Thursday, September 21st, 2023, at 11:00 am
Chairs: Lisa Budzinski & Christin Koch
Bacterial communities have a profound role in human health, environmental systems and industrial processes, which relies on their cellular function and properties – therefore this years’ microbiology session again explores cutting edge technologies in microbial single-cell analysis.
The genetic diversity of microbiomes has been assessed extensively by sequencing technologies, but to elucidate the function of bacterial cells it requires different technological approaches. Single-cell analysis tools enable the investigation of bacterial metabolism such as adaption processes and are essential to contextualize microbial communities in their hosts or environments. Shifting from bulk to single-cell information brings potential of targeted control of microbial processes and allows to understand taxonomic shifts in bacterial communities functionally.
This session will highlight innovative approaches and applications contributing to the understanding of microbiomes in regards to composition, function and management.
Probing microbiome function using single-cell chemical imaging
University of Southampton
Southampton, United Kingdom
Humans and other animals host diverse communities of microorganisms that play fundamental roles in their physiology and health. In order to understand how microorganisms interact with and shape the environments that they inhabit, analysing the phenotype of cells in their native habitat is essential. Stable isotope probing (SIP) is a key tool for this purpose, as it enables tracking of isotopically-labelled atoms into microbial biomarkers and/or cells of interest. We have developed and applied new SIP techniques that exploit non-destructive Raman microspectroscopy to enable the detection of stable isotopes in single cells of bacteria. These techniques can be coupled with methods to specifically identify the labelled bacteria, i.e., to link identity to function and activity. By combining heavy water as a general tracer for metabolic activity, Raman-activated cell sorting and mini-metagenomics we were able to identify a consortium of gut commensal microbes able to reduce pathogen colonization. More recently, we developed a novel high-throughput approach to combine stimulated-Raman scattering (SRS) with fluorescence in situ hybridization (FISH), which is 100-100 times faster than previous approaches, thereby enabling high-throughput single-cell SIP for the first time. We exploited SRS-FISH to identify individual responses of the human gut microbiome to nutrients and pharmaceutical drugs, as well as to detect drug bioaccumulation with unprecedented resolution. Overall, we show that single-cell Raman-SIP approaches are powerful for directly demonstrating microbial functions within complex communities.
Fatima C. Pereira is a Lecturer at the University of Southampton, United Kingdom. Her research combines single-cell activity methods, microspectroscopy, molecular biology and next-generation sequencing to investigate how diet and medication shape the function of the gut microbiome. Fatima obtained her PhD in Molecular Biology from the NOVA University of Lisbon in Portugal, where she investigated the molecular bases of pathogenesis of the gut pathogen Clostridioides difficile. This motivated her to better understand how resident microbes modulate resistance to infection, and she then moved to the University of Vienna, Austria, with a Marie-SkLodowska-Curie (MSCA) Postdoctoral Fellowship to investigate mechanisms of microbiota-mediated colonisation resistance. As a Senior Postdoctoral fellow, Fatima secured major funding from the Austrian Science Fund and the Portuguese Research Agency to investigate the mechanisms through which the microbiomes of mammals (human and mice) and other vertebrates (fish) modulate gut inflammation, nutrition and growth. In August 2022 she moved to the University Southampton, UK, where she established her research group.
Hunting systems for typical and atypical glycan processing in gut microbiomes, one cell at a time
Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
The community of microbes inhabiting the gastrointestinal tract includes a large variety of bacterial species that collectively influence numerous aspects of host health and nutrition. Firmicutes and Bacteroidetes phyla are typically dominant, with specific symbiotic members supplying an arsenal of carbohydrate-active enzymes for the depolymerization and fermentation of otherwise indigestible complex carbohydrates to short-chain fatty acids. This talk will present some of our recent research, which utilizes methodological toolsets that combine traditional culturing, meta-omics (including next-generation sequencing and functional multi-omics), biochemistry and enzymology, to fully elucidate enzymatic pathways that microbes employ for the utilization of nutrients consumed by the host. This includes typical plant-derived polysaccharides, such as β-mannans, and atypical glycans such as the food additive xanthan gum. In particular, coupling of detailed knowledge of microbial saccharolytic mechanisms to unique structural features of β-mannans has allowed us to design intervention strategies to selectively engage beneficial microbes at species level. Additional application of multi-omics has enabled visualization of the impact of β-mannans on the gut microbiota composition and functions, unveiling interactions between key players in degradation of this fiber directly in complex endogenous animal microbiomes and elucidating mechanisms by which these microorganisms affect host biology. We demonstrate that a multi-faceted approach is needed for deciphering and implementing efforts to enhance host health and minimize disease by manipulating gut microbial composition and metabolism.
Sabina Leanti La Rosa received her PhD in Molecular Microbiology from the Norwegian University of Life Sciences in 2014. She then trained with Dr Barbara E. Murray at the University of Texas Health Science Center in Houston (USA), investigating the genetic basis of pathogenicity of clinically relevant gram-positive pathogens. After that, she moved back to Norway to begin work on gut microbiome research, focusing on the enzymatic mechanisms through which gram-positive gut commensals degrade food and feed components. Since 2022, she is an Associate Professor in Microbiology at the Norwegian University of Life Sciences. Sabina’s current research applies multi-omics approaches and enzymology to investigate mechanisms by which gut commensals utilize complex glycans, including hemicellulosic substrates and food additives, with diverse interests on CAZymes discovery, biotechnology applications and prebiotic-based modulation of human and animal gut microbiomes.