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GBP metagenomic assembly

ABSTRACT: EMG produced TPA metagenomics assembly of the Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota (GBP) data set

PROVIDER: PRJEB22519 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1305895.fasta.gz	Fasta.gz
	ERR1305898.fasta.gz	Fasta.gz
	SRR1761773.fasta.gz	Fasta.gz
	SRR1761777.fasta.gz	Fasta.gz
	ERR1305915.fasta.gz	Fasta.gz

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Project description:Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota

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Weight loss following Roux-en-Y gastric bypass surgery leads to changes in the expression of several miRNAs and their predicted target genes in skeletal muscle

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Project description:A prospective, multicenter, cohort study was conducted in patients with severe obesity, who were randomized between two bariatric surgery techniques (Roux-en-Y gastric bypass and one anastomosis gastric bypass). Fecal samples were collected from 45 obese patients before surgery (T0) and 24 months after surgery (T1) and analyzed by shotgun metaproteomics.

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The Epigenome of Spermatozoa is Affected in Obesity and Dynamically Changes after Bariatric Surgery [Lean/Obese MNase]

Project description:Obesity is a heritable disorder, with children of obese fathers at higher risk of developing obesity. Â Environmental factors epigenetically influence somatic tissues, but the contribution of these factors to the establishment of epigenetic patterns in human gametes is unknown. Here, we hypothesized that weight loss remodels the epigenetic signature of spermatozoa in human obesity. Comprehensive profiling of the epigenome of sperm from lean and obese men showed similar histone positioning, but small non-coding RNA expression and DNA methylation patterns were markedly different. In a separate cohort of morbidly obese men, surgery-induced weight loss was associated with a dramatic remodeling of sperm DNA methylation, notably at genetic locations implicated in the central control of appetite. Our data provide evidence that the epigenome of human spermatozoa dynamically changes under environmental pressure, and offers Â insight into how obesity may propagate metabolic dysfunction to the next generation. Examination of the DNA methylation status, histone retention and sncRNA expression of the semen of 13 lean and 10 obese individuals; as well as the DNA methylation status of the semen of 6 obese men undergoing Roux-en-Y GBP surgery, at three time points: approximately 1 week before, 1 week after and 1 year after the surgery.

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Transcriptome analysis of circulating monocytes in obese patients before and three months after bariatric surgery

Project description:Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. Furthermore, weight loss after bariatric surgery is associated with less inflammation. Transcriptome analysis of circulating monocytes from control and obese patients before and after bariatric surgery will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20.3±0.5 kg/m2, mean±SEM) and 18 obese individuals without clinical symptoms of cardiovascular disease (BMI: 45.1±1.4 kg/m2, P<0.001 compared with lean controls). These 18 morbidly obese subjects were referred to our hospital for bariatric surgery. Before they were included, individuals were evaluated by an endocrinologist, an abdominal surgeon, a psychologist and a dietician. Only after multidisciplinary deliberation, the selected patients received a laparoscopic Roux-en-Y gastric bypass. CD14+ monocytes were collected before and three months after bariatric surgery (BMI: 37.5±1.3 kg/m2, P<0.001 compared with before weight loss), total RNA was extracted and subjected to genome-wide expression analysis. Samples consisted of CD14+ monocytes from 6 lean controls and 18 morbidly obese patients before and three months after bariatric surgery. The 6 lean controls were also used to make 6 control pools.

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Systems Signature Reveals Unique Remission-path of Diabetes Generated by Gastric Bypass Surgery

Project description:Gastric bypass surgery (GBP) emerging as a powerful tool for treatment of obesity has been applied for remission of diabetes. However, the GBP global molecular effects on diabetes remission independent of weight loss remain largely unknown. We profiled plasma metabolites and proteins of 10 normoglycemic obese (NO) and 9 diabetic obese (DO) patients at 1-week, 3-months and 1-year stages after Roux-en-Y gastric bypass (RYGB) as well pre-RYGB stage, by which 146 proteins and 128 metabolites were detected from both NO and DO groups at all four stages. By analyzing a set of bi-molecular associations among the corresponding network of the subjects with our newly developed computational method, we defined the representing physiological states (called the edge-states, in contrast to the traditional node-states) and the related molecular networks of NO and DO patients, respectively. The PCA results and hubnetworks of NO subjects were significantly different from those of DO patients; particularly, the hub-network rearrangement of both groups differentially went through after RYGB. In conclusion, by developing network-based systems signatures rather than relying on individual molecules, we for the first time reveal that RYGB generates a unique recovering-path for diabetes remission independent of weight loss.

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Project description:Obesity-related diseases now affect half of the global population, and bariatric surgery is one of the few interventions with long lasting weight loss and cardio-metabolic effects. Here, we investigated the effect of Roux-en-Y gastric bypass surgery on the plasma proteome, hypothesizing that specific proteins or protein patterns may serve as key mediators and markers of the metabolic response. We performed MS-based proteomics on two longitudinal studies encompassing 47 morbidly obese patients, generating quantitative information on more than 1700 proteins. A global correlation matrix incorporating about 200,000 relationships revealed functional connections between proteins and assigned them to physiological processes. The main classes of significantly altered proteins were markers of systemic inflammation and those involved in lipid metabolism, and our data highlight robust correlative and anti-correlative behavior to each other and to clinical parameters. A group of inflammation-related proteins showed distinct inverse relationships to proteins consistently associated with insulin sensitivity.

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MYDIASECRET: RNA-Seq of human skeletal muscle biopsies before and after bariatric surgery

Project description:This study aimed at identifying differentially expressed protein-coding genes after bariatric surgery. Muscle biopsies were taken from vastus lateralis before and 3 months after bariatric surgery (i.e. sleeve gastrectomy or Roux-en-Y gastric bypass).

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Project description:In order to identify mechanisms underlying the long-term beneficial effect of bariatric surgery on abdominal subcutaneous WAT, we performed gene microarray analyses on adipose tissue from a cohort of obese women. Adipose tissue biopsies were obtained before RYGB, and then 2 and 5 years thereafter. To evaluate the long-term effect of Roux-en-Y gastric bypass (RYGB) surgery on WAT, we also compared the WAT gene expression at 5 years postsurgery with that of age-matched nonoperated women.

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Project description:Roux-en-Y gastric bypass surgery changes fungal and bacterial microbiota in morbidly obese patients - A pilot study

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