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J Transl Med. 2018 Sep 3;16(1):244. doi: 10.1186/s12967-018-1619-z.

Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women.

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Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
New York University Langone Medical Center, 423 East 23rd St, New York, NY, 10016, USA.
The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, S1W7 2AZ, UK.
Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
New York University Langone Medical Center, 423 East 23rd St, New York, NY, 10016, USA.
Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, RG6 6AP, UK.



Microbiota and bile acids in the gastrointestinal tract profoundly alter systemic metabolic processes. In obese subjects, gradual weight loss ameliorates adipose tissue inflammation and related systemic changes. We assessed how rapid weight loss due to a very low calorie diet (VLCD) affects the fecal microbiome and fecal bile acid composition, and their interactions with the plasma metabolome and subcutaneous adipose tissue inflammation in obesity.


We performed a prospective cohort study of VLCD-induced weight loss of 10% in ten grades 2-3 obese postmenopausal women in a metabolic unit. Baseline and post weight loss evaluation included fasting plasma analyzed by mass spectrometry, adipose tissue transcription by RNA sequencing, stool 16S rRNA sequencing for fecal microbiota, fecal bile acids by mass spectrometry, and urinary metabolic phenotyping by 1H-NMR spectroscopy. Outcome measures included mixed model correlations between changes in fecal microbiota and bile acid composition with changes in plasma metabolite and adipose tissue gene expression pathways.


Alterations in the urinary metabolic phenotype following VLCD-induced weight loss were consistent with starvation ketosis, protein sparing, and disruptions to the functional status of the gut microbiota. We show that the core microbiome was preserved during VLCD-induced weight loss, but with changes in several groups of bacterial taxa with functional implications. UniFrac analysis showed overall parallel shifts in community structure, corresponding to reduced abundance of the genus Roseburia and increased Christensenellaceae;g__ (unknown genus). Imputed microbial functions showed changes in fat and carbohydrate metabolism. A significant fall in fecal total bile acid concentration and reduced deconjugation and 7-α-dihydroxylation were accompanied by significant changes in several bacterial taxa. Individual bile acids in feces correlated with amino acid, purine, and lipid metabolic pathways in plasma. Furthermore, several fecal bile acids and bacterial species correlated with altered gene expression pathways in adipose tissue.


VLCD dietary intervention in obese women changed the composition of several fecal microbial populations while preserving the core fecal microbiome. Changes in individual microbial taxa and their functions correlated with variations in the plasma metabolome, fecal bile acid composition, and adipose tissue transcriptome. Trial Registration NCT01699906, 4-Oct-2012, Retrospectively registered. URL-


Correlation analysis; Diet-induced weight loss; Fecal bile acids; Fecal bile acids-plasma metabolome; Fecal microbiota; Fecal microbiota-adipose tissue transcriptome; Gut microbiota-fecal bile acids; Gut microbiota-plasma metabolome; Obesity; Plasma metabolome

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