shotgun metagenomics of passalid beetle gut regions - SRA

SRX5145808: shotgun metagenomics of passalid beetle gut regions
1 ILLUMINA (Illumina HiSeq 2500) run: 11.9M spots, 3.6G bases, 2.1Gb downloads

Design: DNA extraction and library preparation. Four passalid beetles that were part of a long-term colony feeding on oak wood were selected and their digestive tracts extracted and separated in their four morphologically differentiated sections. Each gut section was then cut open while submerged in a house-made solution of RNAlater. The lumen content of each section as well as the material attached to the gut wall was removed from the beetle tissue. The separated lumen content from each section was then kept in RNAlater at 4C overnight. RNAlater was removed prior to DNA extraction by centrifuging at 8,000 g for 5 minutes. The extracted gut contents were then transferred to a Lysing Matrix E tube (MP Biomedicals, Santa Clara, CA, USA) containing 500 l of lysis solution (1% CTAB in 0.5 M NaCl). The samples were bead-beaten in a FastPrep Instrument (MP Biomedicals) at 4 m/s for 30 seconds. Lysozyme buffer (180 l; 20 mM Tris-HCl (pH 8.0), 2mM EDTA, 1.2% Triton X) containing 10 mg/ml of lysozyme was added to each tube and the mixture incubated at 37C for 30 min. Five l of proteinase K (Ambion, Grand Island, NY, USA) was added to the tubes, mixed by tapping and incubated at 56C for 30 minutes. After the proteinase K lysis, 500 l of phenol:chloroform:isoamyl alcohol (25:24:1) was added to each tube, and the samples bead-beaten in the FastPrep instrument as before. The samples were centrifuged at 10,000 g for 1 minute at 4C and the supernatants transferred to a MaXtract high density tube (Qiagen, Germantown, MD, USA) containing 500 l of chloroform:isoamyl alcohol (24:1). The samples were centrifuged 10,000 g for 1 minute at 4C, and the supernatants transferred to a microcentrifuge tube containing 1 ml of isopropanol and 1l of linear acrylamide (Ambion, Grand Island, NY, USA). The DNA/RNA mixture was precipitated by incubating for 10 minutes at room temperature and centrifuged at 10,000 g for 5 minutes at 4C, and the isopropanol removed. The obtained pellet was washed with 70% ethanol and centrifuged at 10,000 g for 1 minute at 4C. The ethanol was completely removed, and the pellet dissolved in DEPC-treated water. The DNA was purified with the QIAamp DNA Micro kit (Qiagen) following the manufacturers protocol that was modified to treat the samples with RNase (Ambion) for 5 min before the washing steps. The DNA concentration was determined with the use of a Qubit fluorometer (Qiagen) and the DNA size assessed by bioanalyzer and gel electrophoresis. The extracted DNA from each sample was diluted to yield a final mass of 100 ng for metagenomic library preparation. DNA was sheared using Covaris and the library preparation was performed on the IntegenX Apollo 324 robot.

Submitted by: Lawrence Berkeley National Laboratory

Study: beetle metagenome and metaproteome

PRJNA510434 • SRP173726 • All experiments • All runs

show Abstracthide Abstract

Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, we demonstrate how spatially segregated microbiome functionality facilitates lignocellulose deconstruction and transformation in the passalid digestive tract.Using metagenome and metaproteome analyses, along with spectroscopic, isotopic and analytical chemistry approaches, we reconstructed the pathways for sequential lignocellulose transformation, the subsequent fermentation of lignocellulose products, and the distribution of key microbial catalysts throughout the passalid digestive tract.

Sample: midgut DNA from beetle 2

SAMN10605228 • SRS4156187 • All experiments • All runs

Organism: insect gut metagenome

Library:

Name: Sample_EBJC001_index14

Instrument: Illumina HiSeq 2500

Strategy: WGS

Source: METAGENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 11.9M spots, 3.6G bases, 2.1Gb

Run	# of Spots	# of Bases	Size	Published
SRR8334327	11,887,865	3.6G	2.1Gb	2018-12-18

ID:: 6960303

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity