Hologenomics is the

omics The branches of science known informally as omics are various disciplines in biology whose names end in the suffix '' -omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collect ...

study of

hologenome The hologenome theory of evolution recasts the individual animal or plant (and other multicellular organisms) as a community or a "holobiont" – the host plus all of its symbiotic microbes. Consequently, the collective genomes of the holobiont for ...

s. A hologenome is the whole set of

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

s of a

holobiont A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit through symbiosis, though there is controversy over this discreteness. The components of a holobiont are in ...

, an organism together with all co-habitating

microbes A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

, other life forms, and

viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

. While the term hologenome originated from the

hologenome theory of evolution The hologenome theory of evolution recasts the individual animal or plant (and other multicellular organisms) as a community or a "holobiont" – the host plus all of its symbiotic microbes. Consequently, the collective genomes of the holobiont for ...

, which postulates that

natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charle ...

occurs on the holobiont level,Number 6 in a series of 7 VHS recordings, ''A Decade of PCR: Celebrating 10 Years of Amplification'', Cold Spring Harbor Laboratory Press, 1994. . hologenomics uses an integrative framework to investigate interactions between the

host A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places * Host, Pennsylvania, a village in Berks County People *Jim Host (born 1937), American businessman * Michel Host ...

and its associated

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

. Examples include

gut microbe Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut mic ...

or viral genomes linked to human or animal genomes for host-microbe interaction research. Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges.

History

The origins of hologenomics revolves around the hologenome theory of evolution, which describes individual

multicellular organisms A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni- ...

, microbes, and viruses establishing

symbiotic relationships Symbiosis (from Ancient Greek, Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different Organism, biological organisms, be it Mutualism (biolog ...

and undergoing

coevolution In biology, coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection. The term sometimes is used for two traits in the same species affecting each other's evolution, as well ...

together.

Richard Jefferson Richard Allen Jefferson Jr. (born June 21, 1980) is an American former professional basketball player who is a sports analyst on ESPN. He played college basketball with the Arizona Wildcats. Jefferson was drafted in the first round of the 200 ...

introduced the term 'hologenome' to describe the host-symbiont genome as an evolutionary unit.Number 6 in a series of 7 VHS recordings, ''A Decade of PCR: Celebrating 10 Years of Amplification'', Cold Spring Harbor Laboratory Press, 1994. . Prior to this,

Lynn Margulis Lynn Margulis (born Lynn Petra Alexander; March 5, 1938 – November 22, 2011) was an American evolutionary biologist, and was the primary modern proponent for the significance of symbiosis in evolution. Historian Jan Sapp has said that "Lynn Ma ...

used the term 'holobiont' to describe hosts and their associated species as an ecological unit.

Eukaryotes-prokaryotes coevolution

Earliest evidence of multicellular-unicellular interactions are seen in sponges, which are a well studied hologenomic system.

Porifera Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through th ...

are often described as holobionts because they harbor a wide range of

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

and

algae Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular mic ...

. Microbial communities present have been observed in facilitating

metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...

functions and

immune In biology, immunity is the capability of multicellular organisms to resist harmful microorganisms. Immunity involves both specific and nonspecific components. The nonspecific components act as barriers or eliminators of a wide range of pathogens ...

responses. Offspring inherit these microbial colonies via

vertical Vertical is a geometric term of location which may refer to: * Vertical direction, the direction aligned with the direction of the force of gravity, up or down * Vertical (angles), a pair of angles opposite each other, formed by two intersecting s ...

and/or

horizontal transmission Horizontal transmission is the transmission of organisms between biotic and/or abiotic members of an ecosystem that are not in a parent-progeny relationship. This concept has been generalized to include transmissions of infectious agents, symbiont ...

. Symbiont

colonies In modern parlance, a colony is a territory subject to a form of foreign rule. Though dominated by the foreign colonizers, colonies remain separate from the administration of the original country of the colonizers, the '' metropolitan state'' ...

are transferred through parental

gametes A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce t ...

in vertical transmission, whereas

offspring In biology, offspring are the young creation of living organisms, produced either by a single organism or, in the case of sexual reproduction, two organisms. Collective offspring may be known as a brood or progeny in a more general way. This ca ...

acquire same colonies from their environment in horizontal transmission. Vertical transmission is also seen in

terrestrial Terrestrial refers to things related to land or the planet Earth. Terrestrial may also refer to: * Terrestrial animal, an animal that lives on land opposed to living in water, or sometimes an animal that lives on or near the ground, as opposed to ...

organisms like '' C. ocellatus'', where

gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp ...

in the parental gut is vertically transferred through egg contamination.

Criticism

The hologenome theory evolution is not fully accepted, and research in microbial-host phylogenetics is ongoing. Rather than the selection of corals with certain symbiotic microbial communities,

coral bleaching Coral bleaching is the process when corals become white due to various stressors, such as changes in temperature, light, or nutrients. Bleaching occurs when coral polyps expel the zooxanthellae (dinoflagellates that are commonly referred to as alg ...

may simply be a result of environmental stressors, and bacterial presence in bleached coral may be explained simply as opportunistic

colonization Colonization, or colonisation, constitutes large-scale population movements wherein migrants maintain strong links with their, or their ancestors', former country – by such links, gain advantage over other inhabitants of the territory. When ...

. Ubiquity testing also revealed many different

bacterial Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

and

algal Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular mic ...

symbionts that are not associated with a single species of coral, suggesting that hologenomics just identifies and validates mechanistic interactions between

pathogens In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...

, microbes, and their hosts.

Examples of discoveries with hologenomic approaches

Nanopore sequencing Nanopore sequencing is a third generation approach used in the sequencing of biopolymers — specifically, polynucleotides in the form of DNA or RNA. Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the ne ...

- Profiling organelle genomes in the holobiont '' C. ashmeadii'' revealed that ''

Rhodospirillaceae The Rhodospirillaceae are a family of Pseudomonadota. The majority are purple nonsulfur bacteria, producing energy through photosynthesis; originally all purple nonsulfur bacteria were included here.George M. Garrity, Don J. Brenner, Noel R. ...

'' was dominant among six putative

endosymbionts An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...

. *

16S rRNA 16S rRNA may refer to: * 16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The g ...

sequencing - Sponge-specific microbial communities were profiled with rRNA and rRNA gene sequencing, providing insight into bacterial diversity and activity of those communities. * Metagenomic DNA - Gene profiles of sponge

microbiome A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably well ...

s were compared to surrounding planktonic communities. Core function genes of microbial symbionts expressed consistent patterns of phylogeny and function that differ from planktonic samples, demonstrating host-symbiont co-evolution.

Applications

Medicine

It's hypothesized the continued incidence

non-infectious diseases A non-communicable disease (NCD) is a disease that is not transmissible directly from one person to another. NCDs include Parkinson's disease, autoimmune diseases, strokes, most heart diseases, most cancers, diabetes, chronic kidney disease, oste ...

is a result of

modernization Modernization theory is used to explain the process of modernization within societies. The "classical" theories of modernization of the 1950s and 1960s drew on sociological analyses of Karl Marx, Emile Durkheim and a partial reading of Max Weber, ...

reducing the diversity of symbiotic microbes. The human microbiome has also been correlated to numerous

etiologies Cause, also known as etiology () and aetiology, is the reason or origination of something. The word ''etiology'' is derived from the Greek , ''aitiologia'', "giving a reason for" (, ''aitia'', "cause"; and , ''-logia''). Description In medicine, ...

non-communicable disease A non-communicable disease (NCD) is a disease that is not transmissible directly from one person to another. NCDs include Parkinson's disease, autoimmune diseases, strokes, most heart diseases, most cancers, diabetes, chronic kidney disease, os ...

, such as brain disorders, cancer, and heart disease. Interactions between human microbiome and human health are complex and suggest a hologenomic approach. Disease

biomarkers In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, p ...

can be found by investigating lifestyle, genomic differences, and

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

profiles of the patient and their microbiota. For investigating microbiomes and specifically microbiota subcommunities that may contribute to a disease

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...

longitudinal studies A longitudinal study (or longitudinal survey, or panel study) is a research design that involves repeated observations of the same variables (e.g., people) over short or long periods of time (i.e., uses longitudinal data). It is often a type of obs ...

are recommended as everyone has a personalized microbiome with small differences in microbiome phylotypes. A personalized plan managing a person’s microbiome can then be developed, with

prebiotics Prebiotics are compounds in food that induce the growth or activity of beneficial microorganisms such as bacteria and fungi. The most common example is in the gastrointestinal tract, where prebiotics can alter the composition of organisms in the ...

nurturing beneficial endogenous microbes, and

probiotics Probiotics are live microorganisms promoted with claims that they provide health benefits when consumed, generally by improving or restoring the gut microbiota. Probiotics are considered generally safe to consume, but may cause bacteria-host i ...

manipulating a person’s hologenome.

Immunology

Conditional mutualism, where

parasites Parasitism is a Symbiosis, close relationship between species, where one organism, the parasite, lives on or inside another organism, the Host (biology), host, causing it some harm, and is Adaptation, adapted structurally to this way of lif ...

have mutualistic effects under certain environmental/ecological conditions, have been found with holobiont-holobiont interactions. Maturation of mammalian host immune systems has been known to involve

gastrointestinal The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the digestive system that leads from the mouth to the anus. The GI tract contains all the major organs of the digestive system, in humans and ...

flora Flora is all the plant life present in a particular region or time, generally the naturally occurring (indigenous) native plants. Sometimes bacteria and fungi are also referred to as flora, as in the terms '' gut flora'' or '' skin flora''. E ...

. Understanding microorganism recognition of foreign pathogenic invasion and how host immunity favors the most ideal symbiont may aid in discovering novel therapeutic treatments to combat evolving diseases.

References

Genomics {{Genetics-stub