Table 1.

Microbial taxa positively correlated to select gut conditions in human subjects.

Condition	Study size/details	Microbial taxonomic changes associated with conditiona	Reference
CDI	Fecal samples from n = 14 recurrent CDI patients (4 within this group given FMT)	↑ Proteobacteria, ↓ Bacteroidetes, ↓ Firmicutes	Weingarden et al., 2015
	Fecal samples from n = 94 CDI, and n = 89 non-CDI inpatients	↑ Proteobacteria, ↓ Firmicutes (except Enterococcus and Erysipelotrichia and some Lachnospiraceae)	Schubert et al., 2014
	Fecal samples from n = 9 recurrent CDI patients given FMT in van Nood et al. (2013) study	↑ Proteobacteria, ↑ Bacilli, ↓ Bacteroidetes, ↓ Firmicutes, ↓ overall microbial diversity compared to post-FMT and healthy donor samples	Fuentes et al., 2014
	Fecal samples from n = 22 C. difficile culture-positive elderly subjects, and n = 252 healthy elderly subjects	↑ Proteobacteria, Firmicutes (↓ Enterococcaceae and ↑ Lactobacillaceae), ↓ overall microbial diversity	Rea et al., 2012
	Fecal samples from n = 39 CDI patients, n = 36 C. difficile-negative nosocomial diarrhea patients, and n = 40 healthy control subjects	↓ Firmicutes, ↑ Proteobacteria, ↓ Microbial diversity in both diarrheal groups compared to healthy controls	Antharam et al., 2013
	Stool samples from n = 6 CDI patients given FMT	↑ Proteobacteria, ↓ Bacteroidetes, ↓ Firmicutes (specifically Lachnospiraceae, ↓ overall microbial diversity	Shahinas et al., 2012
UC	Fecal samples from n = 15 UC patients and n = 15 control subjects	↓ Bacteroidetes, ↓ Firmicutes, ↓ overall microbial diversity	Rajilic-Stojanovic et al., 2013
	RCT on FMT for UC (58 fecal samples total from n = 34 UC patients, and n = 24 healthy donors)	↓ Firmicutes, ↑ Proteobacteria  ↑ Bacteroidetes, ↑ Bacilli, no change in bacterial diversity	Rossen et al., 2015
	Sequencing completed on inflamed and non-inflamed mucosal biopsies from n = 6 UC patients, and n = 5 healthy controls	↑ Bacteroidetes, ↓ Firmicutes	Walker et al., 2011
	Fecal samples from n = 36 active UC patients treated with FMT, and n = 34 active UC patients given placebo	Reduced bacterial diversity, no information on phyla, but: ↓ Lachnospiraceae, ↓ Ruminococcus	Moayyedi et al., 2015
	Sigmoid colon biopsies from n = 8 monozygotic twin pairs discordant for UC, and n = 10 healthy individuals	↑ Actinobacteria, ↑ Proteobacteria (↓ Bacteroidetes), no change in Firmicutes, ↓ Overall bacterial diversity	Lepage et al., 2011
Obesity	Gut microbial communities profiled from n = 31 monozygotic twin pairs, and n = 23 dizygotic twin pairs generally concordant for obesity or leanness	↓ Bacteroidetes, ↑ Actinobacteria, no change in Firmicutes	Turnbaugh et al., 2009
	Stool samples from n = 2 lean, and n = 12 obese individuals	↓ Bacteroidetes, ↑ Firmicutes	Ley et al., 2006
	Stool samples from n = 1 normal-weight adolescent, and n = 1 obese adolescent	↓ Bacteroidetes, ↑ Firmicutes	Ferrer et al., 2013
	Collected fecal samples from n = 52 lean, and n = 42 overweight or obese individuals	No change in Firmicutes to Bacteroidetes (F:B) ratio between lean and obese groups	Fernandes et al., 2014
	Stool samples from n = 30 normal range, n = 35 overweight, n = 33 obese (defined by BMI)	↑ Bacteroidetes, no change in Firmicutes	Schwiertz et al., 2010
	Stool samples from n = 9 metabolic syndrome patients undergoing allogenic gut microbiota (n = 9) from healthy lean individuals or autologous FMT (n = 9)	↓ Overall bacterial diversity, and ↑ Bacteroidetes, ↓ Lachnospiraceae in obese subjects compared to lean prior to FMT	Vrieze et al., 2012

Abbreviations: Body mass index (BMI); fecal microbiota transplantation (FMT); Clostridium difficile infection (CDI); randomized controlled clinical trial (RCT); ulcerative colitis (UC).

^aPhylum level taxonomic changes are listed unless otherwise described.