Technical Note

The species on the label and the species in the genome are not always the same

A comparative genomic study published in World Journal of Microbiology & Biotechnology sequenced the Enterococcus faecium in five commercial probiotic products from the Asian market. All five were identified as a different species: Enterococcus lactis.

Published 12 October 2026 · 6 min read

What the study did

Five E. faecium strains isolated from commercial probiotic products were whole-genome sequenced and phenotypically profiled alongside five reference strains. Average Nucleotide Identity (ANI) and Multilocus Sequence Typing identified the product-derived strains as Enterococcus lactis, clustering into two distinct phylogenetic clades (Clade I: ST-812; Clade II: ST-76).

The clades carried coherent but different functional genomic profiles: Clade I was enriched in genes for carbohydrate metabolism and dietary fibre degradation, while Clade II showed a different emphasis, including carotenoid biosynthesis.

On safety, the findings were favourable

All product-derived strains lacked the high-risk resistance gene vanA and the major virulence determinants esp, hyl and gelE;
those determinants were present in the clinical control strain ATCC 51559 in the same study;
phenotypically the strains were susceptible to penicillin, ampicillin, vancomycin and tetracycline, and carried no acquired resistance genes for WHO-defined critically important antibiotics.

In vitro assays, however, showed significant inter-strain variability in gastric acid tolerance, bile salt resistance and bile salt hydrolase (BSH) activity — which the authors take as evidence that functional performance is a strain-level property, not a species-level one.

Why this happens: taxonomy moved ahead of routine identification

A product labelled E. faecium that sequences as E. lactis looks, at first glance, like substitution. The published evidence points to something more ordinary, and more widespread.

E. lactis is a relatively young species, described in 2012 from Italian raw-milk cheeses. Strains isolated, deposited and named before that date were never going to carry the name.
A later genome-based reassignment moved an entire clade. Whole-genome analysis concluded that E. faecium Clade B strains belong to E. lactis; the same work found these strains lack the hospital-infection-associated markers IS16, hyl_Efm and esp, and the PBP5 allelic profile linked to ampicillin resistance.
Routine methods do not separate the two species. A dedicated PCR assay targeting the gluP gene was developed for the purpose — the gene's nucleotide sequence diverges by 90 to 92% between the species. For MALDI-TOF, the same authors describe results as promising but note that a robust library of E. lactis spectra is still needed before routine identification.

"Many probiotics or feed formulas contain E. faecium, which might actually correspond to E. lactis."— Microbiology Spectrum, on distinguishing the two species

In other words, this is not a question of who is substituting what. A species boundary was redrawn, and upstream identification practice has not caught up. For a buyer the consequence is the same either way: the species name on the specification sheet and the species in the genome may not match.

What it means for buyers

1. Regulatory frameworks are written around species names

Permitted-species lists, labels and registration dossiers all reference the species. Where the genomic identity differs from the declared one, what needs rechecking is not a label but a document chain.

2. The supporting literature can break in the middle

A dossier citing E. faecium studies for a strain that is genomically E. lactis has a discontinuity at the species level. The more fundamental point is the next one.

3. Safety and function are strain-level conclusions

This study is itself the illustration: within one dataset, the product-derived strains carried no vanA and no major virulence genes while the clinical control strain did, and acid tolerance, bile salt resistance and BSH activity varied significantly between strains. Neither "this species is safe" nor "this species does X" transfers automatically to an individual strain.

How identity is established: ANI

The species boundary for prokaryotes is currently defined by whole-genome Average Nucleotide Identity, with thresholds generally placed at 95–96%. 16S rRNA sequencing, biochemical panels and standard MALDI-TOF libraries are adequate at genus level and for most species, but not for resolving close relatives such as E. faecium and E. lactis.

How Baifude handles this

Strain identity is something that can be established objectively rather than inherited from a historical name. Where the species assignment of a strain is in question, or where a customer needs it documented for registration and compliance, Baifude can arrange whole-genome sequencing and ANI-based species confirmation on request, with the result recorded in the accompanying documentation — so that the species delivered is the species specified.

If you are reviewing the species assignment of an enterococcal ingredient, or need identification evidence for a specific strain, send us the strain designation and intended application.

References

Comparative genomic and phenotypic profiling of commercial probiotic Enterococcus faecium strains: insights into safety and functional attributes. World Journal of Microbiology & Biotechnology, 27 September 2026. PubMed 42801401
Genome-based studies indicate that the Enterococcus faecium Clade B strains belong to Enterococcus lactis species and lack of the hospital infection associated markers. International Journal of Systematic and Evolutionary Microbiology. Article
Distinction between Enterococcus faecium and Enterococcus lactis by a gluP PCR-based assay. Microbiology Spectrum. Article
Morandi S. et al., Enterococcus lactis sp. nov., from Italian raw milk cheeses, 2012.

This note summarises published research to explain strain identification practice. It is not a claim about the performance of any product, and it is not directed at any particular company or brand. The findings described apply to the strains and conditions reported in the original papers.