Research Topic

Microbiomes for Industrial Bioprocesses and Biorefineries

About this Research Topic

Modern industrial bioprocess engineering and technologies mainly rely on native or genetically engineered strains of microorganism(s) to produce high-value chemicals, commercial products, enzymes, food-feed-fuel, pharmaceuticals and polymers from organic/inorganic resources (e.g. lignocellulose, waste biomass, minerals, etc.) and greenhouse gases (e.g. methane, carbon dioxide, etc). Industrial bioprocess engineering and technologies have also expanded to exploit the microorganisms in processes such as biomining (e.g. metals) and bioremediation of environmental pollutants from soil, air and water. Native strains that are isolated from nature evolve and adapt to their environmental conditions or their growth is optimized to the specific process designs in industrial scale bioreactors. The genetic and metabolic biochemical pathway engineering of native strains has helped to maximize their bioprocessing capacities and resilience towards process variables. However, pure strain applications are limited to specific product development that requires extensive process design optimization and understanding. On the other hand, mixed microbial cultures (i.e. microbiomes) are more robust and self-regulating systems that are suitable for the energy and economics needed for industrial bioprocesses . Microbiomes include complex diversity in way that the different populations co-exist, while their interactions are less understood (e.g. biofermentation, biorefinery and bioremediation systems).

The main aim of this Research Topic on “Microbiomes for Industrial Bioprocesses and Biorefineries” is to establish a fundamental knowledge about Microbiome diversity, core and satellite communities, physical-chemical-biological interactions, nutrient obligations, secretion of metabolic compounds (or excretomes) and the effect on environmental variables to tailor Microbiomes for industrial bioprocesses and bioproduct development. This Research Topic welcomes Original Research and Review articles on, but not limited to, the following topics:

(a) Developing the understanding of microbiome interactions and modelling in complex systems/extreme environments
(b) The role of microbiomes in new bioproduct development and potential industrial application
(c) The role of environmental variables in microbiomes community selections and adaptations
(d) New genetic tools and methods for improving the understanding and manipulation of the microbiome structure
(e) Natural vs. synthetic microbiome communities for industrial applications and case studies

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Drs. Heimann, Strong, and Esteves hold patents related to the theme of this Research Topic and Dr. Marcio Busi Da Silva stands as the Director of Cemvita Factory Inc., Sentinel Environmental LLC., Trtech Inc., and CEO of W2S3 Environmental Consultancy. All other Topic Editors declare no competing interests with regard to the Research Topic subject.


Keywords: Value Chemicals, Bioenergy and Biofuels, Microbial Ecology, Bioreactor Technology, Genetic Engineering, Metabolic Modelling, Bioeconomy


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Modern industrial bioprocess engineering and technologies mainly rely on native or genetically engineered strains of microorganism(s) to produce high-value chemicals, commercial products, enzymes, food-feed-fuel, pharmaceuticals and polymers from organic/inorganic resources (e.g. lignocellulose, waste biomass, minerals, etc.) and greenhouse gases (e.g. methane, carbon dioxide, etc). Industrial bioprocess engineering and technologies have also expanded to exploit the microorganisms in processes such as biomining (e.g. metals) and bioremediation of environmental pollutants from soil, air and water. Native strains that are isolated from nature evolve and adapt to their environmental conditions or their growth is optimized to the specific process designs in industrial scale bioreactors. The genetic and metabolic biochemical pathway engineering of native strains has helped to maximize their bioprocessing capacities and resilience towards process variables. However, pure strain applications are limited to specific product development that requires extensive process design optimization and understanding. On the other hand, mixed microbial cultures (i.e. microbiomes) are more robust and self-regulating systems that are suitable for the energy and economics needed for industrial bioprocesses . Microbiomes include complex diversity in way that the different populations co-exist, while their interactions are less understood (e.g. biofermentation, biorefinery and bioremediation systems).

The main aim of this Research Topic on “Microbiomes for Industrial Bioprocesses and Biorefineries” is to establish a fundamental knowledge about Microbiome diversity, core and satellite communities, physical-chemical-biological interactions, nutrient obligations, secretion of metabolic compounds (or excretomes) and the effect on environmental variables to tailor Microbiomes for industrial bioprocesses and bioproduct development. This Research Topic welcomes Original Research and Review articles on, but not limited to, the following topics:

(a) Developing the understanding of microbiome interactions and modelling in complex systems/extreme environments
(b) The role of microbiomes in new bioproduct development and potential industrial application
(c) The role of environmental variables in microbiomes community selections and adaptations
(d) New genetic tools and methods for improving the understanding and manipulation of the microbiome structure
(e) Natural vs. synthetic microbiome communities for industrial applications and case studies

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Drs. Heimann, Strong, and Esteves hold patents related to the theme of this Research Topic and Dr. Marcio Busi Da Silva stands as the Director of Cemvita Factory Inc., Sentinel Environmental LLC., Trtech Inc., and CEO of W2S3 Environmental Consultancy. All other Topic Editors declare no competing interests with regard to the Research Topic subject.


Keywords: Value Chemicals, Bioenergy and Biofuels, Microbial Ecology, Bioreactor Technology, Genetic Engineering, Metabolic Modelling, Bioeconomy


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

03 July 2020 Abstract
04 December 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

03 July 2020 Abstract
04 December 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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