Integrative Microbiome Sciences Webpage for the Mu Laboratory at Monash University, led by Andre Mu

Research

What we do

We employ both wet lab and dry lab approaches to answer research questions. We analyse large omic datasets to generate novel targeted hypotheses (discovery science) to validate in the lab, and translate towards advancements in biotherapeutic and biotechnological applications.

How we do it

Our lab has expertise in microbial genomics (isolates and microbiomes), integrative multi-omics, and in vitro molecular microbiology techniques.
A key component of our lab’s success is through open and collaborative science. We therefore work closely with world-leading researchers from Monash University, and with colleagues at the Salk Institute for Biological Studies, University of California San Diego, Wellcome Sanger Institute, and Rutgers Health New Jersey Medical School, to address global research challenges of mitigating infectious diseases, antimicrobial resistance, and understanding the links across microbiomes and human health.

What are we working on

Below are highlights of some current research topics in our lab.
We would love to hear from highly-motivated prospective graduate students, and postdoctoral scholars interested in related areas to identify and develop key questions to pursue in their research project. Applicants must submit a concise research proposal (1 - 2 pages written) that aligns with the lab’s establshed topics to ensure appropriate support and mentoring can be provided. Please see research articles below.

Microbial ecology of infectious diseases

Metabolic hand-off processes
Integrative microbiome sciences
Bacterial sepsis
PI-Mu is a Leader at the Centre to Impact AMR

Host microbiome responses to phage therapy

Metagenomics and metabolomics
Phage genomics
Current work is in collaboration with experts at Phage Australia

Discovery of novel phage functions

In silico structural predictions
Integrative omics

Highlighted

Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium
Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium
Andre Mu, Glen P. Carter, Lucy Li, Nicole S. Isles, Alison F. Vrbanac, …, Brunda Nijagal, Malcolm J. McConville, Rob Knight, Benjamin P. Howden, Timothy P. Stinear
mSystems  ·  25 Aug 2020  ·  doi:10.1128/mSystems.00452-20
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Andre Mu, Daniel McDonald, Alan K. Jarmusch, Cameron Martino, Caitriona Brennan, …, Steffanie A. Strathdee, Robert T. Schooley, Pieter C. Dorrestein, Rob Knight, Saima Aslam
Microbiome  ·  14 Apr 2021  ·  doi:10.1186/s40168-021-01026-9
Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.
Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.
Andre Mu, William P Klare, Sarah L Baines, C N Ignatius Pang, Romain Guérillot, …, Stuart J Cordwell, Richard A Strugnell, Timothy P Stinear, Mark A Schembri, Mark J Walker
Nature communications  ·  18 Mar 2023  ·  pmid:36934086

All

2024

Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly
Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly
Yan Shao, Cristina Garcia-Mauriño, Simon Clare, Nicholas J. R. Dawson, Andre Mu, …, Mark D. Stares, Alison Rodger, Peter Brocklehurst, Nigel Field, Trevor D. Lawley
Nature Microbiology  ·  06 Sep 2024  ·  doi:10.1038/s41564-024-01804-9
A gut microbial signature for combination immune checkpoint blockade across cancer types.
A gut microbial signature for combination immune checkpoint blockade across cancer types.
Ashray Gunjur, Yan Shao, Timothy Rozday, Oliver Klein, Andre Mu, …, Jodie Palmer, Jonathan Cebon, Andreas Behren, David J Adams, Trevor D Lawley
Nature medicine  ·  01 Mar 2024  ·  pmid:38429524

2023

Therapeutic blockade of ER stress and inflammation prevents NASH and progression to HCC
Therapeutic blockade of ER stress and inflammation prevents NASH and progression to HCC
Ebru Boslem, Saskia Reibe, Rodrigo Carlessi, Benoit Smeuninx, Surafel Tegegne, …, Janina E. E. Tirnitz-Parker, Peter J. Meikle, Stefan Rose-John, Michael Karin, Mark A. Febbraio
Science Advances  ·  15 Sep 2023  ·  doi:10.1126/sciadv.adh0831
Editorial: Understanding the effects of metabolites and trace minerals on microbes during infection.
Editorial: Understanding the effects of metabolites and trace minerals on microbes during infection.
Thomas Naderer, Andre Mu, Andrew J Monteith, Tania Wong Fok Lung
Frontiers in cellular and infection microbiology  ·  30 Aug 2023  ·  pmid:37712062
Biofilm colonization of stone materials from an Australian outdoor sculpture: Importance of geometry and exposure
Biofilm colonization of stone materials from an Australian outdoor sculpture: Importance of geometry and exposure
Cristina Cattò, Andre Mu, John W. Moreau, Nancy Wang, Francesca Cappitelli, Richard Strugnell
Journal of Environmental Management  ·  01 Aug 2023  ·  doi:10.1016/j.jenvman.2023.117948
Bacteriophage discovery to advance biotechnology and biotherapeutics.
Bacteriophage discovery to advance biotechnology and biotherapeutics.
Andre Mu, Trevor D Lawley
Nature reviews. Microbiology  ·  01 May 2023  ·  pmid:36807633
Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.
Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.
Andre Mu, William P Klare, Sarah L Baines, C N Ignatius Pang, Romain Guérillot, …, Stuart J Cordwell, Richard A Strugnell, Timothy P Stinear, Mark A Schembri, Mark J Walker
Nature communications  ·  18 Mar 2023  ·  pmid:36934086

2022

Gut microbiome signatures and host colonization with multidrug-resistant bacteria
Gut microbiome signatures and host colonization with multidrug-resistant bacteria
Nicole S. Isles, Andre Mu, Jason C. Kwong, Benjamin P. Howden, Timothy P. Stinear
Trends in Microbiology  ·  01 Sep 2022  ·  doi:10.1016/j.tim.2022.01.013
Chronic Leptin Deficiency Improves Tolerance of Physiological Damage and Host-Pathogen Cooperation during Yersinia pseudotuberculosis Infection.
Chronic Leptin Deficiency Improves Tolerance of Physiological Damage and Host-Pathogen Cooperation during Yersinia pseudotuberculosis Infection.
Karina K Sanchez, Katia Troha, Andre Mu, Samuel E Redford, Justin L McCarville, Arianna Insenga, Sarah Stengel, Yujung Michelle Lee, Janelle S Ayres
Infection and immunity  ·  04 Aug 2022  ·  pmid:35924898
Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection
Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection
Tania Wong Fok Lung, Daniel Charytonowicz, Kristin G. Beaumont, Shivang S. Shah, Shwetha H. Sridhar, …, Danielle Ahn, Robert K. Ernst, Benjamin P. Howden, Robert Sebra, Alice Prince
Cell Metabolism  ·  01 May 2022  ·  doi:10.1016/j.cmet.2022.03.009
Adipose triglyceride lipase mediates lipolysis and lipid mobilization in response to iron-mediated negative energy balance
Adipose triglyceride lipase mediates lipolysis and lipid mobilization in response to iron-mediated negative energy balance
Alicia R. Romero, Andre Mu, Janelle S. Ayres
iScience  ·  01 Mar 2022  ·  doi:10.1016/j.isci.2022.103941
The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial
The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial
Erica L. Plummer, Kate Maddaford, Gerald L. Murray, Christopher K. Fairley, Shivani Pasricha, Andre Mu, Catriona S. Bradshaw, Deborah A. Williamson, Eric P. F. Chow
Microbiology Spectrum  ·  23 Feb 2022  ·  doi:10.1128/spectrum.01757-21

2021

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection
Andre Mu, Daniel McDonald, Alan K. Jarmusch, Cameron Martino, Caitriona Brennan, …, Steffanie A. Strathdee, Robert T. Schooley, Pieter C. Dorrestein, Rob Knight, Saima Aslam
Microbiome  ·  14 Apr 2021  ·  doi:10.1186/s40168-021-01026-9
Microbiota control of maternal behavior regulates early postnatal growth of offspring
Microbiota control of maternal behavior regulates early postnatal growth of offspring
Yujung Michelle Lee, Andre Mu, Martina Wallace, Jivani M. Gengatharan, Annalee J. Furst, Lars Bode, Christian M. Metallo, Janelle S. Ayres
Science Advances  ·  29 Jan 2021  ·  doi:10.1126/sciadv.abe6563

2020

Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium
Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium
Andre Mu, Glen P. Carter, Lucy Li, Nicole S. Isles, Alison F. Vrbanac, …, Brunda Nijagal, Malcolm J. McConville, Rob Knight, Benjamin P. Howden, Timothy P. Stinear
mSystems  ·  25 Aug 2020  ·  doi:10.1128/mSystems.00452-20
Subsurface carbon monoxide oxidation capacity revealed through genome resolved metagenomics of a carboxydotroph
Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph
Andre Mu, Brian C. Thomas, Jillian F. Banfield, John W. Moreau
Environmental Microbiology Reports  ·  23 Jul 2020  ·  doi:10.1111/1758-2229.12868
Feeling down A systematic review of the gut microbiota in anxiety depression and irritable bowel syndrome
Feeling down? A systematic review of the gut microbiota in anxiety/depression and irritable bowel syndrome
Carra A. Simpson, Andre Mu, Nick Haslam, Orli S. Schwartz, Julian G. Simmons
Journal of Affective Disorders  ·  01 Apr 2020  ·  doi:10.1016/j.jad.2020.01.124
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity
Kathryn M. Edenborough, Andre Mu, Kristin Mühldorfer, Johanna Lechner, Angelika Lander, Marcel Bokelmann, Emmanuel Couacy-Hymann, Aleksandar Radonic, Andreas Kurth
PLOS ONE  ·  20 Mar 2020  ·  doi:10.1371/journal.pone.0223629

2019

Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis
Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis
Tania Wong Fok Lung, Ian R. Monk, Karen P. Acker, Andre Mu, Nancy Wang, …, Loreani P. Noguera, Felix Dach, Stanislaw J. Gabryszewski, Benjamin P. Howden, Alice Prince
Nature Microbiology  ·  04 Nov 2019  ·  doi:10.1038/s41564-019-0597-0
Mus musculus deficient for secretory antibodies show delayed growth with an altered urinary metabolome
Mus musculus deficient for secretory antibodies show delayed growth with an altered urinary metabolome
Kim R. Simpfendorfer, Nancy Wang, Dedreia L. Tull, David P. De Souza, Amsha Nahid, …, Dianna M. Hocking, John S. Pedersen, Odilia L. C. Wijburg, Malcolm J. McConville, Richard A. Strugnell
Molecular Medicine  ·  03 Apr 2019  ·  doi:10.1186/s10020-019-0077-2
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
Andre Mu, Jason C. Kwong, Nicole S. Isles, Anders Gonçalves da Silva, Mark B. Schultz, …, Glen P. Carter, Deborah A. Williamson, Torsten Seemann, Timothy P. Stinear, Benjamin P. Howden
mSphere  ·  27 Feb 2019  ·  doi:10.1128/msphere.00529-18
Engineering the microbiome for animal health and conservation
Engineering the microbiome for animal health and conservation
Se Jin Song, Douglas C Woodhams, Cameron Martino, Celeste Allaband, Andre Mu, Sandrine Javorschi-Miller-Montgomery, Jan S Suchodolski, Rob Knight
Experimental Biology and Medicine  ·  18 Feb 2019  ·  doi:10.1177/1535370219830075
Can Bacteria Living Underground Help Fight Climate Change
Can Bacteria Living Underground Help Fight Climate Change?
Andre Mu, John W. Moreau
Frontiers for Young Minds  ·  15 Jan 2019  ·  doi:10.3389/frym.2018.00077

2018

Streptococcus gallolyticus subsp. pasteurianus meningitis complicated by venous sinus thrombosis: A case report
Streptococcus gallolyticus subsp. pasteurianus meningitis complicated by venous sinus thrombosis: A case report
Martin Wardle, Andre Mu, Steven Y.C. Tong
International Journal of Infectious Diseases  ·  01 Jun 2018  ·  doi:10.1016/j.ijid.2018.04.005
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
Jason C. Kwong, Courtney R. Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, …, Michelle Sait, Susan A. Ballard, Torsten Seemann, Timothy P. Stinear, Benjamin P. Howden
PeerJ  ·  03 Jan 2018  ·  doi:10.7717/peerj.4210

2015

The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection
The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection
Andre Mu, John W. Moreau
Frontiers in Microbiology  ·  09 Apr 2015  ·  doi:10.3389/fmicb.2015.00263

2014

Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment
Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment
Andre Mu, Chris Boreham, Henrietta X. Leong, Ralf R. Haese, John W. Moreau
Frontiers in Microbiology  ·  14 May 2014  ·  doi:10.3389/fmicb.2014.00209

2013

Biodegradation of thiocyanate by a novel strain i of Burkholderia phytofirmans i from soil contaminated by gold mine tailings
Biodegradation of thiocyanate by a novel strain of Burkholderia phytofirmans from soil contaminated by gold mine tailings
H.P. Vu, A. Mu, J.W. Moreau
Letters in Applied Microbiology  ·  22 Jul 2013  ·  doi:10.1111/lam.12123