Cereal‐based fermented foods in developing countries: ancient foods for modern research

Cereal‐based fermented foods are major contributors to energy intake in developing countries (DC). Their microbiota is dominated by lactic acid bacteria and has been extensively investigated. Diversity studies have been facilitated by molecular methods enabling genotyping of isolates; the rapid development of ‘omics’ approaches should facilitate more comprehensive studies to describe the relation between microbial diversity, cell physiology and product characteristics. Also, the link between the food microbiota and health benefits, in particular in nutrition, should be investigated. There is a need to encourage researches in the field of DC cereal‐based foods in direction of more mechanistic approaches.     

Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding

The aim of this study was to explore the effect of colostrum feeding time on the ileal microbiome of neonatal calves. In this study, 22 male Holstein calves were randomly assigned to different colostrum feeding time treatments: after birth (at 45 min, n = 7); at 6 h after birth (n = 8); and at 12 h after birth (TRT12h; n = 7). At 51 h after birth, calves were killed and ileum digesta was collected for microbiome analysis using shotgun metagenomic sequencing. Bacteria, archaea, eukaryotes, and viruses were identified from the ileum microbiome. For the bacteriome, Firmicutes and Proteobacteria were the predominant phyla, and Escherichia, Streptococcus, Lactobacillus were the 3 most abundant genera. For the archaeal community, Euryarchaeota and Crenarchaeota were the 2 major phyla, and Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the 3 most abundant genera. In total, 116 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified from the ileal microbiome, with “biosynthesis of vancomycin group antibiotics,” “biosynthesis of ansamycins,” “valine, leucine, and isoleucine biosynthesis,” “ribosome,” and “d-alanine metabolism” as the top 5 functions. When the ileal microbiomes were compared among the 3 treatments, the relative abundance of Enterococcus was higher in TRT12h calves, suggesting that calves may have a higher abundance of opportunistic pathogens when the feeding of colostrum is delayed for 12 h. Moreover, among all KEGG pathways, the enriched “taurine and hypotaurine metabolism” (KO00430) pathway was identified in the ileal microbiome of TRT12h calves; however, future studies are needed to understand the effect on the host. Additionally, 2 distinct ileal microbial profiles were identified across all samples, indicating that that host factors may play a significant role in driving varied microbiome changes in response to colostrum feeding time. Whether such microbiome shifts affect long-term gut function and calf performance warrants future studies.     

肠道微生物群落研究进展及合成微生物群落面临的挑战

In recent years, research on the intestinal microbial communities and human health has developed rapidly. However, the regulation and application of the intestinal microbial community are still in their infancy. The reason for this is that our understanding of the structure and function of the human gut microbiome is inadequate. Synthetic microbiota is a new microbial community established by artificial synthesis of multiple species, which is simulated, tested, and optimized by various experimental models and mathematical modeling methods in vitro and in vivo. It is helpful to deepen the understanding of the structure, stability, and functional activity of the complex microbiota in the human gut. We summarized the research methods of the intestinal microbiome, the factors affecting the stability of the intestinal microbiome, and the challenges facing the synthesis of the intestinal microbiome, in order to provide a reference for the bidirectional transformation of the theoretical research and clinical application of intestinal microbial community.     

宏基因组文库新型β-葡萄糖苷酶的筛选、克隆及酶学性质分析

利用宏基因组文库方法,通过功能筛选法从文库中筛选到一个新型β-葡萄糖苷酶基因bgl2238（GenBank：KU320675.1）,对新基因进行生物信息学分析和原核表达,并研究其酶学性质。结果表明,该基因全长2238bp,可编码745个氨基酸,通过氨基酸序列分析,预测bgl2238蛋白分子质量为80.67kDa,pI值为4.95,是一种结构较稳定、疏水性高且无信号肽序列的酸性蛋白质;经同源性分析,发现其与来源于Bacteroides thetaiotaomicron的β-葡萄糖苷酶具有58%的相似性,属于GH3超家族和GH3C超家族酶。将重组质粒pET-32a（＋）-bgl2238转化入Escherichia coli BL2l（DE3）细胞进行异源表达,酶学性质测定结果显示,以对硝基苯基-β-D-吡喃葡萄糖苷（p-nitrophenyl-β-D-glucopyranoside,pNPG）为底物,β-葡萄糖苷酶bgl2238最适反应pH值和温度分别为6.10、44℃,此时该酶最大比活力达到29.1U/mg;且在4～50℃范围内,热处理β-葡萄糖苷酶bgl22384h后仍保留70%以上的酶活力,热稳定性较好;其动力学参数Vmax为576μmoL/（L·min）,Km为0.296mmol/L;不同浓度的K＋、Na＋、Fe2＋、Mg2＋、Mn2＋、Ca2＋、Co2＋和Ni2＋对酶活力均有较大促进作用,其中Fe2＋对bgl2238酶活力的促进作用最大,10mmol/LFe2＋使相对酶活力高达260%,而重金属离子Ag＋、Hg2＋及Cu2＋对酶活力有抑制作用。bgl2238具有良好的酶学性质,可以尝试应用于工业上纤维素降解的生产。     

土壤宏基因组中芽孢杆菌信号肽的克隆及分析

从土壤宏基因组中筛选获得在芽孢杆菌中高效分泌重组蛋白的信号肽。通过数据分析,将预测到的信号肽DNA片段与蛋白酶基因融合,在枯草芽孢杆菌（Bacillus subtilis）WB800和地衣芽孢杆菌（Bacillus licheniformis）DL6中表达,进行胞外蛋白酶酶活测定。筛选得到25个可能来源于G+菌的信号肽序列,胞外蛋白酶活性分析的结果显示,有14个信号肽具有较好的分泌蛋白酶的能力,其中引导效果最好的信号肽（sig20）是蛋白酶自身信号肽的1.64倍。将高分泌信号肽转化到地衣芽孢杆菌中,证实其在地衣芽孢杆菌同样具有较好的引导效果。应用生物信息学与宏基因组学相结合的方法,可有效获得高效的芽孢杆菌信号肽序列,为蛋白质高效分泌表达系统的构建提供丰富的表达元件。     

新型高抗草甘膦N-乙酰转移酶基因的分离及其在大肠杆菌中的表达

利用草甘膦极端污染土壤总DNA,构建了元基因组文库,筛选到一个高抗草甘膦的N-乙酰转移酶(N-acetyltransferase,GAT)基因,并利用原核表达系统对该基因进行了功能鉴定,发现其在大肠杆菌BL21中能耐受高达300 mM的草甘膦.研究结果为进行N-乙酰化途径高抗草甘膦机理研究和新型高抗草甘膦转基因作物的开发提供了理论基础.     

Phospholipases: Occurrence and production in microorganisms,assay for high-throughput screening,and gene discovery from natural and man-made diversity

Various kinds of phospholipids have wide industrial applications such as in food and nutraceuticals, cosmetics, agricultural products, and pharmaceuticals. The demand for reliable biocatalysts for the production of phospholipid products, such as phospholipases A₁, A₂, C, and D, has steadily increased over the past several decades. A large number of microbial phospholipases have been isolated and characterized, and the increasing availability of these enzymes could eventually lead to the sustained development of phospholipid-related biotechnology. Although a number of reactions have been performed using phospholipases, a reliable and efficient supply of superior phospholipases in quantity is still a challenge for their practical application. High-throughput functional assay methods for phospholipases should be devised to develop superior new species from the huge diversity of phospholipases. Recent biotechnological advances in the discovery of new phospholipase genes from natural sources, such as extremophiles of phospholipases by protein engineering, such as directed evolution, can provide valuable means of rapidly developing practical uses of phospholipases for various applications.     

Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss

This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur (https://www.mothur.org/) in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database. After filtering on relative abundance (>0.1%) and penetrance (95%), 25 OTU were selected for the analyses (17 bacteria, 1 archaea, and 7 ciliates). Association with the genetic background of the host animal based on the principal components of a genomic relationship matrix based on single nucleotide polymorphism markers was analyzed using Bayesian methods. Fifty percent of the bacteria and archaea genera were associated with the host genetic background, including Butyrivibrio, Prevotella, Paraprevotella, and Methanobrevibacter as main genera. Forty-three percent of the ciliates analyzed were also associated with the genetic background of the host. In total, 48% of microbes were associated with the host genetic background. The results in this study support the hypothesis and provide some evidence that there exists a host genetic component in cattle that can partially regulate the composition of the microbiome.     

新型碱性低分子量β-葡萄糖苷酶基因的分离与酶学性质研究

目的:获得新型β-葡萄糖苷酶编码基因,并对其表达产物进行酶学性质研究。方法:采用宏基因组学方法提取兔盲肠内微生物总DNA,构建DNA文库,通过筛选培养基获得产β-葡萄糖苷酶的克隆,测序获得其插入基因序列,氨基酸多重序列比对分析其序列特征,并用DNS显色法测定表达产物在不同条件下的酶活力。结果:在文库中获得一个基因片段nglu07,能编码一个低分子量的β-葡萄糖苷酶。nglu07基因片段长180bp,编码60个氨基酸残基。与已提交的糖苷水解酶Ⅰ家族成员进行氨基酸多重序列比对表明nglu07具有预测的活性位点Glu4与底物结合位点Tyr47,其最适反应温度为50℃,最适pH为10.0,粗酶活为8.12U/mL。结论:成功获得一新型低分子量的碱性β-葡萄糖苷酶编码基因,其蛋白温度稳定性高,在pH4.0～11.0的环境中均能保持较高的酶活力,具有作为食品工业用酶以及碱性酶的潜力,尤其在食品饮料加工、棉织品生物整理、洗涤及废纸脱墨等工业方面具有一定的应用价值。