Description: To determine strain-specific driving mechanisms of B. pseudolongum UMB-MBP-01, researchers compared it to porcine tropic strain B. pseudolongum ATCC25526 using cell culture and in vivo experimentation and comparative genomic approaches. The data demonstrates that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution.

Subject of Study

Mouse (C57BL/6)

Subject Domain

Immunity

Keywords

Bifidobacterium

Gastrointestinal Microbiome

Genomics

Immunity, Innate

Access via GenBank
genomes, metagenome, and transcriptome sequences
Accession #: PRJNA809764

Access via GitHub
R codes and input dataset

Access via Article
Immunologic experimental raw data files
Access Restrictions: Unrestricted access
Access Instructions: The assembly of the genomes, metagenome, and transcriptome sequences were submitted to GenBank. R codes and input dataset used to generate the heatmap was deposited in GitHub. Raw data files available to download.
Associated Publications: Ma, B. Gavzy, SJ. Saxena, V. Sang, Y. Piao, W. Lwin, HW. Lakhan, R. Iyyathurai, J. Li, L. France, M. Paluskievica, C. Shirkey, MW. Hittle, L. Munawwar, A. Mongodin, EF. Bromberg, JS. Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum. Sci Rep. 2023 Jan 19;13(1023).
Data Type: Genetic

Genomic
Equipment Used: Accu-Scope EXC-500
Provides sharp, crisp images via Plan achromat or Plan semi-Apochromatic objectives.

Anaerobic microplates
Rapid broad-based identification and characterization product designed for anaerobic bacteria.

Bifido Selective Media agar plates
For the selective isolation and identification of Bifidobacteria.

BioAnalyzer 2100
Automated electrophoresis tool for the sample quality control of biomolecules

CD11c positive selection kit
Magnetic separation of CD11c+ cells by positive selection.

DNA/RNA Shield
DNA and RNA stabilization solution for nucleic acids in any biological sample.

GasPak EZ
Generates a pouch-based anaerobic, microaerophilic or CO2-enriched environment.

Illumina MiSeq System
Capable of automated paired end reads.

Illumina NovaSeq 6000 Sequencing System
Performs whole-genome sequencing

KAPA Hyper Prep kit KK8504

LSRFortessa Flow Cytometer
Multicolor analysis with powerful fluidics systems and novel optics design to maximize signal and enable minimum cross talk.

Microm HM550
Cryostats for sectioning techniques in routine and research.

Nextera XT Flex kit
Prepare sequencing libraries for small genomes, PCR amplicons, plasmids, or cDNA

Phasemaker tubes
A thick liquid polymer that separates and completely isolates the upper aqueous phase of a TRIzol Reagent mix from the organic phase underneath, greatly simplifying removal of the upper phase containing the RNA.

Promega Wizard Genomic DNA Purification Kit
A reliable and widely used kit designed for efficient extraction and purification of high-quality genomic DNA from various biological samples.

RiboZero Plus kit
Removes abundant RNA using enzymatic depletion.

RNA 1000 Nano kit
Provides reliable and reproducible characterization of total RNA and mRNA from multiple sample types.

Sigma-Aldrich RNAlater
Stabilize and protect RNA with immediate RNase inactivation

Spectrophotometer microplate reader
Run standard spectrophotometer and microplate reader applications.

TRIzol Reagent
A complete, ready-to-use reagent for the isolation of high-quality total RNA or the simultaneous isolation of RNA, DNA, and protein from a variety of biological samples

TruSeq Stranded mRNA
Prepare sequencing libraries from mRNA to get a clear view of the coding transcriptome with strand-specific information.

VWR UV CrossLinker
Quick, safe, and efficient sample exposure to a controlled amount of UV radiation.
Software Used: anvi'o pangenome pipeline
Advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies.

anvi'o vers 6.2 workflow
Open source software analysis and visualization platform for microbial genomics.

BMTagger
A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome.

Braken
Highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

clusterProfiler Bioconductor package
Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Cnetplot function
Used as a general method to visualize data relationships in a network diagram.

dbCAN2
Web server for automated Carbohydrate-active enzyme Annotation.

DESeq
Differential gene expression analysis based on the negative binomial distribution

eggNOG-mapper v2
Software tool for functional annotation of large sets of sequences.

enrichGO
Given a vector of genes, this function will return the enrichment GO categories after FDR control.

fastp
Software tool to provide fast all in one preprocessing for FastQ files

FastQC
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines.

FlowJo
Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

Gene Ontology enrichment analysis
Performs enrichment analysis on gene sets.

GhostKOALA
Assigns K numbers to the user's sequence data by GHOSTX search against a nonredundant set of KEGG GENES.

HiSat
Graph-based alignment of next generation sequencing reads to a population of genomes.

HTSeq
Analysing high-throughput sequencing data with Python

HUMAnN2
A pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Kraken2
A set of software tools designed to streamline the analysis of next-generation sequencing data.

MAUVE Contig Mover
Used to order a draft genome relative to a related reference genome.

MUSCLE
Software for multiple sequence alignment, used to align protein or nucleotide sequences for comparative analysis.

Pfam vers34.0
A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

phyloseq
Software for handling and analysis of high-throughput microbiome census data.

PSORTb
Precise bacterial localization prediction tool.

SoftMax Pro 7
A software package for microplate reader control and microplate data analysis.

Sourmash v. 3.3
Software library for sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.

SPAdes

vegan package
Ordination methods, diversity analysis and other functions.

Volocity 3D Image Analysis Software
3D image analysis software to visualize, analyze and validate 3D fluorescence images.
Study Type: Observational
Dataset Format(s): TXT
Data Collection Instruments: Markov Cluster Algorithm

Hidden Markov model

Rao score test

Linear discriminant analysis Effect Size

Kruskal-Wallis

Latent Dirichlet Allocation model

Canonical Correspondence Analysis

polymerase chain reaction assay

Over-representation analyses
Dataset Size: 518 MB

Grant Support: 1U01AI170050/National Institute of Immunology, Allergy and Infectious Diseases

R01HL148672/National Heart, Lung, and Blood Institute

T32AI95190-10/National Institute of Allergy and Infectious Diseases (U.S.)

UMB Data Catalog

Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum
UMB Dataset

Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum UMB Dataset

Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum
UMB Dataset