Why do babies cry? Exploring the role of the gut microbiota in infantile colic, constipation, and cramps in the KOALA birth cohort study

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Barnett D, Thijs C, Mommers M, Endika M, Klostermann C, Schols H, Smidt H, Nauta A, Arts I, Penders J
Journal
Gut microbes
Year
2025
Keywords:
Infant gut microbiota, colic, constipation, functional gastrointestinal symptoms, human milk oligosaccharides
Gastrointestinal symptoms are common during infancy, including infantile colic. Colic can be loosely defined as prolonged and recurrent crying without obvious cause. The cause indeed remains unclear despite much research. Results on infant nutrition are inconclusive, but prior work has linked maternal mental health to infant crying. Recently, several small studies have described associations between gut microbiota and colic. We used a larger cohort to examine the role of the microbiota in infant gastrointestinal health, while also accounting for other biopsychosocial factors. Using fecal 16S rRNA gene amplicon sequencing data from 1,012 infants in the KOALA birth cohort, we examined associations between the 1-month gut microbiota and parent-reported functional gastrointestinal symptoms throughout infancy, including colic, constipation, and cramps. These analyses were adjusted for biopsychosocial factors that were associated with symptoms in a broader analysis involving 2,665 participants. In 257 infants, we also explored associations between breastmilk human milk oligosaccharides (HMOs) and gastrointestinal symptoms. Higher relative abundance of Staphylococcus at one month was associated with less constipation in the first three months of life. Conversely, Ruminococcus gnavus group abundance was associated with more colicky symptoms, particularly between four and seven months. Breastmilk concentrations of the HMOs lacto-N-hexaose (LNH) and lacto-N-neohexaose (LNnH) were associated with less constipation in the first three months. Our results support the conclusion that gut microbiota are relevant in infantile colic and constipation. However more work is needed to elucidate the underlying mechanisms, and explore their interplay with other relevant biopsychosocial factors such as maternal mental health.

Experiment 1


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Subjects

Location of subjects
Netherlands
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
Functional abnormality of the gastrointestinal tract Functional abnormality of the GI tract,GI dysfunction,Functional abnormality of the gastrointestinal tract,functional abnormality of the gastrointestinal tract
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-crude (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-crude (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation: >3 days without defecation in infants <3 months. (full cohort).
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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
Logistic Regression
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)?
Yes

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation > 3d-crude (< 3months)

NCBI Quality ControlLinks
Enterococcus

Revision editor(s): Shulamite

Signature 2

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High constipation > 3d-crude (< 3months)

NCBI Quality ControlLinks
Haemophilus
Lactococcus
Staphylococcus

Revision editor(s): Shulamite

Experiment 2


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-crude (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-crude (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic: Wessel's criteria applied to infants <3 months. (Full cohort)
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-crude (< 3months)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Signature 2

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High colic: wessel-crude (< 3months)

NCBI Quality ControlLinks
Bifidobacterium
Sutterella

Revision editor(s): Shulamite

Experiment 3


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-crude (4 - 7months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-crude (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic: Wessel's criteria applied to infants aged 4–7 months. (Full cohort).
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-crude (4 - 7months)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Experiment 4


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-crude (8 - 12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation >3d-crude (8 - 12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation: >3 days without defecation in infants aged 8–12 months (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation >3d-crude (8 - 12months)

NCBI Quality ControlLinks
Parabacteroides

Revision editor(s): Shulamite

Experiment 5


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic: Wessel's criteria applied to infants <3 months, adjusted for covariates. (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High colic: wessel-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Bifidobacterium

Revision editor(s): Shulamite

Experiment 6


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation: >3 days without defecation in infants <3 months, adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High constipation > 3d-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Haemophilus
Staphylococcus

Revision editor(s): Shulamite

Experiment 7


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps: Occurrence >3 days in infants <3 months, adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): Shulamite

Experiment 8


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (4 - 7months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic: Wessel's criteria applied to infants aged 4–7 months, adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-Covariate adjusted (4 - 7months)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Experiment 9


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps: Occurrence >3 days in infants aged 4–7 months, adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (4 - 7months)

NCBI Quality ControlLinks
Clostridium SS1Clostridium SS1

Revision editor(s): Shulamite

Experiment 10


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic: Wessel's criteria were applied to infants aged 8–12 months, and they were adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High colic: wessel-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Enterococcus

Revision editor(s): Shulamite

Experiment 11


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation: >3 days without defecation in infants aged 8–12 months, adjusted for covariates (Full cohort).
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation > 3d-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Parabacteroides

Revision editor(s): Shulamite

Experiment 12


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps: Occurrence >3 days in infants aged 8–12 months, adjusted for covariates (Full cohort).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Enterococcus
Clostridium SS1Clostridium SS1

Revision editor(s): Shulamite

Experiment 13


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-crude (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-crude (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, crude model) in infants <3 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-crude (< 3months)

NCBI Quality ControlLinks
Sutterella
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Signature 2

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High colic: wessel-crude (< 3months)

NCBI Quality ControlLinks
Bifidobacterium

Revision editor(s): Shulamite

Experiment 14


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-crude (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-crude (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation (>3 days without defecation, crude model) in infants <3 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation > 3d-crude (< 3months)

NCBI Quality ControlLinks
Enterococcus

Revision editor(s): Shulamite

Signature 2

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High constipation > 3d-crude (< 3months)

NCBI Quality ControlLinks
Lactococcus
Staphylococcus

Revision editor(s): Shulamite

Experiment 15


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-crude (4 - 7months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-crude (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, crude model) in infants aged 4–7 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-crude (4 - 7months)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Experiment 16


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-crude (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-crude (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, crude model) in infants aged 8–12 months, with no abx up to 3 months.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-crude (8-12months)

NCBI Quality ControlLinks
Veillonella

Revision editor(s): Shulamite

Experiment 17


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-crude (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-crude (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation (>3 days without defecation, crude model) in infants aged 8–12 months, with no abx up to 3 months.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation > 3d-crude (8-12months)

NCBI Quality ControlLinks
Parabacteroides

Revision editor(s): Shulamite

Experiment 18


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, covariate-adjusted model) in infants <3 months, with no abx up to 3 months.

Lab analysis

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Not specified

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): Shulamite

Experiment 19


Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation (>3 days without defecation, covariate-adjusted model) in infants <3 months, with no abx up to 3 months.
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 platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/02

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High constipation > 3d-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Staphylococcus

Revision editor(s): Shulamite

Experiment 20


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel crude <3 months (Full cohort)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel adjusted <3 months (Full cohort)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel covariate Adjusted <3months in the Full cohort
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel crude <3 months (Full cohort) and Colic:Wessel adjusted <3 months (Full cohort)

Abundance in Group 1: increased abundance in Colic:Wessel adjusted <3 months (Full cohort)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel crude <3 months (Full cohort) and Colic:Wessel adjusted <3 months (Full cohort)

Abundance in Group 1: decreased abundance in Colic:Wessel adjusted <3 months (Full cohort)

NCBI Quality ControlLinks
Staphylococcus
Lactobacillus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 21


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Treatment Treatment,treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel No Antibiotics crude <3 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel No Antibiotics adjusted <3 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel covariate Adjusted No Antibiotics <3months group

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel No Antibiotics crude <3 months and Colic:Wessel No Antibiotics adjusted <3 months.

Abundance in Group 1: increased abundance in Colic:Wessel No Antibiotics adjusted <3 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel No Antibiotics crude <3 months and Colic:Wessel No Antibiotics adjusted <3 months.

Abundance in Group 1: decreased abundance in Colic:Wessel No Antibiotics adjusted <3 months

NCBI Quality ControlLinks
Staphylococcus
Bifidobacterium
Lactobacillus

Revision editor(s): MyleeeA

Experiment 22


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel Breastfed crude <3 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel Breastfed adjusted <3 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel Covariate adjusted <3 months Breastfed group.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel Breastfed <3 months and Colic:Wessel Breastfed adjusted <3 months.

Abundance in Group 1: increased abundance in Colic:Wessel Breastfed adjusted <3 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel Breastfed <3 months and Colic:Wessel Breastfed adjusted <3 months.

Abundance in Group 1: decreased abundance in Colic:Wessel Breastfed adjusted <3 months

NCBI Quality ControlLinks
Lactobacillus

Revision editor(s): MyleeeA

Experiment 23


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Functional abnormality of the gastrointestinal tract Functional abnormality of the GI tract,GI dysfunction,Functional abnormality of the gastrointestinal tract,functional abnormality of the gastrointestinal tract
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel crude 4-7 months (Full cohort)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel adjusted 4-7months (Full cohort)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel covariate Adjusted 4-7 months in the Full cohort

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations betweenColic:Wessel crude 4-7 months (Full cohort) and Colic:Wessel adjusted 4-7 months (Full cohort).

Abundance in Group 1: increased abundance in Colic:Wessel adjusted 4-7months (Full cohort)

NCBI Quality ControlLinks
Mediterraneibacter gnavus
Staphylococcus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations betweenColic:Wessel crude 4-7 months (Full cohort) and Colic:Wessel adjusted 4-7 months (Full cohort).

Abundance in Group 1: decreased abundance in Colic:Wessel adjusted 4-7months (Full cohort)

NCBI Quality ControlLinks
Bifidobacterium
Lactobacillus

Revision editor(s): MyleeeA

Experiment 24


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Treatment Treatment,treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel No Antibiotics crude 4-7 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel No Antibiotics adjusted 4-7 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel covariate Adjusted No Antibiotics 4-7 months group

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel No Antibiotics crude 4-7 months and Colic:Wessel No Antibiotics adjusted 4-7 months.

Abundance in Group 1: increased abundance in Colic:Wessel No Antibiotics adjusted 4-7 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel No Antibiotics crude 4-7 months and Colic:Wessel No Antibiotics adjusted 4-7 months.

Abundance in Group 1: decreased abundance in Colic:Wessel No Antibiotics adjusted 4-7 months

NCBI Quality ControlLinks
Lactobacillus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 25


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colic:Wessel Breastfed crude 4-7 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colic:Wessel Breastfed adjusted 4-7 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colic:Wessel Covariate adjusted 4-7 months Breastfed group.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel Breastfed crude 4-7 months and Colic:Wessel Breastfed adjusted 4-7 months.

Abundance in Group 1: increased abundance in Colic:Wessel Breastfed adjusted 4-7 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Colic:Wessel Breastfed crude 4-7 months and Colic:Wessel Breastfed adjusted 4-7 months.

Abundance in Group 1: decreased abundance in Colic:Wessel Breastfed adjusted 4-7 months

NCBI Quality ControlLinks
Lactobacillus

Revision editor(s): MyleeeA

Experiment 26


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Constipation Constipation,Costiveness,Dyschezia,constipation
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d crude <3 months (Full cohort)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d adjusted <3 months (Full cohort)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d covariate Adjusted <3months in the Full cohort

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d crude <3 months (Full cohort) and Constipation >3d adjusted <3 months (Full cohort)

Abundance in Group 1: increased abundance in Constipation >3d adjusted <3 months (Full cohort)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d crude <3 months (Full cohort) and Constipation >3d adjusted <3 months (Full cohort)

Abundance in Group 1: decreased abundance in Constipation >3d adjusted <3 months (Full cohort)

NCBI Quality ControlLinks
Bifidobacterium
Staphylococcus
Lactobacillus

Revision editor(s): MyleeeA

Experiment 27


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Treatment Treatment,treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d No Antibiotics crude <3 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d No Antibiotics adjusted <3 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d covariate Adjusted <3months in the No Antibiotics group.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d No Antibiotics crude <3 months and Constipation >3d No Antibiotics adjusted <3 months

Abundance in Group 1: increased abundance in Constipation >3d No Antibiotics adjusted <3 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d No Antibiotics crude <3 months and Constipation >3d No Antibiotics adjusted <3 months

Abundance in Group 1: decreased abundance in Constipation >3d No Antibiotics adjusted <3 months

NCBI Quality ControlLinks
Staphylococcus
Lactobacillus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 28


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d Breastfed crude <3 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d Breastfed adjusted <3 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d Covariate adjusted <3 months Breastfed group.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d Breastfed crude <3 months and Constipation >3d Breastfed adjusted <3 months

Abundance in Group 1: increased abundance in Constipation >3d Breastfed adjusted <3 months

NCBI Quality ControlLinks
Lactobacillus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d Breastfed crude <3 months and Constipation >3d Breastfed adjusted <3 months

Abundance in Group 1: decreased abundance in Constipation >3d Breastfed adjusted <3 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus
Staphylococcus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 29


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Constipation Constipation,Costiveness,Dyschezia,constipation
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d crude 4-7 months (Full cohort)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d adjusted 4-7 months (Full cohort)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d covariate Adjusted 4-7 months in the Full cohort

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d crude 4-7 months (Full cohort) and Constipation >3d adjusted 4-7 months (Full cohort).

Abundance in Group 1: increased abundance in Constipation >3d adjusted 4-7 months (Full cohort)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d crude 4-7 months (Full cohort) and Constipation >3d adjusted 4-7 months (Full cohort).

Abundance in Group 1: decreased abundance in Constipation >3d adjusted 4-7 months (Full cohort)

NCBI Quality ControlLinks
Staphylococcus
Lactobacillus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 30


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d Breastfed crude 4-7 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d Breastfed adjusted 4-7 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d Covariate adjusted 4-7 months Breastfed group.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d Breastfed crude 4-7 months and Constipation >3d Breastfed adjusted 4-7 months.

Abundance in Group 1: increased abundance in Constipation >3d Breastfed adjusted 4-7 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d Breastfed crude 4-7 months and Constipation >3d Breastfed adjusted 4-7 months

Abundance in Group 1: decreased abundance in Constipation >3d Breastfed adjusted 4-7 months

NCBI Quality ControlLinks
Staphylococcus
Lactobacillus
Bifidobacterium

Revision editor(s): MyleeeA

Experiment 31


Needs review

Curated date: 2025/05/02

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Treatment Treatment,treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Constipation >3d No Antibiotics crude 4-7 months
Group 1 name Corresponds to the case (exposed) group for case-control studies
Constipation >3d No Antibiotics adjusted 4-7 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Constipation >3d covariate Adjusted No Antibiotics 4-7 months group

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d No antibiotics crude 4-7 months and Constipation >3d No antibiotics adjusted 4-7 months

Abundance in Group 1: increased abundance in Constipation >3d No Antibiotics adjusted 4-7 months

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 5C

Description: Results of regression model testing associations between Constipation >3d No antibiotics crude 4-7 months and Constipation >3d No antibiotics adjusted 4-7 months

Abundance in Group 1: decreased abundance in Constipation >3d No Antibiotics adjusted 4-7 months

NCBI Quality ControlLinks
Lactobacillus
Staphylococcus

Revision editor(s): MyleeeA

Experiment 32


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Constipation <3d Breastfed >3months (Crude)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Constipation <3d Breastfed >3months (Crude)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, had constipation <3days, were >3months and were in the crude group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Constipation <3days, >3 months Breastfed (Crude) stool microbiota core genera

Abundance in Group 1: decreased abundance in High Constipation <3d Breastfed >3months (Crude)

NCBI Quality ControlLinks
Staphylococcus

Revision editor(s): MyleeeA

Experiment 33


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Cramps <3d Breastfed >3months (Crude)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Cramps <3d Breastfed >3months (Crude)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, had cramps <3days, were >3months and were in the crude group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Cramps <3days, >3 months Breastfed (Crude) stool microbiota core genera

Abundance in Group 1: decreased abundance in High Cramps <3d Breastfed >3months (Crude)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): MyleeeA

Experiment 34


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Colic:Wessel Breastfed 4-7months (Crude)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Colic:Wessel Breastfed 4-7months (Crude)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, were Colic:Wessel 4-7 months and were in the crude group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Colic:Wessel Breastfed 4-7 months (Crude) stool microbiota core genera

Abundance in Group 1: increased abundance in High Colic:Wessel Breastfed 4-7months (Crude)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Experiment 35


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Colic:Wessel Breastfed 8-12months (Crude)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Colic:Wessel Breastfed 8-12months (Crude)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, were Colic:Wessel 8-12 months and were in the crude group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Colic:Wessel Breastfed 8-12 months (Crude) stool microbiota core genera

Abundance in Group 1: decreased abundance in High Colic:Wessel Breastfed 8-12months (Crude)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Experiment 36


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Colic:Wessel Breastfed >3months (Covariate adjusted)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Colic:Wessel Breastfed >3months (Covariate adjusted)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, were Colic:Wessel >3 months and were in the Covariate adjusted group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Colic:Wessel Breastfed >3 months (Covariate adjusted) stool microbiota core genera

Abundance in Group 1: decreased abundance in High Colic:Wessel Breastfed >3months (Covariate adjusted)

NCBI Quality ControlLinks
Sutterella

Revision editor(s): MyleeeA

Experiment 37


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Constipation <3d Breastfed >3months (Covariate adjusted)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low Constipation <3d Breastfed >3months (Covariate adjusted)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, had constipation <3days, were >3months and were in the Covariate adjusted group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Constipation <3days, >3 months Breastfed (Covariate adjusted) stool microbiota core genera

Abundance in Group 1: decreased abundance in Low Constipation <3d Breastfed >3months (Covariate adjusted)

NCBI Quality ControlLinks
Staphylococcus

Revision editor(s): MyleeeA

Experiment 38


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Cramps <3d Breastfed >3months (Covariate adjusted)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low Cramps <3d Breastfed >3months (Covariate adjusted)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, had cramps <3days, were >3months and were in the Covariate adjusted group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Cramps <3days, >3 months Breastfed (Covariate adjusted) stool microbiota core genera

Abundance in Group 1: decreased abundance in Low Cramps <3d Breastfed >3months (Covariate adjusted)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): MyleeeA

Experiment 39


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Colic:Wessel Breastfed 4-7 months (Covariate adjusted)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Colic:Wessel Breastfed 4-7 months (Covariate adjusted)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, were Colic:Wessel 4-7 months and were in the Covariate adjusted group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Colic:Wessel Breastfed 4-7 months (Covariate adjusted) stool microbiota core genera

Abundance in Group 1: increased abundance in High Colic:Wessel Breastfed 4-7 months (Covariate adjusted)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Experiment 40


Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low Colic:Wessel Breastfed 8-12months (Covariate adjusted)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low Colic:Wessel Breastfed 8-12months (Covariate adjusted)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Infants who were exclusively breastfed before sampling, were Colic:Wessel 8-12 months and were in the Covariate adjusted group.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/05/03

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Table 6: Part C

Description: Results of regression model testing associations between Colic:Wessel Breastfed 8-12 months (Covariate adjusted) stool microbiota core genera

Abundance in Group 1: decreased abundance in Low Colic:Wessel Breastfed 8-12months (Covariate adjusted)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): MyleeeA

Experiment 41


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Functional abnormality of the gastrointestinal tract Functional abnormality of the GI tract,GI dysfunction,Functional abnormality of the gastrointestinal tract,functional abnormality of the gastrointestinal tract
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted (< 3months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (< 3months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps (>3 days of symptoms, covariate-adjusted model) in infants <3 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (< 3months)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): Shulamite

Experiment 42


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (4 - 7months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, covariate-adjusted model) in infants aged 4–7 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High colic: wessel-Covariate adjusted (4 - 7months)

NCBI Quality ControlLinks
Mediterraneibacter gnavus

Revision editor(s): Shulamite

Experiment 43


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted (4 - 7months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (4 - 7months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps (>3 days of symptoms, covariate-adjusted model) in infants aged 4–7 months, with no abx up to 3 months.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (4 - 7months)

NCBI Quality ControlLinks
Clostriidium SS1Clostriidium SS1

Revision editor(s): Shulamite

Experiment 44


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low colic: wessel-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High colic: wessel-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High colic (Wessel’s criteria, covariate-adjusted model) in infants aged 8–12 months, with no abx up to 3 months.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High colic: wessel-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Enterococcus

Revision editor(s): Shulamite

Experiment 45


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low constipation >3d-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High constipation > 3d-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High constipation (>3 days without defecation, covariate-adjusted model) in infants aged 8–12 months, with no abx up to 3 months.
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

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: increased abundance in High constipation > 3d-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Parabacteroides

Revision editor(s): Shulamite

Experiment 46


Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low cramps >3d-Covariate adjusted (8-12months)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High cramps >3d-Covariate adjusted (8-12months)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
High cramps (>3 days of symptoms, covariate-adjusted model) in infants aged 8–12 months, with no abx up to 3 months.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2025/05/03

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table S6

Description: Results of regression models testing associations between one-month stool microbiota core genera and functional gastrointestinal symptoms.

Abundance in Group 1: decreased abundance in High cramps >3d-Covariate adjusted (8-12months)

NCBI Quality ControlLinks
Enterococcus
Clostridium SS1Clostridium SS1

Revision editor(s): Shulamite