This repository contains raw and intermediate data files as well as analysis code from the manuscript "Evaluating the Analytical Performance of Direct-to-Consumer Gut Microbiome Testing Services". In this analysis a pilot version of the homogenized whole human stool reference material was submitted as a sample to commercial direct to consumer microbiome testing companies. In addition, NIST conducted in house characterization by 16S amplicon sequencing and whole metagenomic sequencing (WMS) on the same sample. Raw sequencing data from the sequencing providers was not obtained for this study; however sequencing files (fastq) both 16S amplicon sequencing analysis and whole metagenomic sequencing (WMS) conducted at NIST are included. In addition, the fastq files from other donors that contributed to the pilot material and included in this analysis to represent biological diversity are also included in this record.

,Using the SHIME (an in vitro simulator of the human gut microbiome) we studied changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). 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. Samples were collected before, during, and after inoculation of the reactors with LGG.,This dataset includes untargeted metabolomics data. Shallow shotgun metagenomic sequencing data 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:,

중국 GB 4789.35-2023 식품 미생물학 검사(유산균 검사) 번역문입니다. 본 콘텐츠는 번역 자료로 해당 내용의 최종 확인은 원문을 참고하시기 바랍니다.

,The impact of lactose on the gut microbiota of healthy adults was examined, using a short-term, in vitro strategy where fecal samples harvested from 18 donors were cultured anaerobically with and without lactose. Donors represented 3 adult age groups. Data collected include: amplicon sequencing of the V1-V2 regions of the 16S rRNA gene (available in the NCBI Sequence Read Archive associated with BioProject PRJNA883645: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA883645), RT-qPCR of Bifidobacterium 16S rRNA genes, and short-chain fatty acid concentrations.,Resources in this dataset:,

,The SHIME® (Simulator of the Human Intestinal Microbial Ecology) was used for in vitro cultivation of the human gut microbiota (3 donors) prior to and following the addition of ivermectin to the system. These additions were performed on bioreactors which had stabilized on a background of media supplemented with either soluble or insoluble fiber or no addition controls. Data collected include 16S rRNA gene amplicon sequencing and short chain fatty acid (SCFA) concentrations.,

,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:,

This repository includes the raw data, analysis code, and results of a systematic analysis of natural transformation (i.e., horizontal gene transfer; HGT) of bacteria in a naturally occurring microbiome (human stool) following exposure to free extracellular DNA (eDNA) that coded for antibiotic resistance. A full description of this effort is available in the associated publication.

,This is a dataset consisting of donor-specific collections of 78 metagenomes (13 / donor) and 143 metagenome-assembled genomes (MAGs) representing the gut microbiomes of six healthy adult human donors. Raw sequencing data and MAG sequence data will be available in NCBI under BioProject accession PRJNA961974 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA961974). Spreadsheets attached to this dataset include individual accession numbers and sequencing depth for the raw data; and assembly and NCBI accession numbers, binning information, quality metrics, and taxonomic assignments for the MAGs.,Resources in this dataset:,,

This repository contains the raw data and analysis scripts supporting the associated publication which introduces a framework to help researchers select fit-for-purpose microbial cell counting methods and optimize protocols for quantification of microbial total cells and viable cells. Escherichia coli cells were enumerated using four methods (colony forming unit assay, impedance flow cytometry - Multisizer 4, impedance flow cytometry - BactoBox, and fluorescent flow cytometry - CytoFLEX LX) and repeated on multiple dates. The experimental design for a single date starts with a cell stock that is divided into 18 sample replicates (3 each for 6 different dilution factors), and each sample is assayed one or two times for a total of 30 observations. Raw data files are provided from the Multisizer 4 (*.#m4) and CytoFLEX LX (*.fcs 3.0). The colony forming unit assay and BactoBox readings are recorded for each date as are the derived results from the Multisizer 4 and CytoFLEX LX. Also provided are an example analysis script for the *.fcs files and the statistical analysis that was performed.