Longitudinal Stool Samples from Infants (n = 2,684)

Longitudinal Stool Samples from Infants (n = 2,684)

Usage

babies

Format

An rbiom object with 2,684 samples. Includes metadata and taxonomy.

Subject ID -

ID1, ID2, ..., ID12

Sex -

Male or Female

Age (days) -

1 - 266

Child's diet -

"Breast milk", "Breast milk and formula", or "Formula"

Sample collection -

"Frozen upon collection" or "Stored in alcohol"

Antibiotic exposure -

Yes or No

Antifungal exposure -

Yes or No

Delivery mode -

Cesarean or Vaginal

Solid food introduced (Age) -

116 - 247

Source

https://www.nature.com/articles/s41467-018-04641-7 and doi:10.1038/s41467-017-01973-8

See also

Other Built-In Datasets: gems, hmp50

Examples

babies
#> 
#> ══ DailyBaby ═══════════════════════════════════════════════
#> 
#> Longitudinal stool microbiome from 12 infants (Muinck &
#> Trosvik, 2018
#> (<https://www.nature.com/articles/s41467-018-04641-7>)).
#> Retrieved from MicrobiomeHD
#> (<https://doi.org/10.1038/s41467-017-01973-8>).
#> 
#>    2684 Samples: SRR7044380, SRR7058817, SRR7039319, ... 
#>     506 OTUs:    ASV085, ASV022, ASV251, ..., and ASV607 
#>       8 Ranks:   .otu, Kingdom, Phylum, ..., and Species 
#>      10 Fields:  .sample, Subject ID, Sex, ... 
#>         Tree:    <absent>
#> 
#> ── 500 reads/sample ────────────────────────── 2018-06-08 ──
#> 
head(babies$metadata$Age)
#> Warning: Unknown or uninitialised column: `Age`.
#> NULL