A team of international researchers has published the first comprehensive comparative pan-genome analysis of lactic acid bacteria (LAB), a family of microorganisms essential to natural ecosystems and the food industry.

Lactobacillus_paracasei

Source: Dr. Horst Neve, Max Rubner-Institut

Lactobacillus paracasei

The study was carried out by scientists from the Novo Nordisk Foundation Center for Biosustainability  (DTU Biosustain) and the University of California, San Diego, and published in the journal Food Microbiology.

Crucial leap

The new study represents a crucial leap in understanding the genetic capabilities of 26 LAB species, in the first of its kind family-wide pangenome analysis.

By analyzing over 2400 publicly available genomes of high quality, the researchers successfully mapped the functional genetic capabilities, metabolic pathways, and biosynthetic gene clusters of individual strains across 26 species in the Lactobacillaceae family.

Researchers developed a novel integrated workflow for large-scale pangenome analysis that includes important steps of data curation, taxonomic definitions, phylogroup identification, pangenome reconstruction, functional annotations and genome mining. This advanced computational analysis resulted in better understanding of functional differences across different LAB species as compared to prior efforts focused on individual species or metagenome studies.

Treasure trove

“In mapping the genetic landscape of LAB, we have cracked open the door to a treasure trove of novel possibilities represented by phylogenetic groups and individual strains for future biotechnological applications,” says Postdoc Omkar Satyavan Mohite from DTU Biosustain who is one of the lead authors of the study.

The outcomes of this groundbreaking research are not confined to data science investigation of microbes - they have real-world applications.

“We’ve laid the groundwork for everything from species identification and functional studies to phylogenetic research and biotechnological innovations. This work can drive advancements in various sectors, including the food industry, healthcare, and environmental sciences,” says Akanksha Rajput, a Postdoctoral Researcher at UCSD and also one of the lead authors of the study.

Data driven insights

This research is especially relevant for experts and investigators across academic, industrial, medical, and environmental domains, all of whom can utilize these data driven insights to prioritizing strains of required genetic background.

According to the researchers, future work will use pan-genomic characteristics as a key tool for delving deeper into bacterial evolution, metabolic pathways, or sequence level variation. The integrated pangenome analysis workflow harvested here could be crucial platform to further investigate other microbial groups of industrial relevance.

The corresponding author of the study is Professor Bernhard O. Palsson. The study was led by Akanksha Rajput (Postdoctoral Researcher at UCSD), Siddarth Chauhan (Ph.D. student at UCSD), and Omkar S. Mohite (Postdoctoral Researcher at DTU Biosustain). Collaboration included teams from DTU Biosustain’s Microbial Foods, the Reconstruction Team, and Genome Analytics.

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