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Low-cost sample preservation methods for high-throughput processing of rumen microbiomes.

Juliana C C Budel1,2, Melanie K Hess1, Timothy P Bilton3

  • 1Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.

Animal Microbiome
|June 6, 2022
PubMed
Summary

New lysis buffer methods (TNx2 and GHx2) offer cost-effective alternatives for preserving rumen microbial community (RMC) DNA. These methods simplify sample processing for RMC profiling, aiding livestock breeding research.

Keywords:
Genotyping-by-sequencingPstIRE-RRSRumen microbial profilesRumen microbiologySuperorganism

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Area of Science:

  • Microbiology
  • Animal Science
  • Genomics

Background:

  • Rumen microbial community (RMC) profiling is crucial for predicting methane emissions in livestock.
  • Current Global Rumen Census (GRC) protocols require time-consuming freeze-drying and grinding, hindering research accessibility.
  • Developing efficient DNA preservation methods is essential for cost-effective RMC profiling.

Purpose of the Study:

  • To evaluate alternative rumen sample preservation methods for RMC profiling.
  • To assess the feasibility of using Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2) lysis buffers.
  • To compare these methods against the standard GRC protocol for DNA yield, quality, and RMC profile accuracy.

Main Methods:

  • Rumen samples from 151 sheep were collected at two time-points.
  • Samples were preserved using TNx2, GHx2, 100% ethanol, and the GRC method.
  • DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing for RMC profiling.

Main Results:

  • TNx2 and GHx2 methods yielded comparable DNA quality and RMC profiles to the GRC method.
  • Ethanol preservation resulted in poorer DNA quality and higher sample failure rates.
  • While minor differences in specific genera abundances were observed, TNx2 and GHx2 showed high consistency (R² > 0.99) with the GRC method for overall RMC profiles.

Conclusions:

  • TNx2 and GHx2 lysis buffers are viable, cost-effective alternatives to the GRC method for sheep RMC profiling.
  • These methods reduce processing time and costs, improving throughput for ruminal sample analysis.
  • Simplified preservation protocols can accelerate the use of RMC profiles in breeding programs for ruminant livestock.