COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/17

Curator: Cabidog

Revision editor(s): Cabidog, Folakunmi, ChiomaBlessing

Subjects

Location of subjects: China

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: Breast , Milk Mamma,Mammary part of chest,Mammary region,Breast,breast,Mammary gland milk,Milk,milk

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to vaccine , Timepoint Response to vaccine,response to vaccine,Timepoint,timepoint

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers at post vaccination timepoints; one week post-first dose, one week post second-dose, one month post-second dose.

Group 0 sample size Number of subjects in the control (unexposed) group: 44

Group 1 sample size Number of subjects in the case (exposed) group: 44

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).: 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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 1.5

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: figure 1g

Description: The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.

Abundance in Group 1: increased abundance in Mothers at post vaccination timepoints

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Acinetobacter ursingii
Roseomonas gilardii
unclassified Brevundimonas
unclassified Gordonia (in: high G+C Gram-positive bacteria)
unclassified Paracoccaceae

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: figure 1g

Description: The most differentially abundant taxa in mothers throughout all post-vaccination timepoints; at one week post-first dose, one week post-second dose and one month post-second dose.

Abundance in Group 1: decreased abundance in Mothers at post vaccination timepoints

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Helicobacter rodentium
unclassified Allobaculum
unclassified Muribaculaceae
unclassified Ralstonia
unclassified Turicibacter

Revision editor(s): Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to vaccine Response to vaccine,response to vaccine

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Low IgA mothers at Baseline

Group 1 name Corresponds to the case (exposed) group for case-control studies: High IgA mothers at Baseline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers with high IgA at baseline

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 18

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.004

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: Figure 2d

Description: Taxonomic differences in baseline microbiota between high- and low-IgA subjects.

Abundance in Group 1: increased abundance in High IgA mothers at Baseline

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Actinomyces massiliensis
Bacillota sensu stricto incertae sedis
Cutibacterium granulosum
Endobacter medicaginis
Fusobacterium
Neisseria elongata
Prevotella histicola
Ruminococcus callidus
Stutzerimonas balearica
unclassified Actinobacillus
unclassified Aggregatibacter
unclassified Alishewanella
unclassified Arachnia
unclassified Castellaniella
unclassified Monoglobus
unclassified Neisseria
unclassified Oscillospiraceae
unclassified Stomatobaculum
unclassified Sutterella
unclassified Terrisporobacter

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2024/02/15

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 2d

Description: Taxonomic differences in baseline microbiota between high- and low-IgA subjects.

Abundance in Group 1: decreased abundance in High IgA mothers at Baseline

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Corynebacterium kroppenstedtii
unclassified Acinetobacter
unclassified Brevundimonas

Revision editor(s): ChiomaBlessing

Experiment 3

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Low IgA mothers at one week post-second dose

Group 1 name Corresponds to the case (exposed) group for case-control studies: High IgA mothers at one week post-second dose

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers with high IgA at one week after receiving the second dose of the SARS-CoV-2 mRNA vaccine (BNT162b2).

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/22

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: Figure 3d

Description: Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects

Abundance in Group 1: increased abundance in High IgA mothers at one week post-second dose

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Bifidobacterium bifidum
Candidatus Marinarcus aquaticus
Streptococcus parasuis
unclassified Acidaminococcus
unclassified Bifidobacterium
unclassified Corynebacterium
unclassified Dorea
unclassified Eubacterium
unclassified Gemmobacter
unclassified Holdemanella
unclassified Leucobacter
unclassified Neptunomonas
unclassified Rhodobacter
unclassified Subdoligranulum
unclassified Vibrio

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2024/02/15

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 3d

Description: Taxonomic differences in microbiota one week post-second dose between high- and low-IgA subjects

Abundance in Group 1: decreased abundance in High IgA mothers at one week post-second dose

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Acinetobacter soli
unclassified Brevundimonas

Revision editor(s): ChiomaBlessing

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Mothers at pre-vaccination timepoint (baseline)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mothers at one week post-first dose

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers at one week after receiving the first dose of BNT162b2 vaccine.

Group 0 sample size Number of subjects in the control (unexposed) group: 44

Group 1 sample size Number of subjects in the case (exposed) group: 44

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 1.5

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: supplementary table 3

Description: differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.

Abundance in Group 1: increased abundance in Mothers at one week post-first dose

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Acinetobacter radioresistens
Acinetobacter soli
Acinetobacter ursingii
Caldibacillus thermoamylovorans
Empedobacter brevis
Eubacterium ventriosum
Haemophilus haemolyticus
Haemophilus parahaemolyticus
Roseomonas gilardii
unclassified Actinobacillus
unclassified Anoxybacillus
unclassified Bacillus (in: firmicutes)
unclassified Bergeyella
unclassified Brevundimonas
unclassified Duganella
unclassified Empedobacter
unclassified Enhydrobacter
unclassified Flavobacterium
unclassified Janthinobacterium
unclassified Microbacterium
unclassified Paracoccaceae
unclassified Providencia
unclassified Pseudarthrobacter
unclassified Shewanella
unclassified Sphingomonadaceae
unclassified Sphingomonas
Clostridiales bacterium CHKCI001
unclassified Gordonia (in: high G+C Gram-positive bacteria)
unclassified Sphingobacterium
unclassified Allorhizobium-Neorhizobium Pararhizobium-Rhizobiumunclassified Allorhizobium-Neorhizobium Pararhizobium-Rhizobium

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2024/02/15

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary Table 3

Description: Differential abundance of mothers one week after first dose of BNT162b2 when compared to baseline.

Abundance in Group 1: decreased abundance in Mothers at one week post-first dose

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Acinetobacter baumannii
Lactobacillus intestinalis
unclassified Allobaculum
unclassified Bacilli
unclassified Comamonadaceae
unclassified Fusicatenibacter
unclassified Parabacteroides
unclassified Ralstonia
unclassified Turicibacter
unclassified Muribaculaceae

Revision editor(s): ChiomaBlessing

Experiment 5

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mothers at one week post-second dose

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers at one week post-second dose of BNT162b2 vaccine.

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

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: supplementary table 3

Description: differential abundance of mothers at one week post second dose of BNT162b2 when compared to baseline.

Abundance in Group 1: increased abundance in Mothers at one week post-second dose

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Acinetobacter baumannii
Acinetobacter soli
Acinetobacter ursingii
Brevundimonas olei
Epilithonimonas hominis
Moraxella atlantae
Moraxella porci
Paenibacillus macerans
Peredibacter starrii
Prevotella melaninogenica
Roseomonas gilardii
unclassified Acinetobacter
unclassified Actinobacillus
unclassified Brevundimonas
unclassified Chitinophagaceae
unclassified Gemmobacter
unclassified Gordonia (in: high G+C Gram-positive bacteria)
unclassified Klebsiella
unclassified Leptotrichia
unclassified Megamonas
unclassified Nautella
unclassified Neptunomonas
unclassified Ochrobactrum
unclassified Paracoccaceae
unclassified Peptoniphilus
unclassified Serratia (in: enterobacteria)
unclassified Vogesella
uncultured Clostridia bacterium
uncultured Paraburkholderia sp.
Clostridiales bacterium
unclassified Eubacterium (in: firmicutes)
unclassified Pseudarcobacter
unclassified Sandaracinobacter

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-15

Curated date: 2024/02/15

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplementary Table 3

Description: Differential abundance of mothers one week after second dose of BNT162b2 when compared to baseline.

Abundance in Group 1: decreased abundance in Mothers at one week post-second dose

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Anaerococcus nagyae
Anaerococcus octavius
Arthrobacter russicus
Bacteroides caecimuris
Phocaeicola plebeius
Phocaeicola vulgatus
Clostridiaceae bacterium
unclassified Oscillospiraceae
Cutibacterium granulosum
Helicobacter rodentium
Ligilactobacillus aviarius
Pseudoxanthomonas kaohsiungensis
Rothia sp. (in: high G+C Gram-positive bacteria)
unclassified Eubacterium
unclassified A0389unclassified A0389
unclassified Akkermansia
unclassified Alcaligenes
unclassified Allobaculum
unclassified Bacilli
unclassified Bacteroides
unclassified Castellaniella
unclassified Bacillota
unclassified Colidextribacter
unclassified Coriobacteriaceae
unclassified Desulfovibrionaceae
unclassified Dubosiella
unclassified Faecalibacterium
unclassified Haliangium
unclassified Halomonadaceae
unclassified Halomonas
unclassified Kurthia
unclassified Lachnospiraceae
unclassified Lactobacillus
unclassified Muribaculaceae
unclassified Parabacteroides
unclassified Parasutterella
unclassified Peptostreptococcaceae
unclassified Prevotellaceae
unclassified Quinella
unclassified Ralstonia
unclassified Romboutsia
unclassified SUP05_clusterunclassified SUP05_cluster
unclassified Sutterella
unclassified Treponema
unclassified Turicibacter
uncultured Odoribacter sp.

Revision editor(s): ChiomaBlessing

Experiment 6

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-16

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mothers at one month post second-dose

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breastfeeding mothers at one month post second-dose of BNT162b2 vaccine.

Group 1 sample size Number of subjects in the case (exposed) group: 44

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-16

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, Chinelsy, ChiomaBlessing

Source: supplementary table 3

Description: differential abundance of mothers at one month post second dose of BNT162b2 when compared to baseline.

Abundance in Group 1: increased abundance in Mothers at one month post second-dose

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Acinetobacter ursingii
Campylobacter showae
Clostridiales bacterium
Dubosiella newyorkensis
Epilithonimonas hominis
Marinobacterium marisflavi
Moraxella atlantae
Neisseria elongata
Prevotella histicola
Prevotella melaninogenica
Pseudoroseomonas aestuarii
Roseomonas gilardii
Stenotrophomonas acidaminiphila
unclassified Acidovorax
unclassified Aeromicrobium
unclassified Atopobium
unclassified Brevundimonas
unclassified Corynebacteriaceae
unclassified Dermacoccaceae
unclassified Formosa
unclassified Gordonia (in: high G+C Gram-positive bacteria)
unclassified Lachnoanaerobaculum
unclassified Microvirga
unclassified Moraxella
unclassified Neisseriaceae
unclassified Novosphingobium
unclassified Paracoccaceae
unclassified Pasteurellaceae
unclassified Pediococcus
unclassified Planococcaceae
unclassified Pseudarcobacter
unclassified Rhizobiaceae
unclassified Serratia (in: enterobacteria)
unclassified Skermanella
unclassified Sphingomonas
unclassified Tepidimonas
uncultured Clostridia bacterium
un-Allorhizobium-Neorhizobium Pararhizobium-Rhizobiumun-Allorhizobium-Neorhizobium Pararhizobium-Rhizobium
unclassified chloroplastunclassified chloroplast

Revision editor(s): Folakunmi, Chinelsy, ChiomaBlessing

Signature 2