2023年9月29日

mLife · Volume 2 · Issue 3

正式出版！

第二卷Issue 3共计12篇文章，包括7篇Original Research，1篇Review，1篇Perspective，1篇Personal Reflection，1篇Method，1篇Correspondence。作者分别来自中国、美国、德国、日本、新加坡、印度、挪威等国家。

▶ Assessing mechanisms for microbial taxa and community dynamics using process models

Linwei Wu, Yunfeng Yang, Daliang Ning, Qun Gao, Huaqun Yin, Naija Xiao, Benjamin Y. Zhou, Si Chen, Qiang He, Jizhong Zhou

北京大学吴林蔚研究员团队研究开发了一种基于过程模型的新框架，通过将消费者-资源模型与中性模型随机微分方程相结合，定量评估微生物物种和群落动态背后的组装机制。基于厌氧生物反应器的时间序列数据，发现组合模型对不稳定环境下的丰富种预测性能最佳，而中性模型对稀有种动态变化的预测更好，表明确定性和随机因素的相对重要性随环境条件和物种丰度而变化。

▶ Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

Xiaoli Yu, Qichao Tu, Jihua Liu, Yisheng Peng, Cheng Wang, Fanshu Xiao, Yingli Lian, Xueqin Yang, Ruiwen Hu, Huang Yu, Lu Qian, Daoming Wu, Ziying He, Longfei Shu, Qiang He, Yun Tian, Faming Wang, Shanquan Wang, Bo Wu, Zhijian Huang, Jianguo He, Qingyun Yan, Zhili He

南方海洋科学与工程广东省实验室（珠海）海洋微生物组贺志理教授团队基于宏基因组测序与环境因子分析，比较了本地种与引进种红树林根际微生物的基因组特征和功能图谱，发现环境选择和进化过程对根际微生物组功能具有重要作用，拓展了对红树林根际微生物组形成机制和功能的认知。

▶ Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin‐derived aromatics

Tiantian Yu, Haining Hu, Xianhong Zeng, Yinzhao Wang, Donald Pan, Longhui Deng, Lewen Liang, Jialin Hou, Fengping Wang

上海交通大学王风平教授团队成功获得了深古菌的富集培养体系，同时发现了一种新的特异性甲基转移酶，用于木质素来源的芳香族化合物去甲基化。编码该酶系统的关键基因广泛存在于深古菌基因组以及近岸沉积物环境中，这表明深古菌在木质素降解中发挥着重要且独特的作用。

▶ Dual functions: A coumarin–chalcone conjugate inhibits cyclic‐di‐GMP and quorum‐sensing signaling to reduce biofilm formation and virulence of pathogens

Yu Zhang, Pramod Bhasme, Dinesh S. Reddy, Dejian Liu, Zhaoxiao Yu, Tianhu Zhao, Yaqian Zheng, Amit Kumar, Haiying Yu, Luyan Z. Ma

中国科学院微生物研究所马旅雁研究员团队基于经孪药设计合成的一系列香豆素-查尔酮共轭物开展了抗细菌生物被膜的实验，发现C9能够通过干扰环二鸟苷酸cyclic-di-GMP、群体感应系统及胞外多糖Psl的合成从而抑制铜绿假单胞菌生物被膜的形成并降低该致病菌的毒性。

▶ Identification of atypical T4SS effector proteins mediating bacterial defense

Xi Shen, Zixiang Yang, Zihan Li, Dan Xiong, Jinxing Liao, Weimei He, Danyu Shen, Xiaolong Shao, Ben Niu, Yongxing He, Yong-Gui Gao, Guoliang Qian

南京农业大学钱国良教授团队建立了一种高效挖掘非典型T4SS效应子的方法，并利用这种创新方法鉴定到两个非典型T4SS效应子。典型效应蛋白通过转运到竞争者细胞中发挥毒性功能，而该研究发现的非典型T4SS效应子则扮演胞内“分子盾牌”的角色来抵御竞争者的进攻，揭示了T4SS效应子功能和进化的多样性。

▶ Protective efficacy of a universal influenza mRNA vaccine against the challenge of H1 and H5 influenza A viruses in mice

Yulei Li, Xi Wang, Xi Zeng, Wenbo Ren, Pu Liao, Baoli Zhu

中国科学院微生物研究所朱宝利研究员团队设计和开发了一种新型的通用流感mRNA疫苗（mHAs）。研究人员利用小鼠模型测试了mHAs疫苗的效力，疫苗引发了针对HA颈干部的强大体液以及特异性细胞免疫应答。重要的是，两剂mHAs疫苗可完全保护小鼠免受异源性H1N1和异亚型H5N8流感病毒的致命挑战，接受疫苗接种的小鼠显示出较少的肺损伤和更低的病毒滴度。这些结果表明，使用HA保守颈干部的mRNA疫苗可能对季节性和其他可能的流感变异提供有效保护。

▶ Acquisition of a novel conjugative multidrug‐ esistant hypervirulent plasmid leads to hypervirulence in clinical carbapenem‐ esistant Klebsiella pneumoniae strains

Gong Li, Ling Jia, Lei Wan, Lijuan Xia, Ang Gao, Runshi Yang, Ruanyang Sun, Minge Wang, Juan Du, Xinlei Lian, Rongmin Zhang, Liangxing Fang, Xiaoping Liao, Yahong Liu, Bao-Tao Liu, Jian Sun

华南农业大学兽医学院孙坚教授团队从黄瓜中分离了一株ST23 碳青霉烯耐药高毒力肺炎克雷伯菌（CR‐HvKP），该菌株携带一个可接合转移的杂合质粒，其可能由住院患者中CR‐HvKP的耐药质粒和毒力质粒杂合而成。该杂合质粒可导致肺炎克雷伯菌对碳青霉烯等多种药物耐药，将CRKP转变为CR‐HvKP菌株并通过食物链在哺乳动物肠道定植，这对人类健康具有重大风险。

▶ Denitrification and the challenge of scaling microsite knowledge to the globe

G. Philip Robertson

Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process‐level knowledge gaps or predicting outcomes under novel environmental conditions. Hybrid models that incorporate well‐calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced. 

▶ Roadmap to tackle antibiotic resistance in the environment under the One Health framework

Liguan Li, Tong Zhang

抗生素抗性基因是全球公共健康面临的巨大挑战。“同一个健康”是应对该问题的重要框架，即人类、动物和环境健康紧密相关。其中，环境被认为是抗性基因产生的重要储库和传播的关键媒介。香港大学张彤教授团队系统阐述了“同一个健康”框架下应对环境中抗性基因传播扩散的思路。

▶ Cultivating the unseen: Lessons from James Tiedje

Yoichi Kamagata

In recounting Dr. James M. Tiedje's outstanding research achievements spanning the past 55 years, it is easy to overlook his early and mid-career endeavors. Specifically, his contribution to the aerobic degradation of pesticides and other chemicals, as well as methanogenic degradation of those compounds retains their brilliance. Many researchers in environmental microbiology have gained invaluable knowledge from these studies, which have been applied to the elucidation of previously uncultivated microorganisms.

▶ A modified isooctane‐ased DNA extraction method from crude oil

Armando Alibrandi, Rolando di Primio, Alexander Bartholomäus, Jens Kallmeyer

The authors present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. They investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, they evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as asolvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit(Qiagen). 

▶ A small, polyphyletic group of Firmicutes synthesizes trimethylamine from L‐carnitine

Marius Vital, Ylenia Heinrich-Sanchez

Gut microbiota-derived trimethylamine (TMA) is associated with cardiometabolic disorders and exemplifies a microbial involvement in the etiology of emerging, noncommunicable diseases, the leading causes of death worldwide. Three biochemical pathways taking dietary compounds as intake have been described with distinct taxa involved that are all present at low relative abundances. A recently discovered pathway is now considered to be the main route for TMA synthesis from l-carnitine involving γ-butyrobetaine as an intermediate product. By comprehensive (meta) genomic screening of publicly available data, namely, genomes of the UHGG catalog (n > 200,000) and 10 metagenomic (transcriptomic) data sets, the authors revealed bacteria synthesizing TMA via this pathway and specified their ecophysiology. Results will contribute to stratification of individuals based on their gut microbiota's potential to synthesize TMA and might aid in the development of strategies restricting TMA formation.