Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.
NPJ Biofilms Microbiomes. 2022 Jun 8;8(1):46. doi: 10.1038/s41522-022-00309-9.
Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.
瘤胃微生物群落通过消化顽固性木质纤维素底物为可利用的营养物质和必需代谢物，促进营养吸收。尽管瘤胃微生物群落结构高度相似，但不同的反刍动物物种可能具有独特的功能能力，使其能够以各种木质纤维素底物为食而茁壮成长。在这里，我们应用基于基因组的宏基因组学来探索形成生物膜的微生物群落的系统发育多样性、木质纤维素降解潜力和发酵代谢，这些微生物群落定植于骆驼瘤胃中 11 种不同的植物底物上。多样性分析显示，定植于不同底物的瘤胃微生物群落的组成存在显著差异，这与它们不同的理化性质相符。宏基因组重建共获得了 590 个细菌分离株和 1 个古菌谱系的基因组序列，这些序列属于 20 个微生物门。与公开的参考基因组和瘤胃宏基因组组装基因组的比较表明，大多数分离株属于没有特征明确代表的新物种。我们发现，某些低丰度的分类群，包括厚壁菌门、浮霉菌门和拟杆菌门的成员，其基因组每兆碱基具有数量不成比例的大量碳水化合物活性酶，这意味着它们具有很高的代谢潜力，可对瘤胃功能做出贡献。总之，我们提供了一幅详细的图景，展示了骆驼瘤胃中定植于不同木质纤维素组成饲料的瘤胃微生物群落的多样性和功能意义。对 591 个宏基因组组装基因组的详细分析揭示了一个相互关联的微生物群落网络，并强调了某些分类群在瘤胃功能中的关键作用，包括那些具有最小基因组的分类群（例如 Patescibacteria）。存在着多种多样的基因簇，编码次生代谢物，揭示了这些生物分子在塑造瘤胃微生物群落结构中的特定功能。
