16S rRNA gene sequencing data from: Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens
Data files
Jun 25, 2025 version files 2.12 GB
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IgG_vs_BSA-fed.zip
276.73 MB
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matAb-sufficient_vs_deficient.zip
1.84 GB
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README.md
11.54 KB
Abstract
Maternal antibodies fundamentally regulate gut immunity in the developing infant, yet the mechanisms underlying this process remain elusive. Here, we show that maternal IgG, ingested in the first week of life, restrains microbiota-dependent adaptive immune responses weeks later, following weaning. Antibodies are key regulators of gut microbiota diversity and composition, prompting us to explore whether alterations in microbiome assembly correlated with immune dysregulation in maternal antibody-deficient offspring. 16S rRNA gene sequencing of ileal and colonic contents did not reveal substantial differences in the diversity of microbes in each sample (alpha diversity) nor between-group distances (beta diversity) between age-matched offspring of µMT+/- or µMT-/- littermate dams and B6 sires. However, the abundance of a small subset of taxa differed significantly between p7 offspring of µMT+/- and µMT-/- dams, and this variation increased with age. Thus, the absence of all breastmilk antibodies correlates with minor alterations in the assembly of the postnatal microbiome. Analysis of p20 progeny of µMT-/- dams and B6 sires fed sIgG or BSA during the first week of life similarly failed to reveal significant differences in alpha or beta diversity as a function of feeding. Instead, litter was a driving factor. Indeed, the provision of IgG resulted in the differential abundance of only a single ileal taxon and two colonic taxa, which were distinct from those identified in p21 offspring of µMT+/- and µMT-/- dams. The similarity in microbiota community structure between IgG and BSA-fed littermates indicates that breastmilk IgG does not significantly alter the composition of the developing microbiome.
Dataset Title
16S rRNA Gene Sequencing Data from: Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens
Principal Investigator Information
Name: Meghan Koch
ORCID: 0000-0002-9539-4027
Institution: Fred Hutchinson Cancer Center
Address: 1100 N. Fairview Ave. Seattle, WA 98109
Email: mkoch@fredhutch.org
Author Information
Name: Meera Shenoy
ORCID: 0000-0002-3986-1321
Institution: Singapore Immunology Network, Agency for Science, Technology, and Research
Address: 8a Biomedical Grove, Singapore 138648
Email: Meera_Shenoy@immunol.a-star.edu.sg
Dates of Data Collection
2016-11-16: Maternal Antibody Sufficient vs. Deficient Version 2
2017-10-26: Maternal Antibody Sufficient vs. Deficient Version 3
2022-05-05: IgG vs. BSA fed
Geographic Location of Data Collection:
Maternal Antibody Sufficient vs. Deficient Versions 2 and 3: Berkeley, CA
IgG vs. BSA fed: Seattle, WA
DATA PROCESSING
Amplification and MiSeq Illumina sequencing were performed by the Alkek Center for Metagenomics and Microbiome Research at Baylor College of Medicine. The V4 region of the 16S rRNA gene was amplified using 515F and 806R primers. Reads were demultiplexed, trimmed, and quality checked with bbduk. The 250bp paired-end reads were then merged using bbmap and run through the MaLiAmPi workflow to generate Amplicon Sequence Variants (ASVs) using DADA2. The Bayesian classifier Pplacer was used to estimate taxonomic classification of ASVs using phylogenetic placement with a likelihood cutoff of 90%. Sequences that could not be assigned unambiguously to a single genus were instead assigned at a higher taxonomic level.
EXPERIMENT SUMMARY
Maternal Antibody Sufficient vs. Deficient Experiment (matAb-sufficient vs. deficient)
We bred µMT-knockout C57Bl/6 dams that lacked antibodies with wild-type sires to produce µMT-heterozygous offspring that received no maternal antibodies yet were capable of producing their own antibodies. We collected intestinal samples from these mice as well as from mice born to µMT-heterozygous C57Bl/6 dams and C57Bl/6 wild-type sires, and sequenced the 16S rRNA gene to characterize the composition of the microbiome in the two groups. µMT-heterozygous and µMT-knockout dams used for experiments were littermates and were cohoused before breeding to promote homogenization of the microbiome.
IgG Feed Experiment (IgG_vs_BSA-fed)
This dataset contains 16S rRNA sequencing reads from pups lacking maternal antibodies that were fed 10 µg of either IgG purified from the serum of specific-pathogen-free (SPF) mice or the protein bovine serum albumin (BSA; control) once daily during the first week of life for a total of eight feedings.
DIRECTORY OVERVIEW
Each experiment directory contains
- .csv metadata file with information about each sample using the data-specific abbreviations described below.
- A directory containing demultiplexed compressed FASTQ files containing forward and reverse paired-end reads for each sample.
- Forward reads filenames end with either 1.fq.gz or R1.fastq.gz.
- Reverse reads filenames end with either 2.fq.gz or R2.fastq.gz.
- Directory containing the ASV counts table, taxa tables (counts and relative abundance), ASV sequences, and ASV classification.
TABULAR METADATA FILE DETAILS
Samples are in rows. Each column includes information about each sample as described below.
matAb-sufficient_vs_deficient_metadata.csv
sampleID
Sample IDs include information about the dam genotype, timepoint, cage ID, mouse number, and sampling location in that order. The sample IDs use the abbreviations described for each column header below. For example, sample Het14A_1_col is from a maternal antibody sufficient mouse, from the day 14 timepoint, cohort A, is mouse #1 from that litter and timepoint, and collected from the colon contents.
damGeno (dam genotype)
Indicates maternal antibody status.
- Het:
Maternal antibody sufficient – mouse was born to and nursed by a C57Bl/6 dam able to produce antibodies (heterozygous for the µMT gene) - KO:
maternal antibody deficient – mouse was born to and nursed by a C57Bl/6 dam not able to produce antibodies (homozygous KO for the µMT gene)
timepoint
Time point of sample collection (postnatal days).
- 7
- 14
- 21
cohort
Groups of litters that were born on or around the same day.
- Cohorts A and B are from Version 2.
- Cohorts C and D are from Version 3.
number
Each mouse with identical parameters was assigned a unique number.
Missing data is represented with "NA".
location1
Site of tissue/intestinal contents sampled.
intestine samples
- col: contents of the distal colon
- ile: contents of the ileum
tissue samples
- lgwall: distal colon wall
- smwall: ileal wall
version
Version 2 (v2): experiment performed in 2016
Version 3 (V3): repeat experiment performed in 2017
IgG_vs_BSA-fed_metadata.csv
sampleID
Sample IDs include the cage ID, mouse number, and sampling site (C=colon lumen, S=ileum lumen).
Sample IDs include information about the dam genotype, timepoint, cage ID, mouse number, and sampling location in that order. The sample IDs use the abbreviations described for each column header below. For example, sample Het14A_1_col is from a maternal antibody sufficient mouse, from the day 14 timepoint, cohort A, is mouse #1 from that litter and timepoint, and collected from the colon contents.
feed
Indicates whether the mouse was fed IgG or BSA (control).
- IgG10: 10 µg IgG
- BSA10: 10 µg BSA
- na: The dams were not fed IgG or BSA as part of this experiment. This is indicated by "na" in this column.
location1
- ColonLumen: Samples are from the contents of the colon lumen.
- Ileum Lumen: Samples are from the contents of the ileal lumen.
- Feces: Fecal pellets, collected from the dams only.
Cage
Indicates which cage the mouse was housed in. Mice with the same cage number are the same age and from the same litter.
Sex
- f: female
- m: male
AgeAtSac
The postnatal day on which the mouse was sacrificed and tissues collected.
type
Indicates whether the sample is from a pup or a dam. Fecal samples from the three dams were collected to compare with the pups’ microbiome.
- pup: experimental mouse (offspring of ADam, BDam, and EDam)
- Adam: from cage 739A
- DDam: dam from cage 739D
- EDam: dam from cage 739E
FASTQ FILENAMES
Each filename includes information about the sample as described below.
matAb-sufficient_vs_deficient_raw_demux_reads_V2_V3
- Versions 2 and 3 were processed at different times and have slight differences in their naming schemes. For more information about each category, please see the TABULAR METADATA FILE DETAILS.
Version 2 files
- MatAb: experiment - Maternal antibody sufficient vs. deficient
- v2: Version 2
- Intestine/Tissue: intestine = intestinal contents, tissue = intestinal wall
- Barton: PI of project - Greg Barton, University of California, Berkeley
- Het/KO: Het = maternal antibody sufficient, KO = maternal antibody deficient
- 7/14/21: timepoint of specimen collection (postnatal day)
- A/B: experimental cohort
- 1/2/3/4/5/6: mouse number
- col/ile/sm_w/lg_w: col = colon, ile = ileum, sm_wall = small intestine wall, lg_w = large intestine wall
- R1/R2: R1 = forward paired-end reads, R2 = reverse paired-end reads
Version 3 files
- 102617: date the files were submitted for sequencing - Oct. 26, 2017
- MatAb: experiment - Maternal antibody sufficient vs. deficient
- V3: Version 3
- Barton: PI - Greg Barton, UCB
- Het/KO: Het = maternal antibody sufficient, KO = maternal antibody deficient
- 7/14/21: timepoint of specimen collection
- C/D: experimental cohort
- col/ile/sm_w/lg_w: col = colon, ile = ileum, sm_wall = small intestine wall, lg_w = large intestine wall
- R1/R2: R1 = forward paired-end reads, R2 = reverse paired-end reads
IgG vs. BSA-fed
- Koch: PI - Meghan Koch, Fred Hutchinson Cancer Center
- A/D/E: litter ID
- 1/2/3/4/5/6: mouse number
- C/S: C = colon contents S = small intestine (ileum) contents
- 1/2: 1 = forward reads, 2 = reverse reads
SPECIMEN IDS IN ASV TABLES AND CLASSIFICATION FILES
Specimen IDs are detailed below.
matAb-sufficient_vs_deficient
Version 2 files
- v2: Version 2
- Intestine/Tissue: Intestine = Intestinal wall, Tissue = Tissue contents
- KO/Het: maternal antibody sufficient or deficient
- 7/14/21: timepoint of collection (postnatal day)
- A/B: A = cohort A, B = cohort B
- 1/2/3/4/5/6: mouse number
- col/ile/sm_w/lg_w: col = colon, ile = ileum, sm_wall = small intestine wall, lg_w = large intestine wall
Version 3 files
- V3: Version 3
- KO/Het: maternal antibody sufficient or deficient
- C/D: C = cohort C, D = cohort D
- 7/14/21: timepoint of collection (postnatal day)
- 1/2/3/4/5/6: mouse number
- col/ile/smwall/lgwall: col = colon contents, ile = ileum contents, smwall = small intestine wall, lgwall = large intestine wall
IgG_vs_BSA-fed
- A/D/E: litter
- 1/2/3/4/5/6: mouse number
- C/S: C = colon contents, S = ileum contents (small wall and large wall samples from this experiment were not included in this analysis)
FILE STRUCTURE
- IgG_vs_BSA-fed
- IgG_vs_BSA-fed_metadata.csv
- IgG_vs_BSA-fed_raw_demux_reads/
- Koch_D1C_1.fq.gz
- Koch_D1C_2.fq.gz
- Koch_D1S_1.fq.gz
- Koch_D1S_2.fq.gz
- …
- ASV_tables_and_classification
- dada2.combined.seqtabs.nochimera.csv (ASV table: ASV counts for each sample)
- dada2.sv.fasta (sequences of each ASV)
- sv_taxonomy.csv (taxonomic classification for each ASV)
- tables
- taxon_wide_nreads.class.csv (Taxa tables: number of each taxon for each sample)
- taxon_wide_nreads.family.csv
- taxon_wide_nreads.genus.csv
- taxon_wide_nreads.order.csv
- taxon_wide_nreads.phylum.csv
- taxon_wide_nreads.species.csv
- taxon_wide_ra.class.csv (RA tables: relative abundance of each taxon for each sample)
- taxon_wide_ra.family.csv
- taxon_wide_ra.genus.csv
- taxon_wide_ra.order.csv
- taxon_wide_ra.phylum.csv
- taxon_wide_ra.species.csv
- matAb-sufficient_vs_deficient
- matAb-sufficient_vs_deficient_metadata.csv
- matAb-sufficient_vs_deficient_raw_demux_reads_V2_V3/
- 102617-MatAb-V3_Barton_Het14C1col_R1.fastq.gz
- 102617-MatAb-V3_Barton_Het14C1col_R2.fastq.gz
- 102617-MatAb-V3_Barton_Het14C1ile_R1.fastq.gz
- 102617-MatAb-V3_Barton_Het14C1ile_R2.fastq.gz
- …
- ASV_tables_and_classification
- dada2.combined.seqtabs.nochimera.csv (ASV table: ASV counts for each sample)
- dada2.sv.fasta (sequences of each ASV)
- sv_taxonomy.csv (taxonomic classification for each ASV)
- tables/
- taxon_wide_nreads.class.csv (Taxa tables: number of each taxon for each sample)
- taxon_wide_nreads.family.csv
- taxon_wide_nreads.genus.csv
- taxon_wide_nreads.order.csv
- taxon_wide_nreads.phylum.csv
- taxon_wide_nreads.species.csv
- taxon_wide_ra.class.csv (RA tables: relative abundance of each taxon for each sample)
- taxon_wide_ra.family.csv
- taxon_wide_ra.genus.csv
- taxon_wide_ra.order.csv
- taxon_wide_ra.phylum.csv
- taxon_wide_ra.species.csv
Amplification and MiSeq Illumina Sequencing of the V4 region of the 16S gene was performed by the Alkek Center for Metagenomics and Microbiome Research (CMMR) at Baylor College of Medicine. Reads were demultiplexed, trimmed and quality checked with bbduk. Paired-end reads were then merged using bbmap and run through the MaLiAmPi workflow to generate Amplicon Sequence Variants (ASVs) using DADA2. The Bayesian classifier Pplacer was used to estimate taxonomic classification of ASVs using phylogenetic placement with a likelihood cutoff of 90%. Alpha diversity estimates were generated by MaLiAmPi and Bray-Curtis dissimilarity was calculated using the R package vegan (v2.6-4) to determine beta diversity estimates. A pseudocount was applied prior to calculating differences in the relative abundance of taxonomic groups and ASVs with fewer than 10 reads across all samples were removed from the dataset. Differential abundance was determined using DESeq2, and data was normalized using the “poscounts” size estimator.