Dr M. Lisandra Zepeda Mendoza

Lisandra Zepeda-Mendoza

Institute of Microbiology and Infection
Lecturer - Marie Curie Fellow

Contact details

University of Birmingham
B15 2TT

Since Summer 2019 Lisandra is working as a European Union Marie Sklodowska-Curie Fellow on the ARCS (‘Antibiotic Resistance in Clinical Sewage microbiome’) project in the group of Prof Willem van Schaik (this research has been funded by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement No 836384).

Lisandra's main driver is bridging the gap between different disciplines for the design of analysis pipelines and the biological interpretation of the results. Her specific research objectives are:

  • alternatives to the use of antibiotics
  • understanding of antibiotic resistance (AR) from a metabolic network and evolution point of view
  • identification and characterization of microbiomes with relevant pathogenic traits

To accomplish these objectives Lisandra uses high-throughput data (DNA, RNA, metabolites) and metabolic/regulatory modelling methods. Lisandra uses genome scale metabolic and regulatory modelling to better guide hypothesis testing in the laboratory to understand metabolic network rewiring leading to AR, thus finding complex genotype-phenotype associations. High-throughput sequencing data is analysed with metagenomic approaches for characterization of different natural and clinical environments.


  • 2013 - 2016 PhD Student, Centre for GeoGenetics, University of Copenhagen, Denmark Dr M Thomas P Gilbert, Natural History Museum of Denmark (SNM). Dissertation: "Comparitive Genomics and metagenomics for analysing non-model organisms with extreme dietary adaptations".
  • 2008 - 2013 BSc Genomics Sciences,National Autonomous University of Mexico (UNAM), Mexico. Top 1st, Graduate with Highest Honours.  Thesis: "A Statistical method to quantitatively identify differential alternative splicing from proteomic and RNA-seq data". Dr Adrian Krainer, Cold Spring Harobor Laboratory, NY, USA.


With a background in Genomic Sciences, Lisandra first worked in the field of ancient DNA from various organisms ranging from maize to frozen lake sediments. She obtained her PhD in Bioinformatics from the University of Copenhagen, where she studied the gut microbiome's role to the host's health and dietary adaptations.

Following Lisandra's PhD and during her experience in the industry, she characterized strains for designing starter cultures for fermented foods. This work made her appreciate the intricate microbial genotype-phenotype relationships and she became interested in microbiology in the clinical setting.


  • 2018 - Instructor of the hands-on workshop "An introduction to metagenomics and metabarcoding" organised by Transmitting Science, March 19-23rd. Crete, Greece.
  • 2017 - Master thesis sensor for Omics Programme, Sino-Danish Centre for Education and Research (SDC).
  • 2016 - Instructor of the module “NGS” from the “Bioinformatics and Systems Biology” Bachelor level course, organized by Dr. Ramneek Gupta, at the Sino-Danish Centre for Education and Research, Chinese Academy of Sciences, Beijing, China. Instructor of the hands-on workshop “Metabarcoding and metagenomics” organized by Professor Thomas Sicheritz-Ponten, at the National Centre for Antarctic and Ocean Research, Goa, India.
  • 2015 - Instructor of the session “DAMe: A toolkit for processing Datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses” at the eDNA Working Group Meeting. Bangor University, UK.

Other activities

  • 2017 -  Bioinformatics Consultant. Roche Innovation Center Copenhagen A/S, Denmark.
  • 2016 - Maersk Management Consultant for PhD training.  Consulting, client relationship, interviewing, case studies, story-telling and pitching


Zepeda Mendoza ML, Graves GR, Manzano Vargas K, Hansen LH, Roggenbuck M, Brunak S, Gilbert MTP and Sicheritz-Pontén T. (2018) Uncovering the health protective role of the vulture facial and gut microbiome. Acta Vet Scand, 11;60(1):61

Zepeda Mendoza ML, Edwards NK, Madsen MG, Abel-Kistrup M, Puetz L, Sicheritz-Ponten T and Swiegers JA. (2018). Influence of Oenococcus oeni and Brettanomyces bruxellensis on Aged Wine Microbial Taxonomic and Functional Profiles. Am. J. Enology Vitic.

Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Thézé J, Streicker D and Gilbert MTP. (2018). Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology & Evolution. 2:659–668.

Paijmans JLA, Barnett R, Gilbert MTP, Zepeda-Mendoza ML, Reumer JWF, de Vos J, Zazula G, Nagel D, Baryshnikov GF, Leonard JA, Rohland N, Westbury MV, Barlow A and Hofreiter M. (2017) Evolutionary history and extinction dynamics of sabre-toothed cats based on ancient mitogenomics. Current Biology, 6;27(21):3330-3336.e5 

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML and Gilbert MTP. (2016) Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends in Ecology and Evolution. 31(9):689-699.

Winther Pedersen M, Ruter A, Schweger C, Friebe H, Staff RA, Kjeldsen KK, Zepeda Mendoza ML, Beaudoin AB, Zutter C, Larsen NK, Potter BA, Nielsen R, Rainville RA, Orlando L, Meltzer DJ, Kjær KH and Willerslev E. (2016) Postglacial viability and colonization in North America’s ice-free corridor. Nature, 1;537(7618):45-49.

Zepeda-Mendoza ML, Bohmann K, Carmona Baez A and Gilbert MTP. (2016) DAMe: A Toolkit for the Initial Processing of Datasets with PCR replicates of Double-tagged Amplicons for DNA Metabarcoding Analyses. BMC Research notes. 3;9(1):255.

Escalera-Zamudio M, Mendoza MLZ, Heeger F, Loza-Rubio E, Rojas-Anaya E, Méndez-Ojeda ML, Taboada B, Mazzoni CJ, Arias CF and Greenwood AD. (2015) A novel endogenous betaretrovirus in the common vampire bat (Desmodus rotundus) suggests multiple independent infection and cross-species transmission events. J Virol. 89(9):5180–4.

Zepeda Mendoza ML, Sicheritz-Pontén T and Gilbert MTP. (2015) Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform. 16(5):745–58.

Zepeda Mendoza ML, Nygaard S and da Fonseca RR. (2014) DivA: detection of non-homologous and very Divergent regions in protein sequence Alignments. BMC Research Notes. 7:806.

Zepeda Mendoza ML and Resendis-Antonio O. (2012) A roadmap towards a systems biology description in bacterial nitrogen fixation. Symbiotic Endophytes, Chapter 2. Aroca, Ricardo (Ed). Springer. Series Soil Biology Vol. 37.

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