From Compartmentalization of Bacteria within Inorganic Macrocellular Beads to the Assembly of Microbial Consortia

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

Design of Binary Nb2O5-SiO2 Self-Standing Monoliths Bearing Hierarchical Porosity and Their Efficient Friedel-Crafts Alkylation/Acylation Catalytic Properties

Alkylation of aromatic hydrocarbons is among the most industrially important reactions, employing acid catalysts such as AlCl₃, H₂SO₄, HF, or H₃PO₄. However, these catalysts present severe drawbacks, such as low selectivity and high corrosiveness. Taking advantage of the intrinsic high acid strength and Lewis and Brønsted acidity of niobium oxide, we have designed the first series of Nb₂O₅-SiO₂(HIPE) monolithic catalysts bearing multiscale porosity through the integration of a sol-gel process and the physical chemistry of complex fluids. The MUB-105 series offers efficient solvent-free heterogeneous catalysis toward Friedel-Crafts monoalkylation and -acylation reactions, where 100% conversion has been reached at 140 °C while cycling. Alkylation reactions employing the MUB-105(1) catalyst have a maximum turnover number (TON) of 104 and a turnover frequency (TOF) of 9 h^-1, whereas for acylation, MUB-105(1) and MUB-105(2) yield maximum TON and TOF values of 107 and 11 h^-1, respectively. Moreover, the catalysts are selective, producing equal amounts of ortho- and para-substituted alkylated products and greater than 90% of the para-substituted acylated product. The highest catalytic efficiencies are obtained for the MUB-105(1) catalyst, bearing the smallest Nb₂O₅ particle sizes, lowest Nb₂O₅ content, and the highest amorphous character. The catalysts presented here are in a monolithic self-standing state, offering easy handling, reusability, and separation from the final products.

Bacterial Expression Systems for Enzymatic Activity in Droplet-Based Microfluidics

Functional screenings in droplet-based microfluidics require the analysis of various types of activities of individual cells. When screening for enzymatic activities, the link between the enzyme of interest and the information-baring molecule, the DNA, must be maintained to relate phenotypes to genotypes. This linkage is crucial in directed evolution experiments or for the screening of natural diversity. Micro-organisms are classically used to express enzymes from nucleic acid sequences. However, little information is available regarding the most suitable expression system for the sensitive detection of enzymatic activity at the single-cell level in droplet-based microfluidics. Here, we compare three different expression systems for l-asparaginase (l-asparagine amidohydrolase, EC 3.5.1.1), an enzyme of therapeutic interest that catalyzes the conversion of l-asparagine to l-aspartic acid and ammonia. We developed three expression vectors to produce and localize l-asparaginase (l-ASNase) in E. coli either in the cytoplasm, on the surface of the inner membrane (display), or in the periplasm. We show that the periplasmic expression is the most optimal strategy combining both a good yield and a good accessibility for the substrate without the need for lysing the cells. We suggest that periplasmic expression may provide a very efficient platform for screening applications at the single-cell level in microfluidics.

Targeted Release of Probiotics from Enteric Microparticulated Formulations

The development of advanced probiotic delivery systems, which preserve bacteria from degradation of the gastrointestinal tract and achieve a targeted release mediated by pH-independent swelling, is of great interest to improve the efficient delivery of probiotic bacteria to the target tissue. Gram-positive and Gram-negative bacteria models (Lactobacillus acidophilus (Moro) Hansen and Mocquot (ATCC® 4356™) and Escherichia coli S17, respectively) have been successfully encapsulated for the first time in pH-independent microparticulate polymethacrylates (i.e., Eudraguard biotic) used for the targeted delivery of nutraceuticals to the colon. These bacteria have also been encapsulated within the mucoadhesive polymethacrylate Eudragit RS 100 widely used as targeted release formulation for active pharmaceutical ingredients. The enteric microparticles remained unaltered under simulated gastric conditions and released the contained viable microbial cargo under simulated intestinal conditions. Buoyancies of 90.2% and 57.3% for Eudragit and Eudraguard microparticles, respectively, and long-term stability (5 months) for the encapsulated microorganisms were found. Cytotoxicity of the microparticles formulated with both polymers was evaluated (0.5-20 mg/mL) on Caco-2 cells, showing high cytocompatibility. These results underline the suitability of the synthesized materials for the successful delivery of probiotic formulations to the target organ, highlighting for the first time the potential use of Eudraguard biotic as an effective enteric coating for the targeted delivery of probiotics.