Faculty Profile

Dr. Michael Berney, Ph.D.

Michael Berney, Ph.D.

Assistant Professor, Department of Microbiology & Immunology

Areas of Research: Mycobacterium tuberculosis metabolic plasticity; drug target discovery; microbial biochemistry in the host-pathogen context.

Professional Interests

Microbes have shown a remarkable ability to evade eradication by antimicrobial agents, such that treatment of bacterial infections once again represents an urgent global challenge. It is estimated that failure to address the problem of antibiotic resistance could result in 10 million deaths every year globally by 2050 and a cost of $ 84 trillion in lost productivity to the global economy. 

Today, Mycobacterium tuberculosis (Mtb) alone kills around 1.8 million people each year, more than any other infectious disease1. This is particularly alarming because the number of multidrug-resistant Mtb clinical isolates is rapidly increasing. Novel antibacterial tactics are urgently required to combat the rise of antibiotic resistance.

My group studies the role of metabolism and bioenergetics in Mycobacterium tuberculosis host adaptation and antibiotic tolerance. Our goals are to identify vulnerable pathways, translate these findings into drug discovery and determine drug mechanism of action. We use a combination of genetic, metabolomic, transcriptomic and biochemical approaches to learn how to defeat the global threat of M. tuberculosis.


09/16/2019: Just out! Our study "Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection" was just published in Nature Communications. Congrats to Erik Hasenoehrl for this first author publication!

09/09/2019: Our new paper entitled "Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex" is now online at Nature Communications

05/09/2019: Welcome to Dr. Claire Mulholland to the group!

11/19/2018: The Berney Lab was just awarded its first RO1 grant from the NIH!

08/06/2018: Congrats to Erik for receiving an F30 award from the NIAID.

07/02/2018: New PhD student Samantha Johnson just joined the group. Welcome Samantha!

06/28/2018: Congrats to Dr. Erik Hasenoehrl for successfully defending his thesis!

06/11/2018: The lab has been awarded an NIH grant to discover new modes of action of antituberculosis agents in a high-throughput fashion. This grant is in collaboration with the Sauer/Zampieri lab at ETH in Switzerland.

06/01/2018: We have just been awarded a Potts Memorial Foundation grant to study the role of terminal oxidation in TB pathogenesis.

07/13/2017: Read the research roundup about our recent publication here.

06/26/2017: New paper published in PNAS! The paper is entitled "Exploiting the synthetic lethality between terminal respiratory oxidases to kill Mycobacterium tuberculosis and clear host infection."  Congrats to Erik Hasenoehrl who is a first author of the study. 

06/12/2017: Funding success: The Berney lab was just awarded a grant from the POTTS Memorial Foundation.

06/08/2017: We just published two new reviews in Microbiology Spectrum, that are also becoming individual book chapters in the second edition of Tuberculosis and the Tubercle Bacilli, ASM Press.

Review 1: "Mycobacterium tuberculosis metabolism in the face of host-imposed nutrient limitation",

Review 2: "OXPHOS as a target space for tuberculosis: success, caution, and future directions".

05/17/16: Dr. Michael Petridu from University of Otago NZ has joined the Berney lab as a visitor for 3 weeks. Welcome Michael!

02/08/16: Our study "Central Role of Pyruvate Kinase in Carbon Co-Catabolism of Mycobacterium tuberculosis." conducted in collaboration with Dr. John S. Blanchard has just been accepted for publication in the Journal of Biological Chemistry.

02/03/16: Grant success! We have just been awarded funding from the NIH for the project:"Inhibition of methionine biosynthesis eliminates persistent M. tuberculosis"

10/06/15: A Spotlight article featuring our PNAS paper on "Methionine-less death" has just been published in Trends in Microbiology.

07/28/15: Our paper "Essential Roles of Methionine and S-adenosylmethionine in the Autarkic Lifestyle of Mycobacterium tuberculosis" has just been published in PNAS. Read the research roundup here

Selected Publications


Hasenoehrl, E. J., D. Rae Sajorda, L. Berney-Meyer, S. Johnson, J. M. Tufariello, T. Fuhrer, G. M. Cook, W. R. Jacobs and M. Berney* (2019). "Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection." Nature Communications 10(1): 4215.

A. Chiner-Oms#M. Berney#, C. Boinett, F. Gonzalez-Candelas, D. B. Young, S. Gagneux, W. R. Jacobs, Jr., J. Parkhill, T. Cortes and I. Comas (2019). "Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex." Nature Communications 10(1): 3994. #equal contributions


Lee BS, Kalia NP, Jin XEF, Hasenoehrl EJ, Berney M, Pethe K. Inhibitors of energy metabolism interfere with antibiotic-induced death in mycobacteria. Journal of Biological Chemistry (IN PRESS)

Sangeeta Tiwari, Andries J. van Tonder, Catherine Vilchèze, Vitor Mendes, Sherine E. Thomas, Adel Malek, Bing Chen, Mei Chen, John Kim, Tom L. Blundell, Julian Parkhill, Brian Weinrick, Michael Berney, William R. Jacobs Jr. Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis PNAS August 24, 2018. 201808874; published ahead of print August 24, 2018. https://doi.org/10.1073/pnas.1808874115; See also commentary published in the PNAS: https://doi.org/10.1073/pnas.1813587115

Karthik Sekar, Roberto Rusconi, Tobias Fuhrer, Elad Noor, Jen Nguyen, Vicente I Fernandez, Marieke F Buffing, Michael Berney, Suckjoon Jun, Roman Stocker, Uwe Sauer. Synthesis and degradation of FtsZ determines the first cell division in starved bacteria. Molecular Systems biology, 14:e8623, 2018 http://msb.embopress.org/content/14/11/e8623. See news coverage in an ETHZ article: https://www.ethz.ch/en/news-and-events/eth-news/news/2018/11/the-protein-with-the-starting-gun.html


Kurthkoti K, Amin H, Marakalala MJ, Ghanny S, Subbian S, Sakatosb A, Livnye J, Fortune SM, Berney M, Rodriguez GM. Mycobacterium tuberculosis' capacity to survive iron-starvation might enable it to persist in iron-deprived microenvironments of human granulomas. mBio 8:e01092-17, 2017

Kalia NP+, Hasenoehrl EJ+, Ab Rahman NB, Koh VH, Ang MLT, Sajorda DR, Hards K, Grüber G, Alonso S, Cook GM, Berney M*,+, Pethe K*,+. Exploiting the synthetic lethality between terminal respiratory oxidases to kill Mycobacterium tuberculosis and clear host infection. PNAS 2017 (EE June 26th), (+equal contributions *corresponding authors) http://www.pnas.org/content/early/2017/06/23/1706139114

Berney M& Berney-Meyer L. Mycobacterium tuberculosis metabolism in the face of host-imposed nutrient limitation. Tuberculosis and the Tubercle Bacilli, Second Edition, ASM PRESS, June 2017 vol. 5 no. 3 doi:10.1128/microbiolspec.TBTB2-0030-2016 http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.TBTB2-0030-2016

Cook GM, Hards K, Dunn E, Heikal A, Nakatani Y, Greening C, Crick DC, Fontes FL, Pethe K, Hasenoehrl E and Berney M. OXPHOS as a target space for tuberculosis: success, caution, and future directions. Tuberculosis and the Tubercle Bacilli, Second Edition, ASM PRESS, June 2017 vol. 5 no. 3 doi:10.1128/microbiolspec.TBTB2-0014-2016 http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.TBTB2-0014-2016


Central Role of Pyruvate Kinase in Carbon Co-Catabolism of Mycobacterium tuberculosis. Noy T, Vergnolle O, Hartman TE, Rhee KY, Jacobs WR, Berney M*, Blanchard JS*. Journal of Biological Chemistry 2016; http://www.jbc.org/content/early/2016/02/08/jbc.M115.707430.abstract


Berney M*, Berney-Meyer L, Wong KW, Wang J, Chen B, Chen M, Kim J, Harris D, Parkhill J, Chan J, Wang F, Jacobs WR*. Essential Roles of Methionine and S-adenosylmethionine in the Autarkic Lifestyle of Mycobacterium tuberculosis. PNAS 2015; http://www.pnas.org/content/early/2015/07/27/1513033112  

Hards K, Robson J, Berney M, Shaw L, Andries K, Koul A, Bald D, Cook GM. Bactericidal mode of action of Bedaquiline. Journal of Antimicrobial Chemotherapy IN PRESS (2015)

Aung HL, Dixon LL, Smith LJ, Sweeney NP, Robson JR, Berney M, Buxton RS, Green J, Cook GMNovel regulatory roles of cAMP receptorproteins (CRPs) in fast-growing environmental mycobacteria. Microbiology-SGM  2015;161:648-661

Greening C, Constant P, Hards K, Morales S, Oakeshott J, Russell R, Taylor M, Berney M, Conrad R, Cook GM. Atmospheric hydrogen scavenging: from enzymes to ecosystems. Applied and Environmental Microbiology 2015 Feb;81(4):1190-9.


Cook GM, Greening C, Hards K, Berney M. Energetics of pathogenic bacteria and opportunities for drug development. Advances in Microbial Physiology 2014;65:1-62. doi:10.1016/bs.ampbs.2014.08.001. 

Hartman T, Weinrick B, Vilcheze C, Berney M, Tufariello J, Cook GM, Jacobs WR. Succinate dehydrogenase is the regulator of respiration in Mycobacterium tuberculosis. PLoS Pathogens 2014 Nov 20; 10.1371/journal.ppat.1004510

Berney M*, Greening C, Conrad R, Jacobs WR, Cook GM. An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia. PNAS 2014 : 1407034111v1-201407034.  Featured with an interview in The Pathologist (https://thepathologist.com/issues/0114/the-survival-artists/) 

Pecsi I, Hards K, Ekanayaka NV, Berney M, Hartman TE, Jacobs WR., Cook GM. Essentiality of Succinate Dehydrogenase in Mycobacterium smegmatis and its Role in the Generation of the Membrane Potential under Hypoxia  mBio 2014 5(4):e01093-14

Greening C, Villas-Bôas SG, Robson J, Berney M, Cook GM. The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2. PLoS ONE 2014 Jul 24;9(7):e103034. 

Berney M*, Hartman T, Jacobs WR*. A Mycobacterium tuberculosis cytochrome bd oxidase mutant is hypersensitive to bedaquiline. mBio 2014; Vol. 5, No. 4, mBio01275-14

Aung HL, Berney M, Cook GM. Hypoxia-activated cytochrome bd expression in Mycobacterium smegmatis is cAMP receptor protein (CRP)-dependent. Journal of Bacteriology Epub 2014 June 16

Greening C, Berney M, Hards K, Cook GM, Conrad R. A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. PNAS 2014 111 (11) 4257-4261; Epub 2014 March 3, doi:10.1073/pnas/1320586111 

Berney M*, Cook GM*. Respiration and Oxidative Phosphorylation in Mycobacteria. In: The Structural Basis of Biological Energy Generation, Springer, Dordrecht 2014; 39:277-293 

Lagautriere T, Bashiri G, Paterson NG, Berney M, Cook GM, Baker EN. Characterization of the proline utilization pathway in Mycobacterium tuberculosis through structural and functional studies. Acta Crystallographica Section D  2014 70(4): Pages 968-980

Cook GM, Hards K, Vilcheze C, Hartman T, Berney M. Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria. In Molecular Genetics of Mycobacteria, Hatfull, G. and Jacobs, Jr., W.R. (Eds) ASM Press, Washington DC. (2014). Available online in Microbiology Spectrum 2014; 2(3):MGM-0015-2013


Berney M, Greening C, Hards K, and Cook GM. Three [NiFe] Hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis. Environmental Microbiology 2014 16(1): 318-330. Epub 2013 Nov 25


Berney M*, Weimar MR, Heikal A, Cook GM*. Regulation of Proline Metabolism in Mycobacteria and Its Role in Carbon Metabolism under Hypoxia. Molecular Microbiology 2012 84(4): 664-681; Epub 2012 April 22

McKenzie JL, Robson JR., Berney M, Smith T, Ruthe A, Arcus VL and Cook GM. A VapBC Toxin-Antitoxin Module is a Post-Transcriptional Regulator of Metabolic Flux in Mycobacteria. Journal of Bacteriology 2012 194(9): 2189-2204; Epub 2012 Feb 24 


Taniguchi N, Suzuki T, Berney M,Yoshida M, Cook GM. The Regulatory C-terminal Domain of Subunit e of FoF1 ATP Synthase is Dispensable for Growth and Survival of Escherichia coli. Journal of Bacteriology 2011 April;193(8): 2046-2052.

Hammes F, Berney M, Egli T. Cultivation-independent assessment of bacterial viabilityAdvances in Biochemical Engineering and Biotechnology, High Resolution Microbial Single Cell Analytics 2011 124:123-150.


Berney M* and GM Cook*. Unique Flexibility in Energy Metabolism Allows Mycobacteria to Combat Starvation and Hypoxia. PLoS One 2010 Jan;5: e8614

Hümpel A., Gebhard, S., Cook GM, Berney M*. The SigF Regulon in Mycobacterium smegmatis Reveals Roles in Adaptation to Stationary Phase, Heat and Oxidative Stress. Journal of Bacteriology 2010 May;192(10):2491-502


McMillan DGG, Keis S, Berney M, Cook GM. Non-Fermentative Thermoalkaliphilic Growth is Restricted to Alkaline Environments. Appl Environ Microbiol 2009 Dec;75:7649-7654

Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederweis M. Physiology of Mycobacteria. Advances in Microbial Physiology 2009;55:81-182, 318-9

Bosshard F., Berney M., Scheifele M., Weilenmann HU, Egli T. Solar disinfection (SODIS) and subsequent dark storage of S. typhimurium and S. flexneri monitored by flow cytometry. Microbiology-SGM 2009 Apr;155:1310-1317


Berney M, Vital M, Hülshoff I, Weilenmann HU, Egli T, Hammes F. Rapid, cultivation-independent assessment of microbial viability in drinking water. Water Res. 2008 Aug;42(14):4010-8. Epub 2008 Jul 22.

Hammes F, Berney M, Wang Y, Vital M, Köster O, Egli T. Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Res. 2008 Jan;42(1-2):269-77. Epub 2007 Jul 14.


Berney M, Hammes F, Bosshard F, Weilenmann HU, Egli T. Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight Kit in combination with flow cytometry. Appl Environ Microbiol. 2007 May;73(10):3283-90. Epub 2007 Mar 23.


Berney M, Weilenmann HU, Egli T. Adaptation to UVA radiation of E. coli growing in continuous culture. J Photochem Photobiol B. 2007 Feb 1;86(2):149-59. Epub 2006 Oct 19.

Berney M, Weilenmann HU, Simonetti A, Egli T. Efficacy of solar disinfection of Escherichia coli, Shigella flexneri, Salmonella Typhimurium and Vibrio choleraeJ Appl Microbiol. 2006 Oct;101(4):828-36.

Berney M, Weilenmann HU, Egli T. Gene expression of Escherichia coli in continuous culture during adaptation to artificial sunlight. Environ Microbiol. 2006 Sep;8(9):1635-47.

Berney M, Weilenmann HU, Egli T. Flow-cytometric study of vital cellular functions in Escherichia coli during solar disinfection (SODIS). Microbiology-SGM. 2006 Jun;152(Pt 6):1719-29.

Berney M, Weilenmann HU, Ihssen J, Bassin C, Egli T. Specific growth rate determines the sensitivity of Escherichia coli to thermal, UVA, and solar disinfection. Appl Environ Microbiol. 2006 Apr;72(4):2586-93.


Looser V, Hammes F, Keller M, Berney M, Kovar K, Egli T. Flow-cytometric detection of changes in the physiological state of E. coli expressing a heterologous membrane protein during carbon-limited fedbatch cultivation. Biotechnol Bioeng. 2005 Oct 5;92(1):69-78.



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