Carbon dioxide valorization into resveratrol via lithoautotrophic fermentation using engineered Cupriavidus necator H16

BACKGROUND

Industrial biomanufacturing of value-added products using CO2 as a carbon source is considered more sustainable, cost-effective and resource-efficient than using common carbohydrate feedstocks. Cupriavidus necator H16 is a representative H2-oxidizing lithoautotrophic bacterium that can be utilized to valorize CO2 into valuable chemicals and has recently gained much attention as a promising platform host for versatile C1-based biomanufacturing. Since this microbial platform is genetically tractable and has a high-flux carbon storage pathway, it has been engineered to produce a variety of valuable compounds from renewable carbon sources. In this study, the bacterium was engineered to produce resveratrol autotrophically using an artificial phenylpropanoid pathway.

RESULTS

The heterologous genes involved in the resveratrol biosynthetic pathway-tyrosine ammonia lyase (TAL), 4-coumaroyl CoA ligase (4CL), and stilbene synthase (STS) -were implemented in C. necator H16. The overexpression of acetyl-CoA carboxylase (ACC), disruption of the PHB synthetic pathway, and an increase in the copy number of STS genes enhanced resveratrol production. In particular, the increased copies of VvSTS derived from Vitis vinifera resulted a 2-fold improvement in resveratrol synthesis from fructose. The final engineered CR-5 strain produced 1.9 mg/L of resveratrol from CO2 and tyrosine via lithoautotrophic fermentation.

CONCLUSIONS

To the best of our knowledge, this study is the first to describe the valorization of CO2 into polyphenolic compounds by engineering a phenylpropanoid pathway using the lithoautotrophic bacterium C. necator H16, demonstrating the potential of this strain a platform for sustainable chemical production.

Adaptive laboratory evolution and transcriptomics-guided engineering of Escherichia coli for increased isobutanol tolerance

As a renewable energy from biomass, isobutanol is considered as a promising alternative to fossil fuels. To biotechnologically produce isobutanol, strain development using industrial microbial hosts, such as Escherichia coli, has been conducted by introducing a heterologous isobutanol synthetic pathway. However, the toxicity of produced isobutanol inhibits cell growth, thereby restricting improvements in isobutanol titer, yield, and productivity. Therefore, the development of robust microbial strains tolerant to isobutanol is required. In this study, isobutanol-tolerant mutants were isolated from two E. coli parental strains, E. coli BL21(DE3) and MG1655(DE3), through adaptive laboratory evolution (ALE) under high isobutanol concentrations. Subsequently, 16 putative genes responsible for isobutanol tolerance were identified by transcriptomic analysis. When overexpressed in E. coli, four genes (fadB, dppC, acs, and csiD) conferred isobutanol tolerance. A fermentation study with a reverse engineered isobutanol-producing E. coli JK209 strain showed that fadB or dppC overexpression improved isobutanol titers by 1.5 times, compared to the control strain. Through coupling adaptive evolution with transcriptomic analysis, new genetic targets utilizable were identified as the basis for the development of an isobutanol-tolerant strain. Thus, these new findings will be helpful not only for a fundamental understanding of microbial isobutanol tolerance but also for facilitating industrially feasible isobutanol production.

De novo biosynthesis of 2'-fucosyllactose by bioengineered Corynebacterium glutamicum

2'-Fucosyllactose (2'-FL) which is well-known human milk oligosaccharide was biotechnologically synthesized using engineered Corynebacterium glutamicum, a GRAS microbial workhorse. By construction of the complete de novo pathway for GDP-L-fucose supply and heterologous expression of Escherichia coli lactose permease and Helicobacter pylori α-1,2-fucosyltransferase, bioengineered C. glutamicum BCGW_TL successfully biosynthesized 0.25 g L-1 2'-FL from glucose. The additional genetic perturbations including the expression of a putative 2'-FL exporter and disruption of the chromosomal pfkA gene allowed C. glutamicum BCGW_cTTLEΔP to produce 2.5 g L-1 2'-FL batchwise. Finally, optimized fed-batch cultivation of the BCGW_cTTLEΔP using glucose, fructose, and lactose resulted in 21.5 g L-1 2'-FL production with a productivity of 0.12 g L-1 •h, which were more than 3.3 times higher value relative to the batch culture of the BCGW_TL. Conclusively, it would be a groundwork to adopt C. glutamicum for biotechnological production of other food additives including human milk oligosaccharides.

Identification of the enantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of 3,6-anhydro-L-galactose

A novel metabolic pathway of 3,6-anhydro-L-galactose (L-AHG), the main sugar component in red macroalgae, was first discovered in the marine bacterium Vibrio sp. EJY3. L-AHG is converted to 2-keto-3-deoxy-galactonate (KDGal) in two metabolic steps. Here, we identified the enantiomeric nature of KDGal in the L-AHG catabolic pathway via stereospecific enzymatic reactions accompanying the biosynthesis of enantiopure L-KDGal and D-KDGal. Enantiopure L-KDGal and D-KDGal were synthesized by enzymatic reactions derived from the fungal galacturonate and bacterial oxidative galactose pathways, respectively. KDGal, which is involved in the L-AHG pathway, was also prepared. The results obtained from the reactions with an L-KDGal aldolase, specifically acting on L-KDGal, showed that KDGal in the L-AHG pathway exists in an L-enantiomeric form. Notably, we demonstrated the utilization of L-KDGal by Escherichia coli for the first time. E. coli cannot utilize L-KDGal as the sole carbon source. However, when a mixture of L-KDGal and D-galacturonate was used, E. coli utilized both. Our study suggests a stereoselective method to determine the absolute configuration of a compound. In addition, our results can be used to explore the novel L-KDGal catabolic pathway in E. coli and to construct an engineered microbial platform that assimilates L-AHG or L-KDGal as substrates. KEY POINTS: • Stereospecific enzyme reactions were used to identify enantiomeric nature of KDGal • KDGal in the L-AHG catabolic pathway exists in an L-enantiomeric form • E. coli can utilize L-KDGal as a carbon source when supplied with D-galacturonate.

Anti-Menopausal Effect of Soybean Germ Extract and Lactobacillus gasseri in the Ovariectomized Rat Model

Menopause is a significant phase in a woman's life. Menopausal symptoms can affect overall well-being and quality of life. Conventionally, hormone replacement therapy (HRT) is used to alleviate menopausal symptoms; however, depending on the conditions, HRT may lead to side effects, necessitating the exploration of alternative therapies with fewer side effects. In this study, we investigated the effects of a combination of soybean germ extract (S30) containing 30% (w/w) isoflavone and a probiotic, Lactobacillus gasseri (LGA1), on menopausal conditions in an ovariectomized (OVX) rat model. We evaluated the impact of S30+LGA on body weight, estrogen markers, uterine and bone health, vascular markers, and neurotransmitter levels. The results revealed that treatment with S30+LGA1 significantly improved body weight and uterine and bone health. Moreover, S30+LGA1 demonstrated promising effects on lipid profile, liver function, and vascular markers and positively impacted serotonin and norepinephrine levels, indicating potential mood-enhancing effects. In conclusion, S30+LGA1, possessing anti-menopausal effects in vitro and in vivo, can be recommended as a soy-based diet, which offers various health benefits, especially for menopausal women.

Characterization and structural analysis of the endo-1,4-β-xylanase GH11 from the hemicellulose-degrading Thermoanaerobacterium saccharolyticum useful for lignocellulose saccharification

Xylanases are important for the enzymatic breakdown of lignocellulose-based biomass to produce biofuels and other value-added products. We report functional and structural analyses of TsaGH11, an endo-1,4-β-xylanase from the hemicellulose-degrading bacterium, Thermoanaerobacterium saccharolyticum. TsaGH11 was shown to be a thermophilic enzyme that favors acidic conditions with maximum activity at pH 5.0 and 70 °C. It decomposes xylans from beechwood and oat spelts to xylose-containing oligosaccharides with specific activities of 5622.0 and 3959.3 U mg-1, respectively. The kinetic parameters, Km and kcat towards beechwood xylan, are 12.9 mg mL-1 and 34,015.3 s-1, respectively, resulting in kcat/Km value of 2658.7 mL mg-1 s-1, higher by 102-103 orders of magnitude compared to other reported GH11s investigated with the same substrate, demonstrating its superior catalytic performance. Crystal structures of TsaGH11 revealed a β-jelly roll fold, exhibiting open and close conformations of the substrate-binding site by distinct conformational flexibility to the thumb region of TsaGH11. In the room-temperature structure of TsaGH11 determined by serial synchrotron crystallography, the electron density map of the thumb domain of the TsaGH11 molecule, which does not affect crystal packing, is disordered, indicating that the thumb domain of TsaGH11 has high structural flexibility at room temperature, with the water molecules in the substrate-binding cleft being more disordered than those in the cryogenic structure. These results expand our knowledge of GH11 structural flexibility at room temperature and pave the way for its application in industrial biomass degradation.

The Feasibility of Fast, Four-Dimensional Computed Tomography-Based O-Ring Linac Plans for Stereotactic Body Radiotherapy in Patients with Poor Performance Status

PURPOSE/OBJECTIVE(S)

As patients with poor performance status cannot endure long treatment times, it can lead to unplanned and prolonged radiation treatment or discontinuation of treatment. Moreover, prolonged radiation treatment appears to negatively affect survival for patients. We aimed to verify the feasibility of fast 4DCT-based O-ring linear accelerator (LINAC) treatment in lung 4D stereotactic body radiotherapy (SBRT).

MATERIALS/METHODS

This study included data of 38 patients who received lung 4D-SBRT. Gating20-70% plans were based on 4DCT data obtained at phase values ranging from 20-70% using a C-arm LINAC. Non-GatingFB plans were retrospectively established based on 4DCT data obtained at phase values of 0-90% using an O-ring LINAC. The prescribed dose of 4,800 cGy was delivered to PTV in four fractions. The conformity index (CI), homogeneity index (HI), and gradient measurement (GM) of the PTV were analyzed to compare dosimetric data between Gating20-70% and Non-GatingFB plans. Organs at risks (OARs) were analyzed in accordance with the RTOG 0915 protocol. Treatment delivery time and total monitor units (MU) were analyzed to compare the efficiency of treatment delivery. Statistical comparisons were performed using the Wilcoxon signed-rank test (p<0.05).

RESULTS

For the PTV, there was no significant difference in the CI or HI between Gating20-70% and Non-GatingFB plans (CI: 1.337±0.137, 1.335±0.174, HI: 0.939±0.015, 0.939±0.016, all at p>0.05). However, there was a significant difference in GM between Gating20-70% and Non-GatingFB plan (1.528±0.206 cm, 1.381±0.222 cm, p<0.001). For OARs, all plans met the criteria for dose constraint. There was a significant difference between Gating20-70% and Non-GatingFB plans except in the spinal cord. In particular, D1000cc and D1500cc values for the ipsilateral lung for Gating20-70% plans were 31.6% and 59.9% lower than those for Non-GatingFB plans (D1000cc: 50.780±132.061 cGy, 34.755±102.480 cGy, p<0.001, D1500cc: 6.641±14.598 cGy, 2.666±7.926 cGy, p<0.001). Treatment delivery time was 92% longer for Gating20-70% plans than for Non-GatingFB plans (5.0±0.4 min, 9.6±3.3 min, p = 0.043). The total MU value for Gating20-70% plans was 9.6% higher than that for Non-GatingFB plans (3665.8±230.7, 4016±236.9, p = 0.039).

CONCLUSION

When compared to OARs both plans were acceptable per RTOG-0915 protocol, but significant differences were between Non-GatingFB and Gating20-70% plans. However, treatment delivery time of Non-GatingFB plans decreased by 47.9% than Gating20-70% plans. We verified the feasibility of fast 4DCT-based O-ring LINAC treatment for patients who cannot endure long treatment times due to poor performance status in lung 4D-SBRT. In further study, we will analyze dosimetric differences and treatment delivery efficiency considering tumor motion according to tumor location.

Mapping the Anatomical Distribution of MRI-Identified Locoregional Recurrence following Robotic-Assisted Laparoscopic Prostatectomy for Prostate Adenocarcinoma

PURPOSE/OBJECTIVE(S)

The pattern of locoregional recurrence specifically after robotic-assisted laparoscopic prostatectomy (RALP) for prostate adenocarcinoma is still unknown. In this study, we reviewed pelvic magnetic resonance images (MRI) after postoperative biochemical recurrence (BCR) and drew a map of locoregional recurrence to support evidence of determining the optimal target volume of salvage radiotherapy in a post-RALP BCR scenario.

MATERIALS/METHODS

We have retrospectively searched 7,583 prostate adenocarcinoma patients who have received RALP in our institution between January 2010 and December 2021, and found a pool of highly selected patients with gross tumor recurrence confirmed by post-BCR pelvic MRIs and did not have other histories of malignancy. BCR was defined as the serum PSA more or equal to 0.2 ng/mL, or three consecutive increases. Patients with serum PSA nadir more or equal to 0.2 ng/mL on the 90th postoperative day (POD 90) were excluded to guarantee successful tumor removal. We have reviewed serum PSA levels using R codes, MRI and pathological reports using Excel, and descriptive statistics using SPSS 25. The gross lesions were contoured on the correlating MRIs using MIM Maestro 7.1. The RT structure DICOM files were merged into a map using MATLAB 2022b. In addition, we have conducted Fisher exacted test, Mann-Whitney U test, and logistic regression to identify risk factors for regional recurrence.

RESULTS

A total of 173 patients were identified with locoregional recurrence from post-BCR pelvic MRIs, and 139 (80.3%) patients were in the high-risk group or very-high-risk group according to the NCCN guidelines: 57 (32.9%) patients with histological grade group 5, 50 (28.9%) patients with initial PSA over 20 ng/mL, 114 (65.9%) patients with extracapsular extension, 55 (31.8%) patients with seminal vesicle invasion, and 15 (9%) patients with pN1. The median follow-up was 4.7 (IQR 2.8-6.9) years for pelvic MRIs and 5.8 (IQR 4.0-8.6) years for serum PSA. The BCF survival was median of 10.7 (IQR 4.6-19.1) months, and the locoregional recurrence-free survival was median of 24.6 (IQR 9.7-49.4) months for this subgroup of patients. At first locoregional recurrence, 148 (85.5%) patients were local only, 20 (11.6%) patients were regional only, and 5 (2.9%) patients were both local and regional. Out of the 25 patients with regional recurrence, the incidence of gross tumor recurrence differed by nodal sites: 3 (12%) in perirectal space, 5 (20%) in internal iliac, 7 (28%) in obturator, 13 (52%) in external iliac, and 6 (24%) in common iliac lymph nodes.

CONCLUSION

We have found 173 patients and were able to map reliable gross tumor recurrence sites after RALP and confirmed by pelvic MRIs following BCR. The map supports evidence of using the existing consensus pelvic clinical target volume of salvage radiotherapy, in a post-RALP BCR scenario.

Prediction of Lymphopenia and Survival with Baseline Absolute Lymphocyte Count and Irradiated Dose to Immune Cells in Patients with Non-Small Cell Lung Cancer Treated with Concurrent Chemoradiotherapy

PURPOSE/OBJECTIVE(S)

This study aimed to investigate the effect of effective dose to immune cell (EDIC) combined with pre-radiotherapy (RT) absolute lymphocyte count (ALC) on treatment-related lymphopenia during RT and treatment outcome in patients with locally advanced non-small cell lung cancer (NSCLC). A subgroup analysis in patients who received consolidation immunotherapy was also conducted.

MATERIALS/METHODS

Between August 2008 and December 2021, 517 patients with locally advanced NSCLC treated with definitive concurrent chemoradiotherapy (CRT) were retrospectively analyzed. All patients had serial complete-blood-count tests at pre-, and during-CRT. Severe lymphopenia was defined as ALC < 0.5x109cells/L during RT. EDIC was calculated according to mean doses of the lung, heart and the total body. The patients were grouped according to high and low EDIC and pre-RT ALC and was assessed for its correlation with radiation induced lymphopenia and survival outcomes.

RESULTS

Of 517 eligible patients, most of the patients received weekly paclitaxel with carboplatin (90.3%) and 195 patients (37.7%) received consolidation immunotherapy following CRT. A median radiation dose of 63 Gy (IQR, 60-64.5) was delivered in 30 fractions. The optimal cutoff value of EDIC and pre-RT ALC for predicting severe lymphopenia were 2.89 Gy and 2.03x109cells/L, respectively. High risk group was defined as EDIC ≥ 2.89 Gy and pre-RT ALC < 2.03x109cells/L, low risk group as EDIC <2.89 Gy and pre-RT ALC ≥ 2.03x109cells/L, and intermediate group as EDIC ≥ 2.89 Gy and pre-RT ALC ≥ 2.03x109cells/L or EDIC < 2.89 Gy and pre-RT ALC < 2.03x109cells/L. The incidence of severe lymphopenia during RT in high, intermediate, and low risk group was 90.1%, 77.1%, and 52.3%, respectively (p<0.001). The risk groups were independent predictors for both progression-free survival (PFS) (p<0.001) and overall survival (OS) (p<0.001). The high-risk group had higher incidence of locoregional and distant recurrences (p<0.001). In the subset of patients who were treated with consolidation immunotherapy, the risk groups were predictive of severe lymphopenia (p = 0.001), PFS (p = 0.004), and OS (p = 0.012).

CONCLUSION

This study demonstrated that the combination of EDIC and pre-RT ALC is a predictor for severe lymphopenia during RT, recurrence, and survival in patients with locally advanced NSCLC who received CRT. Moreover, the combination of EDIC and pre-RT ALC may serve as a potential biomarker for the benefit of maintenance immunotherapy.

Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice

The probiotic yeast Saccharomyces boulardii has great potential for use as a chassis for microbiome engineering because of its high resistance to environmental stress, well-developed genetic tools, and the ability to secrete recombinant proteins in the intestine. As oral feeding of lysozyme has been reported to change the gut microbiome and fecal metabolites, we engineered S. boulardii to secrete human lysozyme, and investigated the changes in the microbiome and fecal metabolites in response to the administration of the engineered probiotic yeast into mice. Administration of S. boulardii changed the structure of the gut microbiome by promoting the growth of clostridia and increasing the diversity of strains. The human lysozyme secreted by S. boulardii in the intestine resulted in a unique gut microbiome structure through selective growth. In addition, the administration of probiotic yeast S. boulardii affected host energy metabolism and decreased blood urea and fructose levels, suggesting a mechanism of health benefits in mice. IMPORTANCE Our study identified changes in the microbiome by administering wild-type S. boulardii in mice to healthy mice based on long-read sequencing and demonstrated that a recombinant protein secreted by engineered S. boulardii in the intestine could change the microbiome. Our results provide valuable information for the development of therapeutics using engineered S. boulardii that changes the gut microbiome and host physiology.

Single-incision robotic colorectal surgery with the da Vinci SP® surgical system: initial results of 50 cases

PURPOSE

The da Vinci SP® (dVSP) surgical system (Intuitive Surgical, Sunnyvale, CA, USA), a robotic platform designed for single-incision surgery, overcame the need for multiple ports in traditional robotic surgery and issues including triangulation and retraction in single-incision laparoscopic surgery. However, previous studies only included case reports or series with small sample sizes. The aim of this study was to assess the safety and performance of the dVSP surgical system and its instruments and accessories for colorectal procedures.

METHODS

The medical records of patients who had surgery with the dVSP from March 2019 to September 2021 at Ewha Womans University Seoul Hospital were investigated. The pathologic and follow-up data of patients who had malignant tumors were analyzed separately to evaluate oncological safety.

RESULTS

Fifty patients (26 male and 24 female) with a median age of 59 years (interquartile range 52.5-63.0 years) were enrolled. The procedures included low anterior resection with total mesorectal excision (n = 16), sigmoid colectomy with complete mesocolic excision and central vessel ligation (CME + CVL) (n = 14), right colectomy with CME + CVL (n = 9), left colectomy with CME + CVL (n = 4), right colectomy (n = 6), and sigmoid colectomy (n = 1). Operative time significantly decreased after 25 cases (early phase vs. late phase; operative time 295.0 min vs. 250.0 min, p = 0.015; docking time 16.0 min vs. 12.0 min, p = 0.001; console time 212.0 min vs. 190.0 min, p = 0.019). Planned procedures were successfully completed in all patients. Postoperative outcomes were acceptable with only six cases of mild adverse events through a 3-month follow-up. No local recurrence and only one case of systemic recurrence occurred within 1 year postoperatively.

CONCLUSIONS

This study demonstrated the surgical and oncological safety and feasibility of dVSP, which may be a novel surgical platform for colorectal surgery.

Enhanced production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) with modulated 3-hydroxyvalerate fraction by overexpressing acetolactate synthase in Cupriavidus necator H16

The elastomeric properties of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a biodegradable copolymer, strongly depend on the molar composition of 3-hydroxyvalerate (3 HV). This paper reports an improved artificial pathway for enhancing the 3HV component during PHBV biosynthesis from a structurally unrelated carbon source by Cupriavidus necator H16. To increase the intracellular accumulation of propionyl-CoA, a key precursor of the 3HV monomer, we developed a recombinant strain by genetically manipulating the branched-chain amino acid (e.g., valine, isoleucine) pathways. Overexpression of the heterologous feedback-resistant acetolactate synthase (alsS), (R)-citramalate synthase (leuA), homologous 3-ketothiolase (bktB), and the deletion of 2-methylcitrate synthase (prpC) resulted in biosynthesis of 42.5 % (g PHBV/g dry cell weight) PHBV with 64.9 mol% 3 HV monomer from fructose as the sole carbon source. This recombinant strain also accumulated the highest PHBV content of 54.5 % dry cell weight (DCW) with 24 mol% 3HV monomer from CO₂ ever reported. The lithoautotrophic cell growth and PHBV production by the recombinant C. necator were promoted by oxygen stress. The thermal properties of PHBV showed a decreasing trend of the glass transition and melting temperatures with increasing 3 HV fraction. The average molecular weights of PHBV with modulated 3 HV fractions were between 20 and 26 × 10⁴ g/mol.

Production of Ethyl-agarobioside, a Novel Skin Moisturizer, by Mimicking the Alcoholysis from the Japanese Sake-Brewing Process

Agarobiose (AB; d-galactose-β-1,4-AHG), produced by one-step acid hydrolysis of agarose of red seaweed, is considered a promising cosmetic ingredient due to its skin-moisturizing activity. In this study, the use of AB as a cosmetic ingredient was found to be hampered due to its instability at high temperature and alkaline pH. Therefore, to increase the chemical stability of AB, we devised a novel process to synthesize ethyl-agarobioside (ethyl-AB) from the acid-catalyzed alcoholysis of agarose. This process mimics the generation of ethyl α-glucoside and glyceryl α-glucoside by alcoholysis in the presence of ethanol and glycerol during the traditional Japanese sake-brewing process. Ethyl-AB also showed in vitro skin-moisturizing activity similar to that of AB, but showed higher thermal and pH stability than AB. This is the first report of ethyl-AB, a novel compound produced from red seaweed, as a functional cosmetic ingredient with high chemical stability.

L-Fucose is involved in human-gut microbiome interactions

L-Fucose is one of the key metabolites in human-gut microbiome interactions. It is continuously synthesized by humans in the form of fucosylated glycans and fucosyl-oligosaccharides and delivered into the gut throughout their lifetime. Gut microorganisms metabolize L-fucose and produce short-chain fatty acids, which are absorbed by epithelial cells and used as energy sources or signaling molecules. Recent studies have revealed that the carbon flux in L-fucose metabolism by gut microorganisms is distinct from that in other sugar metabolisms because of cofactor imbalance and low efficiencies in energy synthesis of L-fucose metabolism. The large amounts of short-chain fatty acids produced during microbial L-fucose metabolism are used by epithelial cells to recover most of the energy used up during L-fucose synthesis. In this review, we present a detailed overview of microbial L-fucose metabolism and a potential solution for disease treatment and prevention using genetically engineered probiotics that modulate fucose metabolism. Our review contributes to the understanding of human-gut microbiome interactions through L-fucose metabolism. KEY POINTS: • Fucose-metabolizing microorganisms produce large amounts of short-chain fatty acids • Fucose metabolism differs from other sugar metabolisms by cofactor imbalance • Modulating fucose metabolism is the key to control host-gut microbiome interactions.

Elucidation of the fucose metabolism of probiotic Lactobacillus rhamnosus GG by metabolomic and flux balance analyses

Lactobacillus rhamnosus GG (LGG) is one of the most widely used probiotics because of its health benefits and safety. Fucose is among the most abundant hexoses in the human intestine, and LGG consumes fucose to produce energy or proliferate. However, no study has elucidated the metabolism by which LGG metabolizes fucose to produce energy, biomass, and extracellular metabolites. We used metabolomics and flux balance analysis to elucidate these mechanisms and highlight how they might affect the host. We found three different metabolic flux modes by which LGG anaerobically metabolizes fucose to produce energy and biomass. These metabolic flux modes differ from homolactic or heterolactic fermentation and account for the production of lactic acid, 1,2-propanediol, acetic acid, formic acid, and carbon dioxide as a result of fucose metabolism in LGG. We also used gas chromatography/time-of-flight mass spectrometry to identify a variety of short-chain fatty acids and organic acids secreted during fucose metabolism by LGG. Our study is the first to elucidate the unique fucose metabolism of LGG in anaerobic condition.

Optimal β-galactosidases for producing high-titer 3,6-anhydro-L-galactose from red-algal agarobiose

3,6-Anhydro-L-galactose (L-AHG) is a monomeric sugar in agarose derived from red macroalgae. Owing to its various physiological activities such as anti-inflammation, moisturizing, skin whitening, anti-colon cancer, and anti-cariogenicity, L-AHG is a potential functional ingredient. In our previous study, a simple and efficient two-step L-AHG production process was designed for high-titer L-AHG production, where a single enzyme was used after the liquefaction of agarose by acid prehydrolysis. However, the enzyme used did not completely hydrolyze agarobiose (AB). Therefore, in this study, for the efficient hydrolysis of AB and the high-titer production of L-AHG, various β-galactosidases belonging to glycoside hydrolase families 1, 2, 35, and 42 were compared by testing their substrate specificities and kinetic parameters. Among the five β-galactosidases, Bga42A, originating from Bifidobacterium longum ssp. infantis ATCC 15,697, showed the highest substrate specificity. Consequently, the two-step process utilizing Bga42A as a single enzyme resulted in a high-titer production of L-AHG at 85.9 g/L, demonstrating the feasibility of producing L-AHG from agarose. KEY POINTS: • L-AHG derived from red macroalgae has various physiological activities. • Various β-galactosidases were evaluated to efficiently hydrolyze agarobiose. • Bga42A showed the highest substrate specificity against agarobiose. • The highest amount of L-AHG with 85.9 g/L was simply produced.

Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO2

Background

A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO₂) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO₂ is still too low for commercialization.

Results

Here, we engineer the carbon fixation metabolism to improve CO₂ utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO₂—fixing metabolism and PHB production were investigated.

Conclusions

The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01962-7.

SGO and the elephant that is still in the room: Wellness, burnout and gynecologic oncology

OBJECTIVE

To measure wellness and burnout among gynecologic oncology clinicians and identify trends and at-risk populations to inform future interventions.

METHODS

Gynecologic oncologist (GO) and advanced practice provider (APP) responses to the 2020 Society of Gynecologic Oncology State of the Society survey were analyzed. The Maslach Burnout Inventory criteria for burnout was used. Work-life balance was scored on a 5-point Likert scale. Chi-square tests were used to compare mental health factors and the prevalence of burnout. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for associations between burnout and gender.

RESULTS

543 survey responses were included for analysis. Most GO (54%) and all APP respondents were female. Female GOs were disproportionately affected by burnout particularly in the Northeast (female(F): 40.9% vs male(M): 19.1%, p = 0.007) and South (F: 42.5% vs M:22.9%, p = 0.01). Burnout in female GOs over 40 was 1.79 (CI: 1.13-2.83; p-value 0.01) times higher than similarly aged males. Females in non-private practice experienced burnout 1.66 times that of males in similar positions (CI: 1.18-2.94; p < 0.0001). Female GOs reported the worst work-life balance across all 5 domains. APPs and female GOs experienced more stress and feeling overwhelmed compared to men. GOs were more reluctant to see a mental health professional (p = 0.0003) or take medication (p = 0.009) than APPs.

CONCLUSIONS

Burnout in gynecologic oncology persists in both genders and is felt most acutely by female GOs. APPs are not immune and would benefit from inclusion in future research to mitigate burnout in healthcare clinicians.

Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing L-fucose, a mammalian mucin component

Background

Saccharomyces boulardii is a probiotic yeast that exhibits antimicrobial and anti-toxin activities. Although S. boulardii has been clinically used for decades to treat gastrointestinal disorders, several studies have reported weak or no beneficial effects of S. boulardii administration in some cases. These conflicting results of S. boulardii efficacity may be due to nutrient deficiencies in the intestine that make it difficult for S. boulardii to maintain its metabolic activity.

Results

To enable S. boulardii to overcome any nutritional deficiencies in the intestine, we constructed a S. boulardii strain that could metabolize l-fucose, a major component of mucin in the gut epithelium. The fucU, fucI, fucK, and fucA from Escherichia coli and HXT4 from S. cerevisiae were overexpressed in S. boulardii. The engineered S. boulardii metabolized l-fucose and produced 1,2-propanediol under aerobic and anaerobic conditions. It also produced large amounts of 1,2-propanediol under strict anaerobic conditions. An in silico genome-scale metabolic model analysis was performed to simulate the growth of S. boulardii on l-fucose, and elementary flux modes were calculated to identify critical metabolic reactions for assimilating l-fucose. As a result, we found that the engineered S. boulardii consumes l-fucose via (S)-lactaldehyde-(S)-lactate-pyruvate pathway, which is highly oxygen dependent.

Conclusion

To the best of our knowledge, this is the first study in which S. cerevisiae and S. boulardii strains capable of metabolizing l-fucose have been constructed. This strategy could be used to enhance the metabolic activity of S. boulardii and other probiotic microorganisms in the gut.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01926-x.

Genetic and clinical characteristics of transthyretin cardiac amyloidosis in Koreans

Background/Introduction

Transthyretin amyloidosis with mutations (aTTRv amyloidosis) have over 100 recognized pathogenic mutations of the TTR gene and its clinical manifestations are very heterogenous. Through the global THAOS (Transthyretin Amyloidosis Outcomes Survey) patient registry, different and several types of mutants and clinical differences have been identified. Awareness of aTTRv amyloidosis is now becoming somewhat significant amongst physicians all over the world. This is a detailed look at such efforts in Korea.

Purpose

We aimed to seek the geologic significance of aTTRv amyloidosis in South Korea.

Methods

This was an analysis of 638 Korean amyloidosis patients in a single center over a period of 16 years from 1995 to October 2021. 95 individuals were found with aTTR mutations.

Results

aTTRv amyloidosis constituted 14.8% (n=95) of amyloidosis patients, and the most commonly involved organ being the heart (61.7%, n=58). Unlike the rest of the world, the mixed phenotype was most common (51.0%, n=48) in Korea and the most universal mutation in Koreans were Asp38Ala, which only constitutes about 1.0% in the THAOS registry. Val30Met mutation, which comprises 76% of the mutation in the THAOS registry, was mostly associated the neurologic phenotypes. However, the same mutations in Korea mixed phenotypes with cardiac (38.4%) and neurologic (37%) symptoms.

Conclusion

aTTRv amyloidosis in Korea is different from other patients worldwide. The mixed phenotype was most common, emphasizing the need for heart failure management in the Korean population. Genotype wise, Koreans held a less common mutation of Asp38Ala. The most common mutation of Val30Met was more likely to be associated cardiac symptoms, which concurs with other studies that suggesting that geological features are more important than mutations itself.

Funding Acknowledgement

Type of funding sources: None.

GC-TOF/MS-Based Metabolomics for Comparison of Volar and Non-Volar Skin Types

Skin has heterogenous identities on different body sites despite similar cellular compositions. There are two types of skin, volar (palmoplantar) and non-volar (dorsal), which are characterized by epidermal thickness, pigmentation, and presence of hair follicles. However, the mechanisms underlying the development of these different skin types remain unclear. To investigate these, we profiled the cellular metabolites of volar and non-volar skin in mice using gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS), and further assessed the metabolic differences between them. In total, 96 metabolites from both volar and non-volar skin of mice were identified using the BinBase database system. Metabolomics analysis revealed important differences associated with amino acid metabolism (phenylalanine, tyrosine, and tryptophan biosynthesis; aspartate and glutamate metabolism), sugar metabolism (pentose phosphate pathway), and nucleotide metabolism (pyrimidine metabolism) in volar skin. Fifty metabolites were identified as potential biomarkers differentiating the physiological characteristics of these skin types. Of these, nine were highly increased whereas 41 were significantly decreased in volar skin compared with those in non-volar skin. Overall, these results provide valuable information for understanding the metabolic differences between volar and non-volar skin.

Non-Targeted Metabolomics Approach Revealed Significant Changes in Metabolic Pathways in Patients with Chronic Traumatic Encephalopathy

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease that is frequently found in athletes and those who have experienced repetitive head traumas. CTE is associated with a variety of neuropathologies, which cause cognitive and behavioral impairments in CTE patients. However, currently, CTE can only be diagnosed after death via brain autopsy, and it is challenging to distinguish it from other neurodegenerative diseases with similar clinical features. To better understand this multifaceted disease and identify metabolic differences in the postmortem brain tissues of CTE patients and control subjects, we performed ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS)-based non-targeted metabolomics. Through multivariate and pathway analysis, we found that the brains of CTE patients had significant changes in the metabolites involved in astrocyte activation, phenylalanine, and tyrosine metabolism. The unique metabolic characteristics of CTE identified in this study were associated with cognitive dysfunction, amyloid-beta deposition, and neuroinflammation. Altogether, this study provided new insights into the pathogenesis of CTE and suggested appealing targets for both diagnosis and treatment for the disease.

Metabolic discrimination of synovial fluid between rheumatoid arthritis and osteoarthritis using gas chromatography/time-of-flight mass spectrometry

INTRODUCTION

Rheumatoid arthritis (RA) and osteoarthritis (OA) are clinicopathologically different.

OBJECTIVES

We aimed to assess the feasibility of metabolomics in differentiating the metabolite profiles of synovial fluid between RA and OA using gas chromatography/time-of-flight mass spectrometry.

METHODS

We first compared the global metabolomic changes in the synovial fluid of 19 patients with RA and OA. Partial least squares-discriminant, hierarchical clustering, and univariate analyses were performed to distinguish metabolites of RA and OA. These findings were then validated using synovial fluid samples from another set of 15 patients with RA and OA.

RESULTS

We identified 121 metabolites in the synovial fluid of the first 19 samples. The score plot of PLS-DA showed a clear separation between RA and OA. Twenty-eight crucial metabolites, including hypoxanthine, xanthine, adenosine, citrulline, histidine, and tryptophan, were identified to be capable of distinguishing RA metabolism from that of OA; these were found to be associated with purine and amino acid metabolism.

CONCLUSION

Our results demonstrated that metabolite profiling of synovial fluid could clearly discriminate between RA and OA, suggesting that metabolomics may be a feasible tool to assist in the diagnosis and advance the comprehension of pathological processes for diseases.

Deep Learning-Based Prediction of the 3D Postorthodontic Facial Changes

With the increase of the adult orthodontic population, there is a need for an accurate and evidence-based prediction of the posttreatment face in 3 dimensions (3D). The objectives of this study are 1) to develop a 3D postorthodontic face prediction method based on a deep learning network using the patient-specific factors and orthodontic treatment conditions and 2) to validate the accuracy and clinical usability of the proposed method. Paired sets (n = 268) of pretreatment (T1) and posttreatment (T2) cone-beam computed tomography (CBCT) of adult patients were trained with a conditional generative adversarial network to generate 3D posttreatment facial data based on the patient's gender, age, and the changes of upper (ΔU1) and lower incisor position (ΔL1) as input. The accuracy was calculated with prediction error and mean absolute distances between real T2 (T2) and predicted T2 (PT2) near 6 perioral landmark regions, as well as percentage of prediction error less than 2 mm using test sets (n = 44). For qualitative evaluation, an online survey was conducted with experienced orthodontists as panels (n = 56). Overall, PT2 indicated similar 3D changes to the T2 face, with the most apparent changes simulated in the perioral regions. The mean prediction error was 1.2 ± 1.01 mm with 80.8% accuracy. More than 50% of the experienced orthodontists were unable to distinguish between real and predicted images. In this study, we proposed a valid 3D postorthodontic face prediction method by applying a deep learning algorithm trained with CBCT data sets.

Multi-Step Enzymatic Production and Purification of 2-Keto-3-Deoxy-Galactonate from Red-Macroalgae-Derived Agarose

2-keto-3-deoxy sugar acids, which have potential as precursors in medicinal compound production, have gained attention in various fields. Among these acids, 2-keto-3-deoxy-l-galactonate (KDGal) has been biologically produced from D-galacturonate originating from plant-derived pectin. KDGal is also found in the catabolic pathway of 3,6-anhydro-l-galactose (AHG), the main component of red-algae-derived agarose. AHG is converted to 3,6-anhydrogalactonate by AHG dehydrogenase and subsequently isomerized to KDGal by 3,6-anhydrogalactonate cycloisomerase. Therefore, we used the above-described pathway to produce KDGal from agarose. Agarose was depolymerized to AHG and to agarotriose (AgaDP3) and agaropentaose (AgaDP5), both of which have significantly higher molecular weights than AHG. When only AHG was converted to KDGal, AgaDP3 and AgaDP5 remained unreacted. Finally, KDGal was effectively purified from the enzymatic products by size-exclusion chromatography based on the differences in molecular weights. These results show that KDGal can be enzymatically produced and purified from agarose for use as a precursor to high-value products.

Activation of ectopic olfactory receptor 544 induces GLP-1 secretion and regulates gut inflammation

Olfactory receptors are ectopically expressed in extra-nasal tissues. The gut is constantly exposed to high levels of odorants where ectopic olfactory receptors may play critical roles. Activation of ectopic olfactory receptor 544 (Olfr544) by azelaic acid (AzA), an Olfr544 ligand, reduces adiposity in mice fed a high-fat diet (HFD) by regulating fuel preference to fats. Herein, we investigated the novel function of Olfr544 in the gut. In GLUTag cells, AzA induces the cAMP-PKA-CREB signaling axis and increases the secretion of GLP-1, an enteroendocrine hormone with anti-obesity effects. In mice fed a HFD and orally administered AzA, GLP-1 plasma levels were elevated in mice. The induction of GLP-1 secretion was negated in cells with Olfr544 gene knockdown and in Olfr544-deficient mice. Gut microbiome analysis revealed that AzA increased the levels of Bacteroides acidifaciens and microbiota associated with antioxidant pathways. In fecal metabolomics analysis, the levels of succinate and trehalose, metabolites correlated with a lean phenotype, were elevated by AzA. The function of Olfr544 in gut inflammation, a key feature in obesity, was further investigated. In RNA sequencing analysis, AzA suppressed LPS-induced activation of inflammatory pathways and reduced TNF-α and IL-6 expression, thereby improving intestinal permeability. The effects of AzA on the gut metabolome, microbiome, and colon inflammation were abrogated in Olfr544-KO mice. These results collectively demonstrated that activation of Olfr544 by AzA in the gut exerts multiple effects by regulating GLP-1 secretion, gut microbiome and metabolites, and colonic inflammation in anti-obesogenic phenotypes and, thus, may be applied for obesity therapeutics.

Isomer-Specific Monitoring of Sialylated N-Glycans Reveals Association of α2,3-Linked Sialic Acid Epitope With Behcet's Disease

Behcet’s disease (BD) is an immune disease characterized by chronic and relapsing systemic vasculitis of unknown etiology, which can lead to blindness and even death. Despite continuous efforts to discover biomarkers for accurate and rapid diagnosis and optimal treatment of BD, there is still no signature marker with high sensitivity and high specificity. As the link between glycosylation and the immune system has been revealed, research on the immunological function of glycans is being actively conducted. In particular, sialic acids at the terminus of glycoconjugates are directly implicated in immune responses, cell–cell/pathogen interactions, and tumor progression. Therefore, changes in sialic acid epitope in the human body are spotlighted as a new indicator to monitor the onset and progression of immune diseases. Here, we performed global profiling of N-glycan compositions derived from the sera of 47 healthy donors and 47 BD patients using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to preferentially determine BD target glycans. Then, three sialylated biantennary N-glycans were further subjected to the separation of linkage isomers and quantification using porous graphitized carbon-liquid chromatography (PGC-LC)/multiple reaction monitoring (MRM)-MS. We were able to successfully identify 11 isomers with sialic acid epitopes from the three glycan compositions consisting of Hex₅HexNAc₄NeuAc₁, Hex₅HexNAc₄Fuc₁NeuAc₁, and Hex₅HexNAc₄NeuAc₂. Among them, three isomers almost completely distinguished BD from control with high sensitivity and specificity with an area under the curve (AUC) of 0.945, suggesting the potential as novel BD biomarkers. In particular, it was confirmed that α2,3-sialic acid at the terminus of biantennary N-glycan was the epitope associated with BD. In this study, we present a novel approach to elucidating the association between BD and glycosylation by tracing isomeric structures containing sialic acid epitopes. Isomer-specific glycan profiling is suitable for analysis of large clinical cohorts and may facilitate the introduction of diagnostic assays for other immune diseases.

Percutaneous coronary intervention in patients with peripheral artery disease and adverse cardiovascular adverse event and bleeding

Background

Peripheral artery disease (PAD) increase the risk of comorbidity and mortality in coronary artery disease (CAD).

Objectives

We evaluate influence of PAD on prognosis in patients undergoing percutaneous coronary intervention (PCI).

Methods

We analyzed all consecutive patients included in our dedicated local registry for PCI between January 2011 and December 2016. Presence of PAD was defined by decreased ankle-brachial index (&lt;0.9). Major adverse cardiovascular event (MACE) was defined as a composite of cardiovascular death, non-fatal myocardial infarct, revascularization, and ischemic stroke. Major bleeding was defined as Bleeding Academic Research Consortium 3 or 5.

Results

Among the 4,747 patients who underwent the PCI, 12.9% (n=610) of PAD were identified. Old age (&gt;60 years), renal dysfunction, reduced ejection fraction, and presence of PAD were predictors with both MACE and major bleeding event. Among them, presence of PAD was an independent risk factor of MACE and major bleeding (MACE, HR 8.26, 95% CI 2.33- 29.41, p=0.036; major bleeding, HR 3.11, 95% CI 1.10–10.63, p=0.040, respectively). The MACE and major bleeding rate at 5-year was significantly increased in patients with PAD (MACE, 30.0% vs. 15.8%, log rank test p&lt;0.001; major bleeding, 6.7 vs. 3.6%, log rank test p=0.003, respectively) (Figure).

Conclusion

Presence of PAD was strongly associated with higher rate of long-term MACE and major bleeding. These findings could have a clinical relevance in requiring individualized pharmacologic strategies to reduce the burden of cardiovascular disease.

Funding Acknowledgement

Type of funding sources: None.

Impact of active and stable cancer on survival in patients undergoing percutaneous coronary intervention

Background

With advances in treatment of ischemic heart disease and cancer treatment, use of percutaneous coronary intervention (PCI) in cancer survivors and patients with active cancer (AC) is expanding.

Objectives

The purpose of this study was to determine the impact of cancer on survival and major cardiovascular events (MACE) in a long-term, single-center cohort of patients treated with PCI.

Methods

Patients treated with PCI between January 2010 and December 2017 were grouped as follows: controls (patients without cancer), stable cancer (SC), and AC. AC was included patients with cancer diagnosed within the past 6 months, patients who had cancer-related therapy within the past 6 months, active metastatic disease, or active recurrence of the cancer. The primary endpoints were 5-year survival and a secondary endpoint was 5-year MACE.

Results

A total of 6,743 patients (age 66±12 years, 68.4% men) treated with PCI were included: 6,404 (95.0%) controls, 245 (3.6%) SC, and 94 (1.4%) AC. Predominant malignancies were gastrointestinal (37.4%), lung (22.7%), and genitourinary cancer (14.7%). No differences were observed between patients with AC, SC and controls regarding 5-year MACE (total MACE, 33.2% vs. 28.1% vs. 17.5%, p=0.072; cardiac death, 13.6% vs. 9.1% vs. 6.7%, p=0.066; non-fatal myocardial infarction, 2.9% vs. 7.5% vs. 7.8%, p=0.820; revascularization, 17.9% vs. 17.6% vs. 11.6%, p=0.794, respectively). Patients with AC and SC had reduced 5-year survival compared with controls (62.0% vs. 81.5% vs. 89.8%, p&lt;0.001) (Figure). AC was associated with a 1.76 (95% CI 1.22 to 2.54, p=0.002) fold increased risk of all-cause 5-year mortality in multivariable adjusted models.

Conclusions

Cumulative incidence of 5-year survival was discriminated by concurrent status of cancer following PCI. Individualized decision making is needed in the routine practice of PCI regarding concurrent cancer-specific treatment and prognosis.

Funding Acknowledgement

Type of funding sources: None.

Pemetrexed plus cisplatin in patients with previously treated advanced sarcoma: a multicenter, single-arm, phase II trial

Background

Patients with advanced sarcomas have a poor prognosis and few treatment options that improve overall survival. We assessed the efficacy and tolerability of pemetrexed and cisplatin combination therapy in patients with refractory bone and soft tissue sarcoma (STS).

Patients and Methods

Patients were included in this multicenter, phase II study (ClinicalTrials.gov identifier NCT03809637) if they progressed after receiving one or more chemotherapy regimens containing an anthracycline and/or ifosfamide. Pemetrexed was first administered intravenously, followed by cisplatin, over a cycle of 21 days, for a maximum of six cycles. The primary endpoint was a progression-free rate (PFR) at 3 months (3-month PFR).

Results

From January 2017 to September 2019, we enrolled 37 patients; of these, 73% had previously undergone three or more rounds of chemotherapy. Five patients (13.5%) exhibited objective responses, including two patients (2/6, 33.3%) with malignant peripheral nerve sheath tumors, one patient (1/4, 25%) with synovial sarcoma, one patient (1/4, 25%) with undifferentiated pleomorphic sarcoma, and one patient (1/4, 25%) with angiosarcoma. The median progression-free survival was 2.6 months, and the 3-month PFR was 45.9% (n = 17). None of the four patients with osteosarcoma exhibited objective responses or were progression free at 3 months. The most frequent treatment-related grade 3-4 toxicities included neutropenia (16.2%), anemia (13.5%), thrombocytopenia (13.5%), and fatigue (8.1%). Among 26 patients (70.3%) available for immunohistochemical assessments, patients in the low-excision repair cross-complementation group 1 (ERCC1) and low-thymidylate synthase expression groups showed a tendency for longer overall survival.

Conclusions

Combination therapy with pemetrexed and cisplatin was associated with clinically meaningful and sustained responses among patients with advanced and refractory STS. The combination therapy met its predefined primary study endpoint.

•

Pemetrexed and cisplatin show promising efficacy for advanced sarcoma treatment, particularly as a salvage therapy option.

•

The combination therapy met its predefined primary endpoint, with a 3-month PFR of 45.9%.

•

Pemetrexed and cisplatin showed acceptable toxicity in heavily treated sarcoma patients.

Production of neoagarooligosaccharides by probiotic yeast Saccharomyces cerevisiae var. boulardii engineered as a microbial cell factory

Background

Saccharomyces cerevisiae var. boulardii is a representative probiotic yeast that has been widely used in the food and pharmaceutical industries. However, S. boulardii has not been studied as a microbial cell factory for producing useful substances. Agarose, a major component of red macroalgae, can be depolymerized into neoagarooligosaccharides (NAOSs) by an endo-type β-agarase. NAOSs, including neoagarotetraose (NeoDP4), are known to be health-benefiting substances owing to their prebiotic effect. Thus, NAOS production in the gut is required. In this study, the probiotic yeast S. boulardii was engineered to produce NAOSs by expressing an endo-type β-agarase, BpGH16A, derived from a human gut bacterium Bacteroides plebeius.

Results

In total, four different signal peptides were compared in S. boulardii for protein (BpGH16A) secretion for the first time. The SED1 signal peptide derived from Saccharomyces cerevisiae was selected as optimal for extracellular production of NeoDP4 from agarose. Expression of BpGH16A was performed in two ways using the plasmid vector system and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system. The production of NeoDP4 by engineered S. boulardii was verified and quantified. NeoDP4 was produced by S. boulardii engineered using the plasmid vector system and CRISPR-Cas9 at 1.86 and 0.80 g/L in a 72-h fermentation, respectively.

Conclusions

This is the first report on NAOS production using the probiotic yeast S. boulardii. Our results suggest that S. boulardii can be considered a microbial cell factory to produce health-beneficial substances in the human gut.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01644-w.

Antidiabetic Effect of Noodles Containing Fermented Lettuce Extracts

The aim of the current study was to examine the antidiabetic effect of noodle containing fermented lettuce extract (FLE) on diabetic mice as a pre-clinical study. The γ-aminobutyric acid (GABA) content, antioxidant capacity, and total polyphenol content of the FLE noodles were analyzed and compared with those of standard noodles. In addition, oral glucose and sucrose tolerance, and fasting blood glucose tests were performed using a high-fat diet/streptozotocin-mediated diabetic mouse model. Serum metabolite profiling of mice feed standard or FLE noodles was performed using gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) to understand the mechanism changes induced by the FLE noodles. The GABA content, total polyphenols, and antioxidant activity were high in FLE noodles compared with those in the standard noodles. In vivo experiments also showed that mice fed FLE noodles had lower blood glucose levels and insulin resistance than those fed standard noodles. Moreover, glycolysis, purine metabolism, and amino acid metabolism were altered by FLE as determined by GC-TOF-MS-based metabolomics. These results demonstrate that FLE noodles possess significant antidiabetic activity, suggesting the applicability of fermented lettuce extract as a potential food additive for diabetic food products.

Characterization of Neoagarooligosaccharide Hydrolase BpGH117 from a Human Gut Bacterium Bacteroides plebeius

α-Neoagarobiose (NAB)/neoagarooligosaccharide (NAO) hydrolase plays an important role as an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase in agarose utilization. Agarose is an abundant polysaccharide found in red seaweeds, comprising 3,6-anhydro-L-galactose (AHG) and D-galactose residues. Unlike agarose degradation, which has been reported in marine microbes, recent metagenomic analysis of Bacteroides plebeius, a human gut bacterium, revealed the presence of genes encoding enzymes involved in agarose degradation, including α-NAB/NAO hydrolase. Among the agarolytic enzymes, BpGH117 has been partially characterized. Here, we characterized the exo-acting α-NAB/NAO hydrolase BpGH117, originating from B. plebeius. The optimal temperature and pH for His-tagged BpGH117 activity were 35 °C and 9.0, respectively, indicative of its unique origin. His-tagged BpGH117 was thermostable up to 35 °C, and the enzyme activity was maintained at 80% of the initial activity at a pre-incubation temperature of 40 °C for 120 min. K_m and V_max values for NAB were 30.22 mM and 54.84 U/mg, respectively, and k_cat/K_m was 2.65 s⁻¹ mM⁻¹. These results suggest that His-tagged BpGH117 can be used for producing bioactive products such as AHG and agarotriose from agarose efficiently.

In Vitro Prebiotic and Anti-Colon Cancer Activities of Agar-Derived Sugars from Red Seaweeds

Numerous health benefits of diets containing red seaweeds or agar-derived sugar mixtures produced by enzymatic or acid hydrolysis of agar have been reported. However, among various agar-derived sugars, the key components that confer health-beneficial effects, such as prebiotic and anti-colon cancer activities, remain unclear. Here, we prepared various agar-derived sugars by multiple enzymatic reactions using an endo-type and an exo-type of β-agarase and a neoagarobiose hydrolase and tested their in vitro prebiotic and anti-colon cancer activities. Among various agar-derived sugars, agarotriose exhibited prebiotic activity that was verified based on the fermentability of agarotriose by probiotic bifidobacteria. Furthermore, we demonstrated the anti-colon cancer activity of 3,6-anhydro-l-galactose, which significantly inhibited the proliferation of human colon cancer cells and induced their apoptosis. Our results provide crucial information regarding the key compounds derived from red seaweeds that confer beneficial health effects, including prebiotic and anti-colon cancer activities, to the host.

Vibration reduction during milling of highly flexible workpieces using active workpiece holder system

The milling of highly flexible workpieces, such as thin-walled structures used in turbine blades, aerospace equipment, and jet engine compressors, requires vibration compensation to improve the quality of the workpiece surface. Vibration can be reduced by selecting appropriate cutting parameters. However, this approach reduces system productivity. This paper presents an active workpiece holder that controls the vibration of general computer numerical control machine tools. The proposed holder, which comprises a flexible guide mechanism, driver, and sensor, measures vibration and actively controls it using piezoactuators. A high-rigidity flexure mechanism was designed for the holder, and finite element method simulation and modal analysis were performed. Finally, the proposed system was fabricated, and experimental verification indicated that the system reduced vibration. The surface quality obtained using the controlled system was ∼50% better than that obtained using the uncontrolled system.

Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

Dual α-1,4- and β-1,4-Glycosidase Activities by the Novel Carbohydrate-Binding Module in α-l-Fucosidase from Vibrio sp. Strain EJY3

Carbohydrates are structurally and functionally diverse materials including polysaccharides, and marine organisms are known to have many enzymes for the breakdown of complex polysaccharides. Here, we identified an α-l-fucosidase enzyme from the marine bacterium Vibrio sp. strain EJY3 (VejFCD) that has dual α-1,4-glucosidic and β-1,4-galactosidic specificities. We determined the crystal structure of VejFCD and provided the structural basis underlying the dual α- and β-glycosidase activities of the enzyme. Unlike other three-domain FCDs, in VejFCD, carbohydrate-binding module-B (CBM-B) with a novel β-sandwich fold tightly contacts with the CatD/CBM-B main body and provides key residues for the β-1,4-glycosidase activity of the enzyme. The phylogenetic tree analysis suggests that only a few FCDs from marine microorganisms have the key structural features for dual α-1,4- and β-1,4-glycosidase activities. This study provides the structural insights into the mechanism underlying the novel glycoside hydrolase activities and could be applied for more efficient utilization in the hydrolysis of complex carbohydrates in biotechnological applications.

Characteristics of silicon nitride deposited by very high frequency (162 MHz)-plasma enhanced atomic layer deposition using bis(diethylamino)silane

Silicon nitrides, deposited by capacitively coupled plasma (CCP)-type plasma enhanced atomic layer deposition (PEALD), are generally applied to today's nanoscale semiconductor devices, and are currently being investigated in terms of their potential applications in the context of flexible displays, etc. During the PEALD process, 13.56 MHz rf power is generally employed for the generation of reactive gas plasma. In this study, the effects of a higher plasma generation frequency of 162 MHz on both plasma and silicon nitride film characteristics are investigated for the purpose of silicon nitride PEALD, using bis(diethylamino)silane (BDEAS) as the silicon precursor, and N₂ plasma as the reactant gas. The PEALD silicon nitride film deposited using the 162 MHz CCP exhibited improved film characteristics, such as reduced surface roughness, a lower carbon percentage, a higher N/Si ratio, a lower wet etch rate in a diluted HF solution, lower leakage current, and higher electric breakdown field, and more uniform step coverage of the silicon nitride film deposited in a high aspect ratio trench, as compared to silicon nitride PEALD using 13.56 MHz CCP. These improved PEALD silicon nitride film characteristics are believed to be related to the higher ion density, higher reactive gas dissociation, and lower ion bombardment energy to the substrate observed in N₂ plasma with a 162 MHz CCP.

Long-Living Budding Yeast Cell Subpopulation Induced by Ethanol/Acetate and Respiration

Budding yeast generate heterogeneous cells that can be separated into two distinctive cell types: short-living low-density and long-living high-density (HD) cells by density gradient centrifugation. We found that ethanol and acetate induce formation of HD cells, and mitochondrial respiration is required. From their transcriptomes and metabolomes, we found upregulated differentially expressed genes in HD cells involved in the RGT2/RGT1 glucose sensing pathway and its downstream genes encoding hexose transporters. For HD cells, we determined an abundance of various carbon sources including glucose, lactate, pyruvate, trehalose, mannitol, mannose, and galactose. Other upregulated differentially expressed genes in HD cells were involved in the TORC1-SCH9 signaling pathway and its downstream genes involved in cytoplasmic translation. We also measured an abundance of free amino acids in HD cells including valine, proline, isoleucine, and glutamine. These characteristics of the HD cell transcriptome and metabolome may be important conditions for maintaining a long-living phenotype.

Characterization of an Antibacterial Agent Targeting Ferrous Iron Transport Protein FeoB against Staphylococcus aureus and Gram-Positive Bacteria

The emergence of multidrug-resistant Staphylococcus aureus strains has become a serious clinical problem. Iron is absolutely required for the bacterial growth, virulence associated with colonization, and survival from the host immune system. The FeoB protein is a major iron permease in bacterial ferrous iron transport systems (Feo) that has been shown to play a crucial role in virulence of some pathogenic bacteria. However, FeoB is still uncharacterized in Gram-positive pathogens, and its effects on S. aureus pathogenesis are unknown. In this study, we identified a novel inhibitor, GW3965·HCl, that targets FeoB in S. aureus. The molecule effectively inhibited FeoB in vitro enzyme activity, bacterial growth, and virulence factor expression. Genome-editing and metabolomic analyses revealed that GW3965·HCl inhibited FeoB function and affected the associated mechanisms with reduced iron availability in S. aureus. Gentamicin resistance and Caenorhabditis elegans infection assays further demonstrated the power of GW3965·HCl as a safe and efficient antibacterial agent. In addition to S. aureus, GW3965·HCl also presented its effectiveness on inhibition of the FeoB activity and growth of Gram-positive bacteria. This novel inhibitor will provide new insight for developing a next-generation antibacterial therapy.

Characterization of BpGH16A of Bacteroides plebeius, a key enzyme initiating the depolymerization of agarose in the human gut

Seaweeds have received considerable attention as sources of dietary fiber and biomass for manufacturing valuable products. The major polysaccharides of red seaweeds include agar and porphyran. In a marine environment, marine bacteria utilize agar and porphyran through the agarase and porphyranase genes encoded in their genomes. Most of these enzymes identified and characterized so far originate from marine bacteria. Recently, Bacteroides plebeius, a human gut bacterium isolated from seaweed-eating Japanese individuals, was revealed to contain a polysaccharide utilization locus (PUL) targeting the porphyran and agarose of red seaweeds. For example, B. plebeius contains an endo-type β-agarase, BpGH16A, belonging to glycoside hydrolase family 16. BpGH16A cleaves the β-1,4-glycosidic linkages of agarose and produces neoagarooligosccharides from agarose. Since it is crucial to study the characteristics of BpGH16A to understand the depolymerization pathway of red seaweed polysaccharides by B. plebeius in the human gut and to industrially apply the enzyme for the depolymerization of agar, we characterized BpGH16A for the first time. According to our results, BpGH16A is an extracellular endo-type β-agarase with an optimal temperature of 40 °C and an optimal pH of 7.0, which correspond to the temperature and pH of the human colon. BpGH16A depolymerizes agarose into neoagarotetraose (as the main product) and neoagarobiose (as the minor product). Thus, BpGH16A is suggested to be an important enzyme that initiates the depolymerization of red seaweed agarose or agar in the human gut by B. plebeius. KEY POINTS: • Bacteroides plebeius is a human gut bacterium isolated from seaweed-eating humans. • BpGH16A is an extracellular endo-type β-agarase with optimal conditions of 40 °C and pH 7.0. • BpGH16A depolymerizes agarose into neoagarotetraose and neoagarobiose.

Metabolomic Elucidation of the Effect of Sucrose on the Secondary Metabolite Profiles in Melissa officinalis by Ultraperformance Liquid Chromatography-Mass Spectrometry

Sucrose induces flavonoid accumulation in plants as a defense mechanism against various stresses. However, the relationship between the biosynthesis of flavonoids as secondary metabolites and sucrose levels remains unknown. To understand the change in flavonoid biosynthesis by sucrose, we conducted secondary metabolite profiling in Melissa officinalis treated with different levels of sucrose using ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry. The partial least squares-discriminant and hierarchical clustering analyses showed significant differences in secondary metabolite profiles in M. officinalis at 50, 150, and 300 mM sucrose levels. The levels of 3 flavonoids such as quercetin 3-O-β-d-glucosyl-(1→2)-β-d-glucoside, 6-methoxyaromadendrin 3-O-acetate, and 3-hydroxycoumarin and 19 flavonoids including 6-methoxyaromadendrin 3-O-acetate, aureusidin, iridin, flavonol 3-O-(6-O-malonyl-β-d-glucoside) quercetin 3-O-glucoside, and rutin increased at 150 and 300 mM sucrose, respectively, compared to 50 mM sucrose, indicating that the flavonoids were accumulated in M. officinalis by a higher concentration of sucrose. This is the first investigation of the change in individual flavonoids as secondary metabolites in M. officinalis by varying sucrose levels, and the results demonstrate that the sucrose causes the accumulation of certain flavonoids as a defense mechanism against osmotic stress.

Zmo0994, a novel LEA-like protein from Zymomonas mobilis, increases multi-abiotic stress tolerance in Escherichia coli

BACKGROUND

Pretreatment processes and subsequent enzymatic hydrolysis are prerequisites to utilize lignocellulosic sugar for fermentation. However, the resulting hydrolysate frequently hinders fermentation processes due to the presence of inhibitors and toxic products (e.g., ethanol). Thus, it is crucial to develop robust microbes conferring multi-stress tolerance.

RESULTS

Zmo0994, a functionally uncharacterized protein from Zymomonas mobilis, was identified and characterized for the first time. A major effect of Zmo0994 was a significant enhancement in the tolerance to abiotic stresses such as ethanol, furfural, 5'-hydroxymethylfurfural and high temperature, when expressed in Escherichia coli. Through transcriptome analysis and in vivo experiments, the cellular mechanism of this protein was revealed as due to its ability to trigger genes, involved in aerobic respiration for ATP synthesis.

CONCLUSIONS

These findings have significant implications that might lead to the development of robust microbes for the highly efficient industrial fermentation processes.

Overproduction of Exopolysaccharide Colanic Acid by Escherichia coli by Strain Engineering and Media Optimization

Colanic acid (CA) is one of the major bacterial exopolysaccharides. Due to its biological activities, CA has a significant commercial value. However, the cultivation conditions have not been optimized for the large-scale production of CA. Here, we constructed a CA-overproducing Escherichia coli strain (ΔwaaF) and statistically optimized its culture media for maximum CA production. Glucose and tryptone were found the optimal carbon and nitrogen sources, respectively. Fractional factorial design indicated tryptone and Na₂HPO₄ as the critical nutrients for CA production. Through further optimization, we achieved a maximum CA production of 1910.0 mg/L, which is approximately 12-fold higher than the amount obtained using the non-optimized medium initially used. The predicted value of CA production was comparable with experimental value (2052.8 mg/L) under the optimized conditions. This study constitutes a successful demonstration of media optimization for increased CA production, and paves the way for future research for achieving large-scale CA production.

Biochemical characterization of bacterial FeoBs: A perspective on nucleotide specificity

Iron is an essential requirement for the survival and virulence of most bacteria. The bacterial ferrous iron transporter protein FeoB functions as a major reduced iron transporter in prokaryotes, but its biochemical mechanism has not been fully elucidated. In the present study, we compared enzymatic properties of the cytosolic portions of pathogenic bacterial FeoBs to elucidate each bacterial strain-specific characteristic of the Feo system. We show that bacterial FeoBs are classified into two distinct groups that possess either a sole GTPase or an NTPase with a substrate promiscuity. This difference in nucleotide preference alters cellular requirements for monovalent and divalent cations. While the hydrolytic activity of the GTP-dependent FeoBs was stimulated by potassium, the action of the NTP-dependent FeoBs was not significantly affected by the presence of monovalent cations. Mutation of Asn11, having a role in potassium-dependent GTP hydrolysis, changed nucleotide specificity of the NTP-dependent FeoB, resulting in loss of ATPase activity. Sequence analysis suggested a possible association of alanine in the G5 motif for the NTP-dependent activity in FeoBs. This demonstration of the distinct enzymatic properties of bacterial FeoBs provides important insights into mechanistic details of Feo iron transport processes, as well as offers a promising species-specific anti-virulence target.

Variation in the synovial fluid metabolome according to disease activity of rheumatoid arthritis

OBJECTIVES

Because genetic and environmental factors both contribute to rheumatoid arthritis (RA), metabolomics could be a very useful tool to elucidate the pathophysiology of RA, and to predict response to treatment. This study was carried out to investigate synovial fluid (SF) metabolic perturbation in RA patients according to the degree of disease activity using gas chromatography/time-of-flight mass spectrometry (GC/TOF MS).

METHODS

SF samples were obtained from 48 RA patients. Disease activity was assessed using DAS28-ESR(3). SF metabolomics profiling was performed using GC/TOF-MS, in conjunction with multivariate statistical analyses and pathway analyses.

RESULTS

Significant discrimination of metabolite profiles between moderate and high disease activity groups was shown by PLS-DA, which provided evidence that SF metabolic profiles predicted disease activity. We found the significant correlation between DAS28-ESR(3) value and the intensities of 12 metabolites. The intensities of glycocyamine and indol-3-lactate positively correlated with DAS28-ESR(3) value. On the other hand, β-alanine, asparagine, citrate, cyano-L-alanine, leucine, nicotinamide, citrulline, methionine, oxoproline, and salicylaldehyde negatively correlated with DAS28-ESR(3) value. We found fifteen pathways that were significantly associated with disease activity in RA and that the higher the disease activity, the more amino acid metabolic processes were affected.

CONCLUSIONS

We found the SF metabolic alterations in RA patients according to disease activity by using GC/TOF MS and identified 12 candidate metabolic biomarkers that may well reflect the disease activity of RA. SF metabolomic approaches based on GC/TOF MS might provide additional information relating to monitoring disease activity in RA.

Systematic re-evaluation of the long-used standard protocol of urease-dependent metabolome sample preparation

In the urinary metabolomics for finding biomarkers in urine, owing to high concentrations of urea, for chromatography-based metabolomic analysis, urea needed to be degraded by urease. This urease pretreatment has been the key step of sample preparation for standard urinary metabolomics until today even for mass spectrometry-based analysis. The urease pretreatment involving incubation of urine with urease contradicts the concept of metabolome sampling, which should immediately arrest metabolic reactions to prevent alterations of a metabolite profile. Nonetheless, the impact of urease pretreatment has not been clearly elucidated yet. We found that activities of urease and endogenous urinary enzymes and metabolite contaminants from the urease preparations introduce artefacts into metabolite profiles, thus leading to misinterpretation.