Table 1.

Taxa dominating the bacterial microbiota of the GI-tract ⁽¹⁾.

Phyla/Division	Class	Family	Genus	Gram (2)
Actinobacteria	Actinobacteria	Micrococcaceae	Rothia *	+
Actinobacteria	Actinobacteria	Bifidobacteriaceae	Bifidobacterium	+
Firmicutes	Bacilli	Streptoccaceae	Streptococcus	+
Firmicutes	Bacilli	Lactobacillaceae	Lactobacillus	+
Firmicutes	Bacilli	Enterococcaceae	Enterococcus	+
Firmicutes	Negativicutes	Veillonellaceae	Veillonella	(−)
Firmicutes	Negativicutes	Veillonellaceae	Dialiser	(−)
Firmicutes	Clostridia	unclassified Clostridiales	Mogibacterium *	+
Firmicutes	Clostridia	Peptostreptococcaceae	Peptostreptococcus *	+
Firmicutes	Clostridia	Lachnospiraceae	Coprococcus	+
Firmicutes	Clostridia	Lachnospiraceae	Dorea	+
Firmicutes	Clostridia	Lachnospiraceae	Roseburia	(−)
Firmicutes	Clostridia	Lachnospiraceae	Butyrivibrio	(−)
Firmicutes	Clostridia	Ruminococcaceae	Ruminococcus	+
Firmicutes	Clostridia	Ruminococcaceae	Faecalibacterium	+
Firmicutes	Clostridia	Ruminococcaceae	Anaerotruncus	+
Firmicutes	Clostridia	Ruminococcaceae	Subdoligranulum	+
Firmicutes	Clostridia	Clostridiaceae	Clostridium	+
Firmicutes	Clostridia	Clostridiaceae	Blautia	+
Firmicutes	Clostridia	Eubacteriaceae	Eubacterium	+
Firmicutes	Clostridia	unclassified	Collinsella	+
Firmicutes	Erysipelotrichia	Erysipelotrichaceae	Holdemania	+
Proteobacteria	Betaproteobacteria	Alcaligenaceae	Sutterella	-
Proteobacteria	Betaproteobacteria	Neisseriaceae	Neisseria	-
Proteobacteria	Deltaproteobacteria	Desulfovibrionaceae	Bilophila	-
Proteobacteria	Gammaproteobacteria	Pasteurellaceae	Haemophilus *	-
Proteobacteria	Gammaproteobacteria	Enterobacteriaceae	Enterobacter *	-
Proteobacteria	Gammaproteobacteria	Enterobacteriaceae	Serratia *	-
Proteobacteria	Gammaproteobacteria	Enterobacteriaceae	Escherichia	-
Proteobacteria	Gammaproteobacteria	Enterobacteriaceae	Klebsiella	-
Proteobacteria	Gammaproteobacteria	Moraxellaceae	Acinetobacter	-
Proteobacteria	Gammaproteobacteria	Pseudomonadaseae	Pseudomonas *	-
Proteobacteria	Gammaproteobacteria	Cardiobacteriaceae	Cardiobacterium	-
Bacteroidetes	Bacteroidia	Prevotellaceae	Prevotella *	-
Bacteroidetes	Bacteroidia	Porphyromonadaceae	Porphyromonas *	-
Bacteroidetes	Bacteroidia	Porphyromonadaceae	Parabacteroides	-
Bacteroidetes	Bacteroidia	Bacteroidaceae	Bacteroides	-
Bacteroidetes	Bacteroidia	Rikenellaceae	Alistipes
Fusobacteria	Fusobacteria	Fusobacteriaceae	Fusobacterium	-
Spirochaetae	Spirochaetes	Brachyspiraceae	Brachyspira	-
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiaceae	Akkermansia	-

⁽¹⁾ Genus identification has been made by direct gene identification, mostly of the 16S rRNA gene by cloning and sequencing; ⁽²⁾ Negative Gram-reaction within parenthesis means that the reaction is negative or variable. It has been shown for Butyrivibrio fibrisolvens that the negative gram-reaction is due to a thin cell wall and that the cell wall has Gram-positive characteristics [44]. Presumably this is also the case for the other Butyrivibrio spp. and perhaps also for other Firmicutes with Gram-negative reaction, i.e., they presumably do not contain lipopolysaccharides (LPS) and are usually associated with a Gram-negative cell wall. * Taxa typically found dominating in the upper GI tract (mouth to jejunum) but mostly much less pronounced in the distal GI tract (ileum to rectum); data from Pettersson et al. [45], Wang et al. [43], Hayashi et al. [46], Bik et al. [47], Lazarevic et al. [48], Li et al. [49], Nasidze et al. [50], Turnbaugh et al. [51] and Qin et al. [40].