Human intestinal microbiota composition is associated with local and systemic inflammation in obesity

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM, Rensen SS
Journal
Obesity (Silver Spring, Md.)
Year
2013
OBJECTIVE: Intestinal microbiota have been suggested to contribute to the development of obesity, but the mechanism remains elusive. The relationship between microbiota composition, intestinal permeability, and inflammation in nonobese and obese subjects was investigated. DESIGN AND METHODS: Fecal microbiota composition of 28 subjects (BMI 18.6-60.3 kg m(-2) ) was analyzed by a phylogenetic profiling microarray. Fecal calprotectin and plasma C-reactive protein levels were determined to evaluate intestinal and systemic inflammation. Furthermore, HbA1c , and plasma levels of transaminases and lipids were analyzed. Gastroduodenal, small intestinal, and colonic permeability were assessed by a multisaccharide test. RESULTS: Based on microbiota composition, the study population segregated into two clusters with predominantly obese (15/19) or exclusively nonobese (9/9) subjects. Whereas intestinal permeability did not differ between clusters, the obese cluster showed reduced bacterial diversity, a decreased Bacteroidetes/Firmicutes ratio, and an increased abundance of potential proinflammatory Proteobacteria. Interestingly, fecal calprotectin was only detectable in subjects within the obese microbiota cluster (n = 8/19, P = 0.02). Plasma C-reactive protein was also increased in these subjects (P = 0.0005), and correlated with the Bacteroidetes/Firmicutes ratio (rs = -0.41, P = 0.03). CONCLUSIONS: Intestinal microbiota alterations in obese subjects are associated with local and systemic inflammation, suggesting that the obesity-related microbiota composition has a proinflammatory effect.

Experiment 1


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects
Netherlands
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
non-obese
Group 1 name Corresponds to the case (exposed) group for case-control studies
obese
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
obesity: BMI 30.5-60.3 kg/m2
Group 0 sample size Number of subjects in the control (unexposed) group
13
Group 1 sample size Number of subjects in the case (exposed) group
15
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
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
Human Intestinal Tract Chip

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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)?
Yes


Signature 1

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

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 2

Description: Differential microbial abundance between obese and non-obese individuals

Abundance in Group 1: increased abundance in obese

NCBI Quality ControlLinks
Dorea formicigenerans
Papillibacter cinnamivorans
[Clostridium] symbiosum

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 2

Description: Differential microbial abundance between obese and non-obese individuals

Abundance in Group 1: decreased abundance in obese

NCBI Quality ControlLinks
Alistipes
Alloprevotella tannerae
Bacteroides fragilis
Bacteroides intestinalis
Bacteroides ovatus
Bacteroides stercoris
Bacteroides uniformis
Hoylesella oralis
Odoribacter splanchnicus
Parabacteroides distasonis
Phocaeicola plebeius
Tannerella
Xylanibacter ruminicola

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Nonobese microbiota cluster
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
obesity: BMI 30.5-60.3 kg/m3

Lab analysis

Statistical Analysis

Alpha Diversity

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased

Signature 1

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Table 2

Description: Association of intestinal microbiota with local and systemic inflammation in obesity

Abundance in Group 1: increased abundance in obese

NCBI Quality ControlLinks
[Clostridium] symbiosum
[Clostridium] colinum
Anaerobutyricum hallii

Revision editor(s): WikiWorks

Signature 2

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Table 2

Description: Association of intestinal microbiota with local and systemic inflammation in obesity

Abundance in Group 1: decreased abundance in obese

NCBI Quality ControlLinks
Alistipes
Bacteroides fragilis
Bacteroides intestinalis
Odoribacter splanchnicus
Oscillospira guilliermondii

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
low BMI
Group 1 name Corresponds to the case (exposed) group for case-control studies
high BMI
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
obesity: BMI 30.5-60.3 kg/m4

Lab analysis

Statistical Analysis

Statistical test
Spearman Correlation
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No


Signature 1

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

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Differential microbial abundance between high-BMI and low-BMI individuals

Abundance in Group 1: increased abundance in high BMI

NCBI Quality ControlLinks
Aneurinibacillus
Bifidobacterium
Dorea formicigenerans
Eubacterium limosum
Klebsiella aerogenes
Klebsiella pneumoniae
Mediterraneibacter gnavus
Papillibacter cinnamivorans
Roseburia intestinalis
Vibrio
Yersinia
[Clostridium] colinum

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

Curated date: 2021/01/10

Curator: Marianthi Thomatos

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Differential microbial abundance between high-BMI and low-BMI individuals

Abundance in Group 1: decreased abundance in high BMI

NCBI Quality ControlLinks
Alcaligenes faecalis
Alistipes
Bacteroides fragilis
Bacteroides intestinalis
Bacteroides uniformis
Coprobacillus cateniformis
Faecalibacterium prausnitzii
Hoylesella oralis
Odoribacter splanchnicus
Parabacteroides distasonis
Phocaeicola plebeius
Phocaeicola vulgatus
Tannerella
Xylanibacter ruminicola

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 4


Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
low C-Reactive Protein
Group 1 name Corresponds to the case (exposed) group for case-control studies
high C-Reactive Protein
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
obesity: BMI 30.5-60.3 kg/m5

Lab analysis

Statistical Analysis

Signature 1

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Differential microbial abundance between high C-reactive protein group and low C-reactive protein group

Abundance in Group 1: increased abundance in high C-Reactive Protein

NCBI Quality ControlLinks
Aneurinibacillus
Lacrimispora sphenoides
Papillibacter cinnamivorans
Roseburia intestinalis
Subdoligranulum variabile

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Differential microbial abundance between high C-reactive protein group and low C-reactive protein group

Abundance in Group 1: decreased abundance in high C-Reactive Protein

NCBI Quality ControlLinks
Alistipes
Bacteroides intestinalis
Odoribacter splanchnicus
Parabacteroides distasonis
Phocaeicola plebeius
Phocaeicola vulgatus
Tannerella

Revision editor(s): WikiWorks, ChiomaBlessing