Glossary

1

16S rRNA gene — A gene encoding a component of the bacterial and archaeal ribosome. Because it is universal, evolves slowly, and contains both conserved and variable regions, it serves as a molecular barcode for identifying prokaryotic organisms. The basis of 16S rRNA gene sequencing.

16S rRNA gene sequencing — A technique for identifying bacteria and archaea in a sample by extracting DNA, amplifying the 16S rRNA gene using PCR, sequencing the amplified fragments, and comparing them to reference databases. Also called amplicon sequencing. Revolutionised microbiome research from the 2000s onward.

A

Agar plate — A shallow dish containing a gel-like nutrient medium (agar) on which bacteria can be grown as visible colonies. Invented in the laboratory of Robert Koch in the late nineteenth century and still widely used in clinical microbiology.

Alphaproteobacteria — A class of bacteria believed to be the evolutionary ancestors of mitochondria, the energy-producing organelles in eukaryotic cells.

Amplicon sequencing — See 16S rRNA gene sequencing.

Archaea — One of the three domains of cellular life, alongside Bacteria and Eukarya. Archaea are single-celled prokaryotic organisms that resemble bacteria in size and shape but differ fundamentally in their cell membrane chemistry, cell wall composition, and molecular biology. In the human microbiome, the most commonly detected archaeon is the methanogen Methanobrevibacter smithii.

ATP (adenosine triphosphate) — A small molecule that serves as the universal energy currency of living cells. Energy released from nutrients is used to build ATP; the cell then spends ATP to power processes such as muscle contraction, nerve signalling, and DNA replication. Most ATP in eukaryotic cells is produced by mitochondria.

B

Bacillus (pl. bacilli) — A rod-shaped bacterium. Not to be confused with the genus Bacillus, which is a specific group of rod-shaped, spore-forming bacteria.

Bacteria — One of the three domains of cellular life. Bacteria are single-celled prokaryotic organisms characterised by ester-linked membrane lipids and, in most species, cell walls containing peptidoglycan. They are the dominant organisms at most human microbiome sites.

Bacteriophage (phage) — A virus that infects bacteria. Phages are the most abundant biological entities on Earth and in the human body, and they play a critical role in regulating bacterial populations in the microbiome. The term was coined by Félix d'Hérelle in 1917.

Baltimore classification — A system for classifying viruses into seven groups based on their genome type (DNA or RNA, single- or double-stranded) and replication strategy (specifically, how they produce messenger RNA). Proposed by David Baltimore in 1971.

C

Capsid — The protein shell that surrounds and protects the genetic material of a virus.

Capsule (bacterial) — A slimy outer layer of polysaccharides surrounding some bacterial cells. The capsule helps bacteria evade the immune system and adhere to surfaces, including human tissues.

Cell membrane (plasma membrane) — The thin, flexible lipid bilayer that encloses every living cell, separating its interior from the external environment. Studded with proteins that control the transport of molecules in and out of the cell.

Cell theory — The foundational principle that all living organisms are composed of cells, that the cell is the basic unit of life, and that all cells arise from pre-existing cells. Formulated by Schleiden, Schwann, and Virchow in the mid-nineteenth century.

Cell wall — A rigid or semi-rigid structure outside the cell membrane of most prokaryotes, many fungi, and all plants. In bacteria, the cell wall is composed of peptidoglycan. In archaea, it may consist of an S-layer or other materials. In fungi, it is made of chitin.

Chloroplast — An organelle found in plant and algal cells, responsible for photosynthesis. Chloroplasts are descended from ancient cyanobacteria that were engulfed by an early eukaryotic cell (see Endosymbiosis).

Chromosome — A structure composed of DNA (and, in eukaryotes, associated histone proteins) that carries genetic information. Bacterial chromosomes are typically single, circular DNA molecules. Eukaryotic chromosomes are linear and housed within the nucleus.

Coccus (pl. cocci) — A spherical bacterium. Examples include Staphylococcus and Streptococcus.

Colony — A visible clump of genetically identical microbial cells, grown on a solid medium from a single ancestor cell. Colonies are the basis of classical culture-based microbiology.

Conjugation — A process by which one bacterium transfers DNA — typically a plasmid — to another bacterium through direct cell-to-cell contact via a pilus. A major mechanism of horizontal gene transfer and antibiotic resistance spread.

Culturing — The process of growing microorganisms outside their natural environment on nutrient media under controlled laboratory conditions. While essential for clinical diagnostics and detailed characterisation, standard culture methods recover only a fraction of the species present in complex microbial communities.

Culturomics — A high-throughput approach to microbial culture that uses dozens to hundreds of different growth conditions — varying nutrient media, atmosphere, temperature, and incubation time — to recover species that standard methods miss. Colonies are identified using MALDI-TOF mass spectrometry. Pioneered by Didier Raoult and colleagues from 2012.

Cyanobacteria — Photosynthetic bacteria responsible for producing much of the oxygen in Earth's atmosphere. Ancient cyanobacteria gave rise to chloroplasts through endosymbiosis.

Cytoplasm — The gel-like material inside a cell, enclosed by the cell membrane. Contains water, salts, organic molecules, and (in prokaryotes) the cell's DNA and ribosomes. In eukaryotic cells, the cytoplasm refers to the material outside the nucleus but within the cell membrane.

Cytoskeleton — A network of protein filaments within eukaryotic cells that provides structural support, enables cell movement, and serves as tracks for intracellular transport. Includes microfilaments, intermediate filaments, and microtubules.

D

DNA (deoxyribonucleic acid) — The molecule that carries genetic information in all cellular life and many viruses. DNA consists of two complementary strands wound into a double helix. See Primer Chapter 3 for a detailed explanation.

Domain — The highest level of biological classification. Life is divided into three domains: Bacteria, Archaea, and Eukarya.

E

Electron microscopy — A family of imaging techniques that use beams of electrons rather than visible light to achieve much higher magnification and resolution than optical microscopy. Includes transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Essential for visualising viruses and subcellular structures.

Endogenous retrovirus — A retroviral sequence permanently integrated into the genome of its host species, inherited vertically from generation to generation. Human endogenous retroviruses (HERVs) make up roughly 8 per cent of the human genome. Most are no longer functional, but some fragments have been co-opted for host functions (e.g., syncytin in placental development). See also Provirus, Retrovirus.

Endogenous retrovirus (ERV) — A retroviral sequence that has been integrated into the germline genome of a host organism and is inherited by subsequent generations. The human genome contains thousands of human endogenous retroviruses (HERVs), some of which have been co-opted for essential functions. See also: Syncytin.

Endoplasmic reticulum (ER) — An extensive network of folded membranes in eukaryotic cells. The rough ER is studded with ribosomes and synthesises proteins for export or membrane insertion. The smooth ER is involved in lipid synthesis and detoxification.

Endosymbiosis — The evolutionary process by which one organism lives inside another, with both partners eventually becoming mutually dependent. The origin of mitochondria and chloroplasts in eukaryotic cells is explained by endosymbiosis: free-living bacteria were engulfed by an ancestral cell and, over billions of years, became permanent organelles.

Envelope (viral) — An outer lipid bilayer membrane that surrounds the capsid of some viruses, acquired by budding through the host cell's membrane. Envelope proteins (such as the spike protein of SARS-CoV-2) are used by the virus to recognise and bind to host cells. Enveloped viruses are more susceptible to soap, alcohol, and environmental degradation than non-enveloped viruses.

Ester linkage — A type of chemical bond found in the cell membranes of bacteria and eukaryotes, linking fatty acids to glycerol. Contrast with the ether linkages found in archaeal membranes.

Ether linkage — A type of chemical bond found in the cell membranes of archaea, linking branched hydrocarbon chains to glycerol. Ether linkages are more chemically stable than ester linkages, which may contribute to the ability of some archaea to survive extreme conditions.

Eukarya (Eukaryota) — The domain of life encompassing all organisms whose cells contain a true nucleus and membrane-bound organelles. Includes animals, plants, fungi, and protists.

Eukaryotic cell — A cell that possesses a membrane-bound nucleus and internal organelles (e.g., mitochondria, endoplasmic reticulum). All animals, plants, fungi, and protists are composed of eukaryotic cells. Contrast with Prokaryotic cell.

Extremophile — An organism that thrives in extreme environmental conditions, such as very high or very low temperatures, high salinity, high acidity, or high pressure. Many extremophiles are archaea, though extremophilic bacteria and eukaryotes also exist.

F

Flagellum (pl. flagella) — A long, whip-like appendage used by many bacteria (and some eukaryotic cells) for locomotion. Bacterial flagella rotate like propellers; eukaryotic flagella undulate in a wave-like motion.

G

Germ-free (animal) — See Gnotobiotic.

Gnotobiotic — Describes an animal raised in a completely sterile environment, harbouring no microorganisms. From Greek gnotos ("known") and bios ("life"). Gnotobiotic mice are the principal experimental model for testing causal effects of specific microbes or microbial communities on host physiology.

Golgi apparatus — A membrane-bound organelle in eukaryotic cells that sorts, modifies, and packages proteins received from the endoplasmic reticulum into vesicles for transport to their final destinations. Named after the Italian physician Camillo Golgi.

Gram stain — A staining technique developed by Hans Christian Gram in 1884 that differentiates bacteria into two major groups (Gram-positive and Gram-negative) based on differences in cell wall structure. One of the most widely used tools in clinical microbiology.

Gram-negative — Describing bacteria that lose the violet dye in the Gram stain procedure and take up the pink counterstain. Gram-negative bacteria have a thin peptidoglycan layer and an additional outer membrane containing lipopolysaccharides. Examples include Escherichia coli and Pseudomonas aeruginosa.

Gram-positive — Describing bacteria that retain the violet dye in the Gram stain procedure. Gram-positive bacteria have a thick peptidoglycan layer and no outer membrane. Examples include Staphylococcus aureus and Streptococcus pneumoniae.

Great plate count anomaly — The observation, named by Staley and Konopka (1985), that the number of microbial cells visible under a microscope in an environmental sample vastly exceeds the number that can be grown on standard laboratory media — typically by a factor of 100 or more.

H

Helical symmetry — A type of viral capsid architecture in which protein subunits are arranged in a spiral around the genome, producing a rod-like or tube-like structure. The tobacco mosaic virus is a classic example.

HERV (human endogenous retrovirus) — See Endogenous retrovirus.

Histone — A spool-like protein around which eukaryotic DNA is wound. Histones help package the long DNA molecule into compact chromosomes and play a role in regulating gene expression. Generally absent from prokaryotes.

Horizontal gene transfer (HGT) — The transfer of genetic material between organisms by mechanisms other than parent-to-offspring (vertical) inheritance. In bacteria, HGT occurs via conjugation, transformation, and transduction. It is a major driver of antibiotic resistance spread.

I

Icosahedral symmetry — A type of viral capsid architecture with twenty triangular faces, approximating a sphere. This is the most common capsid shape among viruses and provides efficient packaging of the viral genome using a minimal number of protein subunits.

Induction (prophage) — The process by which a dormant prophage is reactivated, excises itself from the host bacterium's chromosome, and enters the lytic cycle, producing new viral particles and destroying the host cell. Induction is often triggered by environmental stress, DNA damage, or exposure to certain chemicals.

Integrase — A viral enzyme, particularly associated with retroviruses, that catalyses the insertion of viral DNA into the host cell's genome. Integrase inhibitors are an important class of antiretroviral drugs used in the treatment of HIV infection.

K

Kill the winner — An ecological model in which the most abundant bacterial species in a community (the "winner") becomes disproportionately targeted by bacteriophages, which multiply rapidly on this abundant host and drive its numbers down. This density-dependent predation helps maintain microbial diversity within ecosystems such as the human gut.

Koch's postulates — A set of criteria, developed by Robert Koch in the 1880s, for establishing that a specific microorganism causes a specific disease. The postulates require isolating the organism from a diseased host, growing it in pure culture, reproducing the disease by introducing the culture into a healthy host, and re-isolating the organism from the new host.

L

Light microscope — A microscope that uses visible light and glass lenses to magnify small objects. Also called an optical microscope. Can achieve magnifications up to about 1,000× and resolve structures down to approximately 0.2 micrometres — sufficient to see bacteria but not viruses or most subcellular details.

Lipid bilayer — The double-layered structure formed by phospholipids in cell membranes, with hydrophobic tails pointing inward and hydrophilic heads facing the aqueous environment on both sides.

Lipopolysaccharide (LPS) — A large molecule found in the outer membrane of Gram-negative bacteria. LPS is a potent activator of the human immune system and, when present in the bloodstream in large quantities, can trigger sepsis.

LUCA (Last Universal Common Ancestor) — The hypothetical single-celled organism from which all current cellular life on Earth is descended. LUCA is not a specific species but a theoretical ancestor of all three domains.

Lysogenic conversion — The acquisition of new phenotypic traits by a bacterium as a result of genes carried by an integrated prophage. Notable examples include the cholera toxin (encoded by the CTXφ prophage in Vibrio cholerae) and Shiga toxin (encoded by a prophage in certain pathogenic E. coli strains).

Lysogenic cycle (lysogeny) — A viral replication strategy in which the virus integrates its genome into the host cell's chromosome (as a prophage or provirus) and is replicated passively along with the host's DNA during cell division, without immediately producing new viral particles or harming the host. Under certain conditions, the integrated virus can reactivate and enter the lytic cycle. Contrast with Lytic cycle.

Lysogeny (lysogenic cycle) — A mode of viral reproduction in which the virus integrates its genetic material into the host cell's genome (becoming a prophage in bacteria) and is replicated passively as the host divides. Under stress, the virus may exit lysogeny and enter the lytic cycle, producing new viral particles and destroying the host cell.

Lysosome — A membrane-bound organelle in eukaryotic cells containing digestive enzymes that break down waste materials, cellular debris, and engulfed pathogens. Sometimes called the cell's recycling centre.

Lytic cycle — A viral replication strategy in which the virus takes over the host cell's machinery, produces large numbers of new viral particles, and then destroys (lyses) the host cell to release them. Contrast with Lysogenic cycle.

M

MALDI-TOF mass spectrometry — Matrix-Assisted Laser Desorption/Ionisation Time-Of-Flight mass spectrometry. A rapid technique for identifying microorganisms by analysing the unique pattern of proteins they contain. Widely used in clinical microbiology and in culturomics for high-throughput species identification.

Mass spectrometry — An analytical technique that measures the mass-to-charge ratio of molecules in a sample. In microbiome research, used in metabolomics to identify and quantify small molecules (metabolites) and in MALDI-TOF for microbial identification.

Metabolite — A small molecule produced or modified by metabolic processes. In the context of the microbiome, metabolites include short-chain fatty acids, bile acid derivatives, amino acid metabolites, and signalling molecules produced by microbial communities.

Metabolomics — The large-scale study of metabolites — small molecules produced by cellular processes — in a biological sample. Uses mass spectrometry or NMR spectroscopy to identify and quantify the chemical outputs of microbial communities.

Metagenome — The collective genetic material of all microorganisms in a particular environment. The human gut metagenome, for example, contains between two and twenty million genes — far more than the approximately 20,000 protein-coding genes in the human genome.

Metagenomics — The sequencing and analysis of all DNA extracted from an environmental or biological sample, without prior culturing. Provides both taxonomic and functional information about microbial communities. Also called shotgun metagenomics.

Metatranscriptomics — The sequencing and analysis of all messenger RNA (mRNA) in a microbial community. Provides a snapshot of gene expression — which genes are actively being used — rather than merely which genes are present.

Methanogen — An organism that produces methane as a metabolic by-product. In the human gut, the most common methanogen is the archaeon Methanobrevibacter smithii, which consumes hydrogen and carbon dioxide produced by bacterial fermentation.

Microbiome — The entire habitat of microorganisms associated with a particular environment, including the organisms themselves, their collective genetic material, their metabolic products, and the environmental conditions they create and respond to. Often used interchangeably with microbiota in popular writing.

Microbiota — The community of living microorganisms (bacteria, archaea, fungi, protists, and viruses) inhabiting a particular environment, such as the human gut.

Mitochondrion (pl. mitochondria) — A membrane-bound organelle found in most eukaryotic cells, responsible for generating the majority of the cell's energy through aerobic respiration. Mitochondria are descended from ancient alphaproteobacteria that were engulfed by an ancestral cell (see Endosymbiosis) and retain their own small genome.

Monolayer (membrane) — A single-sheet membrane structure found in some archaea, in which lipid molecules span the entire width of the membrane rather than forming two separate layers. Extremely stable and resistant to harsh environmental conditions.

Multi-omics — An integrative approach that combines two or more omics techniques (e.g., metagenomics, metabolomics, metatranscriptomics, proteomics) to build a more comprehensive picture of microbial community composition and function.

N

Negative-sense RNA — A type of single-stranded viral RNA genome that cannot be directly translated by ribosomes. It must first be copied into a complementary positive-sense RNA strand by a viral RNA-dependent RNA polymerase. Influenza virus is a negative-sense RNA virus. Contrast with Positive-sense RNA.

NMR spectroscopy — Nuclear Magnetic Resonance spectroscopy. An analytical technique used in metabolomics to identify molecules based on how their atomic nuclei behave in a magnetic field.

Nuclear pore — A channel in the double membrane of the eukaryotic nucleus that regulates the transport of molecules between the nucleus and the cytoplasm.

Nucleoid — The region within a prokaryotic cell where the DNA is concentrated. Unlike a eukaryotic nucleus, the nucleoid is not surrounded by a membrane.

Nucleolus — A dense region within the eukaryotic nucleus where ribosomal RNA is synthesised and ribosomal subunits begin to be assembled.

Nucleus — A membrane-bound organelle in eukaryotic cells that contains the cell's DNA. The presence of a nucleus is the defining feature of eukaryotic cells.

O

Obelisk — A recently discovered class of viroid-like circular RNA elements found in the human gut microbiome. Obelisks encode a single protein and do not fit into any previously known category of biological entity. First described by Zheludev et al. in 2024.

Obligate anaerobe — An organism that can survive and grow only in the absence of oxygen and is actively killed by exposure to it. Many dominant gut bacteria, including members of the genera Faecalibacterium and Roseburia, are obligate anaerobes.

Oblin — A novel protein superfamily encoded by obelisks, with no detectable similarity to any previously known protein family. The function of Oblins remains unknown.

Organelle — A specialised, membrane-bound structure within a eukaryotic cell that performs a specific function. Examples include the nucleus, mitochondria, and chloroplasts.

P

Peptidoglycan — A polymer of sugars and amino acids that forms a mesh-like layer in bacterial cell walls, giving the cell structural rigidity. Absent from archaeal cell walls. The target of several classes of antibiotics, including penicillins and cephalosporins.

Phage therapy — The use of bacteriophages to treat bacterial infections. First explored in the early twentieth century, phage therapy fell out of favour in the West with the advent of antibiotics but is now experiencing renewed interest as antibiotic resistance grows. Phage therapy offers the advantage of high specificity, targeting pathogenic bacteria while leaving the beneficial microbiome intact.

Phageome — The complete community of bacteriophages associated with a particular environment, such as the human gut. The gut phageome is highly individual and relatively stable over time within a person.

Phospholipid — A lipid molecule with a hydrophilic (water-attracting) head and two hydrophobic (water-repelling) fatty acid tails. Phospholipids are the primary structural component of cell membranes.

Pilus (pl. pili) — A short, hair-like projection on the surface of many bacteria, used for attachment to surfaces or for transferring DNA during conjugation.

Polymerase chain reaction (PCR) — A laboratory technique that makes millions of copies of a specific segment of DNA from a small starting amount. Uses heat-stable DNA polymerase enzymes, synthetic primers, and repeated cycles of heating and cooling. Essential for 16S rRNA gene sequencing and many other molecular biology applications.

Positive-sense RNA — A type of single-stranded viral RNA genome that can be directly translated by the host cell's ribosomes, functioning as messenger RNA immediately upon entry into the cell. SARS-CoV-2 is a positive-sense RNA virus. Contrast with Negative-sense RNA.

Primer (molecular biology) — A short, synthetic strand of DNA (typically 15–30 nucleotides) designed to bind to a specific target sequence, providing a starting point for DNA replication during PCR. Not to be confused with the primer chapters of this book.

Prion — An infectious agent consisting of a misfolded form of a normal cellular protein (PrP). Prions can induce correctly folded copies of the same protein to adopt the abnormal shape, causing a chain reaction that leads to progressive, fatal brain diseases such as Creutzfeldt-Jakob disease (CJD) in humans.

Prokaryotic cell — A cell that lacks a membrane-bound nucleus and other internal membrane-bound organelles. Bacteria and archaea are prokaryotes. Contrast with Eukaryotic cell.

Prophage — The DNA of a bacteriophage that has been integrated into a bacterial host's genome during the lysogenic cycle. The prophage is replicated along with the host's DNA during cell division and can reactivate under certain conditions.

Protist — An informal term for any eukaryotic organism that is not an animal, plant, or fungus. Protists are a diverse and largely unrelated collection of organisms, mostly single-celled, that include amoebae, algae, and parasites such as Plasmodium (malaria) and Blastocystis.

Provirus — The DNA form of a retroviral genome after it has been reverse-transcribed and integrated into the host cell's chromosomal DNA. The provirus is replicated along with the host's DNA during cell division and can remain latent for extended periods. In bacteria, the equivalent term is prophage.

R

Resistome — The complete collection of antibiotic resistance genes present in a microbial community. Identified through metagenomic sequencing.

Retrovirus — A family of viruses that carry their genome as single-stranded RNA and use the enzyme reverse transcriptase to convert it into DNA, which is then integrated into the host cell's genome as a provirus. HIV (human immunodeficiency virus) is the most well-known retrovirus. Retroviruses are unique in their ability to permanently alter the host's genetic material.

Reverse transcriptase — An enzyme, characteristic of retroviruses, that synthesises DNA from an RNA template — the reverse of the normal flow of genetic information (DNA → RNA). The discovery of reverse transcriptase by David Baltimore and by Howard Temin and Satoshi Mizutani in 1970 overturned the assumption that information could only flow from DNA to RNA. Reverse transcriptase inhibitors are a major class of antiretroviral drugs.

Ribosomal RNA (rRNA) — A structural component of ribosomes, the cellular machinery that translates genetic instructions into proteins. The gene encoding 16S rRNA (in prokaryotes) or 18S rRNA (in eukaryotes) is highly conserved across all life and is widely used for identifying and classifying microorganisms. Carl Woese's comparison of 16S rRNA sequences led to the discovery of the three domains of life.

Ribosome (70S / 80S) — The molecular machine that reads messenger RNA and assembles proteins. Prokaryotic ribosomes are designated 70S; eukaryotic cytoplasmic ribosomes are 80S. The "S" refers to the Svedberg unit, a measure of sedimentation rate. Several antibiotics target the 70S ribosome specifically.

S

S-layer (surface layer) — A crystalline protein lattice that forms the outermost cell wall layer in many archaea and some bacteria. In archaea, the S-layer often serves as the primary cell wall, replacing the peptidoglycan found in bacteria.

Scanning electron microscopy (SEM) — An electron microscopy technique that bounces electrons off the surface of a specimen to produce three-dimensional images. Used to visualise the surface morphology of cells and microorganisms.

Selective toxicity — The principle that an antimicrobial drug should harm the pathogen while leaving the host unharmed. Achieved by targeting structures or pathways present in the pathogen but absent from host cells (e.g., peptidoglycan in bacteria, which human cells lack).

Spirillum (pl. spirilla) — A spiral-shaped bacterium.

Syncytin — A protein essential for the formation of the human placenta, derived from the envelope gene of an ancient endogenous retrovirus. Syncytin mediates the fusion of cells in the outer layer of the placenta, enabling nutrient exchange between mother and foetus.

T

Torque teno virus (TTV) — A small, non-enveloped, single-stranded DNA virus found in more than 90 per cent of the human population. TTV causes no known disease and is considered part of the normal human virome. Its prevalence makes it a subject of interest in studies of viral commensalism and immune modulation.

Transmission electron microscopy (TEM) — An electron microscopy technique that fires electrons through an ultra-thin specimen slice, achieving nanometre-scale resolution. Used to visualise internal cellular structures, viruses, and molecular complexes.

V

Vesicle — A small, membrane-bound sac within a cell, used for transporting materials between organelles or between the cell and its environment.

Vibrio — A comma-shaped or curved-rod bacterium. The genus Vibrio includes the species Vibrio cholerae, which causes cholera.

Virion — A complete, mature viral particle outside of a host cell. A virion consists of the viral genome (DNA or RNA) enclosed in a protein capsid, and in some cases an outer lipid envelope.

Viroid — A small, circular RNA molecule that can infect plant cells and cause disease. Viroids are the smallest known infectious agents and consist of naked RNA with no protein coat.

Virome — The total community of viruses associated with a particular organism or environment, including bacteriophages, eukaryotic viruses, endogenous viral elements, and dietary or environmental viral sequences. The human virome is increasingly recognised as an important component of the microbiome that interacts with bacterial communities and the immune system.

Virus — A non-cellular biological entity consisting of genetic material (DNA or RNA) enclosed in a protein coat (capsid). Viruses cannot reproduce independently and must hijack the machinery of a host cell. They infect organisms across all three domains of life.