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Anaerobic ammonia oxidizing bacteria: ecological distribution, metabolism, and microbial interactions

Dawen Gao, Xiaolong Wang, Hong Liang, Qihang Wei, Yuan Dou, Longwei Li

《环境科学与工程前沿（英文）》 2018年第12卷第3期 doi: 10.1007/s11783-018-1035-x

摘要： Anammox (ANaerobic AMMonia OXidation) is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.

关键词： Anammox Metabolism Metagenome Ecological distribution Microbial interactions

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ARGs-OAP v3.0——抗生素耐药基因数据库的筛选和分析流程优化 Article

Xiaole Yin, Xiawan Zheng, Liguan Li, An-Ni Zhang, Xiao-Tao Jiang, Tong Zhang

《工程（英文）》 2023年第27卷第8期页码 234-241 doi: 10.1016/j.eng.2022.10.011

摘要：

Antibiotic resistance, which is encoded by antibiotic-resistance genes (ARGs), has proliferated to become a growing threat to public health around the world. With technical advances, especially in the popularization of metagenomic sequencing, scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed. To analyze thousands of ARGs in a highthroughput way, standardized and integrated pipelines are needed. The new version (v3.0) of the widely used ARGs online analysis pipeline (ARGs-OAP) has made significant improvements to both the reference database—the structured ARGs (SARG) database—and the integrated analysis pipeline. SARG has been enhanced with sequence curation to improve annotation reliability, incorporate emerging resistance genotypes, and determine rigorous mechanism classification. The database has been further organized and visualized online in the format of a tree-like structure with a dictionary. It has also been divided into sub-databases for different application scenarios. In addition, the ARGs-OAP has been improved with adjusted quantification methods, simplified tool implementation, and multiple functions with userdefined reference databases. Moreover, the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles. The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia, governmental management, and consultation regarding risk assessment of the environmental prevalence of ARGs.

关键词： SARG database ARGs-OAP Antibiotic-resistance genes Environmental metagenome Quantification

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通过原位观察揭示人体肠道微生物组的重建和动态变化 Article

刘小林, 戴敏, Yue Ma, 赵娜, Ziyu Wang, Ying Yu, Yakun Xu, Huijie Zhang, Liyuan Xiang, He Tian, 税光厚, 张发明, 王军

《工程（英文）》 2022年第15卷第8期页码 89-101 doi: 10.1016/j.eng.2021.03.015

摘要：

人体肠道微生物组主要通过使用粪便样本进行研究，这种做法已经得到了关于胃肠道微生物群落的组成和功能的重要知识。然而，这种对粪便材料的依赖限制了对胃肠道其他位置（原位）微生物动力学的研究，并且粪便样本不能随时获得，这也阻碍了在更精细的时间尺度（如小时）下进行分析。在我们的研究中，我们利用结肠途径经内镜肠内导管（一种最初为粪便微生物群移植开发的技术）每天两次对回盲部微生物组进行采样；然后对这些样品进行宏基因组和宏转录组学分析。从5 名健康志愿者身上共收集了43 份回盲部样本及28 份尿液和粪便样本。在5 名志愿者中分析的回盲部和粪便微生物组被发现在宏基因组分析中相似，但它们的活性基因（宏转录组）被发现高度不同。两种微生物组在泻药暴露后都受到干扰；随着时间的推移，它们表现出与治疗前状态的差异减少，从而证明了作为肠道微生物组的先天特性——恢复力，尽管它们在我们的观察时间窗口内没有完全恢复。白天和夜间对回盲部微生物组的采样显示，在一系列细菌种类和功能途径中存在昼夜节律，特别是与短链脂肪酸产生相关的细菌，如痤疮丙酸杆菌和辅酶A生物合成II。自相关分析和波动分解进一步表明了昼夜振荡的显著周期性。粪便和尿液样本中的代谢组学分析反映出了肠道微生物组的扰动和恢复，表明肠道微生物组对参与宿主健康的诸多关键代谢物的重要贡献。这项研究为人体肠道微生物组及其内在恢复力和昼夜节律以及这些对宿主的潜在后果提供了新的见解。

关键词：昼夜节律重建宏基因组宏转录组代谢组经内窥镜肠管

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氯霉素及其产物降解菌群在长期驯化过程中的微生物群落和关键基因演替模式

张家禹, 周开颜, 郭芳亮, 雷华新, 赵仁鑫, 林琳, 李晓岩, 李炳

《工程（英文）》 2023年第31卷第12期页码 59-69 doi: 10.1016/j.eng.2023.07.009

摘要：

氯霉素（CAP）作为一种广泛存在的新污染物，对水环境中的生态群落产生了负面影响。生物处理广泛应用于水体污染物的去除，而功能微生物的性能决定了其效果。本研究从活性污泥中驯化了一个具有强大CAP降解能力的菌群。对硝基苯甲酸（PNB）和2,2-二氯乙酸（DCA）是CAP生物和化学处理过程中产生的主要产物，它们也分别作为菌群的唯一底物进行长期驯化。宏基因组分析揭示了2.5年驯化过程中微生物群落和关键功能基因的演替模式。经过长期驯化，Sphingomonas、Caballeronia和Cupriavidus分别成为CAP、PNB和DCA降解菌群中的优势菌属，并且它们分别是CAP、PNB和DCA的关键降解菌，它们之间的协同合作实现了CAP的高度矿化。PNB转化为原儿茶酸（PCA），然后通过间位和邻位裂解途径被矿化。通过长期驯化，参与CAP、PNB和DCA代谢的关键功能基因，包括CAP乙酰转移酶、CAP氧化还原酶、卤代酸脱卤酶和原儿茶酸双加氧酶，在菌群中显著富集。本研究还发现pH和碳源对CAP的生物降解效率有显著影响。本研究驯化的菌群和分离的菌株可用作加强CAP、PNB和DCA污染环境生物修复的微生物资源。

关键词：抗生素生物降解代谢作用微生物群落演替宏基因组