Modelling of microbial interactions in anaerobic digestion: from black to glass box

Arianna Basile; Guido Zampieri; Adam Kovalovszki; Behzad Karkaria; Laura Treu; Kiran Raosaheb Patil; Stefano Campanaro

doi:10.1016/j.mib.2023.102363

Modelling of microbial interactions in anaerobic digestion: from black to glass box

Arianna Basile^*
, Guido Zampieri
, Adam Kovalovszki
, Behzad Karkaria
, Laura Treu^*
, Kiran Raosaheb Patil
, Stefano Campanaro

^*Corresponding author for this work

University of Cambridge
University of Padua

Research output: Contribution to journal › Review › peer-review

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Abstract

Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.

Original language	English
Article number	102363
Journal	Current Opinion in Microbiology
Volume	75
Number of pages	9
ISSN	1369-5274
DOIs	https://doi.org/10.1016/j.mib.2023.102363
Publication status	Published - 2023

Bibliographical note

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 866028). The authors acknowledge the contribution of the LIFE + financial instrument of the European Union to project LIFE20 CCM/GR/001642-LIFE CO2 to CH4.

UN SDGs

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SDG 3 Good Health and Well-being

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title = "Modelling of microbial interactions in anaerobic digestion: from black to glass box",

abstract = "Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.",

author = "Arianna Basile and Guido Zampieri and Adam Kovalovszki and Behzad Karkaria and Laura Treu and Patil, \{Kiran Raosaheb\} and Stefano Campanaro",

note = "This project has received funding from the European Research Council (ERC) under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant no. 866028). The authors acknowledge the contribution of the LIFE + financial instrument of the European Union to project LIFE20 CCM/GR/001642-LIFE CO2 to CH4.",

year = "2023",

doi = "10.1016/j.mib.2023.102363",

language = "English",

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journal = "Current Opinion in Microbiology",

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TY - JOUR

T1 - Modelling of microbial interactions in anaerobic digestion

T2 - from black to glass box

AU - Basile, Arianna

AU - Zampieri, Guido

AU - Kovalovszki, Adam

AU - Karkaria, Behzad

AU - Treu, Laura

AU - Patil, Kiran Raosaheb

AU - Campanaro, Stefano

N1 - This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 866028). The authors acknowledge the contribution of the LIFE + financial instrument of the European Union to project LIFE20 CCM/GR/001642-LIFE CO2 to CH4.

PY - 2023

Y1 - 2023

N2 - Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.

AB - Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study.

U2 - 10.1016/j.mib.2023.102363

DO - 10.1016/j.mib.2023.102363

M3 - Review

C2 - 37542746

SN - 1369-5274

VL - 75

JO - Current Opinion in Microbiology

JF - Current Opinion in Microbiology

M1 - 102363

ER -

Modelling of microbial interactions in anaerobic digestion: from black to glass box

Abstract

Bibliographical note

UN SDGs

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