16S rRNA gene sequencing data from: Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens

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 antib..., 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 “poscou..., # Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens

#### 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: [[e-mail]](mailto:[e-mail])

#### 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: [[e-mail]](mailto:[e-mail])

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 Col...,

母体抗体可从根本上调控发育中婴儿的肠道免疫功能，但这一过程背后的具体机制仍未明确。本研究证实，出生第一周摄入的母体IgG会在断奶数周后抑制依赖于菌群的适应性免疫应答。抗体是肠道菌群多样性与组成的关键调控因子，因此我们探索了母体抗体缺陷子代的菌群组装改变是否与免疫失调相关。对回肠和结肠内容物进行16S rRNA基因测序后发现，在同周龄的µMT+/-或µMT-/-同窝母鼠与B6父鼠所产后代中，单样本微生物多样性（α多样性）以及组间距离（β多样性）均未出现显著差异。然而，µMT+/-与µMT-/-母鼠所产的出生后第7天（p7）子代中，少数类群的丰度存在显著差异，且这种差异随年龄增长而加剧。因此，所有母乳抗体的缺失…… 本研究通过贝勒医学院宏基因组学与微生物组研究中心（Alkek Center for Metagenomics and Microbiome Research, CMMR）完成了16S基因V4区的扩增及MiSeq Illumina测序。测序读段通过bbduk进行解复用、修剪与质量质控，随后使用bbmap合并双端读段，并通过MaLiAmPi流程结合DADA2生成扩增序列变体（Amplicon Sequence Variants, ASVs）。采用贝叶斯分类器Pplacer，以90%的似然值截断阈值进行系统发育定位，以此估算ASVs的分类学注释。α多样性估算由MaLiAmPi完成，β多样性则通过R包vegan（v2.6-4）计算Bray-Curtis相异度得到。在计算类群与ASVs的相对丰度差异前，我们添加了伪计数；同时将所有样本中读段数少于10的ASVs从数据集中移除。丰度差异分析通过DESeq2完成，数据标准化采用"poscou……
# 母乳IgG调控新生儿免疫系统以指导肠道抗原免疫应答

#### 数据集标题
16S rRNA基因测序数据源自：母乳IgG调控新生儿免疫系统以指导肠道抗原免疫应答

#### 项目负责人信息
姓名：Meghan Koch
ORCID：0000-0002-9539-4027
所属机构：弗雷德·哈钦森癌症研究中心（Fred Hutchinson Cancer Center）
通讯地址：美国华盛顿州西雅图市北费尔维尤大道1100号，邮编98109
电子邮箱：[[e-mail]](mailto:[e-mail])

#### 作者信息
姓名：Meera Shenoy
ORCID：0000-0002-3986-1321
所属机构：新加坡科技研究局新加坡免疫学网络（Singapore Immunology Network, Agency for Science, Technology, and Research）
通讯地址：新加坡生物医学Grove 8a号，邮编138648
电子邮箱：[[e-mail]](mailto:[e-mail])

#### 数据采集日期
2016-11-16：母体抗体充足组与缺陷组 版本2
2017-10-26：母体抗体充足组与缺陷组 版本3
2022-05-05：IgG喂养组与BSA喂养组

#### 数据采集地理范围……