exposed to environmental and animal-specific factors that may cause natural variations. some events may change the relationship into a functioning but altered symbiotic state, whereas extreme stress events may cause dysbiosis or a breakdown of the relationship and interactions. main article: marine microbiome all animals on earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. in the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. however, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. the potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment. the microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges and ctenophores to more complex organisms such as sea squirts and sharks. the relationship between the hawaiian bobtail squid and the bioluminescent bacterium aliivibrio fischeri is one of the best studied symbiotic relationships in the sea and is a choice system for general symbiosis research. this relationship has provided insight into fundamental processes in animal-microbial symbioses, and especially biochemical interactions and signaling between the host and bacterium. the gutless marine oligochaete worm olavius algarvensis is another relatively well-studied marine host to microbes. these three centimetre long worms reside within shallow marine sediments of the mediterranean sea. the worms do not contain a mouth or a digestive or excretory system, but are instead nourished with the help of a suite of extracellular bacterial endosymbionts that reside upon coordinated use of sulfur present in the environment. this system has benefited from some of the most sophisticated 'omics and visualization tools. for example, multi-labeled probing has improved visualization of the microbiome and transcriptomics and proteomics have been applied to examine host–microbiome interactions, including energy transfer between the host and microbes and recognition of the consortia by the worm's innate immune system. the major strength of this system is that it does offer the ability to study host–microbiome interactions with a low diversity microbial consortium, and it also offers a number of host and microbial genomic resources stylophora pistillata coral colony and the bacteria endozoicomonas (ez) probed cells (yellow) within the tentacles of s. pistillata residing in aggregates (ez agg) as well as just outside the aggregate (b). corals are one of the more common examples of an animal host whose symbiosis with microalgae can turn to dysbiosis, and is visibly detected as bleaching. coral microbiomes have been examined in a variety of studies, which demonstrate how variations in the ocean environment, most notably temperature, light, and inorganic nutrients, affect the abundance and performance of the microalgal symbionts, as well as calcification and physiology of the host. studies have also suggested that resident bacteria, archaea, and fungi additionally contribute to nutrient and organic matter cycling within the coral, with viruses also possibly playing a role in structuring the composition of these members, thus providing one of the first glimpses at a multi-domain marine animal symbiosis. the gammaproteobacterium endozoicomonas is emerging as a central member of the coral's microbiome, with flexibility in its lifestyle. given the recent mass bleaching occurring on reefs, corals will likely continue to be a useful and popular system for symbiosis and dysbiosis research. sponges are common members of the ocean's diverse benthic habitats and their abundance and ability to filter large volumes of seawater have led to the awareness that these organisms play critical roles in influencing benthic and pelagic processes in the ocean. they are one of the oldest lineages of animals, and have a relatively simple body plan that commonly associates with bacteria, archaea, algal protists, fungi, and viruses. sponge microbiomes are composed of specialists and generalists, and complexity of their microbiome appears to be shaped by host phylogeny. studies have shown that the sponge microbiome contributes to nitrogen cycling in the oceans, especially through the oxidation of ammonia by archaea and bacteria. most recently, microbial symbionts of tropical sponges were shown to produce and store polyphosphate granules, perhaps enabling the host to survive periods of phosphate depletion in oligotrophic marine environments. the microbiomes of some sponge species do appear to change in community structure in response to changing environmental conditions, including temperature and ocean acidification, as well as synergistic impacts. collecting a sample of blow from a blue whale using a helicopter drone relative abundance of bacterial classes from whale blow, air and seawater samples. cetacean microbiomes can be difficult to assess because of difficulties accessing microbial samples. for example, many whale species are rare and are deep divers. there are different techniques for sampling a cetacean's gut microbiome. the most common is collecting fecal samples from the environment and taking a probe from the center that is non-contaminated. the skin is a barrier protecting marine mammals from the outside world. the epidermal microbiome on the skin is an indicator of how healthy the animal is, and is also an ecological indicator of the state of the surrounding environment. knowing what the microbiome of the skin of marine mammals looks like under typical conditions allows understanding of how these communities different from free microbial communities found in the sea. cetaceans are in danger because they are affected by multiple stress factors which make them more vulnerable to various diseases. they have been high susceptibility to airway infections, but little is known about their respiratory microbiome. sampling the exhaled breath or "blow" of cetaceans can provide an assessment of their state of health. blow is composed of a mixture of microorganisms and organic material, including lipids, proteins , and cellular debris derived from the linings of the airways which, when released into the relatively cooler outdoor air, condense to form a visible mass of vapor, which can be collected. there are various methods for collecting exhaled breath samples, one of the most recent is through the use of aerial drones. this method provides a safer, quieter, and less invasive alternative and often a cost-effective option for monitoring fauna and flora. blow samples are taken to the laboratory where the respiratory tract microbiota are amplified and sequenced. the use of aerial drones has been more successful with large cetaceans due to slow swim speeds and larger blow sizes. plant microbiomes in the plant ecosystem main article: plant microbiome the plant microbiome plays roles in plant health and food production and has received significant attention in recent years. plants live in association with diverse microbial consortia. these microbes, referred to as the plant's microbiota, live both inside (the endosphere) and outside (the episphere) of plant tissues, and play important roles in the ecology and physiology of plants. "the core plant microbiome is thought to comprise keystone microbial taxa that are important for plant fitness and established through evolutionary mechanisms of selection and enrichment of microbial taxa containing essential functions genes for the fitness of the plant holobiont." plant microbiomes are shaped by both factors related to the plant itself, such as genotype, organ, species and health status, as well as factors related to the plant's environment, such as management, land use and climate. the health status of a plant has been reported in some studies to be reflected by or linked to its microbiome. plant and plant-associated microbiota colonise different niches on and inside the plant tissue. all the above-ground plant parts together, called the phyllosphere, are a continuously evolving habitat due to ultraviolet (uv) radiation and altering climatic conditions. it is primarily composed of leaves. below-ground plant parts, mainly roots, are generally influenced by soil properties. harmful interactions affect the plant growth through pathogenic activities of some microbiota members. on the other hand, beneficial microbial interactions promote plant growth. animal principal coordinate analysis of animal gut microbiome data the mammalian gut microbiome has emerged as a key regulator of host physiology, and coevolution between host and microbial lineages has played a key role in the adaptation of mammals to their diverse lifestyles. diet, especially herbivory, is an important correlate of microbial diversity in mammals. most mammalian microbiomes are also strongly correlated with host phylogeny, despite profound shifts in diet. this suggests host factors that themselves change across host phylogeny, such as gut physiology, play an important role in structuring the gut microbiomes across mammals. the vertebrate adaptive immune system is even speculated to have evolved as just such a factor for selective maintenance of symbiotic homeostasis. the importance of phylogeny-correlated factors to the diversity of vertebrate microbiomes more generally is still poorly understood. phylosymbiosis, or the observation that more closely related host species have more similar microbiomes, has been described in a number of nonmammalian taxa. other analyses have found substantial variation in phylosymbiotic signals among mammalian taxa, sometimes with conflicting results. the presence of a robust phylosymbiotic correlation implies that host factors control microbial assembly. even if the specific mechanisms are unknown, variation in the strength or presence of a measurable phylosymbiotic signal across host phylogeny could prove useful for identifying such mechanisms through comparative studies. however, as of 2020 most studies have focused on just a few taxa at a time, and variable methods for both surveying the microbiome and measuring phylosymbiosis and host specificity (or the restriction of microbes to specific host lineages) have made generalisations difficult. without broader evolutionary context, it is unclear how universally conserved patterns of host-microbe phylosymbiosis actually are. growing evidence indicates that the strong patterns identified in mammals are the exception rather than the rule in vertebrates. meta-analyses of fish and birds have failed to detect the strength of correlations to diet and phylogeny reported in mammals. a recent analysis of samples from more than 100 vertebrate species also found the strength of phylogenetic correlation to be much higher in mammals than in birds, reptiles, amphibians, or fish. it is increasingly appreciated in nonvertebrate animals that fundamental aspects of the host’s relationship to its symbiotic community can change drastically between taxa: many insects depend entirely on microbes for key metabolites, while others seem to be devoid of resident gut microbes. human main article: human microbiome the human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. types of human microbiota include bacteria, archaea, fungi, protists and viruses. though micro-animals can also live on the human body, they are typically excluded from this definition. in the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; the term human metagenome has the same meaning. humans are colonised by many microorganisms, with approximately the same order of magnitude of non-human cells as human cells. some microorganisms that colonize humans are commensal, meaning they co-exist without harming or benefiting humans; others have a mutualistic relationship with their human hosts.: 700 conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce, like trimethylamine, which the human body converts to trimethylamine n-oxide via fmo3-mediated oxidation. certain microorganisms perform tasks that are known to be useful to the human host, but the role of most of them is not well understood. those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota. the human microbiome project (hmp) took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina. it reached a milestone in 2012 when it published its initial results. assessment currently available methods for studying microbiomes, so-called multi-omics, range from high throughput isolation (culturomics) and visualization (microscopy), to targeting the taxonomic composition (metabarcoding), or addressing the metabolic potential (metabarcoding of functional genes, metagenomics) to analyze microbial activity (metatranscriptomics, metaproteomics, metabolomics). based on metagenome data, microbial genomes can be reconstructed. while first metagenome-assembled genomes were reconstructed from environmental samples, in recent years, several thousands of bacterial genomes were binned without culturing the organisms behind. for example, 154,723 microbial genomes of