BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

PLoS Computational Biology
Eugen BauerChristoph Kaleta

Abstract

Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena) to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation of emerging metabolic phenotypes in the biofilm over time. In the human gut model community, we found that spatial gradients of mucus glycans are important for niche formations which shape the overall community structure. Additionally, we could provide novel hypothesis concerning the metabolic interactions between the microbes. These results demonstrate the importance of spatial and temporal multi-scale modeling approaches such as BacArena.

References

Aug 1, 1979·Applied and Environmental Microbiology·C O Gill, K H Tan
Jul 1, 1989·Journal of Bacteriology·R Prats, M A de Pedro
Apr 1, 1983·Applied and Environmental Microbiology·C A Carlson, J L Ingraham
Feb 17, 1998·Applied and Environmental Microbiology·M Loferer-KrössbacherR Psenner
May 11, 1999·The American Journal of Gastroenterology·Y BouhnikJ C Rambaud
Jul 21, 2001·Lancet·P S Stewart, J W Costerton
Feb 20, 2003·Journal of Bacteriology·Philip S Stewart
Dec 4, 2003·Metabolic Engineering·R Mahadevan, C H Schilling
Dec 19, 2003·Nucleic Acids Research·Ida SchomburgDietmar Schomburg
Mar 31, 2004·The Journal of Nutrition·Asya SmirnovZehava Uni
Jun 25, 2004·Antimicrobial Agents and Chemotherapy·Giorgia BorrielloPhilip S Stewart
Apr 16, 2005·Science·Paul B EckburgDavid A Relman
Jul 8, 2005·Journal of Clinical Microbiology·Alexander SwidsinskiHerbert Lochs
Nov 15, 2005·Science·Volker GrimmDonald L DeAngelis
Apr 25, 2006·Journal of Clinical Gastroenterology·Julia M W WongDavid J A Jenkins
Jan 15, 2008·Journal of Bacteriology·Matthew A OberhardtJason A Papin
Feb 12, 2008·Nature Reviews. Microbiology·Philip S Stewart, Michael J Franklin
Jul 19, 2008·Biotechnology and Bioengineering·V MuralidharanR M Kelly
Sep 2, 2008·Applied Microbiology and Biotechnology·Joungmin LeeSang Yup Lee
Oct 27, 2009·Nucleic Acids Research·Ron MiloMichael Springer
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Mar 10, 2010·Nature Biotechnology·Jeffrey D OrthBernhard Ø Palsson
Jul 29, 2010·Molecular Systems Biology·Nathan E LewisBernhard Ø Palsson
Oct 19, 2010·International Journal of Medical Microbiology : IJMM·Max Schobert, Dieter Jahn
Dec 3, 2010·PLoS Computational Biology·Niels Klitgord, Daniel Segrè
Mar 17, 2011·Nature Reviews. Microbiology·Michael A McGuckinTimothy H Florin
Jun 17, 2011·Nature·Andrew L KauJeffrey I Gordon
Nov 15, 2011·Mycopathologia·Antonella RellaMaurizio Del Poeta
Mar 1, 2012·Nature Reviews. Microbiology·Nathan E LewisBernhard O Palsson
Mar 28, 2012·Nature Reviews. Microbiology·Karsten Zengler, Bernhard O Palsson
Apr 12, 2012·Nature Reviews. Microbiology·Nicole M KoropatkinEric C Martens
Nov 28, 2012·PLoS Biology·Jonas Schluter, Kevin R Foster
Feb 20, 2013·Biotechnology Journal·Matthew C GonnermanNathan D Price
Nov 15, 2013·BMC Systems Biology·Gabriel Gelius-DietrichMartin J Lercher
Nov 15, 2013·Briefings in Bioinformatics·Himanshu Kaul, Yiannis Ventikos

❮ Previous
Next ❯

Citations

Jun 9, 2018·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mohammad Soheilypour, Mohammad R K Mofrad
Aug 8, 2018·NPJ Systems Biology and Applications·Eugen Bauer, Ines Thiele
May 31, 2019·Biotechnology Journal·Brendan Fu-Long SieowMatthew Wook Chang
Jul 30, 2020·Biochemical Society Transactions·Yoon-Mi ChoiDong-Yup Lee
Jan 30, 2018·Frontiers in Molecular Biosciences·Partho SenMatej Orešič
Jan 31, 2019·Metabolites·Partho Sen, Matej Orešič
Mar 24, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Angela E Douglas
Jul 14, 2020·Frontiers in Bioengineering and Biotechnology·Denny Popp, Florian Centler
May 26, 2018·Natural Product Reports·Glen D'SouzaChristian Kost
Aug 2, 2019·Clinical Microbiology Reviews·Andrew J McBainJudith Fernandez-Piquer
Apr 23, 2020·Frontiers in Microbiology·Ameen EetemadiIlias Tagkopoulos
Jul 25, 2019·Nature Microbiology·Manish KumarJens Nielsen
Aug 17, 2020·PloS One·Georgios MarinosSilvio Waschina
Jun 17, 2020·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Jagir R Hussan, Peter J Hunter
Nov 14, 2018·Bioinformatics·Beatriz García-JiménezJuan Nogales
Jul 17, 2020·Computational and Structural Biotechnology Journal·Clémence FriouxFalk Hildebrand
Dec 29, 2020·Computational and Structural Biotechnology Journal·Daniel Aguirre de Cárcer
Dec 19, 2020·Computational and Structural Biotechnology Journal·Álvaro AltamiranoDaniel Garrido
Jan 12, 2021·Computational and Structural Biotechnology Journal·Beatriz García-JiménezJuan Nogales
Jan 26, 2021·Current Opinion in Biotechnology·Benedict Borer, Dani Or
Jan 8, 2021·BMC Bioinformatics·Nick W SmithWarren C McNabb
Jan 26, 2021·Computational and Structural Biotechnology Journal·Humphrey A MabwiKwang Hyun Cha
Feb 10, 2021·Current Opinion in Biotechnology·Livia S ZaramelaKarsten Zengler
Jan 22, 2021·Microbiome·Jack Jansma, Sahar El Aidy
Feb 20, 2021·Genome Biology·David B BernsteinDaniel Segrè
Dec 15, 2020·Bioinformatics·Jingyi CaiS H Joshua Chan
Feb 7, 2020·Microorganisms·Shomeek Chowdhury, Stephen S Fong
Oct 9, 2019·Current Opinion in Biotechnology·Stephen P LillingtonMichelle A O'Malley
Mar 7, 2021·Microorganisms·Sherli Koshy-ChenthittayilAnna Dongari-Bagtzoglou

❮ Previous
Next ❯

Software Mentioned

R package ReacTran
windows
MatNet
dOptCom
GLPK
R package deSolve
CLP
BacArena
R
COBRA

Related Concepts

Related Feeds

Biofilm & Infectious Disease

Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections.Here is the latest research on biofilm and infectious diseases.

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Biofilms

Biofilms are adherent bacterial communities embedded in a polymer matrix and can cause persistent human infections that are highly resistant to antibiotics. Discover the latest research on Biofilms here.