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Microbiome Engineering: A New Generation of Ideas
Biotechnology Journal ( IF 4.7 ) Pub Date : 2020-10-06 , DOI: 10.1002/biot.202000406
John C. March 1 , Matthew Wook Chang 2
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John C. March Matthew Wook Chang

There has been considerable hype surrounding synthetic biology since its inception. Researchers laid claim to the potential of finally realizing our biological future through genetic manipulation. Unfortunately, early work indicated just how challenging harnessing biology to work for us in the way that electricity and chemistry already had. However, over the past 15 to 20 years the field has learned a great deal about the possibilities and pitfalls of forging microbes for specific applications. This issue presents some of the successes that have finally begun to pay off for this still‐nascent field.

We have gathered six articles from some of the most promising young minds in the field of synthetic biology: looking for their take on where the field is going and to share with the community their latest developments. You will find herein a meticulous review by Rottinghaus, Amrofell, and Moon, describing the very latest in microbial engineering for medical applications (https://doi.org/10.1002/biot.201900319). It is in this area that the field has made the perhaps most progress and this review captures some of the most promising efforts in diagnosing, treating, and preventing disease. The authors also discuss one of the biggest bottlenecks in the development of new strains to treat novel diseases: that of an experimental system akin to the high throughput systems that are frequently used to build strains. The limits of the animal model system are also discussed with ideas about how to replace it.

An article by Tham and co‐workers digs deeper into one specific medical presentation, that of atopic dermatitis (https://doi.org/10.1002/biot.201900322). Here, the concept of the biome is stretched to include skin microbes. Such an approach holds promise for many epidermal maladies. The authors discuss the ramifications of altering the skin microbiome to have less of Staphylococcus aureus and more “beneficial” microbial communities. Such tinkering can lead to unintended dysbiosis and the authors discuss how this can be managed.

One of the ways that microbial pathogens evade detection and removal from the body is to gather in biofilms. The paper by Liu and co‐workers from Chun Loong Ho's lab examines the role of the biofilm in protecting harmful bacteria and the biochemical processes that maintain it (https://doi.org/10.1002/biot.201900320). There are three classes of attack used against biofilms: physical, chemical, and biological. This review presents these with a perspective on what works and what is unlikely to do so.

Over the last ten years, the relationship between gut microbiomes and obesity has been increasingly elucidated. Lim, Lee, and Ooi have provided some clues as to what causative mechanisms in that relationship are (https://doi.org/10.1002/biot.202000013). The explosion of obesity as a global pandemic has been widely reported. What is less well‐known is how obesity and factors such as host genetics, mode of childbirth delivery, diet, lifestyle habits, and use of antibiotics can all play deciding roles in gut microbial health as well as in obesity. Connecting the temporal events is challenging and this review gives the reader a great place to start putting together the pieces of this complex relationship.

It has been known for some time that the biochemical landscape of the human intestine changes constantly with changes in our health and diet. What has been much less known is how this plays out in controlling metabolism. The interaction between microbial populations in the gut and their host is mediated through numerous chemical transformations and exchanges. One such exchange has been linked to several metabolic disorders, including diabetes. Sasaki, Sasaki, and Kondo present their original research on how molecular structure plays a role in the balance of organic acids in the large bowel (https://doi.org/10.1002/biot.201900523). The same acids that facilitate interspecies communication in the gut play a role in directing the body's response to nutrients. Changes in how gut bacteria parse propionate, acetate, and butyrate can have profound impacts on how we metabolize and respond to nutrients. This fascinating paper dives into the conversion chemistry of different metabolites that keep metabolism tightly regulated.

Finally, the last article from Lei Dai's group revisits the concept of “live biotherapeutics” and how they can be improved upon to be more effective with fewer side‐effects (https://doi.org/10.1002/biot.202000155). This article deftly moves between many of the success stories now happening in synthetic biology. From phage therapy for controlling microbial population densities in a consortium to deploying engineered bacteria that can recognize a tumor, swim to it, and dispatch it from the intestine, the authors do a great job of presenting material that demonstrates that success has started to infiltrate the synthetic biological ranks.

These are just a handful of bright young investigators, building more sustainable and compatible technologies for healing. It is expected that a future issue of this magazine might include work on sustainable technologies, such as in chemical production or waste conversion to value‐added products or electricity from batteries comprised of electrochemical microbes. We are proud to present these innovators of the biological realm and hope you will check back regularly to see what they and yet to be named others are working on next. Thank you and enjoy!



中文翻译:

微生物组工程:新一代思想

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John C. March Matthew Wook Chang

自从合成生物学诞生以来,就已经有相当多的宣传。研究人员声称,通过基因操作最终实现我们生物学未来的潜力。不幸的是,早期的工作表明,利用生物学方法以电和化学的方式为我们工作具有挑战性。但是,在过去的15到20年中,该领域已经了解了许多针对特定应用的微生物锻造的可能性和陷阱。本期杂志介绍了在这一仍处于新生阶段的领域中终于获得回报的一些成功。

我们从合成生物学领域的一些最有前途的年轻人那里收集了六篇文章:寻找他们对领域发展的看法,并与社区分享他们的最新进展。您将在这里找到Rottinghaus,Amfofell和Moon的详尽评论,描述了医疗应用中最新的微生物工程技术(https://doi.org/10.1002/biot.201900319)。正是在这一领域,该领域取得了最大的进展,而本综述涵盖了在诊断,治疗和预防疾病方面最有希望的工作。作者还讨论了用于治疗新型疾病的新菌株开发中最大的瓶颈之一:类似于经常用于构建菌株的高通量系统的实验系统。

Tham及其同事的一篇文章更深入地探讨了一种特定的医学表现,即特应性皮炎(https://doi.org/10.1002/biot.201900322)。在这里,生物群系的概念被扩展到包括皮肤微生物。这种方法为许多表皮疾病带来了希望。作者讨论了改变皮肤微生物组以减少金黄色葡萄球菌和更多“有益”微生物群落的后果。这种修补可能会导致意想不到的营养不良,作者讨论了如何进行管理。

微生物病原体逃避检测和从体内清除的方法之一是聚集在生物膜中。Liu和来自Chun Loong Ho实验室的同事的论文研究了生物膜在保护有害细菌以及维持生物膜的生化过程中的作用(https://doi.org/10.1002/biot.201900320)。针对生物膜的攻击分为三类:物理,化学和生物攻击。这篇综述以可行的方法和不太可行的方法提出了观点。

在过去的十年中,人们越来越多地阐明了肠道微生物群与肥胖之间的关系。Lim,Lee和Ooi提供了一些有关这种关系中的成因机制的线索(https://doi.org/10.1002/biot.202000013)。肥胖已成为全球大流行的爆炸事件,已被广泛报道。肥胖和宿主遗传学,分娩方式,饮食,生活习惯和抗生素使用等因素如何在肠道微生物健康以及肥胖中起决定性作用,这一点鲜为人知。连接时间事件具有挑战性,这篇评论为读者提供了一个开始将这种复杂关系的各个部分放在一起的好地方。

一段时间以来,人们就知道随着人类健康和饮食的变化,人体肠道的生化态势也在不断变化。鲜为人知的是它如何控制新陈代谢。肠道中微生物种群与其宿主之间的相互作用是通过许多化学转化和交换来介导的。一种这样的交换与包括糖尿病在内的几种代谢疾病有关。佐佐木(Sasaki),佐佐木(Sasaki)和近藤(Kondo)提出了他们关于分子结构如何在大肠中有机酸平衡中发挥作用的原创研究(https://doi.org/10.1002/biot.201900523)。促进肠道内部种间交流的相同酸在指导人体对营养的反应中发挥作用。肠道细菌解析丙酸盐,乙酸盐,丁酸对我们如何代谢和响应养分产生深远影响。这篇引人入胜的论文深入探讨了各种代谢产物的转化化学过程,这些代谢产物可以严格控制新陈代谢。

最后,雷岱研究小组的最后一篇文章重新审视了“活体生物疗法”的概念,以及如何在副作用较少的情况下对其进行改进以更有效(https://doi.org/10.1002/biot.202000155)。这篇文章巧妙地在合成生物学目前正在发生的许多成功故事之间移动。从控制联盟中微生物种群密度的噬菌体疗法到部署可以识别肿瘤,游动并将其从肠中分离出来的工程菌,作者们在展示能够证明成功已开始渗透到动物体内的材料方面做得很出色。合成生物学行列。

这些只是少数聪明的年轻研究者,他们建立了更加可持续和兼容的治疗技术。预计该杂志的未来一期将包括有关可持续技术的工作,例如化学生产或将废物转化为增值产品或由电化学微生物组成的电池供电。我们很自豪地向您介绍这些生物领域的创新者,并希望您能定期回来查看,看看他们下一步仍在努力寻找哪些人。谢谢你,享受!

更新日期:2020-10-06
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