About this Dataset

Data From: Persistence Of The Probiotic Lacticaseibacillus Rhamnosus Strain GG (LGG) In An In Vitro Model Of The Gut Microbiome

Using the SHIME (an in vitro simulator of the human gut microbiome) we tracked the fate of the probiotic Lacticaseibacillus rhamnosus GG (LGG) over time and across colonic regions. Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Community composition before, during, and after inoculation of the reactors with LGG as well as short chain fatty acid concentrations representing microbiome metabolic outputs. This dataset includes short-chain fatty acid concentrations and qPCR-based cell concentrations. Raw 16S rRNA amplicon sequencing of the V1-V2 regions can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635.

Resources in this dataset:

Resource Title: Short Chain Fatty Acid concentrations File Name: LGG_SCFA_data.csv
Resource Title: LGG qPCR concentrations File Name: LGG_qPCR_data.csv
Resource Title: Sample metadata File Name: LGG_16S_metadata.csv
Organization: Department of Agriculture
Last updated: 2024-03-30T11:22:02.159823
Tags: 16s-rrna-sequence-data, ars, data-gov, np306, probiotics, short-chain-fatty-acids

Tables

LGG QPCR Data

@usgov.usda_gov_data_from_persistence_of_the_probiotic_lactic_aad67293.lgg_qpcr_data

10.2 kB
240 rows
7 columns

CREATE TABLE lgg_qpcr_data (
  "sampleid" VARCHAR,
  "concentration_ml" DOUBLE,
  "sd" DOUBLE,
  "subject" VARCHAR,
  "sample_type" VARCHAR,
  "colon_region" VARCHAR,
  "day_post_inoculation" DOUBLE
);

LGG SCFA Data

@usgov.usda_gov_data_from_persistence_of_the_probiotic_lactic_aad67293.lgg_scfa_data

12.73 kB
196 rows
7 columns

CREATE TABLE lgg_scfa_data (
  "sampleid" VARCHAR,
  "acetic_acid_mm" DOUBLE  -- Acetic Acid(mM),
  "propanoic_acid_mm" DOUBLE  -- Propanoic Acid(mM),
  "n_2methylpropanoic_acid_mm" DOUBLE  -- 2methylpropanoic Acid(mM),
  "butanoic_acid_mm" DOUBLE  -- Butanoic Acid(mM),
  "n_3methylbutanotic_acid_mm" DOUBLE  -- 3methylbutanotic Acid(mM),
  "n_2methylbutanoic_acid_mm" DOUBLE  -- 2methylbutanoic Acid(mM)
);