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[前沿资讯 ] 华中农业大学猪肠道微生物参考基因集及核心优势细菌功能解析研究取得进展 进入全文
华中农业大学
近日，The ISME Journal杂志在线发表了华中农业大学农业微生物资源发掘与利用全国重点实验室、教育部动物育种与健康养殖前沿科学中心、湖北洪山实验室晏向华教授课题组的研究成果，论文题为“Characterizing core microbiota and regulatory functions of the pig gut microbiome”。该研究构建了猪肠道微生物参考基因集，筛选到猪肠道核心优势细菌，并解析其对宿主代谢的调控作用机制，对实施肠道菌群干预改善猪生长与肠道健康具有重要意义。 研究人员综合运用宏基因组学和细菌16S rDNA扩增子测序技术系统解析了7个品种猪（即杜×（长×大）猪、藏猪、莱芜猪、沙子岭猪、从江香猪、环江香猪和宁乡猪）共计56头断奶仔猪和56头育肥末期猪的肠道微生物区系组成。鉴定了11418273个非冗余肠道微生物基因，通过与已发表文献的非冗余肠道微生物基因进行整合，本研究构建了包含17020160个非冗余基因的猪肠道微生物基因集，通过对宏基因组组装数据进行分箱，共重构获得了4910个非冗余原核微生物基因组。研究表明我国地方猪肠道微生物的营养物质（包括脂类、氨基酸、碳水化合物和核苷酸）代谢能力和能量代谢能力比杜×（长×大）商品猪更强。杜×（长×大）商品猪肠道微生物的抗生素抗性基因丰度比中国地方猪更高，研究发现品种和日龄是影响猪肠道微生物区系组成和功能的关键因素。综合评估微生物的出现率、微生物相对丰度和猪生长阶段，利用宏基因组学和细菌16S rDNA扩增子测序共鉴定出3种猪肠道核心优势细菌（Phascolarctobacterium succinatutens、Prevotella copri和Oscillibacter valericigenes），结果表明灌服上述3种核心优势细菌可显著增加无菌小鼠的器官指数（包括心脏、脾脏和胸腺），降低胃肠道的长度，增强肠道上皮屏障功能，增加肠道的隐窝深度，同时上述3种核心优势细菌可显著改变无菌小鼠的营养物质代谢过程（包括初级胆汁酸的生物合成、苯丙氨酸、酪氨酸和色氨酸的生物合成、苯丙氨酸的代谢等）。综上，本研究系统性解析了7个品种猪的肠道微生物的组成与功能，筛选出猪肠道微生物核心优势细菌并证明了其对无菌小鼠器官指数、肠道屏障功能、肠道黏膜形态和营养物质代谢的关键调控作用，为实施肠道菌群干预改善猪生长与肠道健康提供理论依据和新资料。
[前沿资讯 ] 华中农业大学在江汉鸡肠道微生物组解析和益生菌筛选中取得新进展 进入全文
华中农业大学
华中农业大学生命科学技术学院益生菌智造创新团队赵述淼副教授课题组在国际学术期刊Microbiome上发表题为“Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties”的研究论文，研究采用宏基因组测序技术揭示江汉鸡肠道微生物群物种和功能组成以及分离了具有益生菌特性的乳酸片球菌。 研究团队利用宏基因组测序技术分析了长江流域附近四个城市江汉鸡肠道微生物的物种和功能组成。结果表明，江汉鸡肠道菌群的细菌种类组成与其他鸡品种相似，其中Phocaeicola和Bacteroides是最丰富的细菌属。LEfSe 分析显示荆州样品与其他三组样品之间的物种组成和功能特征存在显著差异。功能注释表明，江汉鸡肠道菌群以代谢基因为主，其中与碳水化合物代谢相关的基因数量最多。发现了多个抗生素抗性基因（ARG），并且ARG的组成与集约化笼养鸡相似，表明抗生素广泛存在于江汉鸡的肠道微生物群中。结合宏基因组的研究结果，从鸡肠道中分离、鉴定出了829株微生物，并进行了大规模的益生性评价，其中3 株乳酸片球菌（P. acidilatic）表现出较强的益生潜力。这些发现提供了对江汉鸡独特肠道微生物群的深入了解，并强调了益生菌株在养殖业的潜在应用前景。
[学术文献 ] Discovery of Toxin-Degrading Enzymes with Positive Unlabeled Deep Learning 进入全文
ACS Catalysis
Identifying functional enzymes for the catalysis of specific biochemical reactions is a major bottleneck in the de novo design of biosynthesis and biodegradation pathways. Conventional methods based on microbial screening and functional metagenomics require long verification periods and incur high experimental costs; recent data-driven methods apply only to a few common substrates. To enable rapid and high-throughput identification of enzymes for complex and less-studied substrates, we propose a robust enzyme’s substrate promiscuity prediction model based on positive unlabeled learning. Using this model, we identified 15 new degrading enzymes specific for the mycotoxins ochratoxin A and zearalenone, of which six could degrade >90% mycotoxin content within 3 h. We anticipate that this model will serve as a useful tool for identifying new functional enzymes and understanding the nature of biocatalysis, thereby advancing the fields of synthetic biology, metabolic engineering, and pollutant biodegradation.
[学术文献 ] DIProT: A deep learning based interactive toolkit for efficient and effective Protein design 进入全文
Synthetic and Systems Biotechnology
The protein inverse folding problem, designing amino acid sequences that fold into desired protein structures, is a critical challenge in biological sciences. Despite numerous data-driven and knowledge-driven methods, there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein design. In this paper, we present DIProT, an interactive protein design toolkit. DIProT leverages a non-autoregressive deep generative model to solve the inverse folding problem, combined with a protein structure prediction model. This integration allows users to incorporate prior knowledge into the design process, evaluate designs in silico, and form a virtual design loop with human feedback. Our inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets, with promising sequence recovery and inference time. Case studies further illustrate how DIProT can facilitate user-guided protein design.
[政策法规 ] Risks for animal health related to the presence of ergot alkaloids in feed 进入全文
European Food Safety Authority
The European Commission requested EFSA to provide an update of the 2012 Scientific Opinion of the Panel on Contaminants in the Food Chain (CONTAM) on the risks for animal health related to the presence of ergot alkaloids (EAs) in feed. EAs are produced by several fungi of the Claviceps and Epichloë genera. This Opinion focussed on the 14 EAs produced by C. purpurea (ergocristine, ergotamine, ergocornine, α‐ and β‐ergocryptine, ergometrine, ergosine and their corresponding ‘inine’ epimers). Effects observed with EAs from C. africana (mainly dihydroergosine) and Epichloë (ergovaline/−inine) were also evaluated. There is limited information on toxicokinetics in food and non‐food producing animals. However, transfer from feed to food of animal origin is negligible. The major effects of EAs are related to vasoconstriction and are exaggerated during extreme temperatures. In addition, EAs cause a decrease in prolactin, resulting in a reduced milk production. Based on the sum of the EAs, the Panel considered the following as Reference Points (RPs) in complete feed for adverse animal health effects: for pigs and piglets 0.6 mg/kg, for chickens for fattening and hens 2.1 and 3.7 mg/kg, respectively, for ducks 0.2 mg/kg, bovines 0.1 mg/kg and sheep 0.3 mg/kg. A total of 19,023 analytical results on EAs (only from C. purpurea) in feed materials and compound feeds were available for the exposure assessment (1580 samples). Dietary exposure was assessed using two feeding scenarios (model diets and compound feeds). Risk characterisation was done for the animals for which an RP could be identified. The CONTAM Panel considers that, based on exposure from model diets, the presence of EAs in feed raises a health concern in piglets, pigs for fattening, sows and bovines, while for chickens for fattening, laying hens, ducks, ovines and caprines, the health concern related to EAs in feed is low.
[政策法规 ] Persistence of microbiological hazards in food and feed production and processing environments 进入全文
European Food Safety Authority
Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well‐designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a ‘seek‐and‐destroy’ approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom‐up and top‐down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.
