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Exploring the human respiratory microbiota

Doctoral research that grew and described bacteria never isolated before from the human airways.

16S rRNA phylogenetic tree with Enterococcus timonensis highlighted in red among related Enterococcus species — 16S rRNA tree placing Enterococcus timonensis (red) among its closest relatives.

Scanning electron micrograph of curved rod-shaped bacteria with flagella, scale bar 5 micrometres — Scanning electron micrograph of a new isolate (scale bar 5 µm).

Gram stain showing pink Gram-negative rods under the microscope — Gram stain of a new isolate.

Blood agar plate with small white bacterial colonies along streak lines — Colonies of a new isolate on blood agar.

Five rapid ID 32 A biochemical test strips with coloured wells, one labelled S. felix — rapid ID 32 A biochemical profiles, including Selenomonas felix (fourth strip).

Problem

Most bacteria living in the human respiratory tract had never been grown or described.

Approach

Combined culturomics with metagenomics on clinical samples, and wrote a systematic review of every bacterial species reported from the mouth and airways.

Result

35 new bacterial species described, including 5 new genera; PhD defended in November 2018.

My role

PhD researcher at IHU Méditerranée Infection, Aix-Marseille Université: isolation, characterisation and writing.

Outputs

Multiple bacterial species publications

Methods and tools

Culturomics
taxonogenomics
microbial culture

Skills

Microbial discovery
phenotypic characterization
research writing