Equipping Saccharomyces cerevisiae with an Additional Redox Cofactor Allows F420-Dependent Bioconversions in Yeast

Industrial application of the natural deazaflavin cofactor F420 has high potential for the enzymatic synthesis of high value compounds. It can offer an additional range of chemistry to the use of well-explored redox cofactors such as FAD and their respective enzymes. Its limited access through organisms that are rather difficult to grow has urged research on the heterologous production of F420 using more industrially relevant microorganisms such as Escherichia coli. In this study, we demonstrate the possibility of producing this cofactor in a robust and widely used industrial organism, Saccharomyces cerevisiae, by the heterologous expression of the F420 pathway. Through careful selection of involved enzymes and some optimization, we achieved an F420 yield of ∼1.3 μmol/L, which is comparable to the yield of natural F420 producers. Furthermore, we showed the potential use of F420-producing S. cerevisiae for F420-dependent bioconversions by carrying out the whole-cell conversion of tetracycline. As the first demonstration of F420 synthesis and use for bioconversion in a eukaryotic organism, this study contributes to the development of versatile bioconversion platforms.

Individual or combinational use of phytase, protease, and xylanase for the impacts on total tract digestibility of corn, soybean meal, and distillers dried grains with soluble fed to pigs

OBJECTIVE

This study was to evaluate the effects of individual or combinational use of phytase, protease, and xylanase on total tract digestibility of corn, soybean meal, and distillers dried grains with soluble (DDGS) fed to pigs.

METHODS

Each experiment had four 4×4 Latin squares using 16 barrows. Each period had 5-d adaptation and 3-d collection. All experiments had: CON (no enzyme); Phy (CON+phytase); Xyl (CON+xylanase); Pro (CON+protease); Phy+Xyl; Phy+Pro, Xyl+Pro, Phy+Xyl+Pro. Each Latin square had 'CON, Phy, Xyl, and Phy+Xyl'; 'CON, Phy, Pro, and Phy+Pro'; 'CON, Pro, Xyl, and Xyl+Pro'; and 'Phy+Xyl, Phy+Pro, Xyl+Pro, Phy+Xyl+Pro'.

RESULTS

The digestible energy (DE), metabolizable energy (ME), and nitrogen retention (NR) of corn were not affected by enzymes but the apparent total tract digestibility (ATTD) of phosphorus (P) was improved (p<0.01) by Phy. The DE and ATTD dry matter (DM) in soybean meal were increased (p<0.05) by Phy+Pro and the ATTD P was improved (p<0.01) by Phy, Phy+Pro, and Phy+Xyl. The DE, ME, and ATTD DM in DDGS were improved (p<0.05) by Phy+Xyl and the ATTD P was improved (p<0.01) by Phy, Phy+Pro, and Phy+Xyl.

CONCLUSION

Phytase individually or in combination with xylanase and protease improved the Ca and P digestibility of corn, soybean meal, and DDGS, from the hydrolysis of phytic acid. The supplementation of protease was more effective when combined with phytase and xylanase in the soybean meal and DDGS possibly due to a higher protein content in these feedstuffs. Xylanase was more effective in DDGS diets due to the elevated levels of non-starch polysaccharides in these feedstuffs. However, when xylanase was combined with phytase, it demonstrated a higher efficacy improving the nutrient digestibility of pigs. Overall, combinational uses of feed enzymes can be more efficient for nutrient utilization in soybean meal and DDGS than single enzymes.

Simulated Design-Build-Test-Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Engineering

Combinatorial pathway optimization is an important tool in metabolic flux optimization. Simultaneous optimization of a large number of pathway genes often leads to combinatorial explosions. Strain optimization is therefore often performed using iterative design-build-test-learn (DBTL) cycles. The aim of these cycles is to develop a product strain iteratively, every time incorporating learning from the previous cycle. Machine learning methods provide a potentially powerful tool to learn from data and propose new designs for the next DBTL cycle. However, due to the lack of a framework for consistently testing the performance of machine learning methods over multiple DBTL cycles, evaluating the effectiveness of these methods remains a challenge. In this work, we propose a mechanistic kinetic model-based framework to test and optimize machine learning for iterative combinatorial pathway optimization. Using this framework, we show that gradient boosting and random forest models outperform the other tested methods in the low-data regime. We demonstrate that these methods are robust for training set biases and experimental noise. Finally, we introduce an algorithm for recommending new designs using machine learning model predictions. We show that when the number of strains to be built is limited, starting with a large initial DBTL cycle is favorable over building the same number of strains for every cycle.

Effects of ileocolonic delivered vitamin B2, B3 and C (ColoVit) or the Groningen anti-inflammatory diet on disease course and microbiome of patients with Crohn's disease (VITA-GrAID study): a protocol for a randomised and partially blinded trial

BACKGROUND

Diet plays a pivotal role in the onset and progression of Crohn's disease (CD). Nutritional interventions revealed effects on intestinal inflammation and gut microbial composition. However, data from well-designed and controlled dietary trials are lacking. Therefore, evidence-based dietary recommendations are still unavailable to patients and physicians. Here, we aim to investigate the effects of an evidence-based anti-inflammatory diet, and an ileocolonic-targeted capsule containing vitamin B₂, B₃ and C (ColoVit) on patients with CD and their healthy household members.

METHODS AND ANALYSIS

In this multicentre, randomised, placebo-controlled, partially blinded nutritional intervention trial, we aim to recruit 255 CD patients with Harvey-Bradshaw Index <8 and a faecal calprotectin (FCal) cut-off of ≥100 µg/g at baseline. Participants will be randomised into two experimental intervention groups and one placebo group. In the experimental groups, participants will either adhere to the Groningen anti-inflammatory diet (GrAID) or ingest an ileocolonic-delivered oral vitamin B₂/B₃/C capsule (ColoVit). The study consists of a 12-week controlled interventional phase, which proceeds to a 9-month observational follow-up phase in which patients allocated to the GrAID group will be requested to continue the intervention on their own accord. Household members of participating patients will be asked to participate in the trial as healthy subjects and are allocated to the same group as their peer. The primary study outcome for patients is the change in FCal level from baseline. The primary outcome for household members is the change in gut microbial composition, which is set as secondary outcome for patients.

ETHICS AND DISSEMINATION

The protocol has been approved by the Institutional Review Board of the Stichting Beoordeling Ethiek Biomedisch Onderzoek in Assen, the Netherlands. Written informed consent will be obtained from all participants. Results will be disseminated through peer-reviewed journals and conference presentations.

TRIAL REGISTRATION NUMBER

NCT04913467.

Suitability and safety of L-5-methyltetrahydrofolate as a folate source in infant formula: A randomized-controlled trial

L-5-methyltetrahydrofolate is the predominant folate form in human milk but is currently not approved as a folate source for infant and follow-on formula. We aimed to assess the suitability of L-5-methyltetrahydrofolate as a folate source for infants. Growth and tolerance in healthy term infants fed formulae containing equimolar doses of L-5-methyltetrahydrofolate (10.4 μg/ 100 ml, n = 120, intervention group) or folic acid (10.0 μg/ 100 ml, n = 120, control group) was assessed in a randomized, double-blind, parallel, controlled trial. A reference group of breastfed infants was followed. Both formulae were well accepted without differences in tolerance or occurrence of adverse events. The most common adverse events were common cold, poor weight gain or growth, rash, eczema, or dry skin and respiratory tract infection. Weight gain (the primary outcome) was equivalent in the two groups (95% CI -2.11; 1.68 g/d). In line with this, there was only a small difference in absolute body weight adjusted for birth weight and sex at visit 4 (95% CI -235; 135 g). Equivalence was also shown for gain in head circumference but not for recumbent length gain and increase in calorie intake. Given the nature of the test, this does not indicate an actual difference, and adjusted means at visit 4 were not significantly different for any of these parameters. Infants receiving formula containing L-5-methyltetrahydrofolate had lower mean plasma levels of unmetabolized folic acid (intervention: 0.73 nmol/L, control: 1.15 nmol/L, p<0.0001) and higher levels of red cell folate (intervention: 907.0 ±192.8 nmol/L, control: 839.4 ±142.4 nmol/L, p = 0.0095). We conclude that L-5-methyltetrahydrofolate is suitable for use in infant and follow-on formula, and there are no indications of untoward effects.

Trial registration: This trial was registered at ClinicalTrials.gov (NCT02437721).

Hidden Hunger: Solutions for America's Aging Populations

The global population, including the United States, is experiencing a demographic shift with the proportion of older adults (aged ≥ 65 years) growing faster than any other age group. This demographic group is at higher risk for developing nutrition-related chronic conditions such as heart disease and diabetes as well as infections such as influenza and pneumonia. As a result, an emphasis on nutrition is instrumental for disease risk reduction. Unfortunately, inadequate nutrient status or deficiency, often termed hidden hunger, disproportionately affects older adults because of systematic healthcare, environmental, and biological challenges. This report summarizes the unique nutrition challenges facing the aging population and identifies strategies, interventions, and policies to address hidden hunger among the older adults, discussed at the scientific symposium "Hidden Hunger: Solutions for America's Aging Population", on March 23, 2018.

Potential of a gypsum-free composting process of wheat straw for mushroom production

Wheat straw based composting generates a selective substrate for mushroom production. The first phase of this process requires 5 days, and a reduction in time is wished. Here, we aim at understanding the effect of gypsum on the duration of the first phase and the mechanism behind it. Hereto, the regular process with gypsum addition and the same process without gypsum were studied during a 5-day period. The compost quality was evaluated based on compost lignin composition analysed by py-GC/MS and its degradability by a commercial (hemi-)cellulolytic enzyme cocktail. The composting phase lead to the decrease of the pyrolysis products 4-vinylphenol and 4-vinylguaiacol that can be associated with p-coumarates and ferulates linking xylan and lignin. In the regular compost, the enzymatic conversion reached 32 and 39% for cellulose, and 23 and 32% for xylan after 3 and 5 days, respectively. In absence of gypsum similar values were reached after 2 and 4 days, respectively. Thus, our data show that in absence of gypsum the desired compost quality was reached 20% earlier compared to the control process.