Session: Parallel session 6 - Proteogenomics and metaproteomics
Combining proteogenomics & metaproteomics for in-depth characterisation of non-model species
Proteogenomics offers a comprehensive approach to characterising the proteome of non-model species of both scientific and environmental interest. Advances in next-generation sequencing, particularly RNA long-read sequencing, enable the construction of customized sequence databases tailored to the organisms under investigation, thereby improving protein identification.
In this study, we combined proteogenomics and metaproteomics to characterize the microbiome of the aquatic sentinel species Gammarus fossarum and assess its health status. To explore host-microbiota interactions, we examined the effects of various diets (alder leaf, carrot, spinach, and protein granules) over a 9-day period. We recorded extensive MS/MS datasets from total proteins extracted from pools of intestines collected from the millimetric animals, as well as from the diets themselves. Our results were interpreted using microbial annotated genomes and RNA-seq derived proteogenomic information from the host.
Functional analyses of host and microbial proteins revealed complementary metabolic activities, enabling the degradation of complex polysaccharides like cellulose and chitin, and high levels of signal transduction. Diet was found to shape microbial community structure, with foodborne microorganisms being the main factor of structural changes during short-term feeding in amphipods. These microorganisms remained viable post-ingestion and contributed to food digestion. Functional stability is maintained across different diets, although the protein-rich granules diet induced functional shifts in both the host and its microbiota, reflecting their adaptation to a novel nutrient source. Finally, we identified a core microbiota driving key gut functions, which was less affected by dietary variations. These findings are significant for forthcoming ecotoxicological and biomonitoring investigations, which could leverage the microbiomes of these sentinel animals as pivotal targets.
In this study, we combined proteogenomics and metaproteomics to characterize the microbiome of the aquatic sentinel species Gammarus fossarum and assess its health status. To explore host-microbiota interactions, we examined the effects of various diets (alder leaf, carrot, spinach, and protein granules) over a 9-day period. We recorded extensive MS/MS datasets from total proteins extracted from pools of intestines collected from the millimetric animals, as well as from the diets themselves. Our results were interpreted using microbial annotated genomes and RNA-seq derived proteogenomic information from the host.
Functional analyses of host and microbial proteins revealed complementary metabolic activities, enabling the degradation of complex polysaccharides like cellulose and chitin, and high levels of signal transduction. Diet was found to shape microbial community structure, with foodborne microorganisms being the main factor of structural changes during short-term feeding in amphipods. These microorganisms remained viable post-ingestion and contributed to food digestion. Functional stability is maintained across different diets, although the protein-rich granules diet induced functional shifts in both the host and its microbiota, reflecting their adaptation to a novel nutrient source. Finally, we identified a core microbiota driving key gut functions, which was less affected by dietary variations. These findings are significant for forthcoming ecotoxicological and biomonitoring investigations, which could leverage the microbiomes of these sentinel animals as pivotal targets.