Biology subjects

Pless, L.

Publications and source records attributed to Pless, L..

3 recordsLinked to original sources

bioRxiv2024

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on -MOS and {beta}-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their hitherto poorly characterized gut microbiomes. Our multi-omic analysis revealed that the investigated MDFs (two -mannans and an acetylated {beta}-galactoglucomannan), at a dose of 0.2%, had negligible effects on both host gene expression, and gut microbiome structure and function under studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of {beta}-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of {beta}-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline novel and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon. IMPORTANCEThis study focuses on the potential of MDFs to improve aquaculture production. Despite preliminary 16S rRNA amplicon data suggested that populations in the salmon gut microbiome could utilize structurally complex mannans, our findings indicates that endogenous microbes could not metabolize it, nor the host responds to its dietary inclusion, at least not under the trial conditions investigated in this study. We highlight that high-resolution and host-specific microbiome characterization can greatly improve trial design and selection of candidate MDFs for future nutritional interventions. Understanding the intricate interplay between host and its gut microbiome is paramount in studies seeking to leverage endogenous microbial communities to benefit the host. While each new condition, whether it is a disease onset or a nutritional stressor, has the potential to profoundly reshape the microbial diversity, composition and outputs, the functional microbiome information gained under healthy conditions represent a pivotal step towards designing more effective trials involving microbiome-reprogramming feed additives. Overall, we envisage that these results will lead to improved focus on coupling fundamental microbiome characterization to the design of next-generation feeds for salmon aquaculture.

microbiology↗

bioRxiv2024

Food Fermentation in Space Is Possible, Distinctive, and Beneficial

Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here we investigate whether food fermentation in space is possible, and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days, and compared it with two earthbound controls. Using a specially-built environmental sensing box, we gathered metadata for temperature, relative humidity, pressure, and radiation. We analyzed the three misos with shotgun metagenomics to investigate the microbial communities composition and safety; whole genome sequencing to investigate the mutation rate of Aspergillus oryzae; untargeted metabolomics to quantify aromatic compounds, amino acids and organic acids; colorimetry to quantify color; and sensory analysis to describe the misos flavours and quantify liking and sensory difference. Across these datasets, we found that overall, the space miso is recognizable as a miso, suggesting fermentation in space is possible. We also found certain differences in the space miso: specifically the presence of Bacillus velezensis, a higher mutation rate of A. oryzae, higher attributions of roasted and nutty flavours, and the most different sensory impression. Taken together, these observations suggest unique features of the space environment--what we might call space terroir--which could be harnessed to create more flavorful, nourishing foods for long-term space missions and to address fundamental questions about the biology of novel environments. Significance StatementOur study presents, to our knowledge, the first time a food product has been fermented in space. We demonstrate that fermentation in space is possible with safe and successful results, a proof of concept that offers fermentation as a new tool for space research and future long-term space exploration missions. We also document how the space environment shapes the fermentation process in unique ways, suggesting a space terroir. These findings on the feasibility and novelty of fermentation in space open up directions for further multidisciplinary research across science, health, systems design, and society and culture.

microbiology↗

bioRxiv2023

The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping

The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detected in vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated by in vitro cultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.

microbiology↗