7th joint conference "Joint Microbiology & Infection Conference 2024" of the DGHM and VAAM

Univ.-Prof. Dr.

Chair

Prof.

Host-associated microbiomes and microbe-host interactions 3

Swimming in the host: pathogens and commensals navigating complex environments

RWTH Aachen

Prof

Invited Speaker

Invited Talk

Professor

The octocoral microbiome: from community structure and function to novel chitinases for the circular blue bioeconomy

Host-associated microbiomes and microbe-host interactions

Octocorals are an integral part of benthic marine ecosystems, increasing habitat complexity and biodiversity. They associate with diverse microorganisms, including micro-eukaryotes, prokaryotes, and viruses. Our previous research on temperate octocorals showed that their microbiome is distinct from the environmental surroundings, host genus-specific, and undergoes complex structural changes under dysbiosis [1]. However, the role of microbial symbionts that populate octocorals is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs), spanning 30 prokaryotic species, retrieved from microbial metagenomes of three temperate octocoral species and seawater [2]. Symbionts affiliated with Endozoicomonadaceae, Candidatus Thioglobaceae, and Metamycoplasmataceae, among others. Phylogenomics showed that the Endozoicomonadaceae MAGs represent a novel genus unique to temperate octocorals, denoted Candidatus Gorgonimonas. These symbionts harboured chitinase and chitin-binging protein-encoding genes, indicating that they hydrolyse the most abundant polysaccharide in the ocean. Subsequent examination of &gt;40 genomes of cultured and uncultured Endozoicomonadaceae strains demonstrated that chitinases and other genes involved in chitin degradation are widespread in the Endozoicomonadaceae family, suggesting that these symbionts play important roles in chitin turnover in marine invertebrates and benthic ecosystems [3]. Since Candidatus Gorgonimonas bacteria remain unculturable, we employed synthetic biology and heterologous expression to harness their enzymes. Two novel, active and mesophilic chitinases from octocoral symbionts were successfully produced, holding promise for upcycling of seafood waste as chitin(ase)-derived products find applications in multiple sectors, from biomedicine over the food industry to agriculture. [1] Keller-Costa et al., 2021, Microbiome, 9 https://doi.org/10.1186/s40168-021-01031-y[2] Keller-Costa et al., 2022, Microbiome, 10 https://doi.org/10.1186/s40168-022-01343-7[3] da Silva,….,&amp; Keller-Costa 2023 ISME COMMUN, 3 https://doi.org/10.1038/s43705-023-00316-7

Oral Presentation

Prof. Dr.

The ability of Staphylococcus aureus to proliferate within nasal communities is strain-specific and dependent on resource availability

IntroductionThe asymptomatic nasal colonization of Staphylococcus aureus increases the risk of infection and concerns approximatively 30% of the population. The underlying molecular principles and especially the role of the endogenous microbiota in this carriage pattern are poorly understood. We hypothesize that, depending on their composition and origin, nasal bacterial communities can promote or inhibit the proliferation of S. aureus within nares.GoalsCharacterize how S. aureus interacts with nasal commensals and communities from different volunteers.MethodsThree nasal communities of different composition and S. aureus carriage level were reconstituted by isolating the nasal bacterial species of healthy volunteers. Using these communities and the corresponding resident strains of S. aureus, in addition to a reference S. aureus strain, we performed (i) pairwise interactions experiments between individual strains, (ii) in vitro co-cultivations between S. aureus and synthetic communities and (iii) in vivo nasal co-colonization assays in gnotobiotic mice. Bacterial proliferation, community structure and metabolomics profiles were monitored.ResultsTwo of the tested communities showed predominantly negative pairwise interactions in vitro and inhibited all S. aureus strains regardless of their origin. Instead, the last community was dominated by cooperative interactions, and the corresponding synthetic consortia promoted the survival of S. aureus. This effect appeared to be specific to the S. aureus nasal strain that was co-isolated with the community and promoted in poor medium, suggesting the existence of co-adaptation mechanisms for resource acquisition. First in vivo experiments indicate that, as observed in vitro, this cooperative community does not interfere with nasal colonization of the reference S. aureus strain.ConclusionsNasal communities display different interaction patterns that can either support or hinder S. aureus proliferation. The strain-specific nature of these interactions could explain why certain communities are invaded by this pathogen, and could inform strategies for preventing nasal colonization by S. aureus.

Promoting gut decolonization of multi-drug resistant bacteria via the microbiome

The fight against multi-drug resistant Enterobacteriaceae (MDR-E) has been declared as a high priority by the WHO. Colonization of the human gut with MDR-E, including MDR E. coli, is associated with an increased risk of infection and dissemination within the community. Probiotics developed to selectively decolonize the microbiota of carriers from MDR strains are a promising treatment alternative. We hypothesize that the human gut is a great resource for probiotics, which show the potential to selectively decolonize MDR-E. As a novel resource for the identification of potentially probiotic bacteria, a strain collection of Enterobacteriaceae was generated from 630 donors from four cohorts. As it is of great interest to screen as many strains as possible due to the high genetic diversity of bacterial isolates, we established an ex vivo assay to identify strains with protective properties. Specifically, candidate probiotics and a MDR E. coli strain were spiked into cecum content of mice representing the nutritional environment in vivo. Furthermore, we developed in vivo models for gut (de)colonization of MDR-E and characterized the decolonization properties of specific probiotic candidates. For this approach we selected a panel of commensal isolates which displayed different competitive abilities in the ex vivo assay and observed decolonization of MDR E. coli after precolonization with competitive isolates. To gain mechanistic insights into the competition between protective isolates and the MDR E. coli strain, we conducted growth curves and competition assays in minimal media supplemented with a single carbon source. We observed a general fitness advantage of the protective strain and reduced CFUs of the MDR E. coli strain after co-cultivation in minimal media with specific carbon sources. We could further demonstrate the competition for carbon sources in vivo. For promising candidates we intend to use loss-of-function genetic screens for genes, which may be crucial for the protective effect. We also want to identify potential cooperation partners and microbiome signatures, which are relevant for the protective effect.

Exploring the Genus Peltigera: A Metagenomic Perspective on Lichen Biology

Many fungi engage in symbiotic relationships that span from pathogenic and commensalistic to mutualistic interactions. Lichens are one of the most successful examples of complex mutualistic symbiotic systems, comprising an association predominantly between fungal (mycobiont) and one or more photosynthetic organism(s) (photobiont), including green algae and/or cyanobacteria. Additionally, diverse fungal and bacterial communities occur in the lichen association. Lichens can serve as long term air pollution indicators and 50% of lichen species exhibit antibiotic properties, with many metabolites holding promise as potential antibiotic agent.The genus Peltigera is widespread across several continents and serves as a representative of cyanolichens, through its symbiotic association with a cyanobacterial photobiont of the genus Nostoc. Although lichens have been studied for at least 200 years, they remain poorly understood, despite the increasing interest in their properties. This is largely reflected in the absence in reliable genomic reference data until recently, as lichen genomic characterization is taking off.To address this issue, here we present several metagenome assemblies of the lichen genus Peltigera found in North-Rhine Westphalia, Germany. These genomic assemblies of both photo- and mycobiont were derived using advanced long-read sequencing methodologies. Our analysis shows that the mycobiont genomes are near complete in terms of gene content as measured by BUSCO analysis. Moreover, our metagenomic analyses uncovered additional organisms associated within the lichen community, which will be reported.Our study offers the possibility to gain new insights into the intricate genomic characteristics of lichens, advancing our understanding of these remarkable organisms and make a significant contribution to the upcoming golden age of lichen research.Keywords: Lichen, Metagenome, Symbiosis, Oxford Nanopore Sequencing

Symposium
Microbiomes: From Sequence-Based Analyses to Active Strains and Molecules (Part II)

Appointment

Chair

Topic

Description

Programme

SymposiumMicrobiomes: From Sequence-Based Analyses to Active Strains and Molecules (Part II)

Appointment

Chair

Topic

Description

Programme

Symposium
Microbiomes: From Sequence-Based Analyses to Active Strains and Molecules (Part II)