Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses

Study information

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study design

case-control

Citation

PMID PubMed identifier for scientific articles.

28852182

DOI Digital object identifier for electronic documents.

10.1038/s41598-017-10663-w

URI

Authors

Mancabelli L, Milani C, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ticinesi A, Nouvenne A, Meschi T, van Sinderen D, Ventura M

Journal

Scientific reports

Year

2017

Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS). Notably, the gut microbiota of FC individuals was shown to be depleted of members belonging to Bacteroides, Roseburia and Coprococcus 3. Furthermore, the metabolic capabilities of the gut microbiomes of five FC and five HS individuals were evaluated through shotgun metagenomics using a MiSeq platform, indicating that HS are enriched in pathways involved in carbohydrate, fatty acid and lipid metabolism as compared to FC. In contrast, the microbiomes corresponding to FC were shown to exhibit high abundance of genes involved in hydrogen production, methanogenesis and glycerol degradation. The identified differences in bacterial composition and metabolic capabilities may play an important role in development of FC symptoms.

Experiment 1

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Curated date: 2025/03/23

Curator: MyleeeA

Revision editor(s): MyleeeA

Subjects

Location of subjects: Italy

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: Chronic constipation Chronic constipation,Infrequent bowel movements,chronic constipation

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Functional constipation (FC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Study participants who reported to have been suffering from Functional constipation

Group 0 sample size Number of subjects in the control (unexposed) group: 79

Group 1 sample size Number of subjects in the case (exposed) group: 68

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 week

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: ANOVA

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: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

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Source: Table S4

Description: Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).

Abundance in Group 1: increased abundance in Functional constipation (FC)

NCBI	Quality Control	Links
Acinetobacter sp. CAG:196
Bacteroidetes incertae sedis
Butyricimonas
Cercis gigantea (nom. inval.)
Christensenella
Dehalobacterium
Desulfovibrio
Faecalibacterium
Gelria
Helicobacter
Holdemania
Hydrogenoanaerobacterium
Lachnoanaerobaculum
Lactococcus
Lautropia
Oxalobacter
Papillibacter
Paraprevotella
Peptococcus
Phascolarctobacterium
Polaromonas
Ruminiclostridium
Thomasclavelia
Victivallis
unclassified Bacteria
unclassified Eubacteriales
unclassified Mollicutes
unclassified Oscillospiraceae
unclassified Peptococcaceae
unclassified Porphyromonadaceae
unclassified Pseudomonadota
unclassified Rhodospirillaceae
unclassified Verrucomicrobiota
Defluviitaleaceae UCG-011Defluviitaleaceae UCG-011
Family XIII AD3011 groupFamily XIII AD3011 group
Coprococcus 2Coprococcus 2
Lachnospiraceae NC2004 groupLachnospiraceae NC2004 group
Ruminiclostridium 5Ruminiclostridium 5
Ruminiclostridium 6Ruminiclostridium 6
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group
Ruminococcaceae UCG-003Ruminococcaceae UCG-003
Ruminococcaceae UCG-004Ruminococcaceae UCG-004
Ruminococcaceae UCG-005Ruminococcaceae UCG-005
Ruminococcaceae UCG-007Ruminococcaceae UCG-007
Ruminococcaceae UCG-010Ruminococcaceae UCG-010
Ruminococcaceae UCG-014Ruminococcaceae UCG-014
Unclassified NB-1nUnclassified NB-1n
unclassified Bacteroidales
unclassified Bacteroidota
Unclassified Clostridiales vadinBB60 groupUnclassified Clostridiales vadinBB60 group

Revision editor(s): MyleeeA

Signature 2

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Source: Table S4

Description: Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).

Abundance in Group 1: decreased abundance in Functional constipation (FC)

NCBI	Quality Control	Links
Acetatifactor
Bacteroides
Flavobacterium
Mucispirillum
Parvularcula
Polaromonas
Roseburia
unclassified Peptostreptococcaceae
Coprococcus 3Coprococcus 3
Lachnospiraceae NK4B4 groupLachnospiraceae NK4B4 group

Revision editor(s): MyleeeA

Experiment 2

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Differences from previous experiment shown

Subjects

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 week

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Signature 1

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Source: Figure 2

Description: Differentially abundant taxa between Functional constipation (FC) and Healthy Subjects (HS).

Abundance in Group 1: increased abundance in Functional constipation (FC)

NCBI	Quality Control	Links
Butyricimonas
Faecalibacterium
Paraprevotella
Phascolarctobacterium
Ruminiclostridium
unclassified Bacteroidales
unclassified Mollicutes
unclassified Oscillospiraceae
unclassified Porphyromonadaceae
uncultured Oscillospiraceae bacterium
Ruminococcaceae UCG-003Ruminococcaceae UCG-003
Ruminiclostridium 5Ruminiclostridium 5
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group
Ruminococcaceae UCG-005Ruminococcaceae UCG-005
Ruminococcaceae UCG-010Ruminococcaceae UCG-010
Ruminiclostridium 6Ruminiclostridium 6
Unclassified Clostridiales VadinBB60 groupUnclassified Clostridiales VadinBB60 group
Unclassified NB1-nUnclassified NB1-n
unclassified Eubacteriales