Table.

The Microbiome and Weight

Source	Study Subjects	Comparison	No. of Subjects	Method	Taxonomic Findings	Functional Findings
Studies in Obesity and Medical Weight Loss
Armougam et al,11 2009	Humans	Anorexic, healthy, and obese	49	16S qPCR	Phylum Firmicutes overall had no changes between groups; Lactobacillus species (phylum Firmicutes) increased in the obese group; phylum Bacteroidetes decreased in obese group	NA
Arumugam et al,8 2011	Humans	No specific comparison; BMI in only 6 classified as obese	37	Metagenomics	Phyla not related to BMI	F-type ATPase levels increased with increasing BMI
Balamurugan et al,12 2010	Adolescent humans	Obese vs nonobese	28	16S qPCR	Bacteroides, Prevotella, and Porphyromonas species (phyla Bacteroidetes), Bifidobacterium species (phylum Actinobacteria), and Eubacterium rectale (phylum Firmicutes) all unchanged; Faecalibacterium prausnitzii (phylum Firmicutes) increased in obesity	NA
Duncan et al,13 2008	Humans	Obese, nonobese, and obese using a weight-loss diet	47	FISH	Decreased phylum Firmicutes in obese subjects with weight-loss diet; no changes in phylum Bacteroidetes between nonobese and obese or in obese after weight loss	NA
Ley et al,14 2005	Mice	Ob/ob vs lean with a normal diet	19	16S Sequencing	Firmicutes to Bacteroidetes ratio increased in obesity	NA
Ley et al,10 2006	Obese humans	Before and after weight-loss diet (restricted fat or carbohydrate intake)	12	16S Sequencing	Firmicutes to Bacteroidetes ratio increased in baseline obesity and decreased with weight-loss diet; increases in phylum Bacteroidetes correlated with weight lost	NA
Nadal et al,15 2009	Obese adolescent humans	Before and after 10-wk calorie-restricted diet	39	FISH	Low-weight-loss group showed no significant differences; high-weight-loss group showed significant decreases in Clostridium (phylum Firmicutes) and increases in Bacteroides and Prevotella species (phylum Bacteroidetes)	Trend toward reduction in fecal energy content in high-weight-loss group
Santacruz et al,16 2009	Obese adolescent humans	Before and after diet and exercise for 10 wk	36	16S qPCR	Firmicutes to Bacteroidetes ratio decreased after weight loss and increased at baseline in group with less weight loss	NA
Schwiertz et al,17 2010	Humans	Stratified by BMI (cutoffs 25 and 30)	98	16S qPCR	Firmicutes to Bacteroidetes ratio decreased in obesity; Methanobrevibacter species decreased in obesity	SCFA stool content increased in obesity
Turnbaugh et al,18 2006	Same animals as Ley et al14 (PNAS)	Ob/ob vs lean with a normal diet	19	Metagenomics	Same findings as Ley et al14	Phylum Bacteroidetes associated with carbohydrate metabolism genes and increased SCFA stool content in obesity
Turnbaugh et al,20 2009	Human twins	Stratified by BMI (cutoffs 25 and 30)	154	16S 454 Pyrosequencing and metagenomics	Decreased phylum Bacteroidetes and increased phylum Actinobacteria in obese	Phylum Bacteroidetes associated with carbohydrate metabolism genes and greater diversity than Firmicutes-based genomes
Zhang et al,19 2010	Mice	Wild type vs Apoa-I negative; high-fat vs normal diet	20	16S Pyrosequencing and DGGE	No phyla-order differences observed; diet caused more difference than genotype; Erysipelotrichaceae (phylum Firmicutes) decreased with obesity	NA
Studies After RYGB
Furet et al,23 2010	Humans	Lean controls; obese at baseline and 3 and 6 mo after RYGB	43	16S qPCR	Decreased Bacteroides and Prevotella species in obesity (phylum Bacteroidetes), increasing after RYGB; increased Lactobacillus, Leuconostoc, and Pediococcus species (phylum Firmicutes) and Bifidobacterium (phylum Actinobacteria) in obesity, decreasing after RYGB	Decreased BMI and levels of leptin and inflammatory markers (eg, CRP, IL-6) after RYGB
Li et al,25 2011	Rats	Sham surgery vs RYGB; preoperative vs 2, 4, 6, and 8 wk after RYGB	12	16S Pyrosequencing	Bacteroides species not measured; Lachnospiraceae and Ruminococcaceae (phylum Firmicutes) both decreased after RYGB	Increased fecal amines and cytotoxicity after RYGB
Li et al,24 2011	Rats	Sham surgery vs RYGB; preoperative vs 2, 4, 6, and 8 wk after RYGB	30	16S Pyrosequencing	52-Fold increase in phylum Proteobacteria after RYGB; decrease in total phyla Firmicutes (4.5-fold) and Bacteroidetes (2-fold), and thus decreased Firmicutes to Bacteroidetes ratio after RYGB	Increased carbohydrate fermentation and protein putrefaction with concomitant rise in gut amines after RYGB
Woodard et al,21 2009	Humans after RYGB	RCT; probiotics (lactobacillus) vs placebo	44	Hydrogen breath test	Patients given lactobacillus probiotics (phylum Firmicutes) had increased weight loss compared to those receiving no supplements	Patients given lactobacillus probiotics after RYGB had higher serum levels of vitamin B12 and less bacterial overgrowth via hydrogen breath test
Zhang et al,22 2009	Humans	Control vs obese vs after RYGB (8–15 mo); separate subjects constitute each group	9	16S Pyrosequencing	Prevotellaceae (phylum Bacteroidetes), Coriobacteriaceae (phylum Actinobacteria), Erysipelotrichaceae (phylum Firmicutes), and Alcaligenaceae (phylum Proteobacteria) increased in obese compared with controls Enterobacteriaceae (phylum Proteobacteria) and Fusobacteriaceae (phylum Fusobacteria) markedly increased in the RYGB group; Clostridiales (phylum Firmicutes) decreased in obese and RYGB compared with controls	NA

Abbreviations: Apoa-I, apolipoprotein A-I; ATPase, adenosine triphosphatase; BMI, body mass index (calculated as weight in kilograms divided by height in meters squared); CRP, C-reactive protein; DGGE, denaturing gradient gel electrophoresis; FISH, fluorescent in situ hybridization; IL-6, interleukin 6; NA, not available; ob/ob, obese phenotype leptin knockout mice; PNAS, prudent no added salt (diet); qPCR, quantitative polymerase chain reaction; RCT, randomized controlled trial; RYGB, Roux-en-Y gastric bypass; SCFA, short-chain fatty acids.