scholarly journals Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2861
Author(s):  
Mohamed Mannaa ◽  
Gil Han ◽  
Young-Su Seo ◽  
Inmyoung Park
Keyword(s):  
Fermented Food ◽  
Food Preservation ◽  
Starter Cultures ◽  
Molecular Tools ◽  
Spontaneous Fermentation ◽  
Food Fermentation ◽  
Functional Roles ◽  
Technological Advances ◽  
Ancient Times ◽  
Generation Sequencing

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

scholarly journals Identification of Lactic Acid Bacteria Isolated from Local Commercial Yahe (Fermented Caridean-Shrimp) Products

2021 ◽  
Vol 1 (3) ◽  
Author(s):  
Say Sophakphokea ◽  
Rith Sokuncharya ◽  
Norng Chakriya ◽  
Ang Vichheka ◽  
Chheun Malyheng ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lactobacillus Plantarum ◽  
Lactobacillus Acidophilus ◽  
Starter Culture ◽  
Acid Tolerance ◽  
Food Preservation ◽  
Starter Cultures ◽  
Caridean Shrimp ◽  
Food Fermentation

Fermentation was used since ancient times as an easy method of food preservation, which also maintains and/or improves the nutritional and sensory properties of food. A research as aimed at identifying strain of lactic acid bacteria (LAB) from fermented caridean-shrimp, which properties suitable for starter cultures in food fermentation. A total of 18 LAB stains were obtained from ten different samples, in each sample consisted of commercial LAB strain that isolated from ten samples of caridean-shrimp. The LAB strains from ten samples were screened for resistance to biological barriers (acid and bile salts), and the three most promising strains were selected. The three bacteria strains were isolated from samples of caridean[1]shrimp and were characterized by the API 50 CHL system of identification. Three lactic acid bacteria species were identified and included Lactobacillus plantarum, and Lactobacillus acidophilus. Strain Y’11b,2, Y’11e,2, Y’85,1, which showed probiotic characteristics reducing cell growth of cancer, could be suitable as a starter culture for food fermentation because of its strong acid production and high acid tolerance. This is the first report to describe bacteria, isolated from caridean[1]shrimp, Lactobacillus Plantarum (Y’11b,2, Y’11e,2) and Lactobacillus acidophilus (Y’85,1) which have the probiotic characteristics and the acid tolerance needed for its use as a starter culture in food fermentation.

scholarly journals COCCUS BACTERIA IN FERMENTED DURIAN SPECIFIC FOOD OF BENGKULU

2017 ◽  
Vol 7 (1) ◽  
pp. 37-43
Author(s):  
Hasanuddin Hasanuddin
Keyword(s):  
Lactic Acid ◽  
Organic Acid ◽  
Fermented Food ◽  
Food Preservation ◽  
Laboratory Analysis ◽  
Spontaneous Fermentation ◽  
Traditional Markets ◽  
Durio Zibethinus ◽  
Specific Food

Coccus bactria is the cell of bacteria formed ball or ellip in 0,5 – 1µm diameter. Fermented durian is the fermented food prepared from spontaneous fermentation of durian (Durio zibethinus)with or without salt by wild bacteria. The sources of data in this study was laboratory analysis. Productions center of fermented durian, traditional markets were sampled for the experiment. Sampels were collected weekly in a month. Samples were analyzed microbiologically to determine and identify bacteria infermented durian. There were two species of coccus bacteria involved in fermented durian namely Pediococcus acidilacticiand Leuconostoc mesentroides. The specieseswere included in lactic acid bacteria.Lactic acid (C2H5COOH) is the organic acid that   can serve as a food preservation

scholarly journals The Lactic Acid Bacteria in Fermented Durian (D. Zibethinus )

2021 ◽  
Vol 4 (1) ◽  
pp. 75-81
Author(s):  
Hasanuddin Hasanuddin
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Acidic Solution ◽  
Fermented Food ◽  
Food Preservation ◽  
Biochemical Change ◽  
Lactobacillus Curvatus ◽  
Spontaneous Fermentation ◽  
Durio Zibethinus ◽  
Harmful Organisms

Lactic acid (C2H5COOH) is the organic acid that  can serve as a food preservation. The group of bacteria which can produce lactic acid in their fermentation process known as Lactic Acid Bacteria (LAB). A fundamental biochemical change of fermentation is that an acidic environment is created. Many harmful organisms cannot exist in acidic solution so the fermentation productions are save to eat. Fermented Durian is the fermented food prepared from spontaneous fermentation of durian (Durio zibethinus) with or without salt by wild bacteria. The research was conducted to isolate and identify lactic acid bacteria in tempoyak. The data in this study were laboratory analysis. Samples were collected weekly in a month analyzed microbiologically from traditionl markets in Bengkulu. There were four species of lactic acid bacteria involved in fermented durian namely Leuconostoc mesentroides, Pediococcus acidilactici, Lactobacillus plantarum, and Lactobacillus curvatus.

Molecular Mechanisms Underlying the Functions of Cellular Markers Associated with the Phenotype of Cancer Stem Cells

2019 ◽  
Vol 14 (5) ◽  
pp. 405-420 ◽  
Author(s):  
Eduardo Alvarado-Ortiz ◽  
Miguel Á. Sarabia-Sánchez ◽  
Alejandro García-Carrancá
Keyword(s):  
Stem Cells ◽  
Cancer Stem Cells ◽  
Molecular Mechanisms ◽  
Tumor Biology ◽  
Molecular Tools ◽  
Recent Past ◽  
Functional Roles ◽  
Cellular Population ◽  
Cellular Markers ◽  
A Minor

Cancer Stem Cells (CSC) generally constitute a minor cellular population within tumors that exhibits some capacities of normal Stem Cells (SC). The existence of CSC, able to self-renew and differentiate, influences central aspects of tumor biology, in part because they can continue tumor growth, give rise to metastasis, and acquire drug and radioresistance, which open new avenues for therapeutics. It is well known that SC constantly interacts with their niche, which includes mesenchymal cells, extracellular ligands, and the Extra Cellular Matrix (ECM). These interactions regularly lead to homeostasis and maintenance of SC characteristics. However, the exact participation of each of these components for CSC maintenance is not clear, as they appear to be context- or cell-specific. In the recent past, surface cellular markers have been fundamental molecular tools for identifying CSC and distinguishing them from other tumor cells. Importantly, some of these cellular markers have been shown to possess functional roles that affect central aspects of CSC. Likewise, some of these markers can participate in regulating the interaction of CSC with their niche, particularly the ECM. We focused this review on the molecular mechanisms of surface cellular markers commonly employed to identify CSC, highlighting the signaling pathways and mechanisms involved in CSC-ECM interactions, through each of the cellular markers commonly used in the study of CSC, such as CD44, CD133, CD49f, CD24, CXCR4, and LGR5. Their presence does not necessarily implicate them in CSC biology.

Genes involved in lactose catabolism and organic acid production during growth of Lactobacillus delbrueckii UFV H2b20 in skimmed milk

2012 ◽  
Vol 3 (1) ◽  
pp. 23-32 ◽  
Author(s):  
A. Do Carmo ◽  
M. De Oliveira ◽  
D. Da Silva ◽  
S. Castro ◽  
A. Borges ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Organic Acid ◽  
Acid Production ◽  
Food Preservation ◽  
Starter Cultures ◽  
Lactobacillus Delbrueckii ◽  
Probiotic Properties ◽  
Organic Acid Production ◽  
Probiotic Lactobacillus ◽  
Skimmed Milk

There are three main reasons for using lactic acid bacteria (LAB) as starter cultures in industrial food fermentation processes: food preservation due to lactic acid production; flavour formation due to a range of organic molecules derived from sugar, lipid and protein catabolism; and probiotic properties attributed to some strains of LAB, mainly of lactobacilli. The aim of this study was to identify some genes involved in lactose metabolism of the probiotic Lactobacillus delbrueckii UFV H2b20, and analyse its organic acid production during growth in skimmed milk. The following genes were identified, encoding the respective enzymes: ldh – lactate dehydrogenase, adhE – Ldb1707 acetaldehyde dehydrogenase, and ccpA-pepR1 – catabolite control protein A. It was observed that L. delbrueckii UFV H2b20 cultivated in different media has the unexpected ability to catabolyse galactose, and to produce high amounts of succinic acid, which was absent in the beginning, raising doubts about the subspecies in question. The phylogenetic analyses showed that this strain can be compared physiologically to L. delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis, which are able to degrade lactose and can grow in milk. L. delbrueckii UFV H2b20 sequences have grouped with L. delbrueckii subsp. bulgaricus ATCC 11842 and L. delbrueckii subsp. bulgaricus ATCC BAA-365, strengthening the classification of this probiotic strain in the NCFM group proposed by a previous study. Additionally, L. delbrueckii UFV H2b20 presented an evolutionary pattern closer to that of probiotic Lactobacillus acidophilus NCFM, corroborating the suggestion that this strain might be considered as a new and unusual subspecies among L. delbrueckii subspecies, the first one identified as a probiotic. In addition, its unusual ability to metabolise galactose, which was significantly consumed in the fermentation medium, might be exploited to produce low-browning probiotic Mozzarella cheeses, a desirable property for pizza cheeses.

scholarly journals Genetic Diversity in Casein Gene Cluster in a Dromedary Camel (C. dromedarius) Population from the United Arab Emirates

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1417
Author(s):  
Abdullah Al Mutery ◽  
Naushad Rais ◽  
Walaa KE Mohamed ◽  
Tlili Abdelaziz
Keyword(s):  
Gene Cluster ◽  
United Arab Emirates ◽  
Future Research ◽  
Dromedary Camel ◽  
Functional Impact ◽  
Casein Gene ◽  
Functional Roles ◽  
Targeted Next Generation Sequencing ◽  
Casein Genes ◽  
Generation Sequencing

Genetic polymorphisms, causing variation in casein genes (CSN1S1, CSN1S2, CSN2, and CSN3), have been extensively studied in goats and cows, but there are only few studies reported in camels. Therefore, we aimed to identify alleles with functional roles in the United Arab Emirates dromedary camel (Camelus dromedarius) population to complement previous studies conducted on the same species. Using targeted next-generation sequencing, we sequenced all genes in the casein gene cluster in 93 female camels to identify and characterize novel gene variants. Most variants were found in noncoding introns and upstream sequences, but a few variants showed the possibility of functional impact. CSN2 was found to be most polymorphic, with total 91 different variants, followed by CSN1S1, CSN3 and CSN1S2. CSN1S1, CSN1S2 and CSN2 each had at least two variants while CSN3 had only one functional allele. In future research, the functional impact of these variants should be investigated further.

scholarly journals Production of Nigerian Yoghurt Using Lactic Acid Bacteria as Starter Cultures

2020 ◽  
pp. 32-42
Author(s):  
S. Aforijiku ◽  
S. M. Wakil ◽  
A. A. Onilude
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Proximate Composition ◽  
Room Temperature ◽  
Starter Cultures ◽  
Cow Milk ◽  
Spontaneous Fermentation ◽  
Overall Acceptability ◽  
Fermentation Control ◽  
Better Than

Aim: This work was carried out to investigate the influence of Lactic Acid Bacteria (LAB) on organoleptic quality and proximate composition of yoghurt, and viability of starter cultures in yoghurt. Methods: The LAB starter cultures were selected based on their ability to produce diacetyl and lactic acid. Results: Lactobacillus caseiN1 produced the highest quantity (2.72 g/L) of diacetyl at 48 hrs of incubation while Pediococcus acidilacticiG1 had the lowest amount (0.50 g/L). The pH of produced yoghurt ranged between 4.40 and 5.58 while the corresponding lactic acid contents ranged between 0.70 and 0.96 g/L. Yoghurt produced with cow milk inoculated with L. PlantarumN24 and L. BrevisN10 had the lowest pH (4.40) at significant level of P≤0.05. Yoghurt with mixed culture of L. PlantarumN24 and L. PlantarumN17 had the highest protein content (5.13%) while spontaneous fermentation (control) produced the least (0.48%). Yoghurt produced from cow milk inoculated with L. PlantarumN24 and L. PlantarumN17 was rated best with overall acceptability (9.0) during first day of storage while the commercial yoghurt (5.8) and spontaneous fermentation (6.8) had least overall acceptability at P≤0.05. Conclusion: Yoghurt samples stored in refrigerator had more viable LAB counts for a period of 21 days while the samples stored at room temperature had a day count except for yoghurt produced with cow milk inoculated with L. plantarumN24 which retained its viability at the second day. The yoghurt produced with selected LAB starters are better than commercial yoghurt in terms of sensory properties, proximate composition, pH and viability.

scholarly journals Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

BMC Genetics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 66 ◽  
Author(s):  
Rhyan B Dockter ◽  
David B Elzinga ◽  
Brad Geary ◽  
P Maughan ◽  
Leigh A Johnson ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Molecular Tools ◽  
Generation Sequencing

scholarly journals Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Ming Zhao ◽  
Xiao Q. Su ◽  
Bo Nian ◽  
Li J. Chen ◽  
Dong L. Zhang ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Gallic Acid ◽  
Glycoside Hydrolases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fermented Foods ◽  
Catechol Dioxygenase ◽  
Spontaneous Fermentation ◽  
Food Fermentation

ABSTRACT The microbiome in fermentation has direct impacts on the quality of fermented foods and is of great scientific and commercial interest. Despite considerable effort to explain the microbial metabolism associated with food fermentation, the role of the microbiome in pu-erh tea fermentation remains unknown. Here, we applied integrated meta-omics approaches to characterize the microbiome in two repeated fermentations of pu-erh tea. Metabarcoding analysis of bacterial 16S rRNA genes showed a decrease in the proportion of Proteobacteria and an increase in the abundance of Firmicutes during fermentation. Metabarcoding analysis of fungal internal transcribed spacer (ITS) sequence demonstrated that Rasamsonia, Thermomyces, and Aspergillus were dominant at the intermediate stage, whereas Aspergillus was dominant at other stages in fermentation. Metaproteomics analysis assigned primary microbial metabolic activity to metabolism and identified microbial carbohydrate-active enzymes involved in the degradation of polysaccharides including cellulose, xylan, xyloglucan, pectin, starch, lignin, galactomannan, and chitin. Metabolomics and high-performance liquid chromatography analysis revealed that levels of phenolic compounds, including gallates, decreased whereas contents of gallic acid and ellagic acid significantly increased after fermentation (P < 0.05). The changes in levels of gallates and gallic acid were associated with the hydrolysis of tannase. Glycoside hydrolases, phenol 2-monooxygenase, salicylaldehyde dehydrogenase, salicylate 1-monooxygenase, catechol O-methyltransferase, catechol dioxygenase, and quercetin 2,3-dioxygenases were hypothesized to be related to oxidation, conversion, or degradation of phenolic compounds. We demonstrated microbiota in fermentation and their function in the production of enzymes related to the degradation of polysaccharides, and metabolism of phenolic compounds, resulting in changes in metabolite contents and the quality of pu-erh tea. IMPORTANCE Fermented foods play important roles in diets worldwide and account for approximately one-third of all foods and beverages consumed. To date, traditional fermentation has used spontaneous fermentation. The microbiome in fermentation has direct impacts on the quality and safety of fermented foods and contributes to the preservation of traditional methods. Here, we used an integrated meta-omics approach to study the microbiome in the fermentation of pu-erh tea, which is a well-known Chinese fermented food with a special flavor and healthful benefits. This study advanced the knowledge of microbiota, metabolites, and enzymes in the fermentation of pu-erh tea. These novel insights shed light onto the complex microbiome in pu-erh fermentation and highlight the power of integrated meta-omics approaches in understanding the microbiome in food fermentation ecosystems.

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