Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Robertson SJ, Lemire P, Maughan H, Goethel A, Turpin W, Bedrani L, Guttman DS, Croitoru K, Girardin SE, Philpott DJ
Journal
Cell reports
Year
2019
Keywords:
co-housing, intestinal, littermates, microbiota, microbiota standardization, mouse
The intestinal microbiota is a fundamental factor that broadly influences physiology. Thus, studies using transgenic animals should be designed to limit the confounding effects of microbiota variation between strains. Here, we report the impact on intestinal microbiota of co-housed versus F2-generation littermates, two commonly used techniques to standardize microbiota in animal models. Our results establish that while fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct. In contrast, strain inter-crossing to generate F2 littermates allows robust microbiota standardization in fecal, colon, and ileum sampling locations. Using reciprocal inter-crosses of P1 parents, we identify dissymmetry in F2 community structures caused by maternal transmission, in particular of the Verrucomicrobiaceae. Thus, F2 littermate animals from a unidirectional P1 cross should be used as a standard method to minimize the influence of the microbiota in genotype-phenotype studies.

Experiment 1


Needs review

Curated date: 2024/03/28

Curator: Nayohmee

Revision editor(s): Nayohmee, Aleru Divine

Subjects

Location of subjects
Canada
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
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
Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
JAX group
Group 1 name Corresponds to the case (exposed) group for case-control studies
JAX-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
16
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None

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
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2.0
Matched on Factors on which subjects have been matched on in a case-control study
age

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3D

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Anaeroplasma
Bacteroides
Dehalobacterium
Lactobacillus
Mucispirillum
Oscillospiraceae
Parabacteroides

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3D

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in JAX-CH group

NCBI Quality ControlLinks
Allobaculum
Bifidobacterium

Revision editor(s): Aleru Divine

Experiment 2


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
TAC-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Taconic Farms (TAC-CH).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3E

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in TAC-CH group

NCBI Quality ControlLinks
Anaerostipes
Anaerotruncus
Turicibacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2E

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in TAC-CH group

NCBI Quality ControlLinks
Candidatus Arthromitus
Clostridiaceae
Lachnospiraceae
Oscillospiraceae
Rikenellaceae

Revision editor(s): Aleru Divine

Experiment 3


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC-CH group
Group 1 name Corresponds to the case (exposed) group for case-control studies
JAX-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
Group 0 sample size Number of subjects in the control (unexposed) group
16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3B

Description: LEfSe plots showing differential taxa (family level) in co-housed mice.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Turicibacteraceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3B

Description: LEfSe plots showing differential taxa (family level) in co-housed mice.

Abundance in Group 1: decreased abundance in JAX-CH group

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): Aleru Divine

Experiment 4


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Group 0 name Corresponds to the control (unexposed) group for case-control studies
JAX group
Group 0 sample size Number of subjects in the control (unexposed) group
12

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3I

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Bacteroides
Dehalobacterium
Lactobacillus
Mucispirillum
Parabacteroides

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3I

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in JAX-CH group

NCBI Quality ControlLinks
Allobaculum
Bifidobacterium
Oscillospiraceae
Rikenellaceae
Ruminococcus

Revision editor(s): Aleru Divine

Experiment 5


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
TAC-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Taconic Farms (TAC-CH).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3J

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in TAC-CH group

NCBI Quality ControlLinks
Coprococcus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3J

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in TAC-CH group

NCBI Quality ControlLinks
Clostridiaceae
Dorea
Lachnospiraceae

Revision editor(s): Aleru Divine

Experiment 6


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC-CH group
Group 1 name Corresponds to the case (exposed) group for case-control studies
JAX-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
Group 0 sample size Number of subjects in the control (unexposed) group
16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3G

Description: LEfSe plots showing differential taxa (family level) in co-housed mice.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Anaerovoracaceae
Oscillospiraceae
Turicibacteraceae
Verrucomicrobiaceae
DehalobacteriaceaeDehalobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3G

Description: LEfSe plots showing differential taxa (family level) in co-housed mice.

Abundance in Group 1: decreased abundance in JAX-CH group

NCBI Quality ControlLinks
Porphyromonadaceae
RF39RF39

Revision editor(s): Aleru Divine

Experiment 7


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
JAX group
Group 0 sample size Number of subjects in the control (unexposed) group
12

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3N

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Bacteroides
Dehalobacterium
Mucispirillum
Parabacteroides

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3N

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in JAX-CH group

NCBI Quality ControlLinks
Allobaculum
Bifidobacterium
Rikenellaceae
Staphylococcus

Revision editor(s): Aleru Divine

Experiment 8


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
TAC-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Taconic Farms (TAC-CH).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3O

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: increased abundance in TAC-CH group

NCBI Quality ControlLinks
Turicibacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3O

Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.

Abundance in Group 1: decreased abundance in TAC-CH group

NCBI Quality ControlLinks
Gammaproteobacteria

Revision editor(s): Aleru Divine

Experiment 9


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC-CH group
Group 1 name Corresponds to the case (exposed) group for case-control studies
JAX-CH group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
Group 0 sample size Number of subjects in the control (unexposed) group
16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3L

Description: LEfSe plots showing differential taxa (family level) in co-housed mice.

Abundance in Group 1: increased abundance in JAX-CH group

NCBI Quality ControlLinks
Oscillospiraceae
Turicibacteraceae
Verrucomicrobiaceae
DehalobacteriaceaeDehalobacteriaceae

Revision editor(s): Aleru Divine

Experiment 10


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces , Colon 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,Hindgut,Large bowel,Posterior intestine,Colon,colon
Group 0 name Corresponds to the control (unexposed) group for case-control studies
JAX-CH colon group
Group 1 name Corresponds to the case (exposed) group for case-control studies
JAX-CH fecal pellets group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure S3

Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).

Abundance in Group 1: increased abundance in JAX-CH fecal pellets group

NCBI Quality ControlLinks
Adlercreutzia
Akkermansia
Anaerostipes
Bifidobacterium
Clostridiaceae
Erysipelotrichaceae
Lactobacillus
Rickettsiales
Turicibacter

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure S3

Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).

Abundance in Group 1: decreased abundance in JAX-CH fecal pellets group

NCBI Quality ControlLinks
Anaeroplasma
Anaerotruncus
Coprococcus
Dehalobacterium
Eubacteriales
Lachnospiraceae
Mucispirillum
Oscillospiraceae
Rikenellaceae
Ruminococcus
Ruminococcus sp.

Revision editor(s): Aleru Divine

Experiment 11


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
TAC-CH colon group
Group 1 name Corresponds to the case (exposed) group for case-control studies
TAC-CH fecal pellets group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure S3

Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).

Abundance in Group 1: increased abundance in TAC-CH fecal pellets group

NCBI Quality ControlLinks
Adlercreutzia
Akkermansia
Bacteroides
Bifidobacterium
Clostridiaceae
Erysipelotrichaceae
Lactobacillus
Parabacteroides
Rickettsiales
RF39RF39

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure S3

Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).

Abundance in Group 1: decreased abundance in TAC-CH fecal pellets group

NCBI Quality ControlLinks
Eubacteriales
Mucispirillum
Anaeroplasma
Oscillospiraceae
Oscillospira
Ruminococcus
Ruminococcus sp.
Coprococcus

Revision editor(s): Aleru Divine

Experiment 12


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
P1 JAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Statistical test
Dunn's test
Kruskall-Wallis
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified
Matched on Factors on which subjects have been matched on in a case-control study
Not specified

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: increased abundance in P1 JAX group

NCBI Quality ControlLinks
Akkermansia
Clostridium
Adlercreutzia
Lactobacillus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: decreased abundance in P1 JAX group

NCBI Quality ControlLinks
Parabacteroides
Bacteroides
Candidatus Arthromitus sp. SFB-mouse
Mucispirillum
Oscillospiraceae

Revision editor(s): Aleru Divine

Experiment 13


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 JAX group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 14


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mTAC group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fecal pellet samples from the maternal F1-generation of Taconic farms (mTAC) mice.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 15


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
F1 mTAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in F1 mJAX and mTAC mice

Abundance in Group 1: increased abundance in F1 mJAX group

NCBI Quality ControlLinks
Akkermansia

Revision editor(s): Aleru Divine

Experiment 16


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
P1 JAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: increased abundance in P1 JAX group

NCBI Quality ControlLinks
Akkermansia
Clostridium
Anaeroplasma
Bifidobacterium
Acinetobacter
Rikenellaceae
Muribaculaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: decreased abundance in P1 JAX group

NCBI Quality ControlLinks
Parabacteroides
Bacteroides
Candidatus Arthromitus sp. SFB-mouse
Mucispirillum
Dehalobacterium
Dorea

Revision editor(s): Aleru Divine

Experiment 17


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 JAX group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 18


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mTAC group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon samples from the maternal F1-generation of Taconic farms (mTAC) mice.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 19


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
F1 mTAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: increased abundance in F1 mJAX group

NCBI Quality ControlLinks
Akkermansia
Muribaculaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice

Abundance in Group 1: decreased abundance in F1 mJAX group

NCBI Quality ControlLinks
Candidatus Arthromitus sp. SFB-mouse
Dehalobacterium

Revision editor(s): Aleru Divine

Experiment 20


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
P1 JAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.

Abundance in Group 1: increased abundance in P1 JAX group

NCBI Quality ControlLinks
Akkermansia
Clostridium
Adlercreutzia
Anaeroplasma

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.

Abundance in Group 1: decreased abundance in P1 JAX group

NCBI Quality ControlLinks
Parabacteroides
Bacteroides
Candidatus Arthromitus sp. SFB-mouse
Mucispirillum
Dehalobacterium

Revision editor(s): Aleru Divine

Experiment 21


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 JAX group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 22


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
P1 TAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mTAC group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Ileum samples from the maternal F1-generation of Taconic farms (mTAC) mice.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 23


Needs review

Curated date: 2024/04/15

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
F1 mTAC group
Group 1 name Corresponds to the case (exposed) group for case-control studies
F1 mJAX group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
Group 0 sample size Number of subjects in the control (unexposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/16

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 6 and S7

Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.

Abundance in Group 1: increased abundance in F1 mJAX group

NCBI Quality ControlLinks
Akkermansia

Revision editor(s): Aleru Divine