FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes.

Dietary fibers impact gut colonic health, through the production of short-chain fatty acids. A low-fiber diet has been linked to lower bacterial diversity, obesity, type 2 diabetes, and promotion of mucosal pathogens. Glycoside hydrolases (GHs) are important enzymes involved in the bacterial catabolism of fiber into short-chain fatty acids. However, the GH involved in glycan breakdown (adhesion, hydrolysis, and fermentation) are organized in polysaccharide utilization loci (PUL) with complex modularity. Our goal was to explore how the capacity of strains, from the Bacteroidetes phylum, to grow on fiber could be predicted from their genome sequences. We designed an in silico pipeline called FiberGrowth and independently validated it for seven different fibers, on 28 genomes from Bacteroidetes-type strains. To do so, we compared the existing GH annotation tools and built PUL models by using published growth and gene expression data. FiberGrowth's prediction performance in terms of true positive rate (TPR) and false positive rate (FPR) strongly depended on available data and fiber: arabinoxylan (TPR: 0.89 and FPR: 0), inulin (0.95 and 0.33), heparin (0.8 and 0.22) laminarin (0.38 and 0.17), levan (0.3 and 0.06), mucus (0.13 and 0.38), and starch (0.73 and 0.41). Being able to better predict fiber breakdown by bacterial strains would help to understand their impact on human nutrition and health. Assuming further gene expression experiment along with discoveries on structural analysis, we hope computational tools like FiberGrowth will help researchers prioritize and design in vitro experiments.

Dip-coating of suspensions.

Withdrawing a plate from a suspension leads to the entrainment of a coating layer of fluid and particles on the solid surface. In this article, we study the Landau-Levich problem in the case of a suspension of non-Brownian particles at moderate volume fraction 10% < φ < 41%. We observe different regimes depending on the withdrawal velocity U, the volume fraction of the suspension φ, and the diameter of the particles 2a. Our results exhibit three coating regimes. (i) At small enough capillary number Ca, no particles are entrained, and only a liquid film coats the plate. (ii) At large capillary number, we observe that the thickness of the entrained film of suspension is captured by the Landau-Levich law using the effective viscosity of the suspension η(φ). (iii) At intermediate capillary numbers, the situation becomes more complicated with a heterogeneous coating on the substrate. We rationalize our experimental findings by providing the domain of existence of these three regimes as a function of the fluid and particles properties.