What is a microbiome? Microbiome is a term that can be used to describe a dynamic and interactive community of microbes that share a common environment in certain niches of an organism or on surfaces, in liquids or faeces. The microbiome can also be used to describe the microbiological community in other types of materials such as water or soil. The microbiome in animals and humans, consists mainly of living prokaryotes and eukaryotes, microorganisms such as bacteria, parasites, protists, fungi and algae. The part of the microbiome in which the living microorganisms are included is called the microbiota, which is only part of a microbiome. There are other non-living particles that also share these environments, such as chemical compounds such as signaling molecules, toxins and metabolites, as well as structural elements related to the theater of activity of microorganisms, which include other non-living entities such as viruses, bacteriophages, but also nucleic acids, proteins, lipids, polysaccharides in addition to the environmental conditions involved. All this is part of the formal definition of a microbiome (Berg et al. 2020).
Researchers have now begun to use a more "holistic approach", so that all eukaryotic organisms should be seen as a 'meta-organism' to recognize that the microbiome of this organism, including all its microbes, are also an integral part of the same individual. In some cases, one actually refers to the microbiota as a separate organ, and shows the importance of this also being an essential part of an organism, both for better and for worse. An understanding of the interaction between microorganisms and host organisms and how the balance between different organisms can be changed by internal or external influences is important in order to be able to understand the health status of an animal or human.
Microorganisms that are part of the microbiota of an organism live together in one of three ways. They can be commensal, where one enjoys living together but for the other it does not matter that the organism is there or not. If they are symbionts, both organisms will have benefits from living together. Pathogens, on the other hand, are microbiological organisms that create imbalance, or dysbiosis, in this microbiological community or that directly harm the host organism, and give rise to disease and health problems. Here, for example, bacteria that contain genes that encode toxins can be an example for this. Some species may have several roles depending on the genes they carry, such as E. coli, a common bacterium in the gut, which is mainly a symbiont, and lives in balance with the host, but sometimes it can appear in variants that carry toxin genes, such as EHEC (enterohaemorrhagic E. coli) which can cause disease in humans and animals. A balanced microbiome can be healthy for an organism and prevent pathogens from establishing themselves, and can thus prevent disease. Therefore, it is important to have both good knowledge about which harmful microorganisms can cause disease, but also about which other bacteria help to maintain a good balance and give us and our animals good health.
Microbioms can be characterized with various scientific tools, and can be described either via studies of metagenomes (DNA / RNA), metatranscriptomes (RNA), metaprotomes (proteins) or metabolomes (metabolites), or a combination of these, together with associated clinical or other relevant metadata. In our project we have focused on the most common approach to characterize the microbiota by producing a metagenome, a dataset where the microbiota can be characterized by studying all genetic material in a sample using sequencing technology. The sequencing methodology used will digitalize all genetic material in a sample, but will not distinguish between genetic material from the microbiota or other material that may be found there. In a stool sample, this may be genetic material from the host, or remnants of genetic material from food. Using advanced data analysis, the sequencing data will provide researchers with information about which microorganisms were present in the sample, and provide genetic information about the microbiota, but also provide information about other characteristics of these organisms encoded by the genes they carry with them, such as for example, the presence of genes encoding antibiotic resistance. A microbial community in animals can be shared between other animals and animal groups, and an individual's microbiome will play together with other microbial communities they may be exposed to in the environment in which they live. This also applies in the microbial community in humans and animals. This provides the basis for the One Health concept. A parallel study of microbiomes in animals and animal owners, on such a large scale, where it is also possible to obtain data that can link this to the health status of animals and owners, makes HUNT One Health unique in a global context.
The collection of sample material (including faecal samples) from animal owners who participated in HUNT4 and animals (HUNT One Health), was completed in the spring of 2019. After the sample collection, the project has actively worked on selecting suitable protocols and methods for processing the samples, to give the best possible picture of the microbiome in these samples, and to facilitate the data generated for further use.
Source: Berg G, Rybakova D, Fischer F, Cernava T, Vergès M-CC, Charles T, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8:103. https://doi.org/10.1186/s40168-020-00875-0