<div>A distinct mechanism of generating metagenome is metagenomics which includes sequencing the whole DNA extracted from an environmental sample, mapping it to a reference database followed by gene annotation. Advancement in sequence-based metagenomics has significantly reduced processing costs and has acquired a rapid pace. Metagenomics has been crucial in investigating &ldquo;hidden&rdquo; genetic characteristics and construction biotechnological processes through the discovery of novel genes, enzymes, pathways and bioactive molecules with entirely different or improved biochemical functions. Metagenomics is a fairly recent addition to the molecular toolbox and is the simplest, impartial way of challenging the adaptive ability of microbial populations. Metagenomics is beneficial in recognising the complex consortium of bacteria, protozoa, archaea, fungi, <em>etc.</em> and association amongst them resulting in higher feed utilization and productivity of animals. It allows formulating probiotics feed materials, as well as in immunomodulation in both livestock and poultry. This review emphasizes significant recent achievements in metagenomics, offers insights into the possibilities, modern-day challenges and its utility in livestock and poultry.</div>


<p>Metagenomics: A Novel Tool for Livestock and Poultry Improvement: A Review</p>


<div>The presence of complex microorganisms in the rumen of ruminants are able to process the lignocellulose from low quality feed and fodder into volatile fatty acids, convert non-protein nitrogen into microbial protein and synthesize B vitamins, thus, ruminants are able to produce food of animal origin without competition for feed with non-ruminants and man. On the other hand, they contribute 14 per cent of anthropogenic methane, released annually into the atmosphere. Manipulating the rumen microbiome is considered as an important approach to reduce environmental impact, while increasing production efficiency in ruminants. A systematic literature search was undertaken and relevant research and review articles were downloaded, classified and salient points extracted to prepare the narrative review on &ldquo;Influence of Feed and Feeding strategies on Rumen microbiome&rdquo;. The microbial community in the rumen is the most diverse composed of bacteria, archaea, protozoa, fungi and uncharacterized virome. Differences in ruminal microbial community compositions are predominantly attributable to diet. Dietary manipulation offers a viable solution to alter the rumen microbiome so that the present-day challenges faced by the ruminant livestock industry is addressed.</div>


<p>Influence of Feed and Feeding Strategies on Rumen Microbiome: A Review</p>


<p><strong>Background:</strong> Ruminal microbes support growth, lactation and maintenance of animals by providing energy and protein yielding nutrients. Metagenomics is the study of microbial communities directly in their natural environments such as soil, water, gut samples etc. The 16S rRNA gene sequencing is one of the basic genetic markers for the characterisation of prokaryote microorganism community. Current study exploited complex gut microbial communities present in cattle rumen based on variation in milk fat yield.&nbsp;<br />
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<strong>Methods:</strong> The study was conducted in cattle reared at University Livestock Farm, Kerala Veterinary and Animal Sciences University. Twelve healthy cattle in the initial stages of lactation (less than three months) were selected and divided into two groups of six each based on high and low milk fat composition. Rumen samples were collected and DNA was isolated. Amplicons of 16S rRNA has been generated from metagenomic DNA targeting V3 and V4 hyper variable regions. Qiime2 was used for analysis for 16S rRNA amplicon sequencing.<br />
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<strong>Result:</strong> Results revealed that a total of 38,28,241 sequences were obtained after demultiplexing. Majority of sequence length ranged around 295 to 301 nucleotides for forward reads and 216 to 300 nucleotides for reverse reads. After denoising, a total of 6,62,498 sequences were obtained. Clustering (de-replication) produced 711 unique sequence features. In kingdom level of taxonomy, for bacterial kingdom, there was no significant difference in abundance of organisms for high milk fat yield and low milk fat yield cows. For archaea, significant difference observed between abundance of high milk fat and low milk fat groups at five per cent level in the current study.</p>


Metagenomics: A Novel Tool for Livestock and Poultry Improvement: A Review

Influence of Feed and Feeding Strategies on Rumen Microbiome: A Review

Evaluation of Rumen Microbes For Milk Fat Yield in Cattle Based on 16S rRNA Amplicon Metagenomic Sequencing