The gut microbiome of Mexican children affected by obesity

Study information

Needs review

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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Curated date: 2021/01/10

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Subjects

Location of subjects: Mexico

Host species Species from which microbiome was sampled (if applicable): 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

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

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

Lab analysis

Sequencing type: WMS

Not specified

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

Statistical Analysis

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Chao1 Abundance-based estimator of species richness: decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged
Richness Number of species: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Rimsha Azhar

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Source: Figure 4A

Description: Differentially abundant bacterial genera, families, or species

Abundance in Group 1: increased abundance in Obese

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Megamonas

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Signature 2

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Source: Figure 4A

Description: Differentially abundant bacterial genera, families, or species

Abundance in Group 1: decreased abundance in Obese

NCBI	Quality Control	Links
Deltaproteobacteria
Desulfurococcaceae
Desulfobacterales
Streptococcus thermophilus
Dorea formicigenerans
Anaerostipes hadrus
Anaerostipes
Veillonella parvula
Coprococcus comes
Oscillibacter
Oscillospiraceae
Holdemania
Bacteroides faecis
Enterocloster citroniae
Bilophila wadsworthia
Bacteroides salyersiae
Bacteroides xylanisolvens
Bacteroides ovatus
Bacteroides
Bacteroidaceae

Revision editor(s): WikiWorks