Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions.
Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions.
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DOI：
10.1186/s40168-022-01352-6
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发表时间：
2022-10-05
期刊：
影响因子：
15.5
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中科院分区：
文献类型：
--
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通过充分控制瘤胃微生物区系以增加到达宿主组织的有益脂肪酸的流量，可以获得更健康的反刍动物产品。基因组选择来改变微生物组的功能提供了一个永久和累积的解决方案，这也可能对其他感兴趣的特征产生有利的结果(例如甲烷排放)。可能由于缺乏数据，这一策略从未被探索过。本研究对宿主基因组影响下直接或间接影响牛肉中与人类饮食健康相关的不饱和脂肪酸C18：3N-3、C20：5N-3、C22：5N-3、C22：6N-3或顺式9、反式-11 C18：2和反式-11 C18：1与高胆固醇饱和脂肪酸C12：0、C14：0和C16：0的含量的瘤胃微生物机制进行了全面的鉴定，称为N3和CLA指数。我们首次发现瘤胃中约27.6%(1002/3633)的功能性核心添加剂对数比转化微生物基因丰度(ALR-MG)至少受到宿主基因组的影响(HGFC)。其中，372个ALR-MG与N3指数(n=290)、CLA指数(n=66)或两者同时存在(n=16)相关，表明HGFC对牛肉脂肪酸组成的影响远比微生物脂肪分解和饲料脂肪生物氢化的直接调节复杂得多，N3指数的变化受HGFC变化的影响比CLA更大。在这372个ALR-MG中，110个与N3和/或CLA指数呈同一方向相关，这表明有机会通过微生物组驱动的育种策略同时提高这两个指数。这些微生物基因参与了变形杆菌门中某些属的微生物蛋白质合成(aroF和血清)、碳水化合物代谢和运输(GalT、msmX)、脂多糖生物合成(kdsA、lpxD、lpxB)或鞭毛合成(flgB、flin)。以这些微生物机制为唯一信息标准的微生物群驱动育种策略对两个指数都有正的选择响应(在2.06选择强度下，N3和CLA指数的SD分别为1.36±0.24和0.79±0.21)。在评估我们的微生物驱动的育种策略增加N3和CLA指数对环境性状甲烷排放(g/kg干物质摄入量)的影响时，我们获得了−0.41±0.12SD的相关缓解响应。这项研究为利用瘤胃功能微生物组作为宿主基因组选择的信息的可能性提供了洞察力，这可以同时改善几个感兴趣的微生物组驱动的性状，在这项研究中，肉类品质性状和甲烷排放就是例证。视频摘要在线版本包含可在10.1186/s40168022-01352-6上查阅的补充材料。
Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome function provides a permanent and accumulative solution, which may have also favourable consequences in other traits of interest (e.g. methane emissions). Possibly due to a lack of data, this strategy has never been explored. This study provides a comprehensive identification of ruminal microbial mechanisms under host genomic influence that directly or indirectly affect the content of unsaturated fatty acids in beef associated with human dietary health benefits C18:3n-3, C20:5n-3, C22:5n-3, C22:6n-3 or cis-9, trans-11 C18:2 and trans-11 C18:1 in relation to hypercholesterolemic saturated fatty acids C12:0, C14:0 and C16:0, referred to as N3 and CLA indices. We first identified that ~27.6% (1002/3633) of the functional core additive log-ratio transformed microbial gene abundances (alr-MG) in the rumen were at least moderately host-genomically influenced (HGFC). Of these, 372 alr-MG were host-genomically correlated with the N3 index (n=290), CLA index (n=66) or with both (n=16), indicating that the HGFC influence on beef fatty acid composition is much more complex than the direct regulation of microbial lipolysis and biohydrogenation of dietary lipids and that N3 index variation is more strongly subjected to variations in the HGFC than CLA. Of these 372 alr-MG, 110 were correlated with the N3 and/or CLA index in the same direction, suggesting the opportunity for enhancement of both indices simultaneously through a microbiome-driven breeding strategy. These microbial genes were involved in microbial protein synthesis (aroF and serA), carbohydrate metabolism and transport (galT, msmX), lipopolysaccharide biosynthesis (kdsA, lpxD, lpxB), or flagellar synthesis (flgB, fliN) in certain genera within the Proteobacteria phyla (e.g. Serratia, Aeromonas). A microbiome-driven breeding strategy based on these microbial mechanisms as sole information criteria resulted in a positive selection response for both indices (1.36±0.24 and 0.79±0.21 sd of N3 and CLA indices, at 2.06 selection intensity). When evaluating the impact of our microbiome-driven breeding strategy to increase N3 and CLA indices on the environmental trait methane emissions (g/kg of dry matter intake), we obtained a correlated mitigation response of −0.41±0.12 sd. This research provides insight on the possibility of using the ruminal functional microbiome as information for host genomic selection, which could simultaneously improve several microbiome-driven traits of interest, in this study exemplified with meat quality traits and methane emissions. Video Abstract The online version contains supplementary material available at 10.1186/s40168-022-01352-6.
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