Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach

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Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Subjects

Location of subjects: Spain

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: Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants (0 - 12 months old)

Group 0 sample size Number of subjects in the control (unexposed) group: 43

Group 1 sample size Number of subjects in the case (exposed) group: 38

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months prior to study recruitment

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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: MaAsLin2

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: decreased

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4 and 5

Description: Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.

Abundance in Group 1: increased abundance in Infants

NCBI	Quality Control	Links
Acetanaerobacterium
Adlercreutzia
Alistipes
Anaerotruncus
Anaerovorax
Bacillota
Bacteroidota
Barnesiella
Blautia
Butyricicoccus
Coprobacter
Coprococcus
Coriobacteriaceae
Dialister
Eubacteriales
Faecalibacterium
Fusicatenibacter
Gemmiger
Gordonibacter
Holdemania
Intestinimonas
Mogibacterium
Oscillibacter
Oscillospiraceae
Roseburia
Ruminococcus
Ruminococcus sp.
unclassified Bacteria
Clostridium cluster XIVaClostridium cluster XIVa

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4 and 5

Description: Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to mothers.

Abundance in Group 1: decreased abundance in Infants

NCBI	Quality Control	Links
Actinomyces
Actinomycetota
Atopobium
Bacillariophyta
Bifidobacterium
Candidatus Parcubacteria
Cyanobacteriota
Eggerthella
Enterobacter
Enterococcus
Erysipelotrichaceae
Escherichia/Shigella sp.
Finegoldia
Gemella
Granulicatella
Klebsiella
Lactobacillus
Mesorhizobium
Pseudomonadota
Rothia
Sphingomonas
Staphylococcus
Streptophyta
Veillonella

Revision editor(s): Aleru Divine

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

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: Grandmothers

Group 0 sample size Number of subjects in the control (unexposed) group: 40

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4 and 5

Description: Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.

Abundance in Group 1: increased abundance in Infants

NCBI	Quality Control	Links
Acetanaerobacterium
Adlercreutzia
Aestuariispira
Alistipes
Bacillota
Bacteroidota
Barnesiella
Bilophila
Blautia
Butyricicoccus
Clostridia
Coprobacter
Coprococcus
Coriobacteriaceae
Eubacteriales
Methanobacteriota
Faecalibacterium
Faecalicoccus
Fusicatenibacter
Gemmiger
Holdemania
Intestinimonas
Methanobrevibacter
Olsenella
Oscillibacter
Oscillospiraceae
Phascolarctobacterium
Romboutsia
Roseburia
Ruminococcus
Sporobacter
Turicibacter
unclassified Bacteria
Clostridium cluster XIVbClostridium cluster XIVb

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4 and 5

Description: Differential abundance results at the phylum and genus levels for 16S rRNA gene sequencing in infants compared to grandmothers.

Abundance in Group 1: decreased abundance in Infants

NCBI	Quality Control	Links
Actinomyces
Actinomycetota
Atopobium
Bifidobacterium
Enterobacter
Escherichia/Shigella sp.
Finegoldia
Gemella
Granulicatella
Haemophilus
Klebsiella
Mesorhizobium
Pseudomonadota
Sphingomonas
Staphylococcus
Veillonella

Revision editor(s): Aleru Divine

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

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: Mothers

Group 0 sample size Number of subjects in the control (unexposed) group: 43

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4, 5 and 6

Description: Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.

Abundance in Group 1: increased abundance in Infants

NCBI	Quality Control	Links
Acutalibacter
Adlercreutzia
Adlercreutzia equolifaciens
Adlercreutzia equolifaciens subsp. celatus
Agathobaculum
Agathobaculum butyriciproducens
Agathobaculum sp.
Alistipes
Alistipes senegalensis
Alistipes shahii
Anaeromassilibacillus
Anaeromassilibacillus sp.
Anaerotignum
Anaerotruncus
Anaerotruncus colihominis
Angelakisella massiliensis
Asaccharobacter
Bacillota
Bacillota bacterium
Bacteroides finegoldii
Bacteroides stercoris
Barnesiella
Bittarella (ex Durand et al. 2017)
Blautia massiliensis (ex Durand et al. 2017)
Butyricicoccus
Catenibacillus
Catenibacillus scindens
Chloroflexota
Christensenella
Clostridia bacterium
Clostridiaceae bacterium
Clostridium phoceensis
Coprococcus
Dialister
Dialister sp.
Dielma
Dielma fastidiosa
Dorea
Dorea longicatena
Dorea sp.
Dysosmobacter
Eubacteriales Family XII. Incertae Sedis
Eubacterium
Evtepia
Faecalibacterium
Faecalibacterium prausnitzii
Faecalicatena
Faecalicatena fissicatena
Flavonifractor sp.
Flintibacter
Flintibacter sp.
Fusicatenibacter
Gemmiger
Gordonibacter
Holdemania
Hydrogeniiclostridium
Intestinimonas massiliensis (ex Afouda et al. 2020)
Lachnospira
Lachnotalea
Lactonifactor
Lawsonibacter
Massiliimalia
Massiliimalia timonensis
Merdimmobilis
Mogibacterium
Odoribacter
Odoribacter splanchnicus
Oscillibacter
Oscillibacter sp.
Oscillospira
Oscillospiraceae bacterium
Paenibacillus
Pseudoflavonifractor capillosus
Raoultibacter
Roseburia
Roseburia faecis
Roseburia inulinivorans
Roseburia sp.
Ruminococcus
Ruminococcus bicirculans (ex Liu et al. 2021)
Ruminococcus callidus
Spirochaetota
Streptococcus pneumoniae
Streptococcus sp.
Subdoligranulum
Subdoligranulum variabile
Veillonella atypica
Veillonella tobetsuensis
Xanthomonas
[Clostridium] nexile
unclassified Bacillota
unclassified Bacteria
unclassified Clostridia
unclassified Coriobacteriia
unclassified Eggerthellaceae
unclassified Eubacteriales
unclassified Lachnospiraceae
unclassified Lentisphaeria
unclassified Oscillospiraceae
unclassified Paenibacillaceae
UnmappedUnmapped

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4, 5 and 6

Description: Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to mothers.

Abundance in Group 1: decreased abundance in Infants

NCBI	Quality Control	Links
Actinomycetota
Alistipes communis
Bifidobacterium
Bifidobacterium bifidum
Bifidobacterium breve
Bifidobacterium longum
Bittarella massiliensis (ex Liu et al. 2021)
Blautia glucerasea
Clostridiales bacterium
Coprococcus comes
Dysosmobacter sp.
Enterococcus
Escherichia
Escherichia coli
Eubacterium ramulus
Eubacterium sp.
Gardnerella
Holdemania filiformis
Holdemania massiliensis
Klebsiella
Lachnospira eligens
Lachnotalea sp.
Lactobacillus
Mediterraneibacter butyricigenes
Mogibacterium sp.
Pseudomonadota
Shigella
Streptococcus mitis
Streptophyta
Veillonella
unclassified Actinomycetaceae
unclassified Bifidobacteriaceae
unclassified Enterobacterales
unclassified Enterobacteriaceae
unclassified Streptococcaceae

Revision editor(s): Aleru Divine

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

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: Grandmothers

Group 0 sample size Number of subjects in the control (unexposed) group: 40

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4, 5 and 6

Description: Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.

Abundance in Group 1: increased abundance in Infants

NCBI	Quality Control	Links
Acutalibacter
Adlercreutzia
Adlercreutzia equolifaciens
Adlercreutzia equolifaciens subsp. celatus
Alistipes
Alistipes dispar
Alistipes onderdonkii
Alistipes senegalensis
Alistipes shahii
Anaerobutyricum
Anaeromassilibacillus
Anaeromassilibacillus sp.
Anaerotignum
Angelakisella
Angelakisella massiliensis
Asaccharobacter
Bacillota
Bacillota bacterium
Bilophila
Butyricicoccus
Chloroflexota
Clostridia bacterium
Clostridiaceae bacterium
Clostridiales bacterium
Clostridium phoceensis
Coprococcus
Coprococcus comes
Dorea
Dorea sp.
Dysosmobacter
Eubacterium
Methanobacteriota
Evtepia
Faecalibacterium
Faecalibacterium prausnitzii
Faecalicatena
Faecalicatena fissicatena
Fibrobacterota
Flavonifractor sp.
Flintibacter
Flintibacter sp.
Fusicatenibacter
Gemmiger
Harryflintia
Holdemania
Intestinimonas gabonensis
Lachnoclostridium
Lachnoclostridium sp.
Lachnospira
Lachnotalea
Lawsonibacter
Massiliimalia
Mogibacterium
Mogibacterium sp.
Odoribacter
Oscillibacter
Oscillibacter sp.
Oscillospiraceae
Paenibacillus
Phascolarctobacterium
Phascolarctobacterium faecium
Porphyromonadaceae bacterium
Pseudoflavonifractor
Pseudoflavonifractor capillosus
Romboutsia
Romboutsia timonensis
Roseburia inulinivorans
Roseburia sp.
Ruminococcus
Ruminococcus bromii
Ruminococcus callidus
Spirochaetota
Streptococcus pneumoniae
Streptococcus sp.
Subdoligranulum variabile
Trichuris
Veillonella atypica
Veillonella tobetsuensis
Xanthomonas
[Clostridium] nexile
unclassified Acidaminococcaceae
unclassified Bacilli
unclassified Bacillota
unclassified Bacteria
unclassified Bacteroidota
unclassified Clostridia
unclassified Coriobacteriales
unclassified Coriobacteriia
unclassified Eggerthellaceae
unclassified Eubacteriales
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Paenibacillaceae
UnmappedUnmapped

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/07/21

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Supplemental data 4, 5 and 6

Description: Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing in infants compared to grandmothers.

Abundance in Group 1: decreased abundance in Infants

NCBI	Quality Control	Links
Actinomycetota
Alistipes putredinis
Bifidobacterium
Bifidobacterium bifidum
Bifidobacterium breve
Bifidobacterium longum
Dysosmobacter sp.
Eggerthellaceae bacterium
Escherichia
Escherichia coli
Fusicatenibacter saccharivorans
Gardnerella
Klebsiella
Lachnotalea sp.
Lactobacillus
Lentisphaeria bacterium
Mediterraneibacter butyricigenes
Odoribacter splanchnicus
Pseudomonadota
Shigella
Streptophyta
Tyzzerella
Veillonella
unclassified Bifidobacteriaceae
unclassified Bifidobacteriales
unclassified Enterobacterales
unclassified Enterobacteriaceae
unclassified Streptococcaceae

Revision editor(s): Aleru Divine

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/09/23

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: Mothers and Grandmothers

Group 0 sample size Number of subjects in the control (unexposed) group: 83

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months before study recruitment

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Statistical Analysis

Statistical test: LEfSe

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.0

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/09/23

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 7E

Description: Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Infants – compared to the other two groups (Mothers and Grandmothers)

Abundance in Group 1: increased abundance in Infants

NCBI	Quality Control	Links
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Lactobacillaceae
Lactobacillus

Revision editor(s): Aleru Divine

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/09/23

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: Infants and Grandmothers

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Mothers of the infants

Group 0 sample size Number of subjects in the control (unexposed) group: 78

Group 1 sample size Number of subjects in the case (exposed) group: 43

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/09/23

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 7E

Description: Linear discriminant analysis (LDA) effect size (LEfSe) results showing the taxa enriched in the Mothers – compared to the other two groups (Infants and Grandmothers)

Abundance in Group 1: increased abundance in Mothers

NCBI	Quality Control	Links
Clostridia
Eubacteriales
Bacillota
Blautia
Dialister
Holdemania
Sutterella
Clostridium IIIClostridium III

Revision editor(s): Aleru Divine

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-9-24

Curated date: 2024/09/23

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: Infants and Mothers

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Grandmothers of the infants.

Group 0 sample size Number of subjects in the control (unexposed) group: 81

Group 1 sample size Number of subjects in the case (exposed) group: 40

Lab analysis

Statistical Analysis

Signature 1