New bacterium found in infants’ noses hints at hidden airway microbiome diversity

Scientists have isolated and characterised what appears to be a previously unrecognised bacterial species from the noses of infants in South Africa, offering a rare glimpse into the poorly mapped microbial world of the young human airway. The bacterium, provisionally named Helcococcus ekapensis, was recovered from archived nasopharyngeal samples collected during the Drakenstein Child Health study, a long-running birth cohort based in the Western Cape.

The nasopharynx, the space behind the nose and above the throat, is a major reservoir for both harmless commensal bacteria and disease-causing pathogens. Researchers have increasingly linked the composition of its microbial community to respiratory health and susceptibility to infection in early life. Yet despite growing interest in this ecological niche, some of its inhabitants remain barely characterised, and the genus Helcococcus is a case in point. Although Helcococcus species have been detected in the human respiratory tract before, the group has never been studied in detail within the infant nasopharynx.

In the new study, published in BMC Microbiology, the team led by Celine C. De Allende and Felix S. Dube describes the isolation and culturing of three H. ekapensis isolates, designated SA-HE-C1, SA-HE-207 and SA-HE-338.

Prevalence screening of the cohort samples revealed a striking pattern: colonisation of the infant nasopharynx by H. ekapensis increases with age over the first two years of life. That trajectory suggests the organism establishes itself progressively as the airway microbiome matures, though the study does not establish whether the bacterium benefits, harms or is neutral to its young hosts.

To probe the organism’s biology more deeply, the researchers sequenced draft genomes of all three isolates. The genomes proved remarkably similar, sharing close to 99% average nucleotide identity, a level of similarity consistent with the isolates belonging to a single species. This genomic coherence strengthens the case that the team has encountered a distinct taxon rather than a loose collection of related strains.

The genomic analysis also revealed a strikingly limited metabolic capacity. Many amino acid biosynthesis pathways were incomplete, implying that H. ekapensis depends on its environment to supply building blocks that most free-living bacteria can manufacture themselves.

Alongside the reduced metabolic repertoire, the genomes carried several putative genes that hint at how the bacterium interacts with its surroundings.

The authors caution that this work is an initial characterisation rather than a formal species description. Until then, the name H. ekapensis remains provisional.

Even in its preliminary form, the study adds a new player to the catalogue of organisms inhabiting the developing infant airway. The researchers suggest the bacterium may be relevant to the nasopharyngeal microbiome during early childhood, a period when the composition of that community is thought to influence respiratory health. They frame the work as a foundation for future studies investigating what role, if any, H. ekapensis plays within the nasopharynx, whether as a commensal, a competitor of pathogens or something else entirely.

The discovery also underscores how much remains unknown about the microbes colonising human airways.

Subject of Research: Isolation and initial genomic and phenotypic characterisation of a potentially novel Helcococcus species from the infant nasopharynx in South Africa

Article Title: Initial characterisation of Helcococcus ekapensis isolated from the nasopharynx of infants in Western Cape, South Africa

Article References: De Allende, C. C., Rechsteiner, L., Salter, S. J., Madzinga, M., Nicol, M. P., Parkhill, J., Hathaway, L. J., & Dube, F. S. (2026). Initial characterisation of Helcococcus ekapensis isolated from the nasopharynx of infants in Western Cape, South Africa. BMC Microbiology. https://doi.org/10.1186/s12866-026-05780-4

Image Credits: AI Generated

DOI: 10.1186/s12866-026-05780-4

Keywords: Helcococcus ekapensis, nasopharynx, infants, microbiome, bacteriology, draft genomes, South Africa, Drakenstein Child Health study, bacteriocins, respiratory tract, Initial, characterisation