Lactobacilli have a niche in the human nose

Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat

Exploring the potential and molecular mechanisms of beneficial lactic acid bacteria in mucosal disorders

Abstract: For several decades, it was widely believed that the healthy respiratory tract was sterile. However, advancements in next-generation sequencing techniques have enabled us to unveil the microbial communities residing within the respiratory tract, both in health and disease. However, there is a lack of in-depth functional insights into these communities to design innovative microbiome therapies for the respiratory tract. Nevertheless, such therapies show great promise as they can act via multifactorial mechanism of action improving respiratory health. Specifically for people with cystic fibrosis (CF), microbiome therapies could complement current treatments by preventing chronic colonization of pathogens at early age and by enhancing the effectiveness of therapies such as antibiotics and modulators through creation of a more stable microbial ecosystem. This PhD thesis aimed to expand the knowledge on the microbial communities within various respiratory tract niches and explore the potential of microbiome therapies as a preventive or complementary treatment strategy for CF. First, we studied the salivary microbiome of 246 women using 16S rRNA amplicon sequencing to investigate whether we could detect bacterial biomarkers linked with respiratory disease. We found that the salivary microbiome was highly preserved among healthy women and lifestyle and host-related parameters had only subtle effects on specific taxa. For the detection of bacterial biomarkers linked with respiratory disease, more targeted sampling methods and insights at a lower taxonomic level were needed. Therefore, we next performed shallow metagenomic shotgun sequencing on respiratory tract samples, including nasopharyngeal, oropharyngeal and sputum samples. The host DNA depletion step was found to reduce the presence of Gram-negative taxa, which play an important role in the human airways. Taken this bias into account, we could show the potential of shallow shotgun sequencing in a clinical setting by identifying important CF pathogens at species level in oropharyngeal and sputum samples providing valuable information about the patient\u2019s disease status. Lastly, we aimed to evaluate the potential of probiotics for CF. Lacticaseibacillus casei AMBR2 demonstrated important adaptation and multifactorial probiotic characteristics in vitro with a focus on CF pathogenesis. Moreover, we identified four putative bacteriocin gene clusters in the genome of AMBR2 of which one exhibited high activity against Gram-negative pathogens. This work combined microbiome research (16S rRNA amplicon and shallow metagenomic shotgun sequencing) with functional studies to achieve the research goals. It has enriched the understanding regarding microbe-microbe and microbe-host interactions in the context of CF, paving the way for future therapeutic applications

Subclinical Heart Dysfunction in Relation to Metabolic and Inflammatory Markers: a Community-Based Study.

BACKGROUND: Population studies investigating the contribution of immunometabolic disturbances to heart dysfunction remain scarce. We combined high-throughput biomarker profiling, multidimensional network analyses and regression statistics to identify immunometabolic markers associated with subclinical heart dysfunction in the community. METHODS: In 1,236 individuals (mean age, 51.0 years; 51.5% women), we measured 39 metabolic and inflammatory markers and assessed echocardiographic indexes of left ventricular diastolic dysfunction (LVDD) and left atrial (LA) reservoir dysfunction. We used partial least squares (PLS) to filter the most relevant biomarkers related to the echocardiographic characteristics. Subsequently, we assessed the associations between the echocardiographic features and the biomarkers selected in PLS while accounting for clinical confounders. RESULTS: Influential biomarkers in PLS modeling of echocardiographic characteristics included blood sugar, γ-glutamyl transferase, D-dimer, ferritin, hemoglobin, IL-4, IL-6 and serum insulin and uric acid. In stepwise regression incorporating clinical confounders, higher D-dimer was independently associated with higher E/e' ratio and LA volume index (P≤0.05 for all). In multivariable-adjusted analyses, the risk for LVDD increased with higher blood sugar and D-dimer (P≤0.048). After full adjustment, higher serum insulin and serum uric acid were independently related to worse LA reservoir strain and higher risk for LA reservoir dysfunction (P≤0.039 for all). The focused biomarker panels detected LVDD and LA reservoir dysfunction with 87% and 79% accuracy, respectively (P<0.0001). CONCLUSIONS: Biomarkers of insulin resistance, hyperuricemia and chronic low-grade inflammation were associated with impaired cardiac function. These biomarkers might help to unravel cardiac pathology and improve the detection and management of cardiac dysfunction in clinical practice.status: Published onlin

Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting : a 16S rRNA analysis

Abstract: In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches

Salivary microbiome of healthy women of reproductive age

ABSTRACT The human salivary microbial community plays a crucial role in local and systemic diseases. Biological and lifestyle factors such as menstrual cycle, oral hygiene, and smoking have been documented to impact this community. However, while hormonal contraceptives are the most prescribed drug in healthy women and intimate partners play key roles in microbial exchange between humans, their impact on the salivary microbiome of women of reproductive age have been understudied. Additionally, the role of other lifestyle factors such as diet, allergies, age, and stress on the saliva microbiome of the general population is not well understood. Here, we studied the salivary microbiome of 255 healthy women of reproductive age using self-sampling kits and 16S rRNA amplicon sequencing combined with questionnaires on lifestyle and host-related parameters. A preserved salivary bacterial community of 12 genera (Actinobacillus, Actinomyces, Alloprevotella, Campylobacter, Fusobacterium, Gemella, Granulicatella, Leptotrichia, Neisseria, Prevotella, Streptococcus, and Veillonella) was identified. Contrary to what we expected, the number of intimate partners or specific contraceptive use did not have a major impact on these bacterial communities. However, recent use of oral antibiotics was associated with a significant decrease in richness at genus level and increase in mean relative abundances of several taxa. Being stressed or nervous was associated with a significantly increased richness of the salivary microbiome at the level of amplicon sequencing variants . Nevertheless, these associations with host-related and lifestyle variables only appeared to be subtle, suggesting that the salivary microbiome is mainly driven by the buccal environment and health status of an individual. IMPORTANCE The salivary microbiome has been proven to play a crucial role in local and systemic diseases. Moreover, the effects of biological and lifestyle factors such as oral hygiene and smoking on this microbial community have already been explored. However, what was not yet well understood was the natural variation of the saliva microbiome in healthy women and how this is associated with specific use of hormonal contraception and with the number of different sexual partners with whom microbiome exchange is expected regularly. In this paper, we characterized the salivary microbiome of 255 healthy women of reproductive age using an in-depth questionnaire and self-sampling kits. Using the large metadata set, we were able to investigate the associations of several host-related and lifestyle variables with the salivary microbiome profiles. Our study shows a high preservation between individuals

Cotton and surgical face masks in community settings : bacterial contamination and face mask hygiene

During the current COVID-19 pandemic, the use of face masks has become increasingly recommended and even mandatory in community settings. To evaluate the risk of bacterial cross-contamination, this study analyzed the bacterial bioburden of disposable surgical masks and homemade cotton masks, and surveyed the habits and face mask preferences of the Flemish population. Using culture approaches and 16S rRNA gene amplicon sequencing, we analyzed the microbial community on surgical and/or cotton face masks of 13 healthy volunteers after 4 h of wearing. Cotton and surgical masks contained on average 1.46 × 105 CFU/mask and 1.32 × 104 CFU/mask, respectively. Bacillus, Staphylococcus, and Acinetobacter spp. were mostly cultured from the masks and 43% of these isolates were resistant to ampicillin or erythromycin. Microbial profiling demonstrated a consistent difference between mask types. Cotton masks mainly contained Roseomonas, Paracoccus, and Enhydrobacter taxa and surgical masks Streptococcus and Staphylococcus. After 4 h of mask wearing, the microbiome of the anterior nares and the cheek showed a trend toward an altered beta-diversity. According to dedicated questions in the large-scale Corona survey of the University of Antwerp with almost 25,000 participants, only 21% of responders reported to clean their cotton face mask daily. Laboratory results indicated that the best mask cleaning methods were boiling at 100°C, washing at 60°C with detergent or ironing with a steam iron. Taken together, this study suggests that a considerable number of bacteria, including pathobionts and antibiotic resistant bacteria, accumulate on surgical and even more on cotton face masks after use. Based on our results, face masks should be properly disposed of or sterilized after intensive use. Clear guidelines for the general population are crucial to reduce the bacteria-related biosafety risk of face masks, and measures such as physical distancing and increased ventilation should not be neglected when promoting face mask use

The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms

Summary: Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed Dolosigranulum pigrum as a species clearly associated with nasal health, although isolates obtained from healthy individuals are scarce. In this study, we explored the properties of this understudied lactic acid bacterium by integrating comparative genomics, habitat mining, cultivation, and functional characterization of interaction capacities. Mining 10.000 samples from the Earth Microbiome Project of 17 habitat types revealed that Dolosigranulum is mainly associated with the human nasal cavity. D. pigrum AMBR11 isolated from the nose of a healthy individual exerted antimicrobial activity against Staphylococcus aureus, decreased proinflammatory cytokine production in airway epithelial cells, and Galleria mellonella larvae mortality induced by this important nasal pathobiont. Furthermore, the strain protected the nasal barrier function in a mouse model using interleukin-4 as disruptive cytokine. Hence, D. pigrum AMBR11 is a mutualist with high potential as topical live biotherapeutic product