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Engineering Microbiomes for Green Technologies

Edited by:
Vijai Kumar GuptaCenter for Safe and Improved Food, & Biorefining and Advanced Materials Research Center, Scotland's Rural College, UK
Jack A. GilbertScripps Institution of Oceanography, SIO Biology Section Head, University of California San Diego, USA
Meisam TabatabaeiHigher Institution Centre of Excellence, Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Malaysia

Submission Opens: 1st June 2023   |   Submission Deadline: 31st December 2024


Environmental Microbiome, Microbiome,  Biotechnology for Biofuels and BioproductsFungal Biology and Biotechnology and Microbial Cell Factories are calling for submissions to our Collection on 'Engineering Microbiomes for Green Technologies.'  We invite Research, Review, Correspondence, Methodology, and Brief report papers in this new cross-journal series, looking at the microbiome engineering-based innovations in biomanufacturing.

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Environmental Microbiome

Microbiome

Biotechnology for Biofuels and Bioproducts

Fungal Biology and Biotechnology

Microbial Cell Factories 

About the collection

Environmental Microbiome, Microbiome,  Biotechnology for Biofuels and Bioproducts, Fungal Biology and Biotechnology and Microbial Cell Factories are calling for submissions to our Collection on 'Engineering Microbiomes for Green Technologies.' 

The association of microbial communities with their surrounding environments directly or indirectly influences the biosynthesis of metabolites by regulating metabolic pathways. Functional core microbiomes (FCM) are emerging as novel microbial tools to accelerate the production of biomolecules and bioproducts, with a huge demand for agri-food-energy and environmental sectors. Owing to the complexity of the microbiome's interactions with its respective environment and the large diversity of microbes still remaining poorly described, the precise engineering of FCMs for producing bioproducts will need planned and collective efforts.

On a different front, contaminants seriously impact human health and the sustainability of the environment. Similarly, emerging microbiomes can also be an effective, low-cost and eco-friendly approach for developing biotechnological solutions in this context. Implementation of engineered microbiomes and metagenomics are regarded as advanced solutions for their applications in greener technologies and waste management at lower costs and energy use and in a more environmentally responsible way. The engineering of microbiomes can be utilized to alter the microbiota's structural components and restore ecological equilibrium. Given the above, more advanced technologies and reliable strategies must be developed in this domain. 

The application of microfluidics, synthetic biology, genome editing, machine learning, and big data processing to carry out more complex FCM screening will not only increase our capability in developing FCM(s)-based innovative bioformulations but will also improve specific bioproducts production, particularly the ones which are synthesized in minute quantities. Active collaborations among agriculturists, chemists, engineers, microbiologists, and data analysts are needed to identify/isolate FCMs, develop large data sets from screening platforms, and increase biomics-editing abilities. Engineered FCM can be used to develop renewable biofuels, biochemicals, and therapeutics.  

In light of the above, this Collection on Engineering Microbiomes for Green Technologies will cover recent advancements in the understanding of evolution of microbiome consortia, the latest signature microbiome-based development, and biotechnological solutions for sustainable environmental management and bioproduction systems in the wake of emerging challenges, including climate change. The significance and present use of microbiome engineering will be the key focus, especially on how it affects agriculture, the environment, and human health. This collection also covers the difficulties in engineering microbiomes and their prospective applications. We invite Research, Review, Correspondence, Methodology, and Brief report papers in this new cross-journal series, looking at the microbiome engineering-based innovations in biomanufacturing. Submissions are welcomed to Environmental Microbiome, Microbiome, Fungal Biology and BiotechnologyBiotechnology for Biofuels and Bioproducts, and Microbial Cell Factories.


Image credit: © Lazy_Bear / stock.adobe.com

  1. Biosynthesis of metallic nanoparticles using microorganisms are a fabulous and emerging eco-friendly science with well-defined sizes, shapes and controlled monodispersity. Copper nanoparticles, among other met...

    Authors: Nahla M. Abdel Aziz, Doaa A. Goda, Dina I. Abdel-Meguid, Ebaa E. EL-Sharouny and Nadia A. Soliman
    Citation: Microbial Cell Factories 2024 23:156
  2. Thermotolerance is widely acknowledged as a pivotal factor for fungal survival across diverse habitats. Heat stress induces a cascade of disruptions in various life processes, especially in the acquisition of ...

    Authors: Tuo Li, Yang Liu, Han Zhu, Linhua Cao, Yihao Zhou, Dongyang Liu and Qirong Shen
    Citation: Biotechnology for Biofuels and Bioproducts 2024 17:54
  3. Short-chain fatty acids (SCFAs) are cost-effective carbon sources for an affordable production of lipids. Hexanoic acid, the acid with the longest carbon chain in the SCFAs pool, is produced in anaerobic ferme...

    Authors: Sergio Morales-Palomo, Clara Navarrete, José Luis Martínez, Cristina González-Fernández and Elia Tomás-Pejó
    Citation: Microbial Cell Factories 2024 23:101
  4. Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approa...

    Authors: Huifeng Hu, Jannie Munk Kristensen, Craig William Herbold, Petra Pjevac, Katharina Kitzinger, Bela Hausmann, Morten Kam Dahl Dueholm, Per Halkjaer Nielsen and Michael Wagner
    Citation: Microbiome 2024 12:55
  5. One of the leading current trends in technology is the miniaturization of devices to the microscale and nanoscale. The highly advanced approaches are based on biological systems, subjected to bioengineering us...

    Authors: Joanna Żebrowska, Piotr Mucha, Maciej Prusinowski, Daria Krefft, Agnieszka Żylicz-Stachula, Milena Deptuła, Aneta Skoniecka, Agata Tymińska, Małgorzata Zawrzykraj, Jacek Zieliński, Michał Pikuła and Piotr M. Skowron
    Citation: Microbial Cell Factories 2024 23:81
  6. Biodiesel, an emerging sustainable and renewable clean energy, has garnered considerable attention as an alternative to fossil fuels. Although lipases are promising catalysts for biodiesel production, their ef...

    Authors: Jinsha Huang, Xiaoman Xie, Wanlin Zheng, Li Xu, Jinyong Yan, Ying Wu, Min Yang and Yunjun Yan
    Citation: Biotechnology for Biofuels and Bioproducts 2024 17:33
  7. Eicosapentaenoic acid (EPA) is widely used in the functional food and nutraceutical industries due to its important benefits to human health. Oleaginous microorganisms are considered a promising alternative re...

    Authors: Yu-Lei Jia, Qing-Ming Zhang, Fei Du, Wen-Qian Yang, Zi-Xu Zhang, Ying-Shuang Xu, Wang Ma, Xiao-Man Sun and He Huang
    Citation: Biotechnology for Biofuels and Bioproducts 2024 17:32
  8. Acetoin, a versatile platform chemical and popular food additive, poses a challenge to the biosafety strain Bacillus subtilis when produced in high concentrations due to its intrinsic toxicity. Incorporating the ...

    Authors: Tao Li, Haixiang Li, Lei Zhong, Yufei Qin, Gege Guo, Zhaoxing Liu, Ning Hao and Pingkai Ouyang
    Citation: Microbial Cell Factories 2024 23:58
  9. Pichia pastoris is a widely utilized host for heterologous protein expression and biotransformation. Despite the numerous strategies developed to optimize the chassis host GS115, the potential impact of changes i...

    Authors: Bingjie Cheng, Keyang Yu, Xing Weng, Zhaojun Liu, Xuewu Huang, Yuhong Jiang, Shuai Zhang, Shuyan Wu, Xiaoyuan Wang and Xiaoqing Hu
    Citation: Microbial Cell Factories 2024 23:55
  10. Penicillium oxalicum engineered strain DB2 and its mutant strains with multiple regulatory modules were constructed. Mutant strain RE-4-2 with two regulatory modules showed a significant increase in the reducing ...

    Authors: Chengqiang Xia, Xiaoyu Qi and Xin Song
    Citation: Biotechnology for Biofuels and Bioproducts 2024 17:18
  11. Classical directed evolution is a powerful approach for engineering biomolecules with improved or novel functions. However, it traditionally relies on labour- and time-intensive iterative cycles, due in part t...

    Authors: Shuaili Chen, Zhanhao Yang, Ze Zhong, Shiqin Yu, Jingwen Zhou, Jianghua Li, Guocheng Du and Guoqiang Zhang
    Citation: Biotechnology for Biofuels and Bioproducts 2024 17:9
  12. Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates gen...

    Authors: Karoline Maria Vieira Nogueira, Vanessa Mendes, Karthik Shantharam Kamath, Anusha Cheruku, Letícia Harumi Oshiquiri, Renato Graciano de Paula, Claudia Carraro, Wellington Ramos Pedersoli, Lucas Matheus Soares Pereira, Luiz Carlos Vieira, Andrei Stecca Steindorff, Ardeshir Amirkhani, Matthew J. McKay, Helena Nevalainen, Mark P. Molloy and Roberto N. Silva
    Citation: Microbial Cell Factories 2024 23:22
  13. Color chemicals contaminate pure water constantly discharged from different points and non-point sources. Physical and chemical techniques have certain limitations and complexities for bioenergy production, wh...

    Authors: Aisha Umar, Islem Abid, Mohammed Antar, Laurent Dufossé, Lobna Hajji-Hedfi, Mohamed S. Elshikh, Abeer El Shahawy and Ahmed M. Abdel-Azeem
    Citation: Microbial Cell Factories 2023 22:258
  14. Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and coul...

    Authors: Yu Liang, Shujie Dou, Guangzhong Zhao, Jie Shen, Guangping Fu, Lihong Fu, Shujin Li, Bin Cong and Chunnan Dong
    Citation: Microbial Cell Factories 2023 22:250
  15. Yarrowia lipolytica, one of the most charming chassis cells in synthetic biology, is unable to use xylose and cellodextrins.

    Authors: Yiran Zhang, Moying Li, Rui Zhu, Yu Xin, Zitao Guo, Zhenghua Gu, Zhongpeng Guo and Liang Zhang
    Citation: Biotechnology for Biofuels and Bioproducts 2023 16:186
  16. The physical states and chemical components of bulk sludge determine the occurrence and development of membrane fouling in membrane bioreactors. Thus, regulation of sludge suspensions can provide new strategie...

    Authors: Ji Qi, Qicheng Zhou, Danlei Huang, Zhong Yu and Fangang Meng
    Citation: Microbial Cell Factories 2023 22:230
  17. Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, ...

    Authors: Poonam Kumari, Nikky Deepa, Prabodh Kumar Trivedi, Brajesh K. Singh, Vaibhav Srivastava and Akanksha Singh
    Citation: Microbial Cell Factories 2023 22:226

    The Correction to this article has been published in Microbial Cell Factories 2024 23:1

  18. Zymomonas mobilis is an important industrial bacterium ideal for biorefinery and synthetic biology studies. High-throughput CRISPR-based genome editing technologies have been developed to enable targeted engineer...

    Authors: Yanli Zheng, Hongmei Fu, Jue Chen, Jie Li, Yuejie Bian, Ping Hu, Lei Lei, Yihan Liu, Jiangke Yang and Wenfang Peng
    Citation: Microbial Cell Factories 2023 22:208

Submission Guidelines

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This Collection welcomes submission of Research Article, Review, Correspondence, Methodology, and Brief report papers. Before submitting your manuscript, please ensure you have read the submission guidelines of the journal you are submitting to Environmental Microbiome, Microbiome,  Biotechnology for Biofuels and Bioproducts, Fungal Biology and Biotechnology and Microbial Cell FactoriesArticles for this Collection should be submitted via our submission system, Snapp Environmental Microbiome, Microbiome,  Biotechnology for Biofuels and Bioproducts, Fungal Biology and Biotechnology and Microbial Cell FactoriesDuring the submission process you will be asked whether you are submitting to a Collection, please select "Engineering Microbiomes for Green Technologies" from the dropdown menu.

Articles will undergo the standard peer-review process of the journal they are considered in Environmental Microbiome, Microbiome,  Biotechnology for Biofuels and Bioproducts, Fungal Biology and Biotechnology and Microbial Cell Factories and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Guest Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Guest Editors have competing interests is handled by another Editorial Board Member who has no competing interests.