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Silva CCG, Ribeiro SC. Microorganisms and Their Importance in the Food Industry: Safety, Quality and Health Properties. Foods 2024; 13:1452. [PMID: 38790752 PMCID: PMC11120582 DOI: 10.3390/foods13101452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms can play an important role in food production, especially through fermentation processes [...].
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Affiliation(s)
- Celia C. G. Silva
- Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, 9700-042 Angra do Heroísmo, Portugal;
- School of Agrarian and Environmental Sciences, University of the Azores, 9700-042 Angra do Heroísmo, Portugal
| | - Susana Chaves Ribeiro
- Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, 9700-042 Angra do Heroísmo, Portugal;
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2
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Josephs-Spaulding J, Rajput A, Hefner Y, Szubin R, Balasubramanian A, Li G, Zielinski DC, Jahn L, Sommer M, Phaneuf P, Palsson BO. Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning. mSystems 2024; 9:e0125723. [PMID: 38349131 PMCID: PMC10949432 DOI: 10.1128/msystems.01257-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Limosilactobacillus reuteri, a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied the independent component analysis (ICA) to 117 RNA-seq data sets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. Our findings indicate that the ICA provides a qualitative advancement and captures nuanced relationships within gene clusters that other methods may miss. This study uncovers the fundamental properties of L. reuteri's TRN and deepens our understanding of its arginine metabolism and the co-regulation of riboflavin metabolism and fatty acid conversion. It also sheds light on conditions that regulate genes within a specific biosynthetic gene cluster and allows for the speculation of the potential role of isoprenoid biosynthesis in L. reuteri's adaptive response to environmental changes. By integrating transcriptomics and machine learning, we provide a system-level understanding of L. reuteri's response mechanism to environmental fluctuations, thus setting the stage for modeling the probiotic transcriptome for applications in microbial food production. IMPORTANCE We have studied Limosilactobacillus reuteri, a beneficial probiotic microbe that plays a significant role in our health and production of sustainable foods, a type of foods that are nutritionally dense and healthier and have low-carbon emissions compared to traditional foods. Similar to how humans adapt their lifestyles to different environments, this microbe adjusts its behavior by modulating the expression of genes. We applied machine learning to analyze large-scale data sets on how these genes behave across diverse conditions. From this, we identified 35 unique patterns demonstrating how L. reuteri adjusts its genes based on 50 unique environmental conditions (such as various sugars, salts, microbial cocultures, human milk, and fruit juice). This research helps us understand better how L. reuteri functions, especially in processes like breaking down certain nutrients and adapting to stressful changes. More importantly, with our findings, we become closer to using this knowledge to improve how we produce more sustainable and healthier foods with the help of microbes.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, California, USA
| | | | - Gaoyuan Li
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Leonie Jahn
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Morten Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Patrick Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Bernhard O. Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
- Department of Bioengineering, University of California, San Diego, California, USA
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3
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Langa S, Peirotén Á, Rodríguez S, Calzada J, Prieto-Paredes R, Curiel JA, Landete JM. Riboflavin bio-enrichment of soy beverage by selected roseoflavin-resistant and engineered lactic acid bacteria. Int J Food Microbiol 2024; 411:110547. [PMID: 38150774 DOI: 10.1016/j.ijfoodmicro.2023.110547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
Some lactic acid bacteria (LAB) have the ability to synthesize riboflavin, a trait linked to the presence of ribG, ribB, ribA and ribH genes located in the rib operon. Previous screening of riboflavin producers identified several LAB strains belonging to different species with this ability, but none of them surpassed 0.25 mg/L production of the vitamin. In this study, we explored two strategies to obtain riboflavin-overproducing strains: by roseoflavin selection of mutants, and by the transformation of selected strains with plasmids pNZ:TuR.rib or pNZ:TuB.rib containing the genes ribG, ribB, ribA and ribH from Lactococcus cremoris MG1363. The resulting riboflavin-overproducing strains were able to produce yields between 0.5 and 6 mg/L in culture media and several of them were selected for the fermentation of soy beverages. Riboflavin in bio-enriched soy beverages was evaluated by direct fluorescence measurement and high-performance liquid chromatography-fluorescence analysis. Soy beverages fermented with the recombinant strains Lactococcus cremoris ESI 277 pNZ:TuB.rib and Lactococcus lactis INIA 12 pNZ:TuR.rib showed the highest riboflavin yields (>5 mg/L) after 24 h fermentation. On the other hand, roseoflavin-resistant mutant Limosilactobacillus fermentum INIA P143R2 was able to enrich fermented soy beverages with 1.5 mg/L riboflavin. Riboflavin-overproducing LAB strains constitute a good option for riboflavin enrichment of soy beverages by fermentation and the commercialization of such beverages could be very useful to prevent riboflavin deficiency.
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Affiliation(s)
- Susana Langa
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain.
| | - Ángela Peirotén
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Susana Rodríguez
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Javier Calzada
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Rubén Prieto-Paredes
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - José Antonio Curiel
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - José María Landete
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
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4
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Russo P, Diez-Ozaeta I, Mangieri N, Tamame M, Spano G, Dueñas MT, López P, Mohedano ML. Biotechnological Potential and Safety Evaluation of Dextran- and Riboflavin-Producing Weisella cibaria Strains for Gluten-Free Baking. Foods 2023; 13:69. [PMID: 38201097 PMCID: PMC10778100 DOI: 10.3390/foods13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Gluten consumption causes several immunological and non-immunological intolerances in susceptible individuals. In this study, the dextran-producing Weissella cibaria BAL3C-5 and its derivative, the riboflavin-overproducing strain BAL3C-5 C120T, together with a commercial bakery yeast, were used to ferment gluten-free (GF)-doughs obtained from corn and rice flours at two different concentrations and supplemented with either quinoa, buckwheat, or chickpea to obtain laboratory-scale GF bread. The levels of dextran, riboflavin, and total flavins were determined in the fermented and breads. Both strains grew in fermented doughs and contributed dextran, especially to those made with corn plus quinoa (~1 g/100 g). The highest riboflavin (350-150 µg/100 g) and total flavin (2.3-1.75 mg/100 g) levels were observed with BAL3C-5 C120T, though some differences were detected between the various doughs or breads, suggesting an impact of the type of flour used. The safety assessment confirmed the lack of pathogenic factors in the bacterial strains, such as hemolysin and gelatinase activity, as well as the genetic determinants for biogenic amine production. Some intrinsic resistance to antibiotics, including vancomycin and kanamycin, was found. These results indicated the microbiological safety of both W. cibaria strains and indicated their potential application in baking to produce GF bread.
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Affiliation(s)
- Pasquale Russo
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, 20133 Milan, Italy; (P.R.); (N.M.)
| | - Iñaki Diez-Ozaeta
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), 20018 San Sebastián, Spain;
| | - Nicola Mangieri
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, 20133 Milan, Italy; (P.R.); (N.M.)
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Giuseppe Spano
- DAFNE Department, University of Foggia, 71122 Foggia, Italy;
| | - Maria Teresa Dueñas
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), 20018 San Sebastián, Spain;
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
| | - Mari Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
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5
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Tang H, Huang W, Yao YF. The metabolites of lactic acid bacteria: classification, biosynthesis and modulation of gut microbiota. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:49-62. [PMID: 36908281 PMCID: PMC9993431 DOI: 10.15698/mic2023.03.792] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 03/14/2023]
Abstract
Lactic acid bacteria (LAB) are ubiquitous microorganisms that can colonize the intestine and participate in the physiological metabolism of the host. LAB can produce a variety of metabolites, including organic acids, bacteriocin, amino acids, exopolysaccharides and vitamins. These metabolites are the basis of LAB function and have a profound impact on host health. The intestine is colonized by a large number of gut microorganisms with high species diversity. Metabolites of LAB can keep the balance and stability of gut microbiota through aiding in the maintenance of the intestinal epithelial barrier, resisting to pathogens and regulating immune responses, which further influence the nutrition, metabolism and behavior of the host. In this review, we summarize the metabolites of LAB and their influence on the intestine. We also discuss the underlying regulatory mechanisms and emphasize the link between LAB and the human gut from the perspective of health promotion.
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Affiliation(s)
- Huang Tang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wanqiu Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China.,State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100), Shanghai 200025, China
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Prieto-Paredes R, Landete JM, Peirotén Á, Curiel JA, Langa S. Polymerase chain reaction for molecular detection of the genes involved in the production of riboflavin in lactic acid bacteria. J Microbiol Methods 2023; 206:106678. [PMID: 36708929 DOI: 10.1016/j.mimet.2023.106678] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
Some lactic acid bacteria (LAB) strains have the ability to synthesize riboflavin, a trait linked to the presence of ribG, ribB, ribA and ribH genes in the rib operon. Multiple sequence alignments of these genes showed that these sequences are not identical in different LAB species, so primers designed to detect these genes in one species do not always work with others. Therefore, we designed degenerate primers based on sequences from Lactococcus lactis MG1363, Levilactobacillus brevis ATCC 367 and Limosilactobacillus fermentum IFO3956, and established optimal PCR conditions for the detection of rib genes in different LAB species. Simultaneously, we selected riboflavin-producing LAB strains from our bacterial collection belonging to the species L. brevis, L. fermentum, L. lactis, Leuconostoc mesenteroides and Lactiplantibacillus plantarum, and we were able to detect ribG, ribB, ribA and ribH genes in these strains by PCR using the designed primers. Thus, the development of degenerate primers and optimal PCR conditions for the detection of ribG, ribB, ribA and ribH genes in LAB allowed the detection and the selection of potential riboflavin-producing strains of different species, which could be good candidates for the development of riboflavin-enriched functional foods.
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Affiliation(s)
- Rubén Prieto-Paredes
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - José María Landete
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - Ángela Peirotén
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - José Antonio Curiel
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain
| | - Susana Langa
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040, Madrid, Spain.
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Das R, Tamang B, Najar IN, Thakur N, Mondal K. First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India. Front Microbiol 2023; 14:1158411. [PMID: 37125168 PMCID: PMC10130461 DOI: 10.3389/fmicb.2023.1158411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.
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Affiliation(s)
- Rohit Das
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Buddhiman Tamang
- Department of Microbiology, Sikkim University, Gangtok, India
- *Correspondence: Buddhiman Tamang,
| | | | - Nagendra Thakur
- Department of Microbiology, Sikkim University, Gangtok, India
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Diez-Ozaeta I, Martín-Loarte L, Mohedano ML, Tamame M, Ruiz-Masó JÁ, del Solar G, Dueñas MT, López P. A methodology for the selection and characterization of riboflavin-overproducing Weissella cibaria strains after treatment with roseoflavin. Front Microbiol 2023; 14:1154130. [PMID: 37089563 PMCID: PMC10116070 DOI: 10.3389/fmicb.2023.1154130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
Fermentative processes by lactic acid bacteria can produce metabolites of interest to the health and food industries. Two examples are the production of B-group vitamins, and of prebiotic and immunomodulatory dextran-type exopolysaccharides. In this study, three riboflavin- and dextran-producing Weissella cibaria strains (BAL3C-5, BAL3C-7 and BAL3C-22) were used to develop a new method for selection and isolation of spontaneous riboflavin-overproducing W. cibaria mutants. This method was based on the selection of strains resistant to roseoflavin. The DNA sequencing of the FMN riboswitch of bacterial cell populations treated with various roseoflavin concentrations, revealed the existence of at least 10 spontaneous and random point mutations at this location. Folding and analysis of the mutated FMN riboswitches with the RNA fold program predicted that these mutations could result in a deregulation of the rib operon expression. When the roseoflavin-treated cultures were plated on medium supporting dextran synthesis, the most promising mutants were identified by the yellow color of their mucous colonies, exhibiting a ropy phenotype. After their isolation and recovery in liquid medium, the evaluation of their riboflavin production revealed that the mutant strains synthesized a wide range of riboflavin levels (from 0.80 to 6.50 mg/L) above the wild-type level (0.15 mg/L). Thus, this was a reliable method to select spontaneous riboflavin-overproducing and dextran-producing strains of W. cibaria. This species has not yet been used as a starter or adjunct culture, but this study reinforces the potential that it has for the food and health industry for the production of functional foods or as a probiotic. Furthermore, analysis of the influence of FMN present in the growth medium, on rib mRNA and riboflavin levels, revealed which mutant strains produce riboflavin without flavin regulation. Moreover, the BAL3C-5 C120T mutant was identified as the highest riboflavin-overproducer. Determination of its chromosomal DNA sequence and that of BAL3C-5, revealed a total identity between the 2 strains except for the C120T mutation at the FMN riboswitch. To our knowledge, this work is the first demonstration that only a single alteration in the genome of a lactic acid bacteria is required for a riboflavin-overproducing phenotype.
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Affiliation(s)
- Iñaki Diez-Ozaeta
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Lucía Martín-Loarte
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Mari Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, (IBFG) CSIC-Universidad de Salamanca, Salamanca, Spain
| | - José Ángel Ruiz-Masó
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Gloria del Solar
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - María Teresa Dueñas
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
- *Correspondence: María Teresa Dueñas,
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
- Paloma López,
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9
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Mu Y, Zhang C, Li T, Jin FJ, Sung YJ, Oh HM, Lee HG, Jin L. Development and Applications of CRISPR/Cas9-Based Genome Editing in Lactobacillus. Int J Mol Sci 2022; 23:12852. [PMID: 36361647 PMCID: PMC9656040 DOI: 10.3390/ijms232112852] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 09/25/2023] Open
Abstract
Lactobacillus, a genus of lactic acid bacteria, plays a crucial function in food production preservation, and probiotics. It is particularly important to develop new Lactobacillus strains with superior performance by gene editing. Currently, the identification of its functional genes and the mining of excellent functional genes mainly rely on the traditional gene homologous recombination technology. CRISPR/Cas9-based genome editing is a rapidly developing technology in recent years. It has been widely applied in mammalian cells, plants, yeast, and other eukaryotes, but less in prokaryotes, especially Lactobacillus. Compared with the traditional strain improvement methods, CRISPR/Cas9-based genome editing can greatly improve the accuracy of Lactobacillus target sites and achieve traceless genome modification. The strains obtained by this technology may even be more efficient than the traditional random mutation methods. This review examines the application and current issues of CRISPR/Cas9-based genome editing in Lactobacillus, as well as the development trend of CRISPR/Cas9-based genome editing in Lactobacillus. In addition, the fundamental mechanisms of CRISPR/Cas9-based genome editing are also presented and summarized.
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Affiliation(s)
- Yulin Mu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chengxiao Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Taihua Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yun-Ju Sung
- BioNanotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Long Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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10
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Hernández-Alcántara AM, Chiva R, Mohedano ML, Russo P, Ruiz-Masó JÁ, del Solar G, Spano G, Tamame M, López P. Weissella cibaria riboflavin-overproducing and dextran-producing strains useful for the development of functional bread. Front Nutr 2022; 9:978831. [PMID: 36267909 PMCID: PMC9577222 DOI: 10.3389/fnut.2022.978831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
This work describes a method for deriving riboflavin overproducing strains of Weissella cibaria by exposing three strains (BAL3C-5, BAL3C-7, and BAL3C-22) isolated from dough to increasing concentrations of roseoflavin. By this procedure, we selected one mutant overproducing strain from each parental strain (BAL3C-5 B2, BAL3C-7 B2, and BAL3C-22 B2, respectively). Quantification of dextran and riboflavin produced by the parental and mutant strains in a defined medium lacking riboflavin and polysaccharides confirmed that riboflavin was only overproduced by the mutant strains, whereas dextran production was similar in both mutant and parental strains. The molecular basis of the riboflavin overproduction by the mutants was determined by nucleotide sequencing of their rib operons, which encode the enzymes of the riboflavin biosynthetic pathway. We detected a unique mutation in each of the overproducing strains. These mutations, which map in the sensor domain (aptamer) of a regulatory element (the so-called FMN riboswitch) present in the 5’ untranslated region of the rib operon mRNA, appear to be responsible for the riboflavin-overproducing phenotype of the BAL3C-5 B2, BAL3C-7 B2, and BAL3C-22 B2 mutant strains. Furthermore, the molecular basis of dextran production by the six W. cibaria strains has been characterized by (i) the sequencing of their dsr genes encoding dextransucrases, which synthesize dextran using sucrose as substrate, and (ii) the detection of active Dsr proteins by zymograms. Finally, the parental and mutant strains were analyzed for in situ production of riboflavin and dextran during experimental bread making. The results indicate that the mutant strains were able to produce experimental wheat breads biofortified with both riboflavin and dextran and, therefore, may be useful for the manufacture of functional commercial breads.
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Affiliation(s)
- Annel M. Hernández-Alcántara
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Rosana Chiva
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - María Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Pasquale Russo
- Department of Agriculture Food Natural Science Engineering, University of Foggia, Foggia, Italy
| | - José Ángel Ruiz-Masó
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Gloria del Solar
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Giuseppe Spano
- Department of Agriculture Food Natural Science Engineering, University of Foggia, Foggia, Italy
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain,*Correspondence: Paloma López,
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