Microbiota and molecular diagnostics glossary

The ACMG criteria are the standards published in 2015 by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology for classifying genetic variants into five tiers, from pathogenic to benign.

Akkermansia muciniphila is a strictly anaerobic bacterium of the human gut that uses mucin from the intestinal mucus layer as its energy source. It is studied for possible links with gut barrier function and metabolic health.

Alpha diversity measures the variety of microorganisms within a single sample (how many types and how evenly spread); beta diversity measures how different two or more samples are from each other.

Antimicrobial resistance (AMR) is the ability of bacteria, viruses, fungi or parasites to stop responding to medicines that used to control them, making infections harder to treat.

Bacteraemia is the presence of viable bacteria in the bloodstream, usually confirmed by blood cultures. It can be transient and harmless or part of a serious infection, and it is not the same as sepsis, which is defined by the body's response to infection.

Bacterial vaginosis is a shift in the vaginal microbiota in which lactobacilli decline and anaerobic bacteria such as Gardnerella overgrow. It can cause discharge and odour, but is often symptom-free.

A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, disease processes or responses to a therapeutic intervention. It may be a molecule, a genetic variant or an imaging finding.

A blood culture incubates a blood sample in bottles of nutrient broth to find out whether live bacteria or fungi are circulating in the bloodstream. If anything grows, it is identified and tested against antibiotics to guide treatment.

A breath test is a non-invasive investigation that measures gases in exhaled air, mainly hydrogen and methane, after a sugar is swallowed, to assess carbohydrate malabsorption or small intestinal bacterial overgrowth.

Butyrate is a four-carbon short-chain fatty acid produced by certain colonic bacteria when they ferment fibre. It is the main energy source for colonocytes and contributes to the function of the intestinal barrier.

Candidiasis is an infection caused by Candida yeasts, most often Candida albicans. It commonly affects the vulva and vagina or the mouth, and occurs when the yeast overgrows beyond normal colonisation.

Clinical metagenomics (mNGS) is the untargeted sequencing of the genetic material in a patient sample to detect bacteria, viruses, fungi or parasites without choosing the pathogen in advance. It complements culture and susceptibility testing rather than replacing them.

ClinVar is a free public database run by the NCBI at the US National Institutes of Health that collects interpretations submitted by laboratories and experts on how human genetic variants relate to disease.

Dietary fibre is the group of plant carbohydrates, plus lignin, that the human small intestine cannot digest or absorb. It reaches the colon, where it adds bulk to stools and is partly fermented by the gut microbiota.

Dysbiosis is a change in the composition or function of the microbiota away from what is considered compatible with health: loss of diversity, loss of beneficial microbes or overgrowth of others.

Eubiosis is the state in which the microbiota is stable, diverse and compatible with the host's health. It is the opposite of dysbiosis, although neither term has an agreed operational definition.

Faecal calprotectin is a neutrophil protein measured in stool as a marker of inflammation of the intestinal lining. It helps distinguish inflammatory bowel disease from functional disorders such as irritable bowel syndrome.

The term covers two distinct conditions: fructose malabsorption, a common digestive problem, and hereditary fructose intolerance (HFI), a rare genetic metabolic disease caused by deficiency of the enzyme aldolase B.

Gardnerella vaginalis is a facultatively anaerobic vaginal bacterium associated with bacterial vaginosis. It is also found in women without symptoms, so its presence alone is not enough for a diagnosis.

A genetic variant is any difference in a person's DNA sequence compared with a reference sequence. Most have no effect on health; some are associated with disease or alter risk.

The gut-brain axis is the two-way communication network between the digestive tract and the central nervous system, operating through the vagus nerve, the immune system, hormones and microbial metabolites.

Intestinal permeability is how easily substances in the gut lumen cross the intestinal lining into the bloodstream. It is a normal, regulated property; increased permeability is associated with several diseases.

Lactobacillus is a genus of Gram-positive, lactic acid-producing bacteria. Species such as L. crispatus, L. gasseri, L. iners and L. jensenii commonly dominate the vaginal microbiota of women of reproductive age.

A liquid biopsy is the analysis of tumour-derived material, mainly circulating tumour DNA (ctDNA), in a body fluid such as blood. It allows genetic changes in a cancer to be studied without a tissue biopsy.

Low-grade inflammation is a mild, persistent, systemic inflammatory activation with no acute infection or injury to explain it. It is detected through modest rises in markers such as high-sensitivity CRP.

Metabolomics is the large-scale study of metabolites — the small molecules produced by the activity of cells and microorganisms — in a biological sample such as blood, urine or stool. It reflects what is happening in a system at a given moment.

The microbiome is the microbial community of a habitat together with its "theatre of activity": its genes, metabolites and surrounding environmental conditions. It is broader than the microbiota.

The microbiota is the community of living microorganisms (bacteria, archaea, fungi, protozoa) that inhabits a specific site of the body, such as the gut, mouth, skin or vagina.

Nanopore sequencing is a third-generation technique that reads single DNA or RNA molecules as they pass through a nanometre-scale pore, by measuring changes in electrical current. It produces long reads and data in real time.

NGS (next-generation sequencing) is a family of technologies that read millions of DNA or RNA fragments in parallel in a single run, making it possible to study whole genomes, targeted genes or entire microbial communities at scale.

OTUs (operational taxonomic units) group similar DNA sequences, usually at 97% identity; ASVs (amplicon sequence variants) are exact sequences that can be told apart by a single nucleotide.

PCR (polymerase chain reaction) is a technique that copies a chosen stretch of DNA millions of times so it can be detected. qPCR, or real-time PCR, tracks amplification cycle by cycle, allowing the target to be quantified.

Periodontitis is a chronic inflammatory disease of the tissues that support the teeth, associated with a dysbiotic bacterial biofilm. It causes loss of attachment and bone and, if uncontrolled, can lead to tooth loss.

A postbiotic is a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host, as defined by the 2021 ISAPP consensus. Purified microbial metabolites alone do not qualify.

A prebiotic is a substrate that is selectively utilised by host microorganisms and confers a health benefit, according to the 2017 consensus definition of the International Scientific Association for Probiotics and Prebiotics (ISAPP).

A probiotic is a live microorganism that, when administered in adequate amounts, confers a health benefit on the host. This is the FAO/WHO definition, retained by the ISAPP consensus panel in 2014.

Relative abundance is the share of a microorganism in the total detected in a sample, usually given as a percentage. It reflects its weight within the community, not its absolute quantity.

Sepsis is life-threatening organ dysfunction caused by a dysregulated host response to infection (Sepsis-3 definition, 2016). It is a medical emergency that needs immediate treatment.

A sexually transmitted infection (STI) is an infection caused by bacteria, viruses or parasites that spreads mainly through vaginal, anal or oral sex. Many cause no symptoms, so testing is often the only way to find them.

The Shannon index is an alpha diversity measure that combines how many types of microorganism are present in a sample and how evenly they are distributed: the higher the value, the more diverse the community.

Short-chain fatty acids (SCFAs) are fatty acids with one to six carbon atoms produced by colonic bacteria when they ferment fibre and other non-digestible carbohydrates. The main ones are acetate, propionate and butyrate.

Shotgun metagenomics sequences all the DNA in a sample in an untargeted way, without amplifying a single marker gene. It can identify bacteria, DNA viruses, fungi and parasites, often to species level, and reveal their functional and resistance genes.

SIBO (small intestinal bacterial overgrowth) is the presence of excessive numbers of bacteria in the small intestine, accompanied by digestive symptoms such as bloating, wind, abdominal pain or diarrhoea.

A synbiotic is a mixture of live microorganisms and substrates selectively utilised by host microorganisms that confers a health benefit on the host, according to the 2020 ISAPP consensus.

A urine culture grows a urine sample on culture media to see whether bacteria or fungi are present, count them in colony-forming units per millilitre (CFU/mL) and identify them. If a pathogen grows, antibiotic susceptibility testing follows.

The vaginal microbiota is the community of microorganisms living in the vagina. In many women of reproductive age it is dominated by Lactobacillus species, which produce lactic acid and help keep vaginal pH low.

Zonulin is a human protein, identified as prehaptoglobin-2, that reversibly regulates tight junctions in the intestinal lining. It has been proposed as a marker of intestinal permeability.

16S rRNA gene sequencing amplifies and reads a marker gene found in all bacteria and archaea to show which groups are present in a sample and in what proportions. It is inexpensive but usually resolves to genus level and does not measure function directly.