NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation

Dataset overview

Participants None

Samples None

Reuse readiness 6.0/10 evidence-backed score

NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation.

Moltzau Anderson J, Lipinski S, Sommer F, Pan WH, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, et al. · Cellular and molecular gastroenterology and hepatology · 2020

Abstract

<h4>Background & aims</h4>Loss-of-function variants in nucleotide-binding oligomerization domain-containing protein 2 (NOD2) impair the recognition of the bacterial cell wall component muramyl-dipeptide and are associated with an increased risk for developing Crohn's disease. Likewise, exposure to antibiotics increases the individual risk for developing inflammatory bowel disease. Here, we studied the long-term impact of NOD2 on the ability of the gut bacterial and fungal microbiota to recover after antibiotic treatment.<h4>Methods</h4>Two cohorts of 20-week-old and 52-week-old wild-type (WT) C57BL/6J and NOD2 knockout (Nod2-KO) mice were treated with broad-spectrum antibiotics and fecal samples were collected to investigate temporal dynamics of the intestinal microbiota (bacteria and fungi) using 16S ribosomal RNA and internal transcribed spacer 1 sequencing. In addition, 2 sets of germ-free WT mice were colonized with either WT or Nod2-KO after antibiotic donor microbiota and the severity of intestinal inflammation was monitored in the colonized mice.<h4>Results</h4>Antibiotic exposure caused long-term shifts in the bacterial and fungal community composition. Genetic ablation of NOD2 was associated with delayed body weight gain after antibiotic treatment and an impaired recovery of the bacterial gut microbiota. Transfer of the postantibiotic fecal microbiota of Nod2-KO mice induced an intestinal inflammatory response in the colons of germ-free recipient mice compared with respective microbiota from WT controls based on histopathology and gene expression analyses.<h4>Conclusions</h4>Our data show that the bacterial sensor NOD2 contributes to intestinal microbial community composition after antibiotic treatment and may add to the explanation of how defects in the NOD2 signaling pathway are involved in the etiology of Crohn's disease.

doi:10.1016/j.jcmgh.2020.03.008 ↗ PMID 32289499 ↗ PMC7327897 ↗

Study facts

Organism: —
Platform: Illumina MiSeq
Age group: adult
Disease groups: —
Anatomical sites: —

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Participant-to-sample mapping is available

Limitations

Not documented: feature/otu tables are advertised
Not documented: taxonomic tables are advertised
Not documented: participant counts are documented

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.paired_end`	True	MiSeq with 2 × 300 base pairs Section `Materials and Methods—16S Amplicon Sequencing`, offset 60000
`assay.platform`	Illumina MiSeq	sequenced on an Illumina ... MiSeq with 2 × 300 base pairs Section `Materials and Methods—16S Amplicon Sequencing`, offset 60000
`assay.primers_reported`	True	using the primers ITS1-F(F) ... and ITS2(R) ... to amplify the fungal ITS1 region Section `Materials and Methods—Fungal ITS1 Amplicon Sequencing`, offset 62500
`assay.read_length`	300	MiSeq with 2 × 300 base pairs Section `Materials and Methods—16S Amplicon Sequencing`, offset 60000
`assay.target_region`	16S rRNA V3–V4 and fungal ITS1	The 16S rRNA gene variable region V3–V4 was amplified ... fungal ITS1 ... amplicon sequencing Section `Materials and Methods—16S Amplicon Sequencing; Fungal ITS1 Amplicon Sequencing`, offset 59600

Cohort

Field	Value	Evidence
`cohort.age_group`	adult	Two cohorts of 20-week-old and 52-week-old ... mice Section `Introduction`, offset 3100
`cohort.study_design`	longitudinal	investigate longitudinal dynamics of the bacterial microbiota after a pulsed perturbation Section `Introduction`, offset 3500
`cohort.treatment_exposure_documented`	True	treated with a cocktail of broad-spectrum antibiotics composed of ampicillin ... vancomycin ... neomycin ... and metronidazole Section `Materials and Methods—Antibiotic Treatment`, offset 57400
`cohort.treatment_response_metadata_available`	True	Recovery from antibiotic-induced weight loss occurred earlier and faster in WT mice compared with Nod2-KO mice Section `Results`, offset 7000

Data_Assets

Field	Value	Evidence
`data_assets.open_access`	True from source	"isOpenAccess": "Y" Section `Publication metadata`, offset —
`data_assets.pipeline_or_tool_versions`	True	using Mothur and MacQIIME v1.9.1 Section `Materials and Methods—16S Amplicon Sequencing`, offset 60400
`data_assets.qc_or_negative_controls_reported`	True	Only sequences with less than 450 base pairs ... mean quality score ≥25 were considered Section `Materials and Methods—16S Amplicon Sequencing`, offset 60700
`data_assets.raw_reads`	True	Raw sequencing data ... were uploaded to ... ENA under accession number PRJEB21817 Section `Availability of Data and Materials`, offset 72800

Specimens

Field	Value	Evidence
`specimens.body_site`	gut	the gut bacterial and fungal microbiota to recover after antibiotic treatment Section `Introduction`, offset 3400
`specimens.longitudinal_sampling`	True	16S amplicon sequencing was performed on longitudinally sampled fecal material Section `Materials and Methods—16S Amplicon Sequencing`, offset 59400
`specimens.participant_to_sample_mapping_available`	True inferred	Each dot represents the bacterial composition of an individual fecal sample. Section `Results`, offset 8200
`specimens.sample_type`	stool	Fecal pellets were collected immediately from mice throughout the experiment and stored at -80°C. Section `Materials and Methods—Specific Pathogen–Free Mice`, offset 56500