What is probiotic genomics? From DNA sequencing to next-generation probiotics.

Two bacteria can belong to the same species and still behave differently.

One strain may tolerate acid well, another may carry genes associated with antimicrobial production, and another may contain genetic elements that require additional safety assessment. These differences can be hidden at the level of the genome—the complete genetic information carried by a microorganism.

This is where probiotic genomics becomes important.

By combining microbiology with whole-genome sequencing, bioinformatics and increasingly artificial intelligence, researchers can examine probiotic bacteria at much greater resolution than was possible with traditional identification methods alone. Genomics can help answer an important question: What does this particular microbial strain appear capable of doing, and is its genetic profile consistent with safe and useful application?

However, genomic information is only part of the answer. A DNA sequence can reveal biological potential, but experimental evidence is still needed to demonstrate function, safety and health effects.

1. What is a probiotic?

A widely accepted scientific definition describes probiotics as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. This definition was reaffirmed by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics, or ISAPP.

This definition is important because simply finding a bacterium in fermented food—or identifying an organism that is normally present in the human gut—does not automatically make it a probiotic.

A microorganism must be appropriately identified and supported by evidence relevant to its intended use.

Probiotic effects can also depend strongly on the strain being studied. Different strains belonging to the same species can possess different genes, metabolic abilities and biological characteristics. This is one reason modern probiotic research increasingly uses genomic methods for detailed strain characterization.

2. What is probiotic genomics?

Probiotic genomics is the study of the complete genetic information of microorganisms being investigated or used as probiotics.

In simple terms, researchers read the organism's DNA and then use computational tools to understand what genes are present and what those genes may do.

It helps to separate three related ideas:

A species is a broader biological group. A strain is a particular genetic variant or isolate within that species. The genome is the complete DNA sequence carried by that particular organism.

For example, researchers may identify two bacterial isolates as belonging to the same species, while whole-genome analysis reveals genetic differences between them.

Those differences may influence characteristics such as carbohydrate utilization, stress tolerance, production of antimicrobial compounds or the presence of antimicrobial resistance genes.

For probiotic research, therefore, knowing only the species name may not provide enough information.

3. Why is genome sequencing important in probiotic research?

Whole-genome sequencing, often abbreviated as WGS, allows researchers to examine almost the complete genetic blueprint of a bacterial strain.

WGS can help investigate:

• taxonomic identity and probiotic strain identification;
• genes involved in carbohydrate metabolism;
• vitamin-related metabolic pathways;
• responses to acid, bile and oxidative stress;
• genes associated with surface structures and adhesion;
• bacteriocin and other antimicrobial-related gene clusters;
• antimicrobial resistance genes;
• virulence-associated genetic elements;
• plasmids, transposons and other mobile genetic elements; and
• genes or pathways associated with potentially harmful metabolites.

Current safety frameworks increasingly recognize the value of WGS. EFSA guidance, for example, describes using whole-genome sequence data to investigate genes associated with antimicrobial resistance, virulence, harmful metabolites and other genetic elements of concern in microorganisms used in the food chain.

Genome sequencing can therefore provide a powerful screening and characterization layer.

Finding a gene does not prove a health benefit. Genomics identifies potential; biological experiments determine whether that potential is realized.

A gene may be present but not expressed. A predicted protein may not function as expected under conditions inside the host. A microorganism may also show a desirable genomic feature without producing a measurable clinical effect.

4. From a bacterial sample to a genome

A simplified probiotic genomics workflow can be represented as:

1. Bacterial isolationA candidate microorganism is obtained from a suitable biological, food, environmental or other source and cultured under appropriate laboratory conditions.
2. DNA extractionGenomic DNA is extracted from the microbial cells. DNA quality and quantity matter because poor-quality starting material can reduce sequencing quality.
3. DNA sequencingSequencing technology reads millions of fragments—or, depending on the platform, longer stretches—of DNA.
4. Sequence quality controlResearchers check the sequence reads for technical problems such as low-quality bases, contamination or other issues that could affect later analysis.
5. Genome assemblyComputational tools reconstruct the sequencing reads into longer DNA sequences called contigs and, when possible, complete chromosomes and plasmids.
6. Genome annotationAnnotation identifies genes and other functional elements within the assembled genome. NCBI's Prokaryotic Genome Annotation Pipeline, or PGAP, identifies protein-coding genes, RNA genes and several other genomic features using predictive and comparative methods.
7. Comparative genomicsThe genome can then be compared with reference strains or related organisms.
8. Functional and safety analysisSpecialized tools and databases can be used to search for genes related to metabolic functions, antimicrobial resistance, virulence, bacteriocins, stress response and other characteristics of interest.

5. What can we learn from a probiotic genome?

A probiotic genome can help researchers ask much more detailed questions about a microorganism.

Is this strain really what we think it is?

Genome comparisons can support taxonomic and strain-level identification.

Could the organism survive gastrointestinal stress?

Researchers may investigate genes involved in acid, bile and oxidative stress responses. Such genes can contribute to survival, although they are not unique to probiotics.

Can it metabolize particular carbohydrates?

Genomic analysis may reveal enzymes involved in carbohydrate metabolism and utilization.

Could it produce antimicrobial compounds?

Bacteriocin-associated gene clusters and related pathways can be investigated.

Does it contain concerning genetic elements?

Researchers can screen for known antimicrobial resistance determinants, toxins, virulence-associated genes and mobile genetic elements.

How does it differ from closely related strains?

Comparative genomics can identify mutations, unique genes and larger genomic differences.

These questions show why genomics has become an important component of modern probiotic characterization.

A genome is a map—not the final answer.
A genome provides a detailed map of what a microorganism may be biologically capable of doing. DNA sequence alone cannot show whether every gene is active, how strongly it is expressed, whether its product functions under real biological conditions, or whether the microorganism produces a measurable health benefit.

6. Probiotic genomics and antimicrobial resistance

Antimicrobial resistance, or AMR, is particularly important in probiotic safety evaluation.

Some microorganisms naturally possess resistance characteristics that may be intrinsic to the species. Other resistance determinants may be located on mobile genetic elements such as plasmids or transposons.

The distinction matters because genetic material associated with mobile elements may, under some circumstances, have a greater potential for horizontal transfer between microorganisms.

Whole-genome sequencing can help locate resistance genes and examine their surrounding genomic regions.

A comprehensive probiotic safety assessment therefore should not simply ask: Does this bacterium contain an AMR gene?

It should also ask:

• What gene is it?
• Where is it located?
• Is it functional?
• Is it transferable?
• Does laboratory susceptibility testing agree with the genomic prediction?

This is a good example of why genomic and phenotypic evidence should be interpreted together.

7. Comparative genomics and the pangenome

A genome becomes even more informative when it is compared with the genomes of related strains.

Researchers may identify:

• Core genes — genes shared by nearly all or all strains being compared.
• Accessory genes — genes found in some strains but absent from others.
• Strain-specific genes — genes detected only in a particular strain or small subset of strains.

Together, the genes represented across a collection of strains form the pangenome.

In simple terms, a pangenome is the larger genetic catalogue of a microbial species rather than the genome of only one individual strain. Pangenome analysis can help researchers understand which biological functions are highly conserved and which vary between strains.

For probiotic research, this is valuable because two strains from the same species may share essential cellular machinery while differing in genes that influence environmental adaptation, metabolism or host interaction.

8. How artificial intelligence is entering probiotic genomics

Microbial genomics can produce enormous datasets. A single bacterial genome may contain thousands of genes. Hundreds or thousands of genomes may be compared simultaneously, together with information about metabolism, phenotype, source and biological activity.

This makes the field well suited to computational analysis.

Machine learning and AI can help researchers recognize patterns in complex genomic datasets.

Potential applications include:

• genomic classification;
• identifying combinations of genomic features;
• prediction of selected functional characteristics;
• prioritizing candidate strains for further laboratory investigation;
• analyzing large comparative-genomics datasets; and
• combining genomic information with phenotypic or microbiome data.

However, AI does not replace microbiology. An algorithm may predict that a strain has a desirable characteristic, but the prediction needs appropriate biological validation.

9. From traditional probiotics to next-generation probiotics

Many established probiotics belong to well-studied groups historically associated with fermented foods or the gastrointestinal tract.

Microbiome research is now widening the search. Advances in metagenomics, sequencing, microbial cultivation and computational biology have enabled researchers to investigate previously underexplored members of the microbiota as potential next-generation probiotics.

Examples discussed in the scientific literature include organisms from groups such as Akkermansia and Faecalibacterium, among others.

This expansion brings opportunity but also additional complexity. Some emerging organisms have less history of widespread use than conventional probiotic species. Researchers must therefore pay close attention to safety, manufacturing, stability, mechanism of action and regulatory requirements.

Genome sequencing can support this process, but it cannot replace:

10. Why probiotic genomics matters

Probiotic genomics sits at the intersection of several important scientific areas.

In human health, it can support precise characterization of microorganisms studied for health-related applications.

In animal health, it can contribute to the evaluation of microbial strains being investigated as feed supplements or alternatives within broader microbial-management strategies.

In food biotechnology, genomic data can help characterize cultures used in functional foods and fermentation.

In agriculture, microbial genomics can support investigation of organisms relevant to animal production, food systems and environmental interactions.

From a One Health perspective, genomic surveillance of antimicrobial resistance and mobile genetic elements can also connect questions involving humans, animals, food and the environment.

The important shift is from simply asking:

“Which species is this?”

to asking:

“Which strain is this, what does its genome contain, how does it differ from related organisms, and what biological evidence supports its proposed function?”

Key terms

Genome

The complete genetic material of an organism.

Whole-genome sequencing

A method used to determine most or all of an organism's DNA sequence.

Genome assembly

Computational reconstruction of sequencing reads into longer genomic sequences.

Genome annotation

Identification and description of genes and other functional genomic features.

Comparative genomics

Comparison of genomes to identify similarities and differences.

Pangenome

The combined set of genes found across multiple strains of a species or related group.

Probiotic strain

A specifically identified microbial strain supported by evidence relevant to its probiotic use.

Antimicrobial resistance

The ability of a microorganism to survive or grow despite exposure to an antimicrobial agent that would normally inhibit it.

Looking ahead

The future of probiotic research is likely to depend increasingly on the integration of several disciplines:

Genomics gives researchers unprecedented resolution for examining microbial strains. Bioinformatics turns DNA sequences into interpretable biological information. AI may help recognize complex patterns and prioritize promising candidates.

But the laboratory remains essential.

A strong probiotic candidate is not defined by an interesting genome alone. It emerges from the convergence of genomic evidence, measurable biological function, safety assessment and appropriately designed validation studies.

That combination—not any single technology—will shape the next generation of probiotic discovery.

References

1. Hill C, Guarner F, Reid G, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology. 2014;11:506–514. doi:10.1038/nrgastro.2014.66
2. FAO/WHO Working Group. Guidelines for the Evaluation of Probiotics in Food. London, Ontario, 2002.
3. EFSA. Statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain. EFSA Journal. 2024.
4. Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research. 2016;44(14):6614–6624.
5. United States Pharmacopeia-related expert review. Considerations for determining safety of probiotics: A USP perspective. Regulatory Toxicology and Pharmacology. 2022;136:105266. doi:10.1016/j.yrtph.2022.105266
6. Raethong N, Santivarangkna C, Visessanguan W, et al. Whole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3. Frontiers in Microbiology. 2022;13:969548. doi:10.3389/fmicb.2022.969548
7. Deciphering probiotic potential: a comprehensive guide to probiogenomic analyses. Review describing genomic approaches to functional and safety analysis of probiotic candidates.
8. Hasnain MA, Kang D-K, Moon G-S. Research trends of next generation probiotics. Food Science and Biotechnology. 2024;33:2111–2121. doi:10.1007/s10068-024-01626-9
9. Abouelela ME, Helmy YA. Next-Generation Probiotics as Novel Therapeutics for Improving Human Health: Current Trends and Future Perspectives. Microorganisms. 2024;12:430. doi:10.3390/microorganisms12030430
10. Kern L, Tofield A, Frame J, et al. Next-generation probiotics: an outlook into current applications and future developments. Nature Reviews Microbiology. 2026;24:539–558.