mLife Pub Date : 2022-12-18 DOI: 10.1002/mlf2.12050

Y. Ishino

引用次数: 0

Artificial intelligence-assisted automatic and index-based microbial single-cell sorting system for One-Cell-One-Tube. 人工智能辅助的 "一细胞一试管 "微生物单细胞自动索引分拣系统。

mLife Pub Date : 2022-12-18 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12047

Zhidian Diao, Lingyan Kan, Yilong Zhao, Huaibo Yang, Jingyun Song, Chen Wang, Yang Liu, Fengli Zhang, Teng Xu, Rongze Chen, Yuetong Ji, Xixian Wang, Xiaoyan Jing, Jian Xu, Yuandong Li, Bo Ma

{"title":"Artificial intelligence-assisted automatic and index-based microbial single-cell sorting system for One-Cell-One-Tube.","authors":"Zhidian Diao, Lingyan Kan, Yilong Zhao, Huaibo Yang, Jingyun Song, Chen Wang, Yang Liu, Fengli Zhang, Teng Xu, Rongze Chen, Yuetong Ji, Xixian Wang, Xiaoyan Jing, Jian Xu, Yuandong Li, Bo Ma","doi":"10.1002/mlf2.12047","DOIUrl":"10.1002/mlf2.12047","url":null,"abstract":"Identification, sorting, and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes. In this work, based on an artificial intelligence (AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting, we developed an automatic and index-based system called EasySort AUTO, where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed, \"One-Cell-One-Tube\" manner. The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting. Then, a cross-interface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube, which leads to coupling with subsequent single-cell culture or sequencing. The efficiency of the system for single-cell printing is >93%. The throughput of the system for single-cell printing is ~120 cells/h. Moreover, >80% of single cells of both yeast and Escherichia coli are culturable, suggesting the superior preservation of cell viability during sorting. Finally, AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples, which was validated by downstream single-cell proliferation assays. The automation, index maintenance, and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78544893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carl Woese: Still ahead of our time. 卡尔-沃斯仍然走在时代前列

mLife Pub Date : 2022-12-14 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12049

Patrick Forterre

引用次数: 0

DANMEL: A manually curated reference database for analyzing mobile genetic elements associated with bacterial drug resistance. DANMEL：人工编辑的参考数据库，用于分析与细菌耐药性相关的移动遗传因子。

mLife Pub Date : 2022-12-11 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12046

Peng Wang, Xiaoyuan Jiang, Kai Mu, Ying Jing, Zhe Yin, Yujun Cui, Cuidan Li, Xinhua Luo, Fangzhou Chen, Ting Yu, Zhichen Zhu, Yansong Sun, Fei Chen, Dongsheng Zhou

引用次数: 0

High-efficiency genome editing of an extreme thermophile Thermus thermophilus using endogenous type I and type III CRISPR-Cas systems. 利用内源性 I 型和 III 型 CRISPR-Cas 系统对极端嗜热菌 Thermus thermophilus 进行高效基因组编辑。

mLife Pub Date : 2022-12-07 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12045

Jinting Wang, Junwei Wei, Haijuan Li, Yingjun Li

{"title":"High-efficiency genome editing of an extreme thermophile Thermus thermophilus using endogenous type I and type III CRISPR-Cas systems.","authors":"Jinting Wang, Junwei Wei, Haijuan Li, Yingjun Li","doi":"10.1002/mlf2.12045","DOIUrl":"10.1002/mlf2.12045","url":null,"abstract":"Thermus thermophilus is an attractive species in the bioindustry due to its valuable natural products, abundant thermophilic enzymes, and promising fermentation capacities. However, efficient and versatile genome editing tools are not available for this species. In this study, we developed an efficient genome editing tool for T. thermophilus HB27 based on its endogenous type I-B, I-C, and III-A/B CRISPR-Cas systems. First, we systematically characterized the DNA interference capabilities of the different types of the native CRISPR-Cas systems in T. thermophilus HB27. We found that genomic manipulations such as gene deletion, mutation, and in situ tagging could be easily implemented by a series of genome-editing plasmids carrying an artificial self-targeting mini-CRISPR and a donor DNA responsible for the recombinant recovery. We also compared the genome editing efficiency of different CRISPR-Cas systems and the editing plasmids with donor DNAs of different lengths. Additionally, we developed a reporter gene system for T. thermophilus based on a heat-stable β-galactosidase gene TTP0042, and constructed an engineered strain with a high production capacity of superoxide dismutases by genome modification.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85084275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cytochrome-mediated direct electron uptake from metallic iron by Methanosarcina acetivorans. 由细胞色素介导的 Methanosarcina acetivorans 从金属铁中直接吸收电子。

mLife Pub Date : 2022-11-17 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12044

Dawn E Holmes, Haiyan Tang, Trevor Woodard, Dandan Liang, Jinjie Zhou, Xinying Liu, Derek R Lovley

{"title":"Cytochrome-mediated direct electron uptake from metallic iron by Methanosarcina acetivorans.","authors":"Dawn E Holmes, Haiyan Tang, Trevor Woodard, Dandan Liang, Jinjie Zhou, Xinying Liu, Derek R Lovley","doi":"10.1002/mlf2.12044","DOIUrl":"10.1002/mlf2.12044","url":null,"abstract":"Methane-producing microorganisms accelerate the corrosion of iron-containing metals. Previous studies have inferred that some methanogens might directly accept electrons from Fe(0), but when this possibility was more intensively investigated, H2 was shown to be an intermediary electron carrier between Fe(0) and methanogens. Here, we report that Methanosarcina acetivorans catalyzes direct metal-to-microbe electron transfer to support methane production. Deletion of the gene for the multiheme, outer-surface c-type cytochrome MmcA eliminated methane production from Fe(0), consistent with the key role of MmcA in other forms of extracellular electron exchange. These findings, coupled with the previous demonstration that outer-surface c-type cytochromes are also electrical contacts for electron uptake from Fe(0) by Geobacter and Shewanella species, suggest that the presence of multiheme c-type cytochromes on corrosion surfaces might be diagnostic for direct metal-to-microbe electron transfer and that interfering with cytochrome function might be a strategy to mitigate corrosion.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73546809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. 以微生物组工程原则为指导：环境利用的成就和前景。

mLife Pub Date : 2022-11-03 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12043

Haiyang Hu, Miaoxiao Wang, Yiqun Huang, Zhaoyong Xu, Ping Xu, Yong Nie, Hongzhi Tang

{"title":"Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use.","authors":"Haiyang Hu, Miaoxiao Wang, Yiqun Huang, Zhaoyong Xu, Ping Xu, Yong Nie, Hongzhi Tang","doi":"10.1002/mlf2.12043","DOIUrl":"10.1002/mlf2.12043","url":null,"abstract":"Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91463122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems. 森林生态系统中土壤细菌群落沿生物多样性梯度的抗逆潜力。

mLife Pub Date : 2022-11-03 eCollection Date: 2022-12-01 DOI: 10.1002/mlf2.12042

Jialiang Kuang, Dongmei Deng, Shun Han, Colin T Bates, Daliang Ning, Wensheng Shu, Jizhong Zhou

{"title":"Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems.","authors":"Jialiang Kuang, Dongmei Deng, Shun Han, Colin T Bates, Daliang Ning, Wensheng Shu, Jizhong Zhou","doi":"10.1002/mlf2.12042","DOIUrl":"10.1002/mlf2.12042","url":null,"abstract":"Higher biodiversity is often assumed to be a more desirable scenario for maintaining the functioning of ecosystems, but whether species-richer communities are also more disturbance-tolerant remains controversial. In this study, we investigated the bacterial communities based on 472 soil samples from 28 forests across China with associated edaphic and climatic properties. We developed two indexes (i.e., community mean tolerance breadth [CMTB] and community mean response asynchrony [CMRA]) to explore the relationship between diversity and community resistance potential. Moreover, we examined this resistance potential along the climatic and latitudinal gradients. We revealed that CMTB was significantly and negatively related to species richness, resulting from the changes in balance between relative abundances of putative specialists and generalists. In comparison, we found a unimodal relationship between CMRA and richness, suggesting that higher biodiversity might not always lead to higher community resistance. Moreover, our results showed differential local patterns along latitude. In particular, local patterns in the northern region mainly followed general relationships rather than those for the southern forests, which may be attributed to the differences in annual means and annual variations of climate conditions. Our findings highlight that the community resistance potential depends on the composition of diverse species with differential environmental tolerance and responses. This study provides a new, testable evaluation by considering tolerance breadth and response asynchrony at the community level, which will be helpful in assessing the influence of disturbance under rapid shifts in biodiversity and species composition as a result of global environmental change.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81127931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging-oriented single-cell sequencing. 通过以共焦点荧光成像为导向的单细胞测序技术综合鉴定肠道微生物群中细菌的生长模式和分类群。

mLife Pub Date : 2022-09-26 eCollection Date: 2022-09-01 DOI: 10.1002/mlf2.12041

Juan Gao, Di Sun, Bei Li, Chaoyong Yang, Wei Wang

{"title":"Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging-oriented single-cell sequencing.","authors":"Juan Gao, Di Sun, Bei Li, Chaoyong Yang, Wei Wang","doi":"10.1002/mlf2.12041","DOIUrl":"10.1002/mlf2.12041","url":null,"abstract":"Despite the fast progress in our understanding of the complex functions of gut microbiota, it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis. To gain knowledge of the indigenous growth/division patterns of the diverse mouse gut bacteria with a relatively high throughput, here, we propose an integrative strategy, which combines the use of fluorescent probe labeling, confocal imaging with single-cell sorting, and sequencing. Mouse gut bacteria sequentially labeled by two fluorescent d-amino acid probes in vivo were first imaged by confocal microscopy to visualize their growth patterns, which can be unveiled by the distribution of the two fluorescence signals on each bacterium. Bacterial cells of interest on the imaging slide were then sorted using a laser ejection equipment, and the collected cells were then sequenced individually to identify their taxa. Our strategy allows integrated acquirement of the growth pattern knowledge of a variety of gut bacteria and their genomic information on a single-cell basis, which should also have great potential in studying many other complex bacterial systems.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81606627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip. 利用纳米间隙稳定微流控芯片对单孢发芽链霉菌的整个生命周期进行观察。

mLife Pub Date : 2022-09-24 eCollection Date: 2022-09-01 DOI: 10.1002/mlf2.12039

Dongwei Chen, Mengyue Nie, Wei Tang, Yuwei Zhang, Jian Wang, Ying Lan, Yihua Chen, Wenbin Du

{"title":"Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip.","authors":"Dongwei Chen, Mengyue Nie, Wei Tang, Yuwei Zhang, Jian Wang, Ying Lan, Yihua Chen, Wenbin Du","doi":"10.1002/mlf2.12039","DOIUrl":"10.1002/mlf2.12039","url":null,"abstract":"Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80930369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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