Breast milk infant stool omics - gwcbi/GWDBB GitHub Wiki
Characterizing microbiome functions and dynamics between breast milk and the infant gut microbiome and metabolome
Citation
Characterizing microbiome functions and dynamics between breast milk and the infant gut microbiome and metabolome
Ali Rahnavard, Shira Levy, Keriann Schulkers, Melena Robertson, Tyson Dawson, Sarah Bengtson, Xinyang Zhang, Isabel Hefner, Lesya Tomlinson, David Kling, Nicholas Lee, Raj Baveja, Robin Baker, Keylie M. Gibson, Keith A. Crandall, Suchitra K. Hourigan, 2023+, under preparation
If you have questions, please direct them to: [email protected]
Contents
Description
Breast milk is the optimal source of nutrition for infants, and exclusive breastfeeding for the first six months offers numerous health benefits, reducing the risk of obesity, asthma, necrotizing enterocolitis, diabetes, and gastroenteritis. Breast milk not only provides essential nutrients but also supports the development of the infant gut microbiome, which has a significant impact on health. The composition of the breast milk microbiome varies between individuals and influences the infant gut microbiome through vertical transmission of bacteria. Understanding this relationship is particularly important for premature infants who are at a higher risk of complications related to microbiome imbalances. The nutrient content and microbiome composition of breast milk may differ in women who deliver prematurely, and the use of donor milk is recommended when necessary. The impact of pasteurization and freezing on the breast milk microbiome is not well-studied. Studying the breast milk microbiome's effects on the infant gut microbiome requires advanced techniques like shotgun metagenomic sequencing, which provides a comprehensive view of the microbial diversity in breast milk beyond just bacteria. This study aims to explore this relationship in premature infants using shotgun metagenomics and metabolomics, considering associated factors such as demographics and clinical aspects.
Requirements
Data are available in the R data package GWDBB.
Load Data
library(GWDBB)
data(breastmilk_microbiome)
data(breastmilk_BGC)
data(infant_microbiome)
data(infant_microbiome)
data(stool_BGC)
Data Types
Metadata
Breastmilk
Breastmilk metadata is a table with 36 rows and 34 columns.
The rows include values.
The columns include sampleID, MaternalAge, MaritalStatus, Height, Weight, BMI, Ethnicity, race, etc.
The table can be directly downloaded from Breastmilk Metadata
Infant Stool
Infant Stool metadata is a table with 74 rows and 35 columns.
The rows include values.
The columns include Name, ExternalID, VisitTime, GestationalAgeDay, GestationalAgeWeek, GestationalAgeCategory, BirthWeight, sex, DaysinNICU, etc.
The table can be directly downloaded from Infant Metadata
Microbial Species
Breastmilk
Abundance of Microbial species from breastmilk sample can be found at here: Breastmilk Microbiome
The table includes 201 rows and 42 columns
Row name: Species name
Column name: Sample information: for example - 32a
32 - sample id
a - visit time point
Cell: Each cell means the relative abundance. If we sum up a column, it should be equal to 100.
The tsv file contains all of the individual metaphlan taxanomic profiling results together, we joined all of the tables and combined the each relative abundance information together.
Infant Stool
Abundance of Microbial species from infant stool sample can be found at here: Infant Stool Microbiome
The table includes 201 rows and 61 columns
Row name: Species name
Column name: Sample information: for example - 20d
20 - sample id
d - visit time point (i.e. it could be a, b, c or d)
Cell: Each cell means the relative abundance. If we sum up a column, it should be equal to 100.
The tsv file contains all of the individual metaphlan taxanomic profiling results together, we joined all of the tables and combined the each relative abundance information together.
Microbial Biosynthetic Gene Clusters
Breastmilk
Abundance of Microbial BGC species from breastmilk sample can be found at here: Breastmilk BGC
The table includes 77 rows and 2444 columns
Row name: For example - “15a_m”: The numeric number like “15” means the sample id. The following character like “a,b,c,d” means visit time point. The last part “-m” means it is breastmilk sample and “_f” means it is from fecal sample.
Column name: Each column represents one BGC, it contains the the BGC short description, BGC class.
Cell: Each cell mean the relative abundance. If we sum up a row, it should be equal to 1.
The tsv file contains all of the individual seqSight BGC profiling results together, we joined all of the tables and combined each relative abundance information together.
Infant Stool
Abundance of Microbial BGC species from infant stool sample can be found at here: Infant Stool BGC
The table includes 74 rows and 2444 columns
Row name: For example - “16a_f”: The numeric number like “16” means the sample id. The following character like “a,b,c,d” means visit time point. The last part “-m” means it is breastmilk sample and “_f” means it is from fecal sample.
Column name: Each column represents one BGC, it contains the the BGC short description, BGC class.
Cell: Each cell means the relative abundance. If we sum up a row, it should be equal to 1.
The tsv file contains all of the individual seqSight BGC profiling results together, we joined all of the tables and combined each relative abundance information together.
Metabolite
Infant Stool
Abundance of Metabolite species from infant stool sample can be found at here: Infant Stool Metabolite
The table includes 71 rows and 1157 columns