanding the interplay between animals and microorganisms associated with them has been recognised as an essential step by the European Commission for improving and optimising animal health, welfare, and production worldwide.
To understand the truly relevant biomolecular interactions that impact production processes, researchers are implementing novel strategies based on the analysis of animal genomes, the metagenomes of the associated microorganisms, and the different omic layers interconnecting them — the so-called holo’omic framework.
However, these approaches do not yet capture spatial properties of feeds, microorganisms, and host epithelial tissue, which are known to differ across intestinal sections, time points, and individuals. Neither conventional multi-omics nor histology provide information on how gene expression and biomolecule production of such cells is triggered by proximity of specific bacterial cells and metabolites, and vice versa. Current methods provide us information analogous to what would be learned from studying the functioning of the Amazon rainforest through mixing all living organisms in the jungle in a big pot and quantifying their relative abundances without acknowledging, for instance, which bird nests or which mycorrhizal fungi are associated with which tree.
Now, we are finally capable of breaking these barriers and boosting animal-microbiota research with a groundbreaking technological advancement. In recent years, there has been a rapid development of techniques that, separately, have enabled the generation of multiple omics data, including both microbial and host components, processing very small amounts of biological material, generating 3D reconstructions of biological elements, and analysing complex microbial communities. Hence, the technology required for 3D multi-omics are finally in place and we will use it to develop, implement, and assess a new methodological framework that will revolutionise animal-microbiota research in animal science and beyond. Ultimately, we foresee that our new framework will open new research avenues to improve the generation of animal breeds with enhanced microbiota-related genetic features, probiotics, microbiota - and host-tailored feeds, animal health treatments, and management practices that will enable increasing production efficiency while decreasing environmental impact and improving animal welfare.
To understand the truly relevant biomolecular interactions that impact production processes, researchers are implementing novel strategies based on the analysis of animal genomes, the metagenomes of the associated microorganisms, and the different omic layers interconnecting them — the so-called holo’omic framework.
However, these approaches do not yet capture spatial properties of feeds, microorganisms, and host epithelial tissue, which are known to differ across intestinal sections, time points, and individuals. Neither conventional multi-omics nor histology provide information on how gene expression and biomolecule production of such cells is triggered by proximity of specific bacterial cells and metabolites, and vice versa. Current methods provide us information analogous to what would be learned from studying the functioning of the Amazon rainforest through mixing all living organisms in the jungle in a big pot and quantifying their relative abundances without acknowledging, for instance, which bird nests or which mycorrhizal fungi are associated with which tree.
Now, we are finally capable of breaking these barriers and boosting animal-microbiota research with a groundbreaking technological advancement. In recent years, there has been a rapid development of techniques that, separately, have enabled the generation of multiple omics data, including both microbial and host components, processing very small amounts of biological material, generating 3D reconstructions of biological elements, and analysing complex microbial communities. Hence, the technology required for 3D multi-omics are finally in place and we will use it to develop, implement, and assess a new methodological framework that will revolutionise animal-microbiota research in animal science and beyond. Ultimately, we foresee that our new framework will open new research avenues to improve the generation of animal breeds with enhanced microbiota-related genetic features, probiotics, microbiota - and host-tailored feeds, animal health treatments, and management practices that will enable increasing production efficiency while decreasing environmental impact and improving animal welfare.
During the first 18 months of the project, we have advanced considerably in our way to achieve the operational objectives of 3D'omics.
The first operational objective is to develop the 3D’omics technology to reconstruct 3D multi-omic intestinal landscapes from micro-scale genomic, transcriptomic, metabolomic and imaging data. In the first reporting period, we created sample embedding, slicing, and microdissection protocols for generating micro-scale multi-omic data. We also developed protocols for laser microdissection and micro-sample collection from cryo-slices. We further created synthetic microbial communities to test the resolution and accuracy of the micro-scale genome-reconstruction techniques, and we began testing and optimising several alternative protocols for generating micro-scale genome and transcriptome data. We established four liquid chromatography - mass spectrometry methods for producing non-targeted metabolomics data and twelve tandem mass spectrometry methods for producing fragmentation data for metabolite identification. We also designed probes and began experimenting with multiple fluorescence in situ hybridisation (FISH) techniques that will be compared with 3D’omics reconstructions, as well as gathering detailed information about morphological and physiological characteristics of the animal gut and the associated microbial communities and began performing mathematical simulations of the intestine structure.
Towards achieving the second objective, which is to showcase the 3D’omics technology in two monogastric animal systems: poultry and swine; we conducted 3 proof-of-principle animal trials to obtain samples for technology development and to produce preliminary data to improve the design of the main trials. From samples collected in these trials, we generated and preliminarily analysed host multi-omic data. Regarding the sub-objective to unveil micro-scale pathogen-microbiota-bird interactions using 3D’omics technology to improve animal health in poultry, we developed standardised field sampling, sample storage, sample preservation, and metadata collection procedures for generating 3D’omic data from in vivo and in vitro experiments.
In terms of establishing strong collaborations and knowledge transfer activities with related microbiome initiatives, 3D'omics participated in the first Applied Hologenomics Conference and the consortium joined the joint dissemination network coordinated by its sister project HoloRuminant. The communications manager joined the Sustainable Food Systems Network (SFSN) and became a Microbiome Ambassador, following the initiative of MicrobiomeSupport, as well as leading multiple outreach initiatives.
The first operational objective is to develop the 3D’omics technology to reconstruct 3D multi-omic intestinal landscapes from micro-scale genomic, transcriptomic, metabolomic and imaging data. In the first reporting period, we created sample embedding, slicing, and microdissection protocols for generating micro-scale multi-omic data. We also developed protocols for laser microdissection and micro-sample collection from cryo-slices. We further created synthetic microbial communities to test the resolution and accuracy of the micro-scale genome-reconstruction techniques, and we began testing and optimising several alternative protocols for generating micro-scale genome and transcriptome data. We established four liquid chromatography - mass spectrometry methods for producing non-targeted metabolomics data and twelve tandem mass spectrometry methods for producing fragmentation data for metabolite identification. We also designed probes and began experimenting with multiple fluorescence in situ hybridisation (FISH) techniques that will be compared with 3D’omics reconstructions, as well as gathering detailed information about morphological and physiological characteristics of the animal gut and the associated microbial communities and began performing mathematical simulations of the intestine structure.
Towards achieving the second objective, which is to showcase the 3D’omics technology in two monogastric animal systems: poultry and swine; we conducted 3 proof-of-principle animal trials to obtain samples for technology development and to produce preliminary data to improve the design of the main trials. From samples collected in these trials, we generated and preliminarily analysed host multi-omic data. Regarding the sub-objective to unveil micro-scale pathogen-microbiota-bird interactions using 3D’omics technology to improve animal health in poultry, we developed standardised field sampling, sample storage, sample preservation, and metadata collection procedures for generating 3D’omic data from in vivo and in vitro experiments.
In terms of establishing strong collaborations and knowledge transfer activities with related microbiome initiatives, 3D'omics participated in the first Applied Hologenomics Conference and the consortium joined the joint dissemination network coordinated by its sister project HoloRuminant. The communications manager joined the Sustainable Food Systems Network (SFSN) and became a Microbiome Ambassador, following the initiative of MicrobiomeSupport, as well as leading multiple outreach initiatives.
3D’omics is still immersed in the first part of the project focused on developing and optimising molecular biology techniques to reconstruct microbial landscapes in animal intestines. All preliminary experiments that produced samples for technology optimisation were concluded successfully, and the methodologies for collecting and preserving samples for generating micro-scale multi-omic data have been established. The consortium is now pushing the limits of nucleic acid sequencing and mass spectrometry methods to identify detectability limits and assess the robustness of the methods under scrutiny. Once the technology is ready, we will use it to unveil animal-microbe and microbe-microbe interactions in bird and swine intestines, aiming at addressing different challenges. In the case of poultry, we will focus on pathogen challenges and will identify interactions and mechanistic causal processes between pathogens, microorganisms, animal cells and phenotypes, and how these vary within and between breeds, sexes, management practices, diet and environmental conditions. The swine system will focus on nutrition, through analysing protein deposition and fibre degradation. We will perform trials with pigs with distinct genetic backgrounds at multiple developmental stages, which will enable us to identify the way functional animal-microbiota interactions change responding to feeding and management practices. The gained knowledge will allow us to include data on microbial ecosystems in the models used to analyse phenotypic variability and to perform genetic evaluations, contributing to the efforts to improve resource use and environmental impact of terrestrial livestock production.