Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria.
Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria.
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DOI：
10.3389/fmicb.2016.01854
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发表时间：
2016
影响因子：
5.2
通讯作者：
Huws SA
中科院分区：
文献类型：
--
作者：
Mayorga OL;Kingston-Smith AH;Kim EJ;Allison GG;Wilkinson TJ;Hegarty MJ;Theodorou MK;Newbold CJ;Huws SA
了解摄入的植物材料和附着的微生物组之间的关系对于开发提高反刍动物营养利用效率的方法至关重要。我们以前已经表明，多年生黑麦草（PRG）瘤胃细菌定植事件遵循的主要（最多4小时）和次要（4小时后）模式的基础上的差异，附着的细菌的多样性。在这项研究中，我们研究了时间生态位专业化的初级和次级群体的附着瘤胃微生物群使用宏基因组鸟枪测序以及监测变化的植物化学中红外光谱（FT-IR）。使用子系统技术的宏基因组快速注释（MG-RAST）对鸟枪宏基因组序列的分类学分析表明，无论时间如何，丁酸弧菌属、梭菌属、真杆菌属、普雷沃氏菌属和月形单胞菌属都主导附着的微生物组。MG-RAST还显示，在二次定殖期间，氨基酸球菌属、芽孢杆菌属、丁酸弧菌属和普雷沃氏菌属rDNA的读段丰度增加，而布劳特氏菌属的读段丰度降低。MG-RAST邻位组簇（COG）功能分析还显示，附着的微生物组的主要功能被广泛地分类为“代谢”;主要是氨基酸、碳水化合物和脂质代谢和转运。这些类别中的大多数序列读段丰度（分别为51.6%、43.8%和50.0%的COG家族与氨基酸、碳水化合物和脂质代谢有关）在次级定殖期间丰度较高。京都基因和基因组百科全书（KEGG）途径分析证实，在瘤胃孵育1和4小时时存在的PRG附着微生物群具有相似的功能能力，仅在仅一个孵育时间点中唯一地发现仅少数途径。FT-IR数据的植物残留物也表明，主要的变化，植物化学之间的主要和次要的殖民地是由于增加碳水化合物，氨基酸和脂质代谢。本研究证实了原发性和继发性定植事件，并支持分类学变化导致功能变化的假设。碳水化合物代谢COG家族内的序列仅包含3.2%的纤维素活性，平均跨越两个孵育时间（1和4小时），表明植物细胞壁的降解可能是确保植物内营养素及时地对微生物和最终动物的生物利用度的关键限速因素。这表明，未来提高反刍动物养分利用效率的重点应该是改变反刍动物植物细胞壁组分和/或提高瘤胃微生物群的纤维素分解能力。
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within “metabolism;” predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.
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影响因子：
4.4
作者：
CHENG, KJ;FAY, JP;COSTERTON, JW
通讯作者：
COSTERTON, JW
DOI：
10.1128/genomea.00723-15
发表时间：
2015-07-01
期刊：
GENOME ANNOUNCEMENTS
影响因子：
--
作者：
Kishi, Luciano T.;de Jesus, Raphael B.;de Souza, Jackson A. M.
通讯作者：
de Souza, Jackson A. M.
DOI：
10.5713/ajas.2009.r.11
发表时间：
2009-09-01
期刊：
ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES
影响因子：
--
作者：
Kim, Eun J.;Huws, Sharon A.;Scollan, Nigel D.
通讯作者：
Scollan, Nigel D.
影响因子：
7
作者：
Kingston-Smith, Alison H.;Edwards, Joan E.;Abberton, Michael
通讯作者：
Abberton, Michael
影响因子：
4.4
作者：
Eschenlauer, SCP;McKain, N;Wallace, RJ
通讯作者：
Wallace, RJ