Hernández Ruth, Chaib De Mares Maryam, Jimenez Hugo, Reyes Alejandro, Caro-Quintero Alejandro
Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia.
Front Microbiol. 2022 Mar 25;13:813002. doi: 10.3389/fmicb.2022.813002. eCollection 2022.
Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
牛的生产力取决于我们充分理解和操控牛瘤胃中植物材料发酵过程的能力，这最终会改善动物健康、提高生产力并减少对环境的影响。朝着这个方向迈出的关键一步是对构成瘤胃微生物群的微生物物种进行系统发育和功能表征。为应对这一挑战，我们使用蔗糖密度梯度按大小和密度分离了瘤胃液样本。我们使用了整个样本和最小的部分（5%），以使细菌富集，来组装宏基因组组装基因组（MAGs）。我们总共获得了16个细菌基因组，其中15个在梯度的最小部分中富集。根据最近提出的基因组分类数据库（GTDB）分类法，这些MAGs属于拟杆菌门、厚壁菌门_A、厚壁菌门、变形菌门和螺旋体门。15个MAGs在物种水平上是新的，4个在属水平上是新的。这些MAGs的功能表征表明，它们与目前已知的来自这个复杂环境的特征明确的成员的基因组潜力有所不同。拟杆菌门和螺旋体门的物种显示出在瘤胃中水解植物细胞壁中复杂多糖以及产生复合维生素B和进行蛋白质降解的潜力。相反，属于厚壁菌门和α-变形菌门的MAGs在几个代谢途径中表现出减少；然而，它们有乳酸发酵的基因以及与几丁质降解相关的水解酶和酯酶。我们的结果表明，按大小和密度分离瘤胃微生物群落降低了瘤胃液样本的复杂性，并富集了一些特征不明确的瘤胃细菌，从而能够探索它们的基因组潜力及其在瘤胃生态系统中的功能作用。
