Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms

Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers’ expectations of healthy products

Kernel Correlation-Dissimilarity for Multiple Kernel k-Means Clustering

The main objective of the Multiple Kernel k-Means (MKKM) algorithm is to extract non-linear information and achieve optimal clustering by optimizing base kernel matrices. Current methods enhance information diversity and reduce redundancy by exploiting interdependencies among multiple kernels based on correlations or dissimilarities. Nevertheless, relying solely on a single metric, such as correlation or dissimilarity, to define kernel relationships introduces bias and incomplete characterization. Consequently, this limitation hinders efficient information extraction, ultimately compromising clustering performance. To tackle this challenge, we introduce a novel method that systematically integrates both kernel correlation and dissimilarity. Our approach comprehensively captures kernel relationships, facilitating more efficient classification information extraction and improving clustering performance. By emphasizing the coherence between kernel correlation and dissimilarity, our method offers a more objective and transparent strategy for extracting non-linear information and significantly improving clustering precision, supported by theoretical rationale. We assess the performance of our algorithm on 13 challenging benchmark datasets, demonstrating its superiority over contemporary state-of-the-art MKKM techniques.Comment: 36 pages. This paper was accepted by Pattern Recognition on January 31, 202

Study on retirement program of Japanese Companies : Interview for employee's work contribution.

This paper examines to what degrees employees' work contribution to Japanese companies is currently reflected in their retirement program, by using interview as research method (July−Dec., 2008 ; on eight companies and two public offices). It also examines the content of the programs, such as social environment surrounding the system, company policies, and problems and solutions involved in the operation, as well as the transition of the system after Meiji era. Major findings include the followings. Firstly despite some changes occurred in the system as a result of diversification of employment types and styles and also alteration of company policies, the system itself will be maintained in the future. Secondly, although many companies modified conventional seniority−based salary systems for a retirement program that reflect employees' work contribution more clearly through an adoption of 'point system' and other measures, they still find some problems in new systems in their operation and practicality

Isolation, Identification, Screening and Fermentation Process Optimization of Bacillus Producing High Antimicrobial Lipopeptide

In order to screen out Bacillus sp. with high production of antimicrobial lipopeptide and determine its optimal fermentation conditions, the study isolated and identified antimicrobial lipopeptide-producing Bacillus sp. strains from traditional fermented soybean paste, and adopted orthogonal test to investigate how lipopeptide production by Bacillus sp was affected by fermentation conditions, such as fermentation inoculum amount, fermentation filling volume, fermentation time and fermentation temperature. The results showed that 27 strains of Bacillus sp. were isolated and screened out from 9 portions traditional fermented soybean paste of the Northeast, among which 6 strains were identified by 16S rDNA as having the genes sfp, fenB and ituA for synthesizing lipopeptide. According to the determination of lipopeptide yield and inhibition effect, Bacillus subtilis SN-20 and Bacillus amyloliquefaciens SN-46 showed excellent performance with the yield of 106 and 72 mg of lipopeptide per unit, and strong inhibition effect on both gram-positive and negative indicator bacteria. The optimal fermentation process of Bacillus subtilis SN-20 was found to be 3% inoculum, 20% fermentation filler, 36 h fermentation time and 32 ℃. The optimal fermentation process of Bacillus subtilis SN-46 was 2% inoculum, 40% fermentation filler, 24 h fermentation time and 32 ℃. Under these conditions, the unit biomass yields of lipopeptides for the two strains of Bacillus before optimization were 106.11 and 76.23 mg/g, respectively. After optimization, they increased by 21.85% and 23.84%, respectively. The study results effectively increased the production of antimicrobial lipopeptides from Bacillus

Whole Genome Sequencing of Bacillus subtilis SNBS-3 and Prediction of Its Antimicrobial Substances

As an extension of the previous research, this study aimed to comprehensively characterize the genome of Bacillus subtilis SNBS-3. Illumina second-generation sequencing technology and the third-generation high-throughput Pacbio sequencing platform were used for whole-genome sequencing of B. subtilis SNBS-3 isolated from traditional bean paste to obtain the key information of genome characteristics, gene function annotation and classification, phylogenetic evolution, and secondary metabolites. The results showed that the genome of SNBS-3 was a closed circular DNA of 4 076 387 bp in length containing 4 000 protein-coding genes. A total of 3 209, 2 824, 2 560, 147, 12 and 4 functional genes were annotated in the Clusters of Orthologous Groups (COG), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active Enzymes (CAZyme), Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factor Database (VFDB), respectively. Using the online software AntiSMASH and Bagel4, we found that it contained genes related to the synthesis of surfactin, mycosubtilin, plipastatin, bacilysin and bacillaene, as well as a complete gene cluster for the synthesis of the bacteriocin subtilosin A. Based on the results of antimicrobial test and proteinase K test, it was hypothesized that B. subtilis SNBS-3 had the ability to synthesize subtilosin A. In conclusion, the whole genome sequencing results of B. subtilis SNBS-3 show that it can produce a variety of bacteriostatic substances and thus have biocontrol potential. The results from this study provide a theoretical basis for further development and application of various bacteriostatic substances including the bacteriocin subtilosin A

Optimization of Process Conditions for Fermented Mulberry Leaf Tea and Analysis of Its Antioxidant Activity

In order to optimize the fermentation process conditions of mulberry leaf tea and explore the changes in antioxidant activity of mulberry leaf tea after fermentation. This experiment used response surface analysis to determine the optimal process conditions for fermenting mulberry leaf tea under three variable conditions: Fermentation temperature, fermentation time, and inoculation amount of Aspergillus niger. The content of bioactive substances and antioxidant properties in fermented mulberry leaf tea were determinated. The findings indicated that 5 days and 16 hours of fermentation duration, 30 ℃ of fermentation temperature, and 16.55% of inoculation amount were the ideal process parameters, and that the fermented mulberry leaf tea scored as high as 90 on the sensory scale under these conditions. In addition, the content of total flavonoids, total polysaccharides, polyphenols, free amino acids, rutin, and quercetin in fermented mulberry leaf tea increased by 14.39%, 12.67%, 2.90%, 3.46%, 81.13%, and 19.35%, respectively, compared to mulberry leaf green tea. Tea brown pigment with a content of 7.55%±0.37% was also detected in fermented mulberry leaf tea. In addition, the scavenging rate of hydroxyl radicals, DPPH radicals, superoxide radicals and the chelating rate of divalent iron ions of fermented mulberry leaf tea at the concentration of 1/1000 (g/mL) were 1.16, 1.07, 1.06 and 0.82 times higher than that of mulberry leaf green tea, respectively. The results of this study provide theoretical basis and references for further development and application of mulberry leaf in the future

Modifiers of the effect of maternal multiple micronutrient supplementation on stillbirth, birth outcomes, and infant mortality: a meta-analysis of individual patient data from 17 randomised trials in low-income and middle-income countries

Background: Micronutrient deficiencies are common among women in low-income and middle-income countries. Data from randomised trials suggest that maternal multiple micronutrient supplementation decreases the risk of low birthweight and potentially improves other infant health outcomes. However, heterogeneity across studies suggests influence from effect modifiers. We aimed to identify individual-level modifiers of the effect of multiple micronutrient supplements on stillbirth, birth outcomes, and infant mortality in low-income and middle-income countries.Methods: This two-stage meta-analysis of individual patient included data from 17 randomised controlled trials done in 14 low-income and middle-income countries, which compared multiple micronutrient supplements containing iron-folic acid versus iron-folic acid alone in 112 953 pregnant women. We generated study-specific estimates and pooled subgroup estimates using fixed-effects models and assessed heterogeneity between subgroups with the χ2 test for heterogeneity. We did sensitivity analyses using random-effects models, stratifying by iron-folic acid dose, and exploring individual study effect.Findings: Multiple micronutrient supplements containing iron-folic acid provided significantly greater reductions in neonatal mortality for female neonates compared with male neonates than did iron-folic acid supplementation alone (RR 0·85, 95% CI 0·75–0·96 vs 1·06, 0·95–1·17; p value for interaction 0·007). Multiple micronutrient supplements resulted in greater reductions in low birthweight (RR 0·81, 95% CI 0·74–0·89; p value for interaction 0·049), small-for-gestational-age births (0·92, 0·87–0·97; p=0·03), and 6-month mortality (0·71, 0·60–0·86; p=0·04) in anaemic pregnant women (haemoglobin \u3c110g/L) as compared with non-anaemic pregnant women. Multiple micronutrient supplements also had a greater effect on preterm births among underweight pregnant women (BMI \u3c18·5 kg/m2; RR 0·84, 95% CI 0·78–0·91; p=0·01). Initiation of multiple micronutrient supplements before 20 weeks gestation provided greater reductions in preterm birth (RR 0·89, 95% CI 0·85–0·93; p=0·03). Generally, the survival and birth outcome effects of multiple micronutrient supplementation were greater with high adherence (≥95%) to supplementation. Multiple micronutrient supplements did not significantly increase the risk of stillbirth or neonatal, 6-month, or infant mortality, neither overall or in any of the 26 examined subgroups.Interpretation: Antenatal multiple micronutrient supplements improved survival for female neonates and provided greater birth-outcome benefits for infants born to undernourished and anaemic pregnant women. Early initiation in pregnancy and high adherence to multiple micronutrient supplements also provided greater overall benefits. Studies should now aim to elucidate the mechanisms accounting for differences in the effect of antenatal multiple micronutrient supplements on infant health by maternal nutrition status and sex.Funding: None

A home calendar and recall method of last menstrual period for estimating gestational age in rural Bangladesh: a validation study

Background: The best method of gestational age assessment is by ultrasound in the first trimester; however, this method is impractical in large field trials in rural areas. Our objective was to assess the validity of gestational age estimated from prospectively collected date of last menstrual period (LMP) using crown-rump length (CRL) measured in early pregnancy by ultrasound. Methods: As part of a large, cluster-randomized, controlled trial in rural Bangladesh, we collected dates of LMP by recall and as marked on a calendar every 5 weeks in women likely to become pregnant. Among those with a urinetest confirmed pregnancy, a subset with gestational age of <15 weeks (n = 353) were enrolled for ultrasound follow-up to measure CRL. We compared interview-assessed LMP with CRL gestational age estimates and classification of preterm, term, and post-term births. Results: LMP-based gestational age was higher than CRL by a mean (SD) of 2.8 (10.7) days; differences varied by maternal education and preterm birth (P < 0.05). Lin\u2019s concordance correlation coefficient was good at ultrasound [0.63 (95 % CI 0.56, 0.69)] and at birth [0.77 (95 % CI 0.73, 0.81)]. Validity of classifying preterm birth was high but post-term was lower, with specificity of 96 and 89 % and sensitivity of 86 and 67 %, respectively. Results were similar by parity. Conclusions: Prospectively collected LMP provided a valid estimate of gestational age and preterm birth in a rural, low-income setting and may be a suitable alternative to ultrasound in programmatic settings and large field trials. Trial registration: ClinicalTrials.gov NCT0086047

mTOR independent alteration in ULK1 Ser758 phosphorylation following chronic LRRK2 kinase inhibition

Unc-51 Like Kinase 1 (ULK1) is a critical regulator of the biogenesis of autophagosomes, the central component of the catabolic macroautophagy pathway. Regulation of ULK1 activity is dependent upon several phosphorylation events acting to repress or activate the enzymatic function of this protein. Phosphorylation of Ser758 ULK1 has been linked to repression of autophagosome biogenesis and was thought to be exclusively dependent upon mTOR complex 1 kinase activity. In this study, a novel regulation of Ser758 ULK1 phosphorylation is reported following prolonged inhibition of the Parkinson's disease linked protein Leucine Rich Repeat Kinase 2 (LRRK2). Here, modulation of Ser758 ULK1 phosphorylation following LRRK2 inhibition is decoupled from the repression of autophagosome biogenesis and independent of mTOR complex 1 activity

Using dengue epidemics and local weather in Bali, Indonesia to predict imported dengue in Australia.

BACKGROUND: Although the association between dengue in Bali, Indonesia, and imported dengue in Australia has been widely asserted, no study has quantified this association so far. METHODS: Monthly data on dengue and climatic factors over the past decade for Bali and Jakarta as well as monthly data on imported dengue in Australia underwent a three-stage analysis. Stage I: a quasi-Poisson regression with distributed lag non-linear model was used to assess the associations of climatic factors with dengue in Bali. Stage II: a generalized additive model was used to quantify the association of dengue in Bali with imported dengue in Australia with and without including the number of travelers in log scale as an offset. Stage III: the associations of mean temperature and rainfall (two climatic factors identified in stage I) in Bali with imported dengue in Australia were examined using stage I approach. RESULTS: The number of dengue cases in Bali increased with increasing mean temperature, and, up to a certain level, it also increased with increasing rainfall but dropped off for high levels of rainfall. Above a monthly incidence of 1.05 cases per 100,000, dengue in Bali was almost linearly associated with imported dengue in Australia at a lag of one month. Mean temperature (relative risk (RR) per 0.5 °C increase: 2.95, 95% confidence interval (CI): 1.87, 4.66) and rainfall (RR per 7.5 mm increase: 3.42, 95% CI: 1.07, 10.92) in Bali were significantly associated with imported dengue in Australia at a lag of four months. CONCLUSIONS: This study suggests that climatic factors (i.e., mean temperature and rainfall) known to be conducive of dengue transmission in Bali can provide an early warning with 4-month lead time for Australia in order to mitigate future outbreaks of local dengue in Australia. This study also provides a template and framework for future surveillance of travel-related infectious diseases globally