Table 3.

Group of bacteria modifications associated with CDI and IBD. Main characteristics and role in disease and fecal microbiota transplant treatment.

Bacteria group at genus level	Taxonomy	Main characteristics and role in the intestinal metabolic activity◊	Gut ecosystem modifications observed	Fecal microbiota transplant treatment
				Expected changes after taxa restoration	Main microbiota communities identified in bacteriotherapy studies for gut restoration (∇)
Alistipes	Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae	Gram-stain negative Straight or slightly curved rods Non-spore forming Non-motile Obligately anaerobic Produce succinic acid (major glucose metabolic end product) and acetic acid (minor) Produce indole and digest gelatin Bile tolerant	Depletion in children with both CDI and IBD100	– Stable engraftment and restoration of the structure of the gut microbiota. Cessation of CD-related changes and resolution of other gastrointestinal symptoms (in combination with genera Bacteroides and Parabacteroides)104	Alistipes and Blautia (positively correlated with colonic melatonin receptor expression) (AM)114
Blautia	Firmicutes Clostridia Clostridiales Lachnospiraceae	Gram-stain-positive, non-motile coccoid or oval-shaped short rods Obligate anaerobe Growth is stimulated by fermentable carbohydrates. End products after fermentation include acetate, ethanol, lactate, butyrate, and succinate - Some species also produce bile salt hydrolase (B. obeum)	Depletion in adult patients with both CDI and IBD76	- Increase of butyrate production (negative correlation with the presence of C. difficile)81 - Restitution of microbiota bile salt hydrolases (restoration of gut bile metabolism)87	Blautia Bacteroides and Ruminococcus (in detriment of Enterococcus, Escherichia, Shigella) (CDI)81 Blautia producta, Escherichia coli, Clostridium bifermentans (to antagonize C. difficile and restore Bacteroides levels) (CDI)82 Blautia and Ruminococcaceae (associated to colonization resistance) (CDI)83 Blautia hansenii (protective against infection) (CDI)83 Blautia, Coprococcus, Faecalibacterium (restoration after FMT) (CDI)84 Blautia and Blautia producta (Taxa used in bacteriotherapy studies) (CDI)85 Blautia and Alistipes (positively correlated with colonic melatonin receptor expression)114 Blautia, Dorea, Roseburia, Oscillobacter (CDI)115
Dorea	Firmicutes Clostridia Clostridiales Lachnospiraceae	Gram-stain-positive rods, non-spore forming, non-motile. Obligately anaerobic and chemo-organotrophic. Major end products of glucose metabolism include ethanol, formate, acetate, H2, and CO2	Depletion in adult patients with both CDI and IBD76	- Recovery of short fatty acid production and therefore the metabolic activity of the microbial community (related with CDI remission)115	Dorea (CDI)85 Dorea, Blautia Roseburia, Oscillobacter (CDI)115
Clostridium	Firmicutes Clostridia Clostridiales Clostridiaceae	Usually Gram-stain-positive rods. Motile or non-motile (when motile, cells usually are peritrichous) The majority of species form oval or spherical endospores that usually distend the end.	Increase in the gut of patients with CDI and IBD76 (although altered patterns of Clostridium group are not always the same in CDI and IBD patients separately)	- Restore the phylogenetic richness of the gut (restoration of Firmicutes/Bacteroidetes ratio)115 - Increase of butyrate production (negative correlation with the presence of C. difficile)81	Clostridium bifermentans, Clostridium innocuum, Clostridium ramosum, Clostridium cocleatum85 Blautia producta, Escherichia coli, Clostridium bifermentans (to antagonize C. difficile and restore Bacteroides levels) (CDI)82
Enterococcus	Firmicutes Bacilli Lactobacillales Enterococcaceae	Gram-stain-positive rods, non-spore forming. Some strains motile by scanty flagella Cells are ovoid Facultative anaerobic Carboxyphilic (C02 dependant)	Increase in the gut of patients with both CDI and IBD76 (although altered patterns of Enterococcus group are not always the same in CDI and IBD patients studied separately)	- Reduction of lactic acid-producing bacteria and their metabolites - Restitution of the intestinal homeostasis	Enterococcus faecalis (CDI)85
Faecalibacterium	Firmicutes Clostridia Clostridiales Ruminococcaceae	Usually Gram-stain-negative Rod-shaped cells Non-motile Non-sporulating Butyrate production Metabolize pectin, uronic acids, and N-acetyl glucosamine	Depletion in children with both CDI and IBD100	- Increase methionine biosynthesis to improve intestinal antioxidant capacity105 - Increase the anti-inflammatory response in the gut49	Faecalibacterium prausnitzii and Bacteroides ovatus (CDI)115 Faecalibacterium, Blautia, Coprococcus (CDI)84
Roseburia	Firmicutes Clostridia Clostridiales Lachnospiraceae	Gram-stain-negative to variable stain reaction Rod-shaped cells Non-sporulating Motile (37ºC) by flagella Chemo-organotrophic Strictly anaerobic Use of carbohydrates as a carbon and energy source Produces H2, CO2 and large amounts of butyrate after fermentation of glucose and acetate May produce lactate, formate, and ethanol	Depletion in children with both CDI and IBD100	- Increase methionine biosynthesis to improve intestinal antioxidant capacity105 - Increase of butyrate production (negative correlation with dysbiosis in UC)74	Roseburia, Oscillobacter, Blautia, Dorea (CDI)115
Ruminococcus gnavus	Firmicutes Clostridia Clostridiales Ruminococcaceae	Gram-stain positive cell wall structure (but many stain Gram-negative) Cells are coccoid, in pairs and chains Only few motile (flagella) Chemo-organotrophic Strictly anaerobic Growth is stimulated by fermentable carbohydrates and the end products include acetate, formate, ethanol, lactate, and succinate Mucin degradation	Increase of Ruminococcus gnavus in adult patients with both CDI and IBD76 Depletion (genus level) in children with both CDI and IBD100	- Reduction of digestive endogenous mucin substrate to prevent other bacteria proliferation and to allow host bacteria to multiply67	Ruminococcus, Blautia, Bacteroides (in detriment of Enterococcus, Escherichia, Shigella) (CDI)81 Ruminococcaceae, Blautia (associated to colonization resistance) (CDI)83

◊ According to Bergey´s Manual of Systematics of Archea and Bacteria.

∇ Specific studies addressing the efficacy of different bacterial species in the restoration of the gut microbiota after inflammation and/or infection.

CDI: Clostridium difficile infection.

AM: animal model.