Publications

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer
2020
International Journal of Systematic and Evolutionary Microbiology

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus , which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term ‘lactobacilli’ will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Applications of plant-based fermented foods and their microbes

S. Wuyts, W. Van Beeck, C. Allonsius, M. van den Broek and S. Lebeer
2020
Current Opinion in Biotechnology

Plant-based fermentations and their microbes provide an underexplored source for novel biotechnological applications. Recent data highlight that a diverse array of lactic acid bacteria (LAB) frequently dominate these plant fermentations. Because of the long history of safe LAB use in fermented foods, we argue here that various novel probiotic, symbiotic and a range of other industrial applications can be produced based on new insights in the functional and genetic potential of these LAB.

Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities

Charlotte De Rudder, Marta Calatayud Arroyo, Sarah Lebeer, Tom Van de Wiele
2020
Sphere

Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity, and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis

Ilke De Boeck, Stijn Wittouck, Katleen Martens, Jos Claes, Mark Jorissen, Brecht Steelant, Marianne F. L. van den Broek, Sven F. Seys, Peter W. Hellings, Olivier M. Vanderveken, Sarah Lebeer
2019
mSphere

It is generally believed that the microbiome plays a role in chronic rhinosinusitis (CRS), though its exact contribution to disease development and severity remains unclear. In this study, samples were collected from different human body sites from the upper respiratory tract of CRS patients, when these patients underwent sinus surgery. The microbial community was collected from these samples and identified via molecular sequencing. The bacterial profiles that we obtained were then compared with the profiles that we earlier collected from healthy individuals (see earlier publication in Frontiers in microbiology). In addition, we also collected several data of our patients, such as disease parameters, patient characteristics (e.g., age and sex) and some markers in the blood.

Our data indicate that the microbiome in the different upper respiratory tract (URT) locations in CRS patients is very similar to each other, with the microbiome in the nose being most similar to the sinus microbiome. We could find some bacterial species that were more associated with CRS patients and are thus potentially associated with the disease, such as Corynebacterium tuberculostearicum, Haemophilus influenzae/H. aegyptius, and Staphylococcus bacteria. On the other hand, some bacteria, such as the lactic acid bacteria Dolosigranulum pigrum, might have a protective effect as they were more associated with our healthy controls.

Impact of spray-drying on the pili of Lactobacillus rhamnosus GG

Kiekens S, Vandenheuvel D, Broeckx G, Claes I, Allonsius C, De Boeck I, Thys S, Timmermans JP, Kiekens F, Lebeer S.
2019
Microbial Biotechnology

The preservation of the viability of microorganisms in probiotic formulations is the most important parameter ensuring the adequate concentration of live microorganisms at the time of administration. The formulation and processing techniques used to produce these probiotic formulations can influence the preservation of the microbial viability. However, it is also required that the bacteria maintain their key probiotic capacities during these processes. In this study, we investigated the impact of spray-drying on the model probiotic strain Lactobacillus rhamnosus GG by looking at its adherence capacity to human intestinal epithelial cells. We found that spray-drying did significantly affect the adherence capacity of L. rhamnosus GG. Microscopy confirmed that the pili, key surface factors for adherence, were lost during the spray-drying process. These data thus highlight that both the functionality and viability of probiotics should be assessed during the spray-drying process and subsequent storage.