complexity and describe the term microbiome as encompassing the genomes of microorganisms only. microbiome definitions definition type examples ecological definitions based on ecology describe the microbiome following the concepts derived from the ecology of multicellular organisms. the main issue here is that the theories from the macro-ecology do not always fit the rules in the microbial world. "a convenient ecological framework in which to examine biocontrol systems is that of the microbiome. this may be defined as a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. the term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". "this term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. this definition is based on that of “biome,” the biotic and abiotic factors of given environments. others in the field limit the definition of microbiome to the collection of genes and genomes of members of a microbiota. it is argued that this is the definition of metagenome, which combined with the environment constitutes the microbiome. the microbiome is characterized by the application of one or combinations of metagenomics, metabonomics, metatranscriptomics, and metaproteomics combined with clinical or environmental metadata". "others use the term microbiome to mean all the microbes of a community, and in particular, for the plant microbiome, those microbial communities associated with the plant which can live, thrive, and interact with different tissues such as roots, shoots, leaves, flowers, and seeds". "ecological community of commensal, symbiotic and pathogenic microorganisms within a body space or other environment". organisms/host-dependent the host-dependent definitions are based on the microbial interactions with the host. the main gaps here concern the question whether the microbial-host interaction data gained from one host can be transferred to another. the understanding of coevolution and selection in the host-dependent definitions is also underrepresented. "a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body". "human microbiome project (hmp): the human microbiome is the collection of all the microorganisms living in association with the human body. these communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses". genomic/ method-driven there is a variety of microbiome definitions available that are driven by the methods applied. mostly, these definitions rely on dna sequence-based analysis and describe microbiome as a collective genome of microorganisms in a specific environment. the main bottleneck here is that every new available technology will result in a need for a new definition. "the collective genomes of microorganisms inhabiting a particular environment and especially the human body". "the microbiome comprises all of the genetic material within a microbiota (the entire collection of microorganisms in a specific niche, such as the human gut). this can also be referred to as the metagenome of the microbiota". "microbiome is a term that describes the genome of all the microorganisms, symbiotic and pathogenic, living in and on all vertebrates. the gut microbiome consists of the collective genome of microbes inhabiting the gut including bacteria, archaea, viruses, and fungi". "different approaches to define the population provide different information. a | microbiota: 16s rrna surveys are used to taxonomically identify the microorganisms in the environment. b | metagenome: the genes and genomes of the microbiota, including plasmids, highlighting the genetic potential of the population. c | microbiome: the genes and genomes of the microbiota, as well as the products of the microbiota and the host environment". "totality of genomes of a microbiota. often used to describe the entity of microbial traits (=functions) encoded by a microbiota." combined there are some microbiome definitions available that fit several categories with their advantages and disadvantages. "a microbiome is the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space." "the microbiome is the sum of the microbes and their genomic elements in a particular environment". "the genes and genomes of the microbiota, as well as the products of the microbiota and the host environment". in 2020, a panel of international experts, organised by the eu-funded microbiomesupport project, published the results of their deliberations on the definition of the microbiome. the panel was composed of about 40 leaders from diverse microbiome areas, and about one hundred further experts from around the world contributed through an online survey. they proposed a definition of the microbiome based on a revival of what they characterised as the "compact, clear, and comprehensive description of the term" as originally provided by whipps et al. in 1988, amended with a set of recommendations considering subsequent technological developments and research findings. they clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. the term microbiome encompasses both the microbiota (community of microorganisms) and their "theatre of activity" (structural elements, metabolites/signal molecules, and the surrounding environmental conditions. the panel extended the whipps et al. definition, which contains all important points that are valid even 30 years after its publication in 1988, by two explanatory paragraphs differentiating the terms microbiome and microbiota and pronouncing its dynamic character, as follows: the microbiome is defined as a characteristic microbial community occupying a reasonable well-defined habitat which has distinct physio-chemical properties. the microbiome not only refers to the microorganisms involved but also encompass their theatre of activity, which results in the formation of specific ecological niches. the microbiome, which forms a dynamic and interactive micro-ecosystem prone to change in time and scale, is integrated in macro-ecosystems including eukaryotic hosts, and here crucial for their functioning and health. the microbiota consists of the assembly of microorganisms belonging to different kingdoms (prokaryotes (bacteria, archaea), eukaryotes (algae, protozoa, fungi etc), while "their theatre of activity" includes microbial structures, metabolites, mobile genetic elements (such as transposons, phages, and viruses), and relic dna embedded in the environmental conditions of the habitat. membership microbiota main article: microbiota the microbiota comprises all living members forming the microbiome. most microbiome researchers agree bacteria, archaea, fungi, algae, and small protists should be considered as members of the microbiome. the integration of phages, viruses, plasmids, and mobile genetic elements is a more controversial issue in the definition of the microbiome. there is also no clear consensus as to whether extracellular dna derived from dead cells, so-called "relic dna", belongs to the microbiome. relic dna can be up to 40% of the sequenced dna in soil, and was up to 33% of the total bacterial dna on average in a broader analysis of habitats with the highest proportion of 80% in some samples. despite its omnipresence and abundance, relic dna had a minimal effect on estimates of taxonomic and phylogenetic diversity. when it comes to the use of specific terms, a clear differentiation between microbiome and microbiota helps to avoid the controversy concerning the members of a microbiome. microbiota is usually defined as the assemblage of living microorganisms present in a defined environment. as phages, viruses, plasmids, prions, viroids, and free dna are usually not considered as living microorganisms, they do not belong to the microbiota. the term microbiome, as it was originally postulated by whipps and coworkers, includes not only the community of the microorganisms but also their "theatre of activity". the latter involves the whole spectrum of molecules produced by the microorganisms, including their structural elements (nucleic acids, proteins, lipids, polysaccharides), metabolites (signalling molecules, toxins, organic, and inorganic molecules), and molecules produced by coexisting hosts and structured by the surrounding environmental conditions. therefore, all mobile genetic elements, such as phages, viruses, and "relic" and extracellular dna, should be included in the term microbiome, but are not a part of microbiota. the term microbiome is also sometimes confused with the metagenome. metagenome is, however, clearly defined as a collection of genomes and genes from the members of a microbiota. microbiome studies sometimes focus on the behaviour of a specific group of microbiota, generally in relation to or justified by a clear hypothesis. more and more terms like bacteriome, archaeome, mycobiome, or virome have started appearing in the scientific literature, but these terms do not refer to biomes (a regional ecosystem with a distinct assemblage of (micro) organisms, and physical environment often reflecting a certain climate and soil) as the microbiome itself. consequently, it would be better to use the original terms (bacterial, archaeal, or fungal community). in contrast to the microbiota, which can be studied separately, the microbiome is always composed by all members, which interact with each other, live in the same habitat, and form their ecological niche together. the well-established term virome is derived from virus and genome and is used to describe viral shotgun metagenomes consisting of a collection of nucleic acids associated with a particular ecosystem or holobiont. viral metagenomes can be suggested as a semantically and scientifically better term. networks co-occurrence networks help visualising microbial interactionsnodes usually represent taxa of microorganisms, and edges represent statistically significant associations between nodes.–––––––––––––––––––––––––––testing of the hypotheses resulted from the network analyses is required for a comprehensive study of microbial interactions. microbes interact with one another, and these symbiotic interactions have diverse consequences for microbial fitness, population dynamics, and functional capacities within the microbiome. the microbial interactions can either be between microorganisms of the same species or between different species, genera, families, and domains of life. the interactions can be separated into positive, negative, and neutral types. positive interactions include mutualism, synergism, and commensalism. negative interactions include amensalism, predation, parasitism, antagonism, and competition. neutral interactions are interactions where there is no observed effect on the functional capacities or fitness of interacting species microbial life strategy concepts. co-occurrence networks show difference in gut microbiota between herbivorous and carnivorous cichlidsnodes coloured according to phylum. the herbivore network has higher complexity (156 nodes and 339 edges) compared to the carnivore network (21 nodes and 70 edges). microbiomes exhibit different adaptive strategies. oligotrophs are organisms that can live in an environment offering very low levels of nutrients, particularly carbon. they are characterised by slow growth, low rates of metabolism, and generally low population density. oligotrophic environments include deep oceanic sediments, caves, glacial and polar ice, deep subsurface soil, aquifers, ocean waters, and leached soils. in contrast are the copiotrophs, which thrive in much higher carbon concentrations, and do well in high organic substrate conditions such as sewage lagoons. in addition to oligotrophic and copiotrophic strategists, the competitor–stress tolerator–ruderals framework can influence the outcomes of interactions. for example, microorganisms competing for the same source can also benefit from each other when competing for the same compound at different trophic levels. stability of a complex microbial ecosystem depends on trophic interactions for the same substrate at different concentration levels. as of 2020 microbial social adaptations in nature have been understudied. here molecular markers can provide insight into social adaptations by supporting the theories, e.g., of altruists and cheaters in native microbiomes. coevolution shift in the understanding of the microbial-host coevolution from "separation" theories to a holistic approach in a holistic approach, the hosts and their associated microbiota are assumed to have coevolved with each other according to the "separation" approach, the microorganisms can be divided into pathogens, neutral, and symbionts, depending on their interaction with their host. the coevolution between host and its associated microbiota may be accordingly described as antagonistic (based on negative interactions) or mutualistic (based on positive interactions). as of 2020, the emergence in publications about opportunistic pathogens and pathobionts has produced a shift towards a holistic approach in the coevolutions theory. the holistic approach sees the host and its associated microbiota as one unit (the so-called holobiont), that coevolves as one entity. according to the holistic approach, holobiont's disease state is linked to dysbiosis, low diversity of the associated microbiota, and their variability: a so-called pathobiome state. the healthy state, on the other hand, is accompanied with eubiosis, high diversity, and uniformity of the respective microbiota. types marine marine animal host-microbiome relationship relationships are generally thought to exist in a symbiotic state, and are normally