Citation: Sanjorjo, R.A.; Tseten, T.; Kang, M.-K.; Kwon, M.; Kim, S.-W. In Pursuit of Understanding the Rumen Microbiome. Fermentation 2023, 9, 114. https://doi.org/10.3390/ fermentation9020114 Academic Editor: Hiroshi Kitagaki Received: 30 December 2022 Revised: 20 January 2023 Accepted: 23 January 2023 Published: 25 January 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). fermentation Review In Pursuit of Understanding the Rumen Microbiome Rey Anthony Sanjorjo 1,† , Tenzin Tseten 1,† , Min-Kyoung Kang 1 , Moonhyuk Kwon 2, * and Seon-Won Kim 1, * 1 Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea 2 Division of Life Science, ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea * Correspondence: mkwon@gnu.ac.kr (M.K.); swkim@gnu.ac.kr (S.-W.K.) † These authors contributed equally to this work. Abstract: The rumen plays an indispensable role in ruminants to utilize ligno-cellulosic material and convert non-protein nitrogen into nutrients otherwise unavailable for human consumption. Recent advancements in the sequencing technology and omics approach have provided profound insights into the rumen world, wherein a consortium of archaea, bacteria, protozoa, fungi, and viruses exist and interact. These ruminal microbes alter the ruminal environment and execute several interlinked metabolic cascades that produce substrates for the host’s energy and body requirements. Methane is emitted as a by-product during this complex fermentation process in ruminants leading to a loss in productivity while negatively impacting the environment. As ruminants play an ever-increasing role in our food supply chain, manipulating the rumen is the critical step towards maximizing the ruminant product’s nutritional value while reducing its carbon footprint. Diet is the most straightforward way to alter the rumen microbiome, possibly in conjunction with phytobiotics and probiotics as feed supplements. Early life interventions allow the manipulation of microbial population structure and function that could persist later on in adult life. It has also been proven that the host exerts influence on the rumen microbiome as a heritable trait. The goal of this review is to provide a better understanding of the rumen, its key organisms, and its development to better identify, characterize, and engineer the rumen microbiome for efficient feed conversion and methane reduction. Keywords: ruminants; rumen microbiome; rumen fermentation; methane; global warming 1. Introduction Ruminants are cloven-hoofed mammals of the Artiodactyla order, with domesticated cattle, sheep, and goats comprising 95% of the total ruminant population [1]. They do not produce cellulolytic or hemicellulolytic enzymes, but rely on the cooperative works among rumen microbes to degrade complex plant polysaccharides [2]. The rumen microbiome is the most diverse gut ecosystem in the animal kingdom and is composed of bacteria, protozoa, fungi, archaea, and phages [3,4]. Anaerobic rumen fermentation by a complex group of rumen microbes converts indigestible forages, food by-products, and non-protein nitrogen into high-grade meat and dairy products for human consumption [5]. The primary products of the rumen fermentation are short volatile fatty acids (SVFAs; predominantly acetate, propionate, and butyrate) and microbial crude protein. The SVFAs serve as an essential energy source, providing up to 70–80% of the host energy requirements [6] and, in the process, generates ATP for the synthesis of microbial cellular protein. Upon digestion, this microbial protein supplies 60% to 85% of the amino acids reaching the small intestine [7]. However, methane is generated during this fermentative process, which is then eructed into the environment, increasing methane concentration in the atmosphere [8]. This gas by-product is a short-lived climate pollutant with a lifetime of only 12.5 years in the atmo- sphere and 80 times more potent than carbon dioxide over 10–20 years [9,10]. According to Fermentation 2023, 9, 114. https://doi.org/10.3390/fermentation9020114 https://www.mdpi.com/journal/fermentation