Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/18

Curator: Aishat

Revision editor(s): Aishat, Victoria, Scholastica

Subjects

Location of subjects: South Africa

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: Infants who are HIV unexposed and uninfected (iHUU) at week 1

Group 1 name Corresponds to the case (exposed) group for case-control studies: Infants who are HIV exposed but uninfected (iHEU) at week 1

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants at 1 week of age born to mothers from South Africa who have HIV but are not themselves infected with HIV

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 61

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: 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).: centered log-ratio

Statistical test: ANCOM

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/18

Curator: Aishat

Revision editor(s): Aishat, Scholastica

Source: Table 2

Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa

Abundance in Group 1: increased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 1

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Klebsiella variicola
unclassified Sutterella
unclassified Holdemanella
Parabacteroides merdae
unclassified Catenibacterium
Blautia obeum
unclassified Senegalimassilia
Bifidobacterium breve
Klebsiella quasipneumoniae
unclassified Parolsenella
unclassified Blautia
[Ruminococcus] torques
Collinsella aerofaciens
unclassified Subdoligranulum
Phocaeicola vulgatus
Klebsiella pneumoniae
unclassified Megamonas
Romboutsia ilealis
unclassified Faecalibacterium
Fusobacterium mortiferum
Enterococcus faecium
Parabacteroides distasonis

Revision editor(s): Aishat, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/18

Curator: Aishat

Revision editor(s): Aishat, Scholastica

Source: Table 2

Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa

Abundance in Group 1: decreased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 1

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unclassified Actinomyces
Parabacteroides distasonis

Revision editor(s): Aishat, Scholastica

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/06/24

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Infants who are HIV unexposed and uninfected (iHUU) at week 15

Group 1 name Corresponds to the case (exposed) group for case-control studies: Infants who are HIV exposed but uninfected (iHEU) at week 15

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV adjusted by mode of feeding

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "mode of feeding" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.mode of feeding

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/06/24

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding

Abundance in Group 1: increased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 15

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Bifidobacterium adolescentis
Collinsella aerofaciens
Dorea formicigenerans
Enterococcus faecalis
Enterococcus gilvus
Enterococcus raffinosus
Faecalibacterium prausnitzii
Klebsiella quasipneumoniae
Lactococcus lactis
Streptococcus gallolyticus
Veillonella atypica
unclassified Enterococcus
unclassified Granulicatella
unclassified Staphylococcus
unclassified Clostridium innocuum groupunclassified Clostridium innocuum group

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/06/24

Curator: Scholastica

Revision editor(s): Scholastica

Source: Table 2

Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding

Abundance in Group 1: decreased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 15

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Bacteroides caccae
Klebsiella michiganensis
Lacticaseibacillus rhamnosus
Lactobacillus gasseri
Megasphaera elsdenii
Segatella copri
[Ruminococcus] torques
unclassified Olsenella
unclassified Prevotella

Revision editor(s): Scholastica

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/06/24

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants at 15 weeks of age born to mothers from South Africa who have HIV but are not themselves infected with HIV when adjusted for reported antibiotic (co-trimoxazole) prophylaxis history adjusted by mode of feeding and reported antibiotics history

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: antibiotic exposure, Confounders controlled for: "mode of feeding" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.mode of feeding

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/06/24

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S2

Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 15 weeks of age in South Africa adjusted by mode of feeding and reported antibiotics history

Abundance in Group 1: increased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 15

NCBI	Quality Control	Links
Collinsella aerofaciens
Klebsiella quasipneumoniae
Bifidobacterium adolescentis
Streptococcus gallolyticus
Enterococcus gilvus
Lactococcus lactis
Enterococcus raffinosus
unclassified Clostridium innocuum groupunclassified Clostridium innocuum group
Dorea formicigenerans
Corynebacterium propinquum
Faecalibacterium prausnitzii
Leuconostoc lactis
unclassified Granulicatella
Rothia mucilaginosa
Streptococcus salivarius
Streptococcus peroris

Revision editor(s): Scholastica

Signature 2