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

Abstract

Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol. Results Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p < 0.0001). Ethanol exhibited poorer quality DNA (A260/A230 < 2) and more failed samples compared to the other methods. Samples preserved using the GRC method had smaller relative abundances in gram-negative genera Anaerovibrio, Bacteroides, Prevotella, Selenomonas, and Succiniclasticum, but larger relative abundances in the majority of 56 additional genera compared to TNx2 and GHx2. However, log10 relative abundances across all genera and time-points for TNx2 and GHx2 were on average consistent (R2 > 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ± 0.11) between time-points within a preservation method. Conclusions The two modified lysis buffers solutions (TNx2 and GHx2) proposed in this study were shown to be viable alternatives to the GRC method for RMC profiling in sheep. Use of these preservative solutions reduces cost and improves throughput associated with processing and sequencing ruminal samples. This development could significantly advance implementation of RMC profiles as a tool for breeding ruminant livestock.

Comparison of DNA quantity and quality from fecal samples of mammals transported in ethanol or lysis buffer

“…For instance, research assessing the use of dimethyl sufoxide saline buffer found that this reagent significantly outperformed ethanol, resulting in a 44% increase in amplification success and 17% improvement in genotyping accuracy [ 30 ], findings consistent with our study. Additionally, other studies have reported similar results when examining rumen samples to assess microbiota; in these cases, ethanol yielded lower quality outcomes in comparison to two lysis buffers, namely Tris-NaCl-EDTA-SDS and guanidine hydrochlorate [ 31 ]. Consistency in results across various studies has led to recommendations favoring the use of buffers for the long-term preservation of DNA extracted from fecal samples [ 32 , 33 ].…”

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

“…Metagenomics is increasingly used to characterise species and resistome diversity in polymicrobial samples such as those from sink drains, but the results may be significantly affected by sampling methodology, including storage conditions [13] and delays between sample collection and processing such as those resulting from transportation to the laboratory [14, 15]. Sample stabilisers, such as boric acid, which has been shown to limit bacterial overgrowth in urine samples and is widely used for community urine sampling [16], may offer a cheap and straightforward approach to maintaining sample microbial composition for environmental surveys using metagenomics.…”