TABLE 1.

Non-exhaustive list of prominent keystone taxa of the human gut microbiome.

Keystone species (in alphabetical order)	Function	Method of identification	Example of reported disease association in humans
Akkermansia muciniphila	Mucin degrader	Empirical (Belzer et al., 2017)	Intestinal inflammation, obesity and metabolic diseases (Yassour et al., 2016)
Bacteroides thetaiotaomicron	Degradation of complex carbohydrates (arabinogalactan); selective BSH activity (Yao et al., 2018)	Empirical (Cartmell et al., 2018)	Unclear – Controversial association with IBD (Sitkin and Pokrotnieks, 2019)
Bifidobacterium longum	Degradation of complex carbohydrates, particularly Human Milk Oligosaccharides; BSH activity (Tanaka et al., 2000)	Empirical (Yu et al., 2013; Gotoh et al., 2019)	Highly prevalent in healthy newborns (Favier et al., 2003)
Bifidobacterium pseudolongum	Degradation of complex carbohydrates	Empirical (Centanni et al., 2018)	Highly prevalent human breast milk (Lugli et al., 2020)
Christensenella minuta	Stimulate ecosystem diversity (Mazier et al., 2021); acetate producer (Morotomi et al., 2012); BSH activity (Déjean et al., 2021)	Co-occurrence networks (Goodrich et al., 2014; Kumpitsch et al., 2020 ahead of publication) Empirical (Ruaud et al., 2020; Mazier et al., 2021)	Obesity and metabolic diseases (Goodrich et al., 2014); Crohn’s disease (Pascal et al., 2017)
Faecalibacterium prausnitzii	Butyrate producer	Presence/absence (Leylabadlo et al., 2020)	Crohn’s disease (Sokol et al., 2008), Ulcerative Colitis (Varela et al., 2013)
Methanobrevibacter smithii	Produces methane from H2 and acetate	Empirical and co-occurrence networks (Goodrich et al., 2014; Kumpitsch et al., 2020 ahead of publication)	Obesity (Goodrich et al., 2014), Crohn’s disease (Pascal et al., 2017)
Ruminococcus bromii	Resistant starch degrader; Butyrate producer	Empirical (Ze et al., 2012)	Highly prevalent microbe in healthy individuals (Beghini et al., 2021)