2025-03-30
ENA first public
ERC000011
ENA-CHECKLIST
School of Health and Life Sciences
INSDC center name
public
INSDC status
ERS18293202
SRA accession
E-MTAB-13807:Sample 4
Submitter Id
ArrayExpress
broker name
not collected
collection date
Protocols: Soaked Rice (Panta Bhat) was prepared following traditional Bangladeshi methods. In brief, whole Basmati rice grains, collected from a local supermarket, were washed and cooked with water at 100 °C for 20-30 minutes in an aluminium pan and then cooled to room temperature. Rice was separated in two clean sterile mud pots, maintaining sterile conditions by mixing rice with water using sterile utensils. Then all the rice soaked in water was kept overnight at room temperature for 12 to 14 hours for further analysis. The rice was prepared by the individual participants for their own consumption as per the ethical approval. DNA from rice samples soaked at 20 °C and 30 °C was extracted using the DNeasy® PowerFood® Microbial Kit, following a modified protocol designed for optimal DNA yield as per the manufacturer's guidelines. Initially, 0.25 g of soaked rice sample was combined with 1.8 ml of rice broth in a 2 ml microcentrifuge tube. The samples were homogenized using a FastPrep-24™ 5G Homogenizer at a speed of 8 m/s for 6 mins.  The resulting microbial food culture was centrifuged, and the supernatant was removed. This process was repeated until 10 ml of soaked rice broth was centrifuged to obtain a concentrated rice pellet.  The cell pellet was resuspended in 450 µl of pre-warmed (55°C) MBL solution and transferred to a PowerBead Tube. Instead of using a vortex adapter, the PowerBead Tubes were placed in the FastPrep-24™ 5G Homogenizer, vortexed horizontally for 10 min at maximum speed. After centrifugation, the supernatant was transferred to a clean tube, and IRS solution was added and incubated before another centrifugation step. The resulting supernatant was mixed with MR solution and loaded onto an MB Spin Column. After several wash steps, the purified DNA was eluted using 50 µl of elution buffer (EB).  The purified DNA samples were quantified using a NanoDropTM ( One Microvolume UV-Vis Spectrophotometer, ThermoScientific). Samples with a concentration of at least 10 ng/µl were selected and sent to Novogene (Genomic services, Cambridge, UK) for sequencing. The V4 region of the 16S rRNA gene was amplified using primers 515F (5’ GTGCCAGCMGCCGCGGTAA 3’) and 806R (5’ GGACTACHVGGGTWTCTAAT 3’).
description
not collected
geographic location (country and/or sea)
unsoaked rice at 20 degree Celsius
growth condition
not applicable
isolate
mixed sample
organism
mixed sample
organism
microbial community
sample type
mixed sample
scientific_name
Sample 4
title