Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/23
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chen X, Sun H, Jiang F, Shen Y, Li X, Hu X, Shen X, Wei P
Journal
PeerJ
Year
2020
Keywords:
16S rRNA gene sequencing, Alpha diversity, Bacterial compositions, Beta Diversity, Childhood obesity, Gut microbiota
Background: Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods: According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results: The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P = 0.008). Principal coordinate analysis (PCoA) and Nonmetric multidimensional scaling (NMDS) revealed significant differences in gut microbial community structure between the normal weight group and the obese group. The liner discriminant analysis (LDA) effect size (LEfSe) analysis showed that fifty-five species of bacteria were abundant in the fecal samples of the normal weight group and forty-five species of bacteria were abundant in the obese group. In regard to phyla, the gut microbiota in the obese group had lower proportions of Bacteroidetes (51.35%) compared to the normal weight group (55.48%) (P = 0.030). There was no statistical difference in Firmicutes between the two groups (P = 0.436), and the Firmicutes/Bacteroidetes between the two groups had no statistical difference (P = 0.983). At the genus level, Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Haemophilus were significantly more abundant in the obese group than in the normal weight group (P = 0.048, P = 0.018, P < 0.001, P = 0.040, and P = 0.003, respectively). The fecal microbiota of children in the obese group had lower proportions of Oscillospira and Dialister compared to the normal weight group (P = 0.002 and P = 0.002, respectively). Conclusions: Our results showed a decrease in gut microbiota abundance and diversity as the BMI increased. Variations in the bacterial community structure were associated with obesity. Gut microbiota dysbiosis might play a crucial part in the development of obesity in Chinese children.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/23

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects
China
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
volunteers between the ages of 6-11 years old who were determined to be obese by BMI
Group 0 sample size Number of subjects in the control (unexposed) group
23
Group 1 sample size Number of subjects in the case (exposed) group
28
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
4 weeks

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

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)?
No

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2, Text

Description: Relative abundance of microbial taxa in normal weight group vs obese group

Abundance in Group 1: increased abundance in obese children

NCBI Quality ControlLinks
Faecalibacterium
Haemophilus
Lachnospira
Megamonas
Phascolarctobacterium

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2, Text

Description: Relative abundance of microbial taxa in normal weight group vs obese group

Abundance in Group 1: decreased abundance in obese children

NCBI Quality ControlLinks
Dialister
Oscillospira

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Source: Figure 5

Description: Relative abundance of microbial taxa in normal weight group vs obese group

Abundance in Group 1: increased abundance in obese children

NCBI Quality ControlLinks
Acetitomaculum ruminis
Actinobacillus
Aggregatibacter
Alcaligenaceae
Bacilli
Betaproteobacteria
Burkholderiales
Campylobacter
Carnobacteriaceae
Clostridiaceae
Clostridium perfringens
Amedibacillus dolichus CAG:375
Fusobacteriota
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacterium
Granulicatella
Haemophilus
Haemophilus influenzae
Haemophilus parainfluenzae
Lachnospira
Lactobacillales
Leptotrichiaceae
Megamonas
Micrococcaceae
Pasteurellales
Pasteuriaceae
Peptostreptococcaceae
Phascolarctobacterium
Phocaeicola coprophilus
Segatella copri
Pseudomonadota
Rothia
Rothia mucilaginosa
Streptococcaceae
Streptococcus
Sutterella
Turicibacter
Veillonella
Veillonella dispar
[Clostridium] colinum
Mediterraneibacter gnavus
Turicibacteraceae

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/29

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Merit

Source: Figure 5

Description: Relative abundance of microbial taxa in normal weight group vs obese group

Abundance in Group 1: decreased abundance in obese children

NCBI Quality ControlLinks
Actinomycetota
Adlercreutzia
Alistipes
Alistipes indistinctus
Anaerotruncus
Bacteroides uniformis
Barnesiellaceae
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Bifidobacterium adolescentis
Bilophila
Christensenella
Christensenellaceae
Clostridium
Collinsella
Collinsella aerofaciens
Coriobacteriaceae
Coriobacteriales
Coriobacteriia
Defluviitalea
Deltaproteobacteria
Desulfovibrio
Desulfovibrionaceae
Desulfovibrionales
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Eubacterium
Hathewaya
Holdemania
Mollicutes
Mycoplasmatota
Oscillospira
Oxalobacter
Oxalobacter formigenes
Oxalobacteraceae
Roseateles saccharophilus
Peptococcaceae
Prevotella
Rickettsiella massiliensis
Rikenellaceae
Ruminococcus
Sporobacter
Streptococcus gordonii

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks, Merit