Description: This dataset was used to overview the taxonomic composition of the gastrointestinal microbiomes during the first two years of life with the intent to better understand the effects of the invasive pathogen, Shigella. Data was collected through a two year longitudinal study of a mother-infant cohort in Malawi, using 16S rRNA amplicon sequencing to characterize the gastrointestinal microbiota. Rectal swab samples were collected every 6 six months during well-child visits or when an infant visiting the clinic presented diarrhea to diagnose Shigella infection. 16S rRNA gene amplicon libraries yielded an average of 23,720 reads per sample with a total of 8,729,027 reads and a total of 325 taxa were identified after quality filtering.
Timeframe: 2016 - 2018
Geographic Coverage: Malawi

Subject of Study

Human

Subject Domain

Gastrointestinal Microbiome

Genomics

Shigella

Population Age

Infant (1 to 23 months of age)

Infant, Newborn (first 28 days after birth)

Keywords

Sequence Analysis, RNA

Shannon diversity index

Access via NCBI SRA
Raw sequencing data
Accession #: PRJNA834726

Access via Supplemental Material
Datasets, figures, and tables
Access Restrictions: Unrestricted access
Access Instructions: All of the raw sequencing data were deposited into NCBI SRA under BioProject ID PRJNA834726. Additional data supporting the article are present in the Supplementary Materials.
Associated Publications: Ndungo, E., Holm, J. B., Gama, S., Buchwald, A. G., Tennant, S. M., Laufer, M. K., Pasetti, M. F., & Rasko, D. A. (2022). Dynamics of the Gut Microbiome in Shigella-Infected Children during the First Two Years of Life. mSystems, 7(5), e0044222. https://doi.org/10.1128/msystems.00442-22
Data Type: Genomic
Equipment Used: DNA/RNA Shield
DNA and RNA stabilization solution for nucleic acids in any biological sample.

Hamilton StarPlus Automated Liquid Handler
Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack.

QIAamp DNA Stool Extraction Kit
Used for the isolation of genomic, bacterial, viral, and parasite DNA

Qiagen Microbiome RNA/DNA isolation kit
Used for automated isolation of microbial RNA and DNA

Qiagen Tissue Lyser II
RNA and DNA purification analyzer
Software Used: DADA2 v1.5.2
Package for inferring amplicon sequence variants (ASVs)

QIIME
Performs microbiome analysis

Ribosomal Database Project (RDP) Classifier
Used to assign sequences derived from bacterial and archaeal 16S genes and fungal 28S gene to the corresponding taxonomy model

Silva v138
rRNA database

TagCleaner v0.16
Used to automatically detect and remove tag sequences from genomic and metagenomic sequence data
Study Type: Longitudinal
Dataset Format(s): XLSX, FASTQ
Dataset Size: 8082 Mb

Grant Support: U19AI110820/NIH

R01AI117734/NIH

R01AI125841/NIH

T32DK067872/NIH

3R01AI117734-04S1/NIH

1UL1TR003098/National Center for Advancing Translational Sciences (U.S.)

UMB Data Catalog

Dynamics of the Gut Microbiome in Shigella-Infected Children During the First Two Years of Life
UMB Dataset

Dynamics of the Gut Microbiome in Shigella-Infected Children During the First Two Years of Life UMB Dataset

Dynamics of the Gut Microbiome in Shigella-Infected Children During the First Two Years of Life
UMB Dataset