Juan Pablo Cárdenas, PhD.

Principal Investigator and Assistant Professor

Microbiome Genomics and Evolution Laboratory

PhD in Biotechnology, Universidad Andrés Bello, Chile.


Líneas de Investigación

  • Transferencia génica horizontal y adaptación de microorganismos de la microbiota intestinal

Microbiome Genomics and Evolution Laboratory

The gut microbiota is currently considered as an additional "organ" among living beings. The microbes that live inside us have co-evolved with us, generating an impact on our health. How did these organisms change to colonize the human being? How have they changed once they have become part of our bodies? What kind of changes has caused some of these native organisms to become relevant to our health?

There are several strategies to answer these questions. Our strategy is to analyze the properties of genes and genomes from these organisms and compare them with their close relatives that inhabit other environments or, in the case of the study of the human microbiome, with organisms that inhabit other mammals. Our hypothesis is that those microbes inhabiting the human body had to acquire new functions by means of horizontal gene transfer (HGT), whereas they lost many of their original genes associated with lifestyles in other niches.

In order to test our hypothesis, we are analyzing genomes from isolates and MAGs, searching for candidate genes for HGT, as well as searching for gene gain/loss patterns when those genomes are compared with their closest non-microbiome relatives.


Juan Pablo Cárdenas (ORCID) has a BSc in Biochemistry from the University of Santiago de Chile (USACH) and a Ph.D. in Biotechnology from the Andrés Bello University (UNAB, Chile). With previous experience in biotechnology start-ups working on the human microbiome, JPCA started at Nov. 2019 his position as assistant professor at the Center for Genomics and Bioinformatics (CGB).

Selected publications

Ortiz RL, Melis-Arcos F, Covarrubias PC, Ugalde JA, Apte ZS, Pérez-Donoso J, Cárdenas JP, Almonacid DE. Draft Genome Sequence of Blautia luti DSM 14534T, Isolated from Human Stool. Microbiol Resour Announc. 2020;9(19):e00088-20. doi: 10.1128/MRA.00088-20.

Bik EM, Bird SW, Bustamante JP, Leon LE, Nieto PA, Addae K, Alegría-Mera V, Bravo C, Bravo D, Cardenas JP, Carson GA, Caughey A, Covarrubias PC, Pérez-Donoso J, Gass G, Gupta SL, Harman K, Hongo DMB, Jiménez JC, Kraal L, Melis-Arcos F, Morales EH, Morton A, Navas CF, Nuñez H, Olivares E, Órdenes-Aenishanslins N, Ossandon FJ, Phan R, Pino R, Soto-Liebe K, Varas I, Vera-Wolf P, Walton NA, Almonacid DE, Goddard AD, Ugalde JA, Zneimer S, Richman J, Apte ZS. A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. PLoS One. 2019;14(5):e0215945. doi: 10.1371/journal.pone.0215945. eCollection 2019.

Gupta S, Palmer C, Bik EM, Cardenas JP, Nuñez H, Kraal L, Bird SW, Bowers J, Smith A, Walton NA, Goddard AD, Almonacid DE, Zneimer S, Richman J, Apte ZS. Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs. Front Public Health. 2018; 6:77. doi: 10.3389/fpubh.2018.00077.

Almonacid DE, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JP, Bik EM, Goddard AD, Richman J, Apte ZS. 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS One. 2017; 12:e0176555. doi: 10.1371/journal.pone.0176555.

Nuñez H, Moya-Beltrán A, Covarrubias PC, Issotta F, Cárdenas JP, González M, Atavales J, Acuña LG, Johnson DB, Quatrini R. Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon. Front Microbiol. 2017; 8:30. doi: 10.3389/fmicb.2017.00030.

Cardenas JP, Quatrini R, Holmes DS. Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment. Front Microbiol. 2016; 7:1822. doi: 10.3389/fmicb.2016.01822.

Cardenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol. 2016; 167(7):529-538. doi: 10.1016/j.resmic.2016.06.007



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