Comparing the healthy nose and nasopharynx microbiota reveals continuity as well as niche- specificity

How can bacteria in the respiratory tract maintain our health and prevent infections from occurring? To answer this question, a better characterization of the collection of bacteria that are present in this human body niche is necessary. A good starting point is the identification of all bacteria that are present under healthy conditions. Therefore, we set up a large-scale citizen-science study, where we collected samples from 100 enthusiastic healthy volunteers. These volunteers were willing to donate a swab sample of their nose and nasopharynx. The bacterial DNA from all these samples was collected.

After processing of all these samples, we got a better idea about the bacteria that are present in the nose of healthy people. Our results, published in Frontiers in Microbiology, show that overall, the healthy nose and nasopharynx are mostly dominated by only a few bacterial species. Furthermore, these bacterial profiles in the nasopharynx could be grouped into at least four bacterial types (you can compare this to blood types) dependent on the bacterium that is most present: a type dominated by Moraxella, by Streptococcus or by Fusobacterium, and finally a mixed type of Staphylococcus, Dolosigranulum and Corynebacterium. Almost all individuals could be grouped into one of these four bacterial types. Interestingly, in the nose, only the Moraxella and the mixed type were found.


Applying for a PhD at the University of Antwerp?

We always welcome applications by students who want to obtain their own funding for a PhD study in line with the existing topics, alone or in cooperation with other universities or companies. In the Lab for Applied Microbiology and Biotechnology (LAMB) of prof. Sarah Lebeer, possible PhD research topics include (but are not limited to) probiotics for skin, urogenital and nasal applications, fermented vegetables, genetic characterization lactobacilli, characterization of molecular structures of lactobacilli such as pili, nasal microbiome in relation to air pollution, novel non-vertebrate animal models for probiotic research, … If you are interested in joining us, please contact Sarah Lebeer ( with a statement of interest about your research, and the scholarship programme to which you aim to apply.
Note that the University of Antwerp only offers PhD scholarships for specific research projects; these will be advertised in the job opportunities section of the faculty of Sciences

The main funding agencies for PhD scholarships in Flanders are:

For general information on the PhD programme, see the website of the Antwerp Doctoral School.

Congratulations dr. van den Broek!

PhD defence Marianne van den Broek. LTR: Prof. Malhotra, Prof. Cos, Marianne van den Broek, Prof. Lebeer, dr. Nauta

On Friday, February 16th 2018, Marianne van den Broek finalised her PhD about the ‘In vitro and in vivo probiotic potential of Lactobacillus spp. for otitis media’ with a public defence.

In this thesis the following questions regarding the probiotic potential of lactobacilli were addressed:

  1. Can lactobacilli inhibit the three main otitis media pathogens: Moraxella catarrhalis, Streptococcus pneumoniae and Haemophilus influenzae?
  2. What are important antimicrobial compounds?
  3. Can lactobacilli mediate more indirect mechanisms such as pathogen exclusion and the inhibition of production of inflammation markers by the otitis media pathogens?
  4. Can orally administered Lactobacillus rhamnosus GG transfer to URT niches and influence the local microbiota?

The PhD thesis can be found here and part of the results were recently published as a research article in ‘Beneficial Microbes’

Multifactorial inhibition of lactobacilli against the respiratory tract pathogen Moraxella catarrhalis

Probiotics, mainly lactic acid bacteria (LAB), are widely focused on gastrointestinal applications. However, recent microbiome studies indicate that LAB can be endogenous members of other human body sites such as the upper respiratory tract (URT). Interestingly, DNA-based microbiome research suggests an inverse correlation between the presence of LAB and the occurrence of important URT pathogens such as Moraxella catarrhalis which linked to otitis media, sinusitis and chronic obstructive pulmonary disease. However, a direct interaction between these microbes has not been explored in detail. Our results, now published in ‘Beneficial Microbes’ demonstrate that many of the Lactobacillus strains tested, exhibit antipathogenic activities against M. catarrhalis using agar-based assays, time course analysis, biofilm assays and MIC testing. Lactic acid was shown to be a key metabolite in these activities. In addition, cell line assays for adhesion competition and immunomodulation were used to substantiate the inhibitory effect of lactobacilli against M. catarrhalis. The well-documented strain Lactobacillus rhamnosus GG was shown to decrease the adhesion of M. catarrhalis to Calu-3 nasopharyngeal cells and to inhibit inflammation markers which were activated by M. catarrhalis.

This study suggests that several lactobacilli and their key metabolite lactic acid are possible candidates for probiotic therapeutic interventions against URT infections.

Large-scale genome analysis of Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus reveals taxonomic inconsistencies

The closely related species of the Lactobacillus casei group (L. casei, L. paracasei and L. rhamnosus) are extensively studied because of their applications in food fermentations and as probiotics. Our results, now published in mSystems, show that many strains in this group are incorrectly classified. Surprisingly many bacteria classified as L. casei are misclassified and should be relabeled as L. paracasei instead. We found that reclassifying them to their most closely related type strain improves the functional predictive power of their taxonomy.

In addition, our findings may spark increased interest in the L. casei species. We found that after reclassification, only 10 genomes remain classified as L. casei. Moreover, these strains show very interesting properties. First, they all appear to be catalase positive. This suggests that they have an increased oxidative stress resistance. Second, we isolated a L. casei strain, AMBR2, from the human upper respiratory tract and discovered that it harbors one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this strain as a potential probiotic organism.

Read more about our open access study on: