Karen Pendergrass, Standards Team

Lactobacillus iners is the most prevalent Lactobacillus species of the vaginal microbiome and a genuine transitional species: it has probiotic traits but offers less protection than Lactobacillus crispatus and is frequently abundant during bacterial vaginosis. It behaves as both a vaginal symbiont and an opportunist depending on the environment.

Coprobacter is an under-characterized genus of anaerobic Bacteroidota found in the human gut, comprising Coprobacter fastidiosus and Coprobacter secundus. It is a proteolytic and carbohydrate-fermenting resident whose health role is still being defined; one species has been associated with sarcopenia.

Bacteroides eggerthii is a common fiber-degrading Bacteroides of the human gut. Like its relatives it breaks down complex carbohydrates, but its role is context-dependent: in a mouse model of colitis it enhanced rather than protected against inflammation, so its meaning depends on the gut environment.

Alistipes is a relatively new genus of Bacteroidota gut bacteria with genuinely mixed implications for health. Depending on the species and context, its members are associated with protection against colitis, liver fibrosis, and cardiovascular disease, or with colorectal cancer and depression, making it a nuanced, context-dependent taxon.

Parasutterella is a core, near-universal member of the human and mouse gut microbiota. It is asaccharolytic, produces succinate, and appears to contribute to bile acid maintenance and cholesterol metabolism, filling a distinct metabolic niche rather than acting as a clear beneficial or harmful microbe.

BACKGROUND: Graves' disease (GD), characterized by immune aberration, is associated with gut dysbiosis.

Collinsella is a genus of anaerobic Actinomycetota commensals of the human gut, led by Collinsella aerofaciens. It is context-dependent rather than clearly beneficial or harmful: its abundance responds strongly to diet and it is often enriched in obesity, metabolic syndrome, and some inflammatory conditions.

Streptococcus salivarius is a pioneer commensal of the human mouth and upper digestive tract and a well-known probiotic. Friendly strains such as K12 produce bacteriocins that suppress oral and throat pathogens, and in a randomized trial K12 reduced severe radiotherapy-induced oral mucositis while enriching healthy oral commensals.

Using the curatedMetagenomicData Biocondutor package (>=3.2.1): we calculated taxa prevalence of healthy child control samples for each body site and at species/genus levels.

Bacteroides thetaiotaomicron is a keystone fiber-degrading symbiont of the human gut and the model organism for polysaccharide utilization. Its many carbohydrate-processing gene clusters break down complex dietary fibers into short-chain fatty acids that feed the host and cross-feeding microbes, and it helps shape a stable, healthy gut community.

Akkermansia muciniphila is a mucin-degrading symbiont of the intestinal mucus layer and a leading next-generation probiotic. It strengthens the gut barrier, feeds other beneficial microbes, and is consistently more abundant in lean, metabolically healthy people, with lower levels tied to obesity, type 2 diabetes, and inflammation.

Blautia wexlerae is a beneficial anaerobic gut commensal that is inversely correlated with obesity and type 2 diabetes. Its distinctive amino-acid and carbohydrate metabolism produces anti-inflammatory metabolites, and oral administration reduced diet-induced obesity and diabetes in mice, marking it as a promising next-generation probiotic.

Anaerobutyricum hallii, formerly Eubacterium hallii, is a beneficial gut commensal and a metabolic hub that converts leftover acetate and lactate into butyrate, also forms propionate, and produces vitamin B12. It improves insulin sensitivity in preclinical models and is a leading next-generation probiotic candidate.

Roseburia intestinalis is a flagellated, butyrate-producing gut commensal widely treated as a marker of intestinal health. Its butyrate fuels the colon lining, tempers inflammation, and supports motility, and its depletion is associated with inflammatory bowel disease, type 2 diabetes, and other conditions.

Methanobrevibacter smithii is the dominant methanogenic archaeon of the human gut. It consumes the hydrogen that bacteria produce during fermentation and converts it to methane, which improves fermentation efficiency but is also linked to obesity and to methane-associated constipation. Its methane-making machinery is fundamentally nickel-dependent, running on the nickel cofactor coenzyme F430.

Citrobacter is a genus of enteric Enterobacteriaceae that live as gut commensals and act as emerging, often multidrug-resistant, opportunistic pathogens in hospitals, most commonly causing urinary tract and bloodstream infections. As an enteric coliform it shares the family's nickel-dependent enzyme systems, a target of the nickel-restriction strategies this database tracks.

Klebsiella is a genus of encapsulated Enterobacteriaceae, led by Klebsiella pneumoniae, that colonize the gut and act as opportunistic pathogens in the lungs, urinary tract, and bloodstream. The genus depends on metal acquisition: iron piracy by siderophores and a nickel-dependent urease that nickel chelation can block.

Klebsiella pneumoniae is an encapsulated Enterobacteriaceae that colonizes the gut and turns opportunistic pathogen outside it, causing pneumonia, urinary tract infections, bloodstream infections, and liver abscesses. It is an ESKAPE pathogen with two converging threats, carbapenem resistance and hypervirulence, and it depends on metal acquisition: iron piracy by siderophores for invasion, and a nickel-dependent urease that nickel chelation can block.

Helicobacter is a genus of spiral, motile Gram-negative bacteria led by the gastric pathogen Helicobacter pylori, alongside enterohepatic species linked to gut and hepatobiliary disease. Several members depend on the metal nickel for the urease and hydrogenase enzymes that power host colonization.

Helicobacter pylori is a spiral gastric pathogen that infects about half the world and is the leading cause of gastric cancer. It is built around the metal nickel: its urease and [NiFe] hydrogenase are nickel enzymes essential for surviving stomach acid, which makes nickel handling both its strength and a drug target.

Salmonella enterica is the species behind essentially all human Salmonella disease, spanning typhoid fever and non-typhoidal gastroenteritis. It invades host cells with type III secretion systems and thrives in the inflamed gut by defeating the host's metal-withholding defenses, a nutritional-immunity battle that is also its weak point.

Salmonella is a genus of foodborne Gram-negative pathogens, led by the species Salmonella enterica. It invades host cells with type III secretion systems and thrives in the inflamed gut by defeating the host's metal-withholding defenses, a nutritional-immunity battle that is also its weak point.

Christensenellaceae is a family of beneficial gut bacteria most strongly and reproducibly linked to leanness and metabolic health. It is the most heritable taxon in the human gut, and on this database its signal usually marks a healthier, leaner community.

Faecalibacterium prausnitzii is one of the most abundant beneficial bacteria in the healthy gut and a major butyrate producer. It is anti-inflammatory and depleted in conditions such as Crohn's disease, so on this database its signal is usually one of protective loss, and the lever to support it is dietary fiber.