We develop and apply bioinformatics tools to study microbial genomes and proteomes, understand their evolution and address questions in microbiology, symbiosis and biotechnology.
Overview
The Bioinformatics group is a recently established group that emerged from the need to develop new bioinformatics tools for analysing next-generation sequencing (NGS) data. Initially, its work focused on designing dedicated pipelines and processing data to classify and separate reads from different samples (demultiplexing) obtained through signature-tagged mutagenesis (STM) coupled with high-throughput sequencing. The aim was to identify key genetic determinants of competitiveness in root colonisation and survival in inoculant formulations. The STM-seq-count tool was developed to process these sequencing data.
The group subsequently diversified its research to include the evolution of synonymous codon usage bias in bacteria (CUBES) and differences in insertion-sequence locations in closely related genomes (ISCompare). Further tools were developed to search for homologous proteins with a defined domain architecture (ArchMMer), identify and compare gene clusters (Scan cluster), and optimise primer design (ColabPCR).
Our current research focuses on identifying, predicting and characterising small open reading frames (smORFs) and their protein products (smORF-encoded polypeptides, SEPs) through proteomic data analysis and artificial intelligence models. In recent years, the team has also made a strong commitment to postgraduate training in bioinformatics by supervising and co-supervising doctoral theses.
Research areas
Identification and characterisation of small open reading frames (smORFs) in microorganisms associated with eukaryotic hosts
Small open reading frames (smORFs) are DNA sequences with the potential to encode small polypeptides, known as SEPs (smORF-encoded polypeptides). Long dismissed as non-coding or ‘junk’ DNA, many have now been shown to be actively transcribed and translated thanks to advances in sequencing and proteomics.
SEPs participate in essential cellular processes including stress responses, antibiotic resistance, transport, signalling, cell division and host interactions, playing key roles in microbial physiology.
This research area identifies smORFs in bacterial genomes, particularly those of bacteria associated with eukaryotic hosts, using and developing bioinformatics tools. We have explored intraspecies conservation as a predictor of coding potential and are currently developing deep learning methods based on protein and nucleic acid language models.
Bioinformatics searches for conserved gene clusters
Bacterial gene clusters play a fundamental role in soil bacterial ecology by shaping adaptation, survival and plant interactions. Clusters specialised in symbiosis, nodulation and root-exudate catabolism (such as rCGCs) enable precise molecular communication with hosts, rhizosphere dominance and coordinated responses to biotic and abiotic stress.
We develop methods to search for gene clusters, particularly those involved in agriculturally relevant activities such as plant growth promotion. We developed Scan cluster to search for and compare bacterial gene clusters. Future work will develop artificial intelligence methods for cluster identification and prediction of traits of interest in microbial strains.
Evolution of symbiotic genes, population diversity and synonymous codon usage in legumes
Legumes such as common bean, lentil and chickpea offer an important alternative with growing demand as meat substitutes: they provide high-quality food, preserve soil health and reduce greenhouse gas emissions.
Legumes establish nitrogen-fixing symbioses with soil bacteria, supporting sustainable agriculture through the gradual replacement of synthetic nitrogen fertilisers. We have studied the evolution of selected genes involved in nitrogen-fixing symbiosis, their allelic variants and synonymous codon usage biases in the nuclear genome.
Evolutionary conservation of codon usage harmonisation in bacteria and its relationship with cotranslational folding
Although the genetic code is universal, organisms differ in the codons most frequently used to encode each amino acid. Some codons are frequent and others rare, giving rise to synonymous codon usage bias.
Successful protein expression in heterologous systems—for example, human proteins in bacteria or plants—requires compatible coding sequences. One approach replaces rare codons with those used by the target organism. To maximise expression, all codons are often replaced with the most frequent ones, a process known as codon usage optimisation. However, this can cause problems when the rate of protein synthesis is important for correct folding (cotranslational folding).
In such cases, reproducing the original organism’s codon usage bias position by position (harmonisation) has been shown to be a better option. Using different codon usage metrics, we investigate whether this information is evolutionarily conserved.
Collaborative research areas
Genes required for rhizosphere and endophytic colonisation of alfalfa
Identification of genes required for Pantoea LPU12 to colonise alfalfa (Medicago sativa). Joint work with Sofía Erdozain and Antonio Lagares.
Evolutionary and functional characterisation of the S. meliloti plasmidome
Joint work with Abril Pagnutti and Antonio Lagares. Abril’s doctoral thesis is supervised by Antonio Lagares and co-supervised by Mauricio J. Lozano.
Adaptation and persistence of the Burkholderia cepacia complex in cystic fibrosis
Genome-wide searches for molecular markers associated with adaptation and persistence in the respiratory tract of children with cystic fibrosis, and characterisation of the plasmidome of Burkholderia cepacia complex organisms. Collaboration with Dr Alejandra Bosch and doctoral co-supervision.
Metabolic reprogramming of ATR(+) phenotypes in Sinorhizobium meliloti
Joint work with Walter Draghi and Carlos Ulises Molfesa Kaczoruk.
Proteins of interest in bacteria from the Neuquén oil basin
Searches for proteins involved in polycyclic aromatic hydrocarbon degradation, surfactin production and quorum sensing in genomes of bacteria isolated from consortia from the Neuquén oil basin. Collaboration with Dr Bibiana Copotelli and co-supervision of Octavio Ellehoj’s undergraduate final project.
Second-messenger signalling in B. diazoefficiens
Bioinformatic and evolutionary identification and characterisation of proteins involved in second-messenger signalling in B. diazoefficiens. Collaboration with Dr Elías Mongiardini, also including genomic analysis of type IV pili in Bradyrhizobium.
Evolution of the NtrBC/XY two-component systems
Evolutionary study of orthologues of the NtrBC/XY two-component systems in B. diazoefficiens. Collaboration with Dr Silvina López García and Dr Florencia Del Papa from the Molecular Microbiology and Bacterial Signal Transduction group.
Genomic variants and flagellar systems in B. diazoefficiens
Single-nucleotide polymorphism (SNP) analysis in more motile B. diazoefficiens strains obtained by directed evolution, and bioinformatic characterisation of polar and subpolar flagellar-system proteins. Collaboration with Dr Julia Althabegoiti also includes subpolar and lateral flagellin analysis in Bradyrhizobium and variant searches in more motile B. diazoefficiens USDA10 strains.
Other shared research areas
Genetic determinants of rhizobia required for rhizosphere colonization
Genome-scale search and identification of genes that enable rhizobia to establish and compete in the rhizosphere.
We combine genomics, genetics, bioinformatics and functional assays to understand how rhizobia adapt to the soil environment, recognize their hosts and colonize their roots. Determinants associated with motility, signaling, adaptation to adverse conditions and interaction with other microorganisms are studied.
The aim is to relate genetic information to colonization and nodulation efficiency, providing a basis for designing more persistent and effective inoculants in agricultural systems.
Participants: María Eugenia Salas, Mauricio Javier Lozano and Antonio Lagares.
Environmental microbiology and evolution of soil bacteria
Analysis of adaptation, evolution and population structure of bacteria from agricultural and natural environments.
We investigate how acidity, nutrient availability and the presence of contaminants shape soil bacterial communities. We integrate comparative genomics, phylogenomics, bioinformatics and experimental evolution to study the acquisition of adaptive functions.
We pay special attention to horizontal gene transfer and plasmid dynamics, with a view to understanding bacterial responses to environmental pressures and their potential application in biotechnology, soil restoration and biofertilization.
Participants: Mauricio Lozano, Walter Draghi and Antonio Lagares.
Functional genomics of bacteria of agricultural and biotechnological interest
Sequencing and functional analysis of bacterial genomes to discover mechanisms and genes of applied interest.
We sequence, assemble and annotate genomes of bacteria isolated from agricultural soils in different regions. Through data mining and comparison with international databases we identify genes related to stress tolerance, metabolite production and plant–microorganism interaction.
The integrative approach of functional genomics and systems biology provides knowledge to design next-generation bacterial inoculants and more sustainable and efficient agricultural solutions.
Participants: Mauricio Lozano, Antonio Lagares and Gonzalo Torres Tejerizo.
Team
- Mauricio Javier LozanoGroup director · Principal investigator · CONICET Associate Researcher · Doctorate, Faculty of Exact Sciences, UNLP
- Antonio LagaresGroup director · CONICET Superior Investigator
- Ezequiel Gerardo MogroCONICET postdoctoral fellow · Doctorate, Faculty of Exact Sciences, UNLP
- Dardo DallachiesaCONICET doctoral completion fellow · Licenciatura in Biotechnology, Faculty of Exact Sciences, UNLP
- Gonzalo Martín ZapataAgencia I+D doctoral fellow · Licenciatura in Biotechnology, Faculty of Exact Sciences, UNLP
- Abril Lourdes PagnuttiCONICET doctoral fellow · Licenciatura in Biotechnology, Faculty of Exact Sciences, UNLP · Supervisor: Antonio Lagares; co-supervisor: Mauricio J. Lozano
- Macarena AlgañarasCONICET doctoral completion fellow · Licenciatura in Biotechnology and specialisation in Bioinformatics, Faculty of Exact Sciences, UNLP / CINDEFI
People linked through theses or collaboration
- Carlos Ulises Molfesa KaczorukLicenciatura in Biotechnology, Faculty of Exact Sciences, UNLP · CONICET doctoral fellowship · Supervisors: Walter Draghi and Mauricio J. Lozano
- Octavio EllehojBiotechnology undergraduate student · Final project supervised by Bibiana Copotelli (CINDEFI, UNLP–CONICET) and co-supervised by Mauricio J. Lozano
Macarena Algañaras and Abril Pagnutti, listed in the team, are also linked through theses and collaboration.
Projects and funding
- Identification and characterisation of small open reading frames (smORFs) in microorganisms associated with eukaryotic hosts. PICT 2021-0168 (ANPCyT, Open Topics — Recently Formed Research Team, track II). Period: 2023–2027. Duration: four years. Director: Mauricio J. Lozano. This funding enabled the launch of one of the group’s main research areas.
- Molecular determinants of the acid-tolerant phenotype (ATR) of Sinorhizobium meliloti, an alfalfa symbiont. PICT 2021-0118 (ANPCyT, Open Topics — Recently Formed Research Team, track II). Period: 2023–2027. Duration: four years. Director: Dr Walter Draghi. The group contributes bioinformatics activities; Mauricio J. Lozano is a member of the responsible research team and jointly supervises a doctoral fellow working on the project’s topic.
- IDPFun2 — Integrating novel data, artificial intelligence and molecular behaviour to expand functional characterization of intrinsically disordered proteins. HORIZON-MSCA-2023-SE-01 (MSCA Staff Exchanges 2023). Action type: HORIZON-TMA-MSCA-SE. Grant Agreement 101182949. Director: Silvio Tosatto. Period: October 2024–October 2028. Accrediting institution: European Union. The group participates through secondments in consortium laboratories, conducting bioinformatics studies on the role and evolution of disordered proteins in bacteria. Mauricio J. Lozano also undertakes administrative work for the UNLP node alongside principal investigator Antonio Lagares and serves as an Extended Board Member.
- Identification and study of bacterial determinants involved in nitrogen-fixing symbiosis with alfalfa through multi-omics approaches. Project 11/X1019 (UNLP). Period: 2024–2027. Director: Gonzalo A. Torres Tejerizo. Co-director: Mauricio J. Lozano. The group searches for orthologous genes, domains and proteins and conducts their bioinformatic and evolutionary characterisation.
- REFRACT: participation in activities providing resources for visits by European researchers.
Selected scientific output
Selected publications associated with the group’s research areas and members. Work predating the reorganisation retains its institutional provenance; each shared publication has one catalogue record.
- ColabPCR: A Validated Google Colaboratory Notebook for Reproducible and Precise Primer Design
- Scan Cluster: A versatile database-independent prediction tool for multi-genome identification of homologous gene clusters
- A study on the codon usage bias of arenavirus common genes
- A Survey of Annotated smORF-Encoded Polypeptides in Bacteria Interacting with Eukaryotic Hosts
- Identification and functional analysis of recent IS transposition events in rhizobia
- Identification of Ensifer meliloti genes required for survival during peat-based bioinoculant maturation by STM-seq
- Improved detection and phylogenetic analysis of plant proteins containing LysM domains
- Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate Desmanthus spp. in Northwest Argentina
- Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
- Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
- Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
- Comparative analysis of three Bradyrhizobium diazoefficiens genomes show specific mutations acquired during selection for a higher motility phenotype and adaptation to laboratory conditions
- Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation
Quartiles shown are those reported by the group.
Collaborations
- Alejandra Bosch (CINDEFI, CONICET–UNLP): genomics and adaptation of Burkholderia cepacia complex bacteria in cystic fibrosis; co-supervision of Macarena Algañaras’s doctorate.
- Walter Draghi (IBBM, CONICET–UNLP): metabolic reprogramming of acid-tolerant S. meliloti phenotypes; joint doctoral supervision of Carlos Ulises Molfesa Kaczoruk.
- Bibiana Copotelli (CINDEFI, CONICET–UNLP): characterisation of bacteria from the Neuquén oil basin; co-supervision of Octavio Ellehoj’s undergraduate final project.
- Rhizobia–Soybean Interactions (IBBM, CONICET–UNLP): genomic analysis of type IV pili and second-messenger signalling in Bradyrhizobium with Dr Elías Mongiardini; evolution of NtrBC/XY systems with Dr Silvina López García and Dr Florencia Del Papa from the Molecular Microbiology and Bacterial Signal Transduction group; analysis of subpolar and lateral flagellins and variants in more motile B. diazoefficiens USDA10 strains with Dr Julia Althabegoiti.
- VACSAL (IBBM, CONICET–UNLP; Dr Daniela Hozbor and Dr Daniela Bottero): bioinformatics searches for vaccine candidates and identification of SEPs in Bordetella pertussis.
- Computational Biology and Data Mining laboratory (Dr Miguel Andrade, Johannes Gutenberg University, Mainz, Germany): Gonzalo Zapata’s DAAD 2026 fellowship. Project: Leveraging Protein Language Models to Classify smORF-Encoded Polypeptides (SEPs) by Coding Potential.
- ERGO Biotech: bioinformatics studies in Daucus carota.
Capabilities
Genomic data analysis, genome comparison, homologue and gene-cluster searches, protein evolution and computational tool development. ColabPCR integrates primer design and specificity checks; its code is available on GitHub.
Tools and software
Development of STM-seq-count for STM-seq data processing; CUBES for codon usage bias studies; ISCompare for comparing insertion-sequence locations; ArchMMer for finding homologous proteins with defined domain architectures; Scan cluster for gene-cluster identification and comparison; and ColabPCR for optimising primer design.
Contact
Mauricio Javier Lozano · mjlozano@biol.unlp.edu.ar