Metagenomic sequencing of the human gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes: correlation with inflammatory and metabolic parameters

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

23032991

DOI Digital object identifier for electronic documents.

10.1038/tpj.2012.43

URI

Authors

Graessler J, Qin Y, Zhong H, Zhang J, Licinio J, Wong ML, Xu A, Chavakis T, Bornstein AB, Ehrhart-Bornstein M, Lamounier-Zepter V, Lohmann T, Wolf T, Bornstein SR

Journal

The pharmacogenomics journal

Year

2013

Roux-en-Y gastric bypass (RYGB) has become a prominent therapeutic option for long-term treatment of morbid obesity and type 2 diabetes mellitus (T2D). Cross talk and pathogenetic consequences of RYGB-induced profound effects on metabolism and gut microbiome are poorly understood. The aim of the present study therefore was to characterize intra-individual changes of gut microbial composition before and 3 months after RYGB by metagenomic sequencing in morbidly obese patients (body mass index (BMI)>40 kg m(-)(2)) with T2D. Subsequently, metagenomic data were correlated with clinical indices. Based on gene relative abundance profile, 1061 species, 729 genera, 44 phyla and 5127 KO (KEGG Orthology) were identified. Despite high diversity, bacteria could mostly be assigned to seven bacterial divisions. The overall metagenomic RYGB-induced shift was characterized by a reduction of Firmicutes and Bacteroidetes and an increase of Proteobacteria. Twenty-two microbial species and 11 genera were significantly altered by RYGB. Using principal component analysis, highly correlated species were assembled into two common components. Component 1 consisted of species that were mainly associated with BMI and C-reactive protein. This component was characterized by increased numbers of Proteobacterium Enterobacter cancerogenus and decreased Firmicutes Faecalibacterium prausnitzii and Coprococcus comes. Functional analysis of carbohydrate metabolism by KO revealed significant effects in 13 KOs assigned to phosphotransferase system. Spearmen's Rank correlation indicated an association of 10 species with plasma total- or low-density lipoprotein cholesterol, and 5 species with triglycerides. F. prausnitzii was directly correlated to fasting blood glucose. This is the first clinical demonstration of a profound and specific intra-individual modification of gut microbial composition by full metagenomic sequencing. A clear correlation exists of microbiome composition and gene function with an improvement in metabolic and inflammatory parameters. This will allow to develop new diagnostic and therapeutic strategies based on metagenomic sequencing of the human gut microbiome.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects: Germany

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity

Group 0 name Corresponds to the control (unexposed) group for case-control studies: after surgery

Group 1 name Corresponds to the case (exposed) group for case-control studies: before surgery

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Roux-en-Y gastric-bypass operation were recruited according to the S3 guidelines of the German Society for Obesity

Group 0 sample size Number of subjects in the control (unexposed) group: 6

Group 1 sample size Number of subjects in the case (exposed) group: 6

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 weeks

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: ANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2021/08/2

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): Fatima, WikiWorks

Source: Table 2 &Table 3

Description: gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes

Abundance in Group 1: increased abundance in before surgery

NCBI	Quality Control	Links
Acinetobacter johnsonii
Anaerostipes
Anaerostipes caccae
Brachyspira hyodysenteriae
Coprococcus
Coprococcus comes
Faecalibacterium
Faecalibacterium prausnitzii
Fibrobacter succinogenes
Fusobacterium periodonticum
Helicobacter
Lactobacillus acidophilus
Leptospira interrogans
Limosilactobacillus reuteri
Mycobacterium kansasii
Nakamurella multipartita
Ectopseudomonas mendocina
Staphylococcus epidermidis
Thermomicrobium roseum
Treponema pallidum
Thomasclavelia spiroformis
Dictyostelium
Epidinium

Revision editor(s): Fatima, WikiWorks

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Fatima on 2021/08/2

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): Fatima, WikiWorks

Source: Table 2 &Table 3

Description: gut microbiome before and after bariatric surgery in obese patients with type 2 diabetes

Abundance in Group 1: decreased abundance in before surgery

NCBI	Quality Control	Links
Citrobacter
Enterobacter
Enterobacter cancerogenus
Salmonella
Salmonella enterica
Shigella boydii
Veillonella
Veillonella dispar
Veillonella parvula
Neurospora

Revision editor(s): Fatima, WikiWorks