How scientists are reading the DNA of beneficial bacteria to revolutionize our health
For thousands of years, humans have unknowingly harnessed the power of lactic acid bacteria (LAB) to create fermented foods like yogurt, cheese, and sourdough bread. Today, a genomic revolution is transforming our understanding of these microscopic allies, revealing the profound secrets hidden within their genetic code and unlocking unprecedented ways to boost human health, prevent disease, and even conserve endangered species.
Lactic acid bacteria are a group of Gram-positive microorganisms that produce lactic acid as a key metabolite during carbohydrate fermentation . Found in diverse environments ranging from fermented foods to the human gut and vaginal tract, these bacteria have long been valued for their beneficial properties.
The term "probiotic" refers to live microorganisms that, when administered in adequate amounts, confer a health benefit on the host 3 . Among the most studied probiotics are lactic acid bacteria from genera such as Lactobacillus, Lactococcus, and Bifidobacterium 7 .
What makes today's research particularly exciting is the emergence of "Lactobacillomics"—an interdisciplinary approach that integrates multiple "omics" technologies including genomics, transcriptomics, proteomics, and metabolomics to comprehensively understand lactic acid bacteria 1 . This holistic perspective allows scientists to move beyond simply observing what these bacteria do to understanding exactly how and why they do it at a molecular level.
DNA sequencing and analysis
Gene expression profiling
Metabolite analysis
The advent of whole-genome sequencing has dramatically accelerated our ability to identify and characterize probiotic strains 2 . By reading the complete DNA sequence of lactic acid bacteria, researchers can now:
Modern genomics relies on sophisticated technologies and bioinformatics tools that allow researchers to sequence, assemble, and interpret bacterial DNA.
| Research Tool | Primary Function | Application in LAB Research |
|---|---|---|
| Whole-Genome Sequencing | Determining complete DNA sequence | Characterizing genetic blueprint of probiotic strains 3 |
| CRISPRDetect | Identifying CRISPR arrays | Detecting antiviral defense systems in bacterial genomes 9 |
| antiSMASH | Predicting biosynthetic gene clusters | Identifying genes for antimicrobial compound production 2 |
| Prokka | Rapid genome annotation | Labeling genes and other features in sequenced genomes 2 |
| BAGEL | Detecting bacteriocin clusters | Finding genes for antimicrobial peptide production 2 |
Modern sequencing technologies can sequence an entire bacterial genome in just a few hours, a process that used to take months or even years!
To understand how genomic research unfolds in practice, let's examine a fascinating 2025 study that isolated and characterized lactic acid bacteria from an unexpected source: the feces of the crested ibis, a rare bird species subject to conservation efforts in China 5 .
The research team followed a systematic approach combining traditional microbiology with cutting-edge genomics:
Researchers collected fresh fecal samples from healthy adult crested ibises at a breeding base in Sichuan Province, China 5 .
Samples were diluted and plated on MRS agar (a specialized growth medium for lactic acid bacteria), then incubated under anaerobic conditions to promote the growth of LAB 5 .
Isolates were tested for acid tolerance (at pH 1.0-3.0), bile salt resistance (at 0.3%-2%), antibacterial activity against pathogens, antibiotic susceptibility, and cell surface hydrophobicity 5 .
The most promising isolate, strain E7, was identified as Lactiplantibacillus plantarum through 16S rDNA sequencing and underwent complete genome sequencing using both Nanopore PromethION48 and Illumina Novaseq platforms 5 .
The assembled genome was annotated to identify genes associated with probiotic functions such as adhesion, stress tolerance, and beneficial metabolite production 5 .
The genomic analysis revealed that L. plantarum E7 consists of a circular chromosome and two circular plasmids, encoding 3024 genes in total 5 . Crucially, researchers identified specific genes associated with:
Acid and bile salt tolerance genes explaining the strain's survival in harsh conditions
Genes indicating ability to colonize the intestinal tract
Genes for bacteriocins that inhibit pathogens
Genes potentially protective against cellular damage
pH 3.0 (3 hours)
High survival rate0.3% Bile Salts (4 hours)
High survival ratepH 2.0 (3 hours)
Moderate survival rate2.0% Bile Salts (4 hours)
Moderate survival rateThis research demonstrates how genomics can identify novel probiotic candidates from unconventional sources. The crested ibis strain not only showed excellent probiotic properties but also provided insights that could help improve the health of these endangered birds through targeted probiotic supplements 5 .
The implications of genomic research on probiotic lactic acid bacteria extend far beyond academic curiosity. These tiny genetic revelations are driving innovations across multiple fields:
Genomic analysis enables the development of strain-specific probiotics tailored to individual needs.
Synthetic biology approaches design probiotic lactic acid bacteria with specialized therapeutic functions 7 .
Probiotics identified through genomic analysis can support wildlife conservation 5 .
| Bacterial Chassis | Therapeutic Molecule | Application | Reference |
|---|---|---|---|
| Lactobacillus jensenii | Cyanovirin-N | Prevention of HIV infection | 7 |
| Lactococcus lactis | Glucagon-like peptide-1 | Treatment of Type 2 diabetes | 7 |
| Lactococcus lactis | KiSS1 protein | Cancer therapy | 7 |
| Lacticaseibacillus casei | Listeria adhesion protein | Protection against Listeria infection | 7 |
A 2025 study of older adults identified specific types of Lactobacillus and Bifidobacterium linked to individual traits, cognitive skills, and brain characteristics, supporting the creation of customized probiotic strategies for different populations 2 .
As genomic technologies continue to advance, we can expect even more sophisticated applications of probiotic lactic acid bacteria. The integration of artificial intelligence with genomic data promises to accelerate the discovery of novel strains with unique beneficial properties.
Machine learning algorithms can analyze genomic data to predict probiotic functions and identify novel strains with desired properties.
Engineered probiotics will deliver targeted therapies for conditions ranging from metabolic disorders to neurological diseases.
The emerging field of "Lactobacillomics" represents a paradigm shift in how we understand and utilize these microscopic workhorses 1 . By viewing lactic acid bacteria through a genomic lens, we're not only uncovering the genetic basis for their health-promoting properties but also learning how to enhance, customize, and target their benefits with unprecedented precision.
From improving digestive health to combating infectious diseases and even aiding wildlife conservation, the genomic revolution in probiotic research promises a future where we can harness the full potential of these tiny titans within—all by reading the instruction manual written in their DNA.
As research continues to evolve, one thing becomes increasingly clear: within the microscopic world of lactic acid bacteria lie solutions to some of our most pressing health challenges, waiting to be discovered—one gene at a time.