DOI: 10.5061/dryad.547d7wmfk
title: Data from: Effects of fermented vegetables on the gut microbiota for prevention of cardiovascular disease

description: This study investigated the impact of regular consumption of fermented
 vegetables on inflammation and the composition of the gut microbiota in
 adults at increased risk for cardiovascular disease. Eighty-seven adults
 ages 35-64 were randomized into a Fermented Vegetable (FV) group, who
 consumed 100g fermented vegetables daily at least 5x/wk for eight weeks,
 or a Usual Diet (UD) group. Blood and stool samples were obtained before
 and after the intervention. Dependent samples t-tests and adjusted linear
 models were used for within and between group comparisons. Mean age and
 BMI of participants were 45 years and 30 kg/m2, and 80% were female.
 Bloating or gas was the most common side effect reported (19.3% FV group
 vs 9.4% UD group). There were no changes in C-Reactive Protein, oxidized
 LDL-receptor 1, angiopoietin-like protein 4, trimethylamine oxide, and
 lipopolysaccharide binding protein or bacterial alpha diversity between
 groups. Our findings indicate that consuming 100g of fermented vegetables
 at least five days per week for eight weeks does not change inflammatory
 biomarkers or microbial alpha diversity as measured by the Shannon index.
 It is possible that higher doses of fermented vegetables are necessary to
 elicit a significant response by gut bacteria.
description: Participants received stool
 collection kits prior to their clinic visits and were instructed to
 collect three stool samples on three separate days on two timepoints (week
 0 and week 8). Each stool collection kit contained three flushable stool
 collection sheets, three DNA/RNA Shield Fecal Collection tubes (Zymo
 Research, Irvine, CA) one biohazard bag, and detailed instructions for
 stool collection. Participants were asked to record the date and time of
 stool collection on each tube and store the tubes at room temperature
 until their clinic visit appointments. The time between collection of
 stool samples and the clinic visits ranged between one and six
 days. DNA was extracted
 from the frozen stool samples with the DNeasy PowerLyzer PowerSoil Kit
 (Qiagen, Germantown, MD, USA) per manufacturer’s protocol. A NanoDrop One
 (Thermo Fisher Scientific, Madison, WI, USA) was used to measure DNA
 concentration and diluted to 10 ng/μL. Next-generation sequencing of the
 V4 region of the 16S rRNA gene was performed. Amplicon PCR was performed
 on the V4 region of 16S rRNA using the forward (5′-GTGCCAGCMGCCGCGGTAA-3′)
 and reverse (5′-GACTACHVGGGTWTCTAAT-3′) primers. PCR amplicons were
 barcoded and pooled in equal concentrations using the SequalPrep
 Normalization Plate Kit (Invitrogen, Carlsbad, CA, USA). qPCR was used to
 quantify and consolidate libraries using the Kappa Library Quantification
 Kit (Roche, Indianapolis, IN, USA), and the quality of the library will be
 determined by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
 Positive and negative controls were sequenced for quality control. The
 ZymoBIOMICS™ Microbial Community Standard (Zymo Research, Irvine, CA, USA)
 were used to provide a commercial community DNA for a positive control,
 and DNA extraction and PCR amplification provided the negative controls.
 Sequencing was performed in a pair-end modality on the Illumina MiSeq 500
 platform rendering 2 x 150 bp paired-end sequences (Illumina, San Diego,
 CA, USA)). Sequencing reads after quality control were denoised using
 Deblur integrated with QIIME2 (2022.02 released), alignment against a 16S
 reference database (SILVA v132), and clustering into amplicon sequence
 variants (ASVs) with 100% identity threshold. A total of 515 fecal samples
 were extracted for DNA and processed into QIIME2 pipeline. After filtering
 and denoising, 484 samples were retained for microbiome
 analysis. All biological
 samples were processed and stored at -70C until analysis. Blood was
 collected in two 8-mL tubes and left at room temperature for 30 minutes
 before centrifugation at 25C for 10 minutes at 1400 rpm. Serum was
 transferred to 1.5 mL cryogenic tubes in 1-mL aliquots. C-reactive protein
 (CRP) (RandD Systems, Minneapolis, MN - Cat#DCRP00), Angiopoetin-like
 protein 4 (ANGPTL4) also known as Fiaf (RandD Systems, Minneapolis, MN -
 Cat#DY3485), Oxidized low density lipoprotein receptor 1 (LOX-1) (RandD
 Systems, Minneapolis, MN – Cat#DY1798) and trimethylamine oxide (TMAO)
 (AFG Bioscience, Northbrook, IL - Cat#EK715704) were measured with
 commercial ELISA kits. Lipopolysaccharide Binding Protein (LBP) was
 measured by a Pierce LAL chromogenic endotoxin quantitation kit
 (Cat#88282, ThermoFisher Scientific, Waltham, MA). All analyses were
 conducted in the laboratory of Dr. Arikawa at the University of North
 Florida.
description: # Effects of Fermented Vegetables on the Gut Microbiota for Prevention of
 Cardiovascular Disease [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.547d7wmfk) This dataset includes data
 on amplicon sequence variants (ASVs) derived from next-generation
 sequencing of the V4 region of 16S rRNA isolated from human stool samples.
 Sequencing was performed in a pair-end modality on the Illumina MiSeq 500
 platform rendering 2 x 150 bp paired-end sequences. These data were
 obtained from subjects who were either randomized into a fermented
 vegetable group, consuming 100 g of fermented vegetables on at least 5
 days per week for 8 weeks, or a control group who were asked to not change
 anything in their diet. All subjects had at least one risk factor for
 cardiovascular disease and ages ranged from 35 to 60 years of age. ##
 Description of the data and file structure #### File name:
 ASV\_table\_dryad.xlsx File description: This file contains the output
 from next-generation sequencing using the Illumina MiSeq platform. It
 contains data on microbial alpha and beta diversity, as well as amplicon
 sequencing variants (ASVs). The file includes the following data: * Column
 A: subject ID * Column B: Timepoint – 1 is for baseline and 2 is for
 follow up (8 weeks later) * Column C: Treatment – 1 = control and 2 =
 fermented vegetable * Column D: Observed features – number of ASVs
 detected * Column E: Chao1 – indicator of species richness (total number
 of species in a sample) * Column F: Simpson – indicator of species
 evenness (proportional distribution of the number of each species in a
 sample) * Columns G, H, I: Bray Curtis index PCOA plot distances * Columns
 J, K, L: Jaccard index PCOA plot distances * Columns M, N, O: Weighted
 unifrac PCOA plot distances * Columns P, Q, R: Unweighted unifrac PCOA
 plot distances * All other columns: Amplicon sequence variants (ASVs)
 Subjects in this study collected three stool samples at baseline and three
 stool samples at 8 weeks, therefore, there are six rows per person. ####
 File name: Inflammatory\_markers File description: This file contains data
 on inflammatory markers measured in serum collected from study
 participants at baseline  (time point 1) and at week 8 (time point 2). 
 The file includes the following data: * Column A: subject ID * Column B:
 TMAO_1ngmL - Serum Trimethylamine oxide (ng/mL) at time point 1 * Column
 C: TMAO_2ngmL - Serum Trimethylamine oxide (ng/mL) at time point 2 (8
 weeks later) * Column D: LBP1_ngmL - Serum Lipopolysaccharide binding
 protein (ng/mL) at time point 1 * Column E: LBP2_ngmL - Serum
 Lipopolysaccharide binding protein (ng/mL) at time point 2 (8 weeks later)
 * Column F: Ferr1_ngmL - Serum Ferritin (ng/mL) at time point 1 * Column
 G: Ferr2_ngmL - Serum Ferritin (ng/mL) at time point 2 (8 weeks later) *
 Column H: CRP1_ngmL - Serum C-reactive protein (ng/mL) at time point 1 *
 Column I: CRP2_ngmL - Serum C-reactive protein (ng/mL) at time point 2 (8
 weeks later) * Column J: LOX1_pgmL - Serum Oxidized LDL Receptor
 (pg/mL) at time point 1 * Column K: LOX2_pgmL - Serum Oxidized LDL
 Receptor (pg/mL) at time point 2 (8 weeks later) * Column L: Fiaf1_ngmL -
 Serum angiopoietin-like protein 4 at time point 1 * Column M: Fiaf2_ngmL -
 Serum angiopoietin-like protein 4 at time point 2 (8 weeks later) Cells
 marked with a '.' indicate a missing value