Foundry120 atlas

Additional file 2 of A diet based on cured acorn-fed ham with oleic acid content promotes anti-inflammatory gut microbiota and prevents ulcerative colitis in an animal model

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Dataset overview

Participants 20
Samples None
Reuse readiness 6.7/10 evidence-backed score

A diet based on cured acorn-fed ham with oleic acid content promotes anti-inflammatory gut microbiota and prevents ulcerative colitis in an animal model.

Abstract

<h4>Background</h4>Diets based on meat products are not recommended in the case of ulcerative colitis (UC). The objective here is to test if some traditional cured meat products, as acorn-fed ham (high levels of oleic acid), may be useful for controlling inflammatory diseases as UC in animal models, which could represent a new dietary complementary intervention in the prevention of this inflammatory disease in humans.<h4>Methods</h4>Two rat cohorts have been used: conventional vegetable rat feed and acorn-fed ham. UC was induced with DSS in drinking water ad libitum for 1 week. Short-chain fatty acids (SCFAs) and 16S rRNA metagenomics from bacterial populations were analyzed in cecum samples. Colon samples were analyzed for histological parameters.<h4>Results</h4>Acorn-fed ham diet induced changes in gut microbiota composition, with pronounced enrichments in anti-inflammatory bacterial genera (Alistipes, Blautia, Dorea, Parabacteroides). The animals with this diet showed a strong reduction in most parameters associated to ulcerative colitis: disease activity index, macroscopic score of colitis, epitelium alteration in colon mucosa, inflammatory cell density in colon, myeloperoxidase titers in colon, proinflammatory cytokines (IL-17, IFN-γ). Also, acorn-fed ham diet animals showed increased total antioxidant activity an oleic acid levels in plasma, as well as higher short-chain fatty acid concentrations in cecum (isobutyric, isovaleric and valeric).<h4>Conclusions</h4>In the acorn-fed ham cohort, as a result of the dietary intake of oleic acid and low intake of omega-6 fatty acids, a strong preventive effect against UC symptoms was observed.

Study facts

Organism
Platform
ION PGM System
Age group
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
  • Taxonomic tables are advertised
  • Participant-to-sample mapping is available
  • Participant counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.platform ION PGM System
on the ION PGM™ System

Section gDNA extraction and 16S rRNA sequencing for metagenomics, offset 27000

assay.sequencing_type amplicon_16s
gDNA extraction and 16S rRNA sequencing for metagenomics

Section gDNA extraction and 16S rRNA sequencing for metagenomics, offset 25700

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Finally, disease activity index (DAI) was measured in all animals.

Section Effect of acorn-feed ham on body weight and disease activity index, offset 30000

cohort.total_participants 20
A total of 20 male Fischer 344 rats

Section Animals and experimental design, offset 6500

cohort.treatment_exposure_documented True
UC was induced in 8 rats from each cohort... using autoclaved drinking water containing 3% DSS

Section UC induction and monitoring, offset 8500

cohort.treatment_response_metadata_available True
Finally, disease activity index (DAI) was measured in all animals.

Section Effect of acorn-feed ham on body weight and disease activity index, offset 30000

Data_Assets

FieldValueEvidence
data_assets.open_access True
Creative Commons Attribution 4.0 International

Section datacite_record, offset 9000

data_assets.pipeline_or_tool_versions True
QIIME 2 (v.2017.6.0)... R software (v3.2.4)

Section Phylogenetic analysis, offset 29200

data_assets.raw_reads True
All raw metagenomics data have been deposited at NCBI SRA database (submission PRJNA524796).

Section Phylogenetic analysis, offset 29200

data_assets.taxonomic_table True
This excel table includes the percentages for each taxonomic level

Section Phylogenetic analysis, offset 28600

Specimens

FieldValueEvidence
specimens.body_site cecum
frozen (− 80 °C) cecum feces

Section gDNA extraction and 16S rRNA sequencing for metagenomics, offset 25700

specimens.inflamed_status_available True
UC was induced in 8 rats from each cohort

Section UC induction and monitoring, offset 8500

specimens.participant_to_sample_mapping_available True inferred
used for comparing frequencies between rat individuals and cohorts

Section Phylogenetic analysis, offset 29200

specimens.sample_type stool
gDNA was extracted from 200 mg of frozen (− 80 °C) cecum feces

Section gDNA extraction and 16S rRNA sequencing for metagenomics, offset 25700