The gut microbiome of Mexican children affected by obesity

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30366118

DOI Digital object identifier for electronic documents.

10.1016/j.anaerobe.2018.10.009

URI

Authors

Maya-Lucas O, Murugesan S, Nirmalkar K, Alcaraz LD, Hoyo-Vadillo C, Pizano-Zárate ML, García-Mena J

Journal

Anaerobe

Year

2019

Keywords:

Cholesterol, Gut microbiome, High-throughput sequencing, Mexican children, Obesity, Triglycerides

Obesity is a metabolic disorder and global health issue. In Mexico 34.4% of children between 5 and 11 years-old are overweight or obese. Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity. We performed metagenomic shotgun-sequencing of DNA isolated from fecal samples from a cohort of normal weight and obese Mexican children using Illumina platform with HiSeq 2500. We also examined their metabolic factors and fecal short-chain fatty acids concentration. The results show that a remarkable dysbiosis of bacteria, archaea and viruses was not observed in the obese children group compared to the normal weight group; however, the archaeal community exhibited an increase of unclassified Methanobrevibacter spp. in obese children. The bacterial communities of all participants were clustered into three different enterotypes. Most normal weight children have a gut bacterial community dominated by Ruminococcus spp. (Enterotype 3), while most obese children had a community dominated by Prevotella spp. (Enterotype 2). On the other hand, changes in the gut microbiome were correlated with clinical metadata and could be used to stratify individuals based on their phenotype. The species Megamonas spp. were over-represented in obese children, whereas members of the family Oscillospiraceae were depleted in the same individuals and negatively correlated with levels of serum cholesterol. A microbiome comparative metabolic pathway analysis showed that two KEGG pathway modules of glycolysis, Glycolysis I (from Glucose 6-Phosphate), and Glycolysis II (from Fructose 6-Phosphate) were significantly overrepresented in normal weight children. Our results establish specific alterations in the gut microbiome of Mexican children affected of obesity, along with clinical alterations, providing information on the microbiome composition that may be useful for prognosis, diagnosis, and treatment.

Experiment 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects: Mexico

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: Normal weight children

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Obese children aged between 9 and 11 years-old

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None.

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: LEfSe

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

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Curator: Rimsha Azhar

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Source: Figure 4A

Description: Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.

Abundance in Group 1: increased abundance in Obese children

NCBI	Quality Control	Links
Megamonas
unclassified Megamonas

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Signature 2

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Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Figure 4A

Description: Differentially abundant bacterial genera, families, or species in obese children compared to normal weight children.

Abundance in Group 1: decreased abundance in Obese children

NCBI	Quality Control	Links
Anaerostipes
Anaerostipes hadrus
Bacteroidaceae
Bacteroides faecis
Bacteroides ovatus
Bacteroides salyersiae
Bacteroides xylanisolvens
Bilophila wadsworthia
Coprococcus comes
Deltaproteobacteria
Desulfobacterales
Desulfurococcaceae
Dorea formicigenerans
Enterocloster citroniae
Holdemania
Oscillibacter
Oscillospiraceae
Streptococcus thermophilus
Veillonella parvula
Desulfovibrionaceae
Desulfovibrionales
Lachnospiraceae bacterium 7_1_58FAA
unclassified Oscillibacter
Ruminococcus sp. 5_1_39BFAA

Revision editor(s): WikiWorks, ChiomaBlessing