Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants

Abstract

Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

“…Metagenomics and metatranscriptomics can collect the microorganism's entire genome and transcriptome range by sequencing add up to DNA/ RNA from different natural tests, delivering useful data with high determination. The metatranscriptomics represents valuable devices for all-inclusive cataloging microbial quality and transcript profiles and reflecting generally metabolic capacities [71]. Falk et al [72] uncovered that microbial genomic potential can be remade by metagenomic investigation of environmentally extracted DNA, metatranscriptomics can shed light on the deciphered items of DNA, giving riches of data on add up to flag-bearer RNA (mRNA) yield; an intermediary for quality expression.…”

“…A few programs have been created for this step, primarily counting Trimmomatic, PRINSEQ, FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_ toolkit/), and NGS QC Toolkit. Among these programs, Trimmomatic may be an adaptable and proficient preprocessing apparatus that is particularly planned for Illumina yields and can create results prevalent to, or at slightest competitive with, other programs such as PRINSEQ and Fastx-Toolkit [71].…”

Bayesian modeling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows

“…In such instances OTUs may not accurately reflect the diversity in prokaryotic species and strains and are not necessary the closest proxy to true biological diversity in a sample. Taxonomical classification of OTUs can overcome the overestimation of strains and subspecies inherent in de novo OTU picking, however this method is reliant on four publicly available databases [63], and the accuracy and reliability of these databases has not been assessed for rumen prokaryotes. This limits the discovery of OTUs to those already included in the database and cannot capture new variation.…”

PCR and qPCR-based applications in rumen microbiology research: a review

“…Such analysis are carried out using bioinformatics tools in order to study genetic materials from uncultured microorganisms. These tools have proven to be efficient in characterising the rumen microbiota according to function on the basis of their genomes as well as high throughput analysis of amplified taxonomic marker genes (Li et al, 2017). In metagenomics, the template DNA is sequenced without prior amplification of specific genes which results in a snapshot of the gene pool and functional potential of the microbiome while in transcriptomics, mRNA is analyzed to provide a measure of gene expression within the intestinal microbiome (Suchodolski, 2012).…”

“…To characterise biomass-degrading genes and genomes, 268 gigabases of metagenomic DNA from rumen microbes (which are viscid to plant fiber incubated in cow rumen), Hess et al, identified 27,755 putative carbohydrate-active genes and 90 expressed candidate proteins, of which 57% were enzymatically active against cellulosic substrates (Hess et al, 2011). However, recent studies reported that the rumen microbes are under-represented in the public databases (Li et al 2017;Stewart et al, 2017;Stewart et al, 2018). From these recent studies, 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic data were presented and the comparative analysis of these sequences against current publicly available genomes shows that over 90% of these sequences represent previously non-sequenced strains and species of bacteria and archaea.…”