Data_Sheet_1_Metagenomic sequencing identified microbial species in the rumen and cecum microbiome responsible for niacin treatment and related to intramuscular fat content in finishing cattle.XLSX

IntroductionNiacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary niacin significantly elevated intramuscular fat content (IMF) in castrated finishing steers. Whether niacin affects fat deposition by regulating the microbial composition and functional capacities of gastrointestinal microbiome has been unknown yet.
MethodsIn this study, 16 castrated Xiangzhong Black cattle were randomly assigned into either control group fed with a basal concentrate diet (n = 8) or niacin group fed with a basal concentrate diet added 1000 mg/kg niacin (n = 8). Seven rumen samples and five cecum content samples were randomly collected from each of control and niacin groups for metagenomic sequencing analysis.
ResultsA total of 2,981,786 non-redundant microbial genes were obtained from all tested samples. Based on this, the phylogenetic compositions of the rumen and cecum microbiome were characterized. We found that bacteria dominated the rumen and cecum microbiome. Prevotella ruminicola and Ruminococcus flavefaciens were the most abundant bacterial species in the rumen microbiome, while Clostridiales bacterium and Eubacterium rectale were predominant bacterial species in the cecum microbiome. Rumen microbiome had significantly higher abundances of GHs, GTs, and PLs, while cecum microbiome was enriched by CBMs and AAs. We found a significant effect of dietary niacin on rumen microbiome, but not on cecum microbiome. Dietary niacin up-regulated the abundances of bacterial species producing lactic acid and butyrate, fermenting lactic acid, and participating in lipid hydrolysis, and degradation and assimilation of nitrogen-containing compounds, but down-regulated the abundances of several pathogens and bacterial species involved in the metabolism of proteins and peptides, and methane emissions. From the correlation analysis, we suggested that niacin improved nutrient digestion and absorption, but reduced energy loss, and Valine, leucine and isoleucine degradation of rumen microbiome, which resulted in the increased host IMF.
ConclusionThe results suggested that dietary manipulation, such as the supplementation of niacin, should be regarded as the effective and convenient way to improve IMF of castrated finishing steers by regulating rumen microbiome.

引言
烟酸是哺乳动物必需维生素之一，在维持瘤胃（rumen）微生态稳态中发挥关键作用。本研究前期发现，日粮添加烟酸可显著提升阉割育肥公牛的肌内脂肪含量（intramuscular fat content, IMF）。目前尚不清楚烟酸是否通过调控胃肠道微生物组的组成与功能特性来影响脂肪沉积。

方法
本研究共纳入16头阉割湘中黑牛，随机分为两组：对照组（n=8）饲喂基础精料日粮，烟酸组（n=8）饲喂添加1000 mg/kg烟酸的基础精料日粮。分别从对照组与烟酸组中随机采集7份瘤胃样本、5份盲肠（cecum）内容物样本，用于宏基因组测序（metagenomic sequencing）分析。

结果
所有受试样本共获得2981786个非冗余微生物基因。基于此，我们对瘤胃与盲肠微生物组的系统发育组成进行了表征。研究发现，细菌为瘤胃与盲肠微生物组的绝对优势类群。瘤胃微生物组中丰度最高的细菌物种为产琥珀酸拟杆菌（Prevotella ruminicola）与黄色瘤胃球菌（Ruminococcus flavefaciens），而盲肠微生物组的优势细菌物种则为梭菌目未培养细菌（Clostridiales bacterium）与直肠真杆菌（Eubacterium rectale）。瘤胃微生物组的糖苷水解酶（glycoside hydrolases, GHs）、糖基转移酶（glycosyltransferases, GTs）与多糖裂解酶（polysaccharide lyases, PLs）丰度显著更高，而盲肠微生物组则富集了碳水化合物结合模块（carbohydrate-binding modules, CBMs）与氨基酸（amino acids, AAs）相关功能通路。我们发现日粮烟酸对瘤胃微生物组具有显著调控效应，但对盲肠微生物组无显著影响。日粮烟酸上调了产乳酸、产丁酸、发酵乳酸以及参与脂质水解、含氮化合物降解与同化作用的细菌物种丰度，而下调了多种病原菌以及参与蛋白质与肽代谢、甲烷生成的细菌物种丰度。通过相关性分析，我们推测烟酸可改善宿主营养物质的消化与吸收，减少能量损失，并下调瘤胃微生物组的缬氨酸、亮氨酸与异亮氨酸降解通路，最终促使宿主肌内脂肪含量提升。

结论
本研究结果表明，通过日粮调控手段（如添加烟酸）可通过调节瘤胃微生物组，作为一种高效便捷的途径提升阉割育肥公牛的肌内脂肪含量。