Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

32143621

DOI Digital object identifier for electronic documents.

10.1186/s12934-020-01319-y

URI Uniform resource identifier for web resources.

Authors

Gallardo-Becerra L, Cornejo-Granados F, García-López R, Valdez-Lara A, Bikel S, Canizales-Quinteros S, López-Contreras BE, Mendoza-Vargas A, Nielsen H, Ochoa-Leyva A

Journal

Microbial cell factories

Year

2020

BACKGROUND: In the last decade, increasing evidence has shown that changes in human gut microbiota are associated with diseases, such as obesity. The excreted/secreted proteins (secretome) of the gut microbiota affect the microbial composition, altering its colonization and persistence. Furthermore, it influences microbiota-host interactions by triggering inflammatory reactions and modulating the host's immune response. The metatranscriptome is essential to elucidate which genes are expressed under diseases. In this regard, little is known about the expressed secretome in the microbiome. Here, we use a metatranscriptomic approach to delineate the secretome of the gut microbiome of Mexican children with normal weight (NW) obesity (O) and obesity with metabolic syndrome (OMS). Additionally, we performed the 16S rRNA profiling of the gut microbiota. RESULTS: Out of the 115,712 metatranscriptome genes that codified for proteins, 30,024 (26%) were predicted to be secreted, constituting the Secrebiome of the gut microbiome. The 16S profiling confirmed an increased abundance in Firmicutes and decreased in Bacteroidetes in the obesity groups, and a significantly higher richness and diversity than the normal weight group. We found novel biomarkers for obesity with metabolic syndrome such as increased Coriobacteraceae, Collinsela, and Collinsella aerofaciens; Erysipelotrichaceae, Catenibacterium and Catenibacterium sp., and decreased Parabacteroides distasonis, which correlated with clinical and anthropometric parameters associated to obesity and metabolic syndrome. Related to the Secrebiome, 16 genes, homologous to F. prausniitzi, were overexpressed for the obese and 15 genes homologous to Bacteroides, were overexpressed in the obesity with metabolic syndrome. Furthermore, a significant enrichment of CAZy enzymes was found in the Secrebiome. Additionally, significant differences in the antigenic density of the Secrebiome were found between normal weight and obesity groups. CONCLUSIONS: These findings show, for the first time, the role of the Secrebiome in the functional human-microbiota interaction. Our results highlight the importance of metatranscriptomics to provide novel information about the gut microbiome's functions that could help us understand the impact of the Secrebiome on the homeostasis of its human host. Furthermore, the metatranscriptome and 16S profiling confirmed the importance of treating obesity and obesity with metabolic syndrome as separate conditions to better understand the interplay between microbiome and disease.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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: normal weight
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: children aged 7-10 years old
Group 0 sample size Number of subjects in the control (unexposed) group: 7
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): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 1

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

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

Signature 1

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Needs review

Curated date: 2020-07-10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks743

Source: Figure 2

Description: Differentially abundant taxa in association with groups and their distribution in the samples.

Abundance in Group 1: increased abundance in obese

NCBI	Links
Bifidobacterium adolescentis
Porphyromonas
Faecalibacterium
Faecalibacterium prausnitzii

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Signature 2

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Curated date: 2020-07-10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks743

Source: Figure 2

Description: Differentially abundant taxa in association with groups and their distribution in the samples.

Abundance in Group 1: decreased abundance in obese

NCBI	Links
Phascolarctobacterium

Revision editor(s): WikiWorks743

Experiment 2

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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: normal weight
Group 1 name Corresponds to the case (exposed) group for case-control studies: obesity with metabolic syndrome
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: children aged 7-10 years old
Group 0 sample size Number of subjects in the control (unexposed) group: 7
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): 3 months

Lab analysis

Sequencing type: 16S

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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 1

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

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

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2020-07-10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks743

Source: Figure 2

Description: Differentially abundant taxa in association with groups and their distribution in the samples.

Abundance in Group 1: increased abundance in obesity with metabolic syndrome

NCBI	Links
Coriobacteriia
Mycobacteriales
Coriobacteriaceae
Collinsella
Collinsella aerofaciens
Bacillota
Bacilli
Clostridia
Eubacteriales
Coprococcus
Erysipelotrichia
Erysipelotrichales
Erysipelotrichaceae
Catenibacterium
Pseudomonadota