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

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Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
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
Keywords:
AAR, CAZY, Metabolic syndrome, Metatranscriptome, Metatranscriptomics, Microbiome, Microbiota, Obesity, Secrebiome, Secretome
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


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

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 Quality ControlLinks
Bifidobacterium adolescentis
Porphyromonas
Faecalibacterium
Faecalibacterium prausnitzii

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

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 Quality ControlLinks
Phascolarctobacterium

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
obesity with metabolic syndrome

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

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 Quality ControlLinks
Coriobacteriia
Mycobacteriales
Coriobacteriaceae
Collinsella
Collinsella aerofaciens
Bacillota
Bacilli
Clostridia
Eubacteriales
Coprococcus
Erysipelotrichia
Erysipelotrichales
Erysipelotrichaceae
Catenibacterium
Pseudomonadota

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 2

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

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

NCBI Quality ControlLinks
Bacteroidota
Bacteroidales
Bacteroidia

Revision editor(s): WikiWorks