Dr Miguel Fernandez-Nino PhD

Food Scientist and Synthetic Biologist

Dr Miguel Fernández-Niño is a food scientist with expertise in food biochemistry, Food microbiology, synthetic biology, food waste valorisation, and industrial biotechnology. He writes and reviews content on these topics.

Dr. Fernández-Niño’s Highlights:

  •  Colombian scientist, with a Ph.D. in Biochemical Engineering from the Jacobs University Bremen (Germany).


  • Alexander von Humboldt Postdoctoral Fellow at the Leibniz Institute of Plant Biochemistry in Halle (Germany).


  • Expertise in using multi-omics approaches (e.g., metabolomics, metagenomics, and metatranscriptomics) to re-engineer products and processes of relevance for the food industry.


  • Expertise in designing microorganisms (microbial biofactories and starter cultures) to produce value-added products and food waste valorisation.


“My professional goal is to contribute to the education and research in Food Engineering and Food Biotechnology. The major incentive of my career is to contribute to the diffusion of scientific knowledge in society, thus promoting rational thinking and evidence-based decision-making”- Dr. Fernández-Niño’s, PhD.


Professional Experience:

Dr Fernández-Niño works as an Alexander von Humboldt Postdoctoral Fellow, at the Leibniz Institute of Plant Biochemistry, in Halle (Germany). He leads a project that aims to improve fine-flavour cocoa bean fermentation for local farmers in Colombia through controlled fermentation systems. 

Previously, Dr Fernández-Niño worked as a Postdoctoral Fellow on the bio-catalytic synthesis of isoferulic acid (BMBF project) in the same institution.

Dr Fernández-Niño also worked as a Postdoctoral researcher at the Department of Chemical and Food Engineering at Los Andes University in Colombia, working on the development of a platform to produce novel aroma precursor compounds and high value-added products from analysis of cocoa fermentation. 

In addition, Dr. Fernández-Niño worked on the assembly of a platform for heterologous polyphenols production in E. coli from analysis of cacao fermentation pathways, in the same institution.


Dr. Fernández-Niño has been an occasional scientific adviser of Casa Luker S.A. (leader in the Colombian chocolate market), working on projects related to the post-harvesting of fine-flavour cocoa. He also worked as instructor and coordinator of the lab course General Biochemistry and Molecular Biology II Lab (Course No. CH02-520121) at Jacobs University Bremen (Germany) and as a Resident Associate in the same institution.

Finally, Dr Miguel Fernández-Niño has experience as Part-Time Assistant Professor, Occasional Professor, and Master Teaching Assistant.



  • 2009 B.Sc. Biologist at Universidad Nacional de Colombia
  • 2012 Master in Science – Biochemistry (Thesis “magna cum laude”) at Universidad Nacional de Colombia
  • 2017 PhD in Biochemical Engineering at Jacobs University Bremen-Germany


The main publications of Dr Miguel Fernández-Niño are:

Fabio Herrera-Rocha, Miguel Fernández-Niño*, Mónica P. Cala, Jorge Duitama, Andrés Fernando González Barrios (2023) Omics approaches to understand cocoa processing and chocolate flavor development: A review. Food Research International. https://doi.org/10.1016/j.foodres.2023.112555

Fernández-Niño Miguel* and Burgos-Toro Daniela (2022) Engineering microbial biofactories for a sustainable future. Chapter edited by Catalina Correa & Adriana Suarez-Gonzalez in the book: Genomics and the Global Bioeconomy -1st Edition-. ISBN 9780323916011. Publisher: ELSEVIER: https://www.elsevier.com/books/genomics-and-the-global-bioeconomy/patrinos/978-0-323-91601-1

Fabio Herrera-Rocha, Mónica P. Cala, Ana Maria León-Inga, Jenny Lorena Aguirre Mejía, Claudia M. Rodríguez-López, Sergio Leonardo Florez, María José Chica, Héctor Hugo Olarte, Jorge Duitama, Andrés Fernando González Barrios, Miguel Fernández-Niño* (2022) Lipidomic profiling of bioactive lipids during spontaneous fermentations of fine-flavor cocoa. Food Chemistry. Volume 397. 133845, ISSN 0308-8146. https://doi.org/10.1016/j.foodchem.2022.133845.

Díaz-Bustamante ML, Fernández-Niño M, Reyes LH and Alvarez Solano OA (2022) Multiscale Approach to Dairy Products Design. Front. Chem. Eng. 4:830314. doi: https://doi.org/10.3389/fceng.2022.830314.

Ramón E. Jaimez*, Luigy Barragan, Miguel Fernández-Niño*, Ludger A. Wessjohann, George Cedeño-Garcia, Ignacio Sotomayor, Francisco Arteaga, (2022): Theobroma cacao L. cultivar CCN 51: A comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects. PeerJ 10:e12676 https://doi.org/10.7717/peerj.12676.

Fabio Herrera‑Rocha, Mónica P. Cala, Jenny Lorena Aguirre Mejía, Claudia M. Rodríguez‑López, María José Chica, Héctor Hugo Olarte, Miguel Fernández‑Niño* & Andrés Fernando Gonzalez Barrios*. (2021): Dissecting fine‑flavor cocoa bean fermentation through metabolomics analysis to break down the current metabolic paradigm. Scientific Reports 11(21904) DOI: https://doi.org/10.1038/s41598-021-01427-8.

Fernández-Niño, M., Rodríguez-Cubillos, MJ., Herrera-Rocha, F., Anzola, JM., Cepeda-Hernández, ML., Aguirre, L., Chica, MJ., Olarte, HH., Rodríguez, CM., Calderón, D., Ramírez-Rojas, A., Del Portillo, P., Restrepo, S., González Barrios, A.* (2021): Dissecting on-farm industrial fermentations of fine-flavour cocoa through metagenomic analysis. Scientific Reports 11(8638) DOI: https://doi.org/10.1038/s41598-021-88048-3.

Buitrago Mora, HM., Arango Piñeros, M., Espinosa Moreno, D., Restrepo, S., Cardona Jaramillo, JEC., Álvarez Solano, OA., Fernandez-Niño, M., González Barrios, A.* (2019): Multiscale design of a dairy beverage model composed of Candida utilis single cell protein supplemented with oleic acid. Journal of Dairy Science. 102(11) 9749-9762 DOI: https://doi.org/10.3168/jds.2019-16729.

Fernández-Niño, M., Giraldo, D., Gomez-Porras, JL., Dreyer, I., González Barrios, A., Arevalo-Ferro, C.* (2017): A synthetic multi-cellular network of coupled self-sustained oscillators. PLOS ONE 12(6): e0180155 DOI: https://doi.org/10.1371/journal.pone.0180155.

Fernández-Niño, M., Marquina, M. Swinnen, S.,Rodríguez-Porrata, B., Nevoigt, E.*, Ariño, J. (2015):The Cytosolic pH of Individual Saccharomyces cerevisiae Cells Is a Key Factor in Acetic Acid Tolerance. Appl Environ Microbiol 81(22): 7813-7821 DOI: https://doi.org/10.1128/AEM.02313-15.

Swinnen, S., Fernández-Niño, M., González-Ramos, D., van Maris, AJ., Nevoigt, E.* (2014): The fraction of cells that resume growth after acetic acid addition is a strain-dependent parameter of acetic acid tolerance in Saccharomyces cerevisiae. FEMS Yeast Res 14(4): 642-653 DOI: https://doi.org/10.1111/1567-1364.12151.

Conference appearances and other speaking engagements

Selected courses delivered:

Course: Current technologies in the production of chocolates. (20 hours course). Invited as professor by the Department of Chemical and Food Engineering / Faculty of Engineering at Los Andes University-Colombia. July (2021).

Course: Design and assembly of microorganisms for the biomedical industry (20 horas course). Invited as professor by the School of Engineering and Science- Instituto Tecnologico de Monterrey (México). January 15-17 (2019)

Selected oral presentations and conferences:

Conference: Dissecting fine-flavour cocoa bean fermentation through multi-omics approaches. Speaker invited by the Organic Chemistry Department at The University of Buenos Aires -Argentina. Sep. 07 (2022).

Conference: Theobroma cacao L. cultivar CCN 51. Association of Producers of Fine Cocoa and Aroma (APROCAFA), Ecuador. March 15 (2022).

Conference: Biology of probiotics and prebiotics. Speaker invited by the Chemical and Food Engineer Department at Los Andes University-Colombia. June 27 (2020).

Conference: Pandemic food revolution. Speaker invited by the Chemical and Food Engineer Department at Los Andes University-Colombia. May 5 (2020).

Conference: Biochemistry and microbiology of cocoa fermentation. Speaker invited to the elective course: cocoa and Chocolate, organized by Casa Luker and the Department of Chemical Engineering at Los Andes University-Colombia. February 5 and 7 (2019)

Oral presentation: Lipidomic profiling of bioactive lipids during spontaneous fermentation of fine-flavour cocoa. Metabolomics 2022. Valencia, Spain. June 19-23 (2022).

Oral presentation: Exploration of Saccharomyces cerevisiae intra-species diversity for the identification of novel genetic determinants for acetic acid tolerance with the help of pooled-segregant RNA sequencing. ISSY33 International Specialized Symposium on Yeasts at University College Cork, Cork, Ireland, June 24-29. (2017)

You can view some of Dr Miguel’s work below and links to his professional profile.











Published Posts: