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Li Y, He W, Liu S, Hu X, He Y, Song X, Yin J, Nie S, Xie M. Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects. Compr Rev Food Sci Food Saf 2024; 23:e70030. [PMID: 39379298 DOI: 10.1111/1541-4337.70030] [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: 04/06/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 10/10/2024]
Abstract
Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.
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Affiliation(s)
- Yuhao Li
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Weiwei He
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Shuai Liu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Xiaoyi Hu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Yuxing He
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Xiaoxiao Song
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Junyi Yin
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
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Tritean N, Dimitriu L, Dima ȘO, Ghiurea M, Trică B, Nicolae CA, Moraru I, Nicolescu A, Cimpean A, Oancea F, Constantinescu-Aruxandei D. Bioactive Hydrogel Formulation Based on Ferulic Acid-Grafted Nano-Chitosan and Bacterial Nanocellulose Enriched with Selenium Nanoparticles from Kombucha Fermentation. J Funct Biomater 2024; 15:202. [PMID: 39057323 PMCID: PMC11277923 DOI: 10.3390/jfb15070202] [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: 05/19/2024] [Revised: 07/13/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Selenium nanoparticles (SeNPs) have specific properties that result from their biosynthesis particularities. Chitosan can prevent pathogenic biofilm development. A wide palette of bacterial nanocellulose (BNC) biological and physical-chemical properties are known. The aim of this study was to develop a hydrogel formulation (SeBNCSFa) based on ferulic acid-grafted chitosan and bacterial nanocellulose (BNC) enriched with SeNPs from Kombucha fermentation (SeNPsK), which could be used as an adjuvant for oral implant integration and other applications. The grafted chitosan and SeBNCSFa were characterized by biochemical and physical-chemical methods. The cell viability and proliferation of HGF-1 gingival fibroblasts were investigated, as well as their in vitro antioxidant activity. The inflammatory response was determined by enzyme-linked immunosorbent assay (ELISA) of the proinflammatory mediators (IL-6, TNF-α, and IL-1β) in cell culture medium. Likewise, the amount of nitric oxide released was measured by the Griess reaction. The antimicrobial activity was also investigated. The grafting degree with ferulic acid was approximately 1.780 ± 0.07% of the total chitosan monomeric units, assuming single-site grafting per monomer. Fourier-transform infrared spectroscopy evidenced a convolution of BNC and grafted chitosan spectra, and X-ray diffraction analysis highlighted an amorphous rearrangement of the diffraction patterns, suggesting multiple interactions. The hydrogel showed a high degree of cytocompatibility, and enhanced antioxidant, anti-inflammatory, and antimicrobial potentials.
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Affiliation(s)
- Naomi Tritean
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
- Faculty of Biology, University of Bucharest, Spl. Independentei nr. 91-95, Sector 5, 50095 Bucharest, Romania;
| | - Luminița Dimitriu
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Ștefan-Ovidiu Dima
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Marius Ghiurea
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Bogdan Trică
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Cristian-Andi Nicolae
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Ionuț Moraru
- Laboratoarele Medica Srl., Frasinului Str. nr. 11, 075100 Otopeni, Romania;
| | - Alina Nicolescu
- “Petru Poni” Institute for Macromolecular Chemistry, Aleea Grigore Ghica Voda 41A, 700487 Iasi, Romania;
| | - Anisoara Cimpean
- Faculty of Biology, University of Bucharest, Spl. Independentei nr. 91-95, Sector 5, 50095 Bucharest, Romania;
| | - Florin Oancea
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
| | - Diana Constantinescu-Aruxandei
- Bioresource and Polymer Department, National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, Splaiul Independenței nr. 202, Sector 6, 060021 Bucharest, Romania; (N.T.); (L.D.); (Ș.-O.D.); (M.G.); (B.T.); (C.-A.N.)
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Nguyen AV, Yaghoobi M, Zhang S, Li P, Li Q, Dogan B, Ahnrud GP, Flock G, Marek P, Simpson KW, Abbaspourrad A. Adaptive Laboratory Evolution of Probiotics toward Oxidative Stress Using a Microfluidic-Based Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306974. [PMID: 38247174 DOI: 10.1002/smll.202306974] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/28/2023] [Indexed: 01/23/2024]
Abstract
Adaptive laboratory evolution (ALE) can be used to make bacteria less susceptible to oxidative stress. An alternative to large batch scale ALE cultures is to use microfluidic platforms, which are often more economical and more efficient. Microfluidic ALE platforms have shown promise, but many have suffered from subpar cell passaging mechanisms and poor spatial definition. A new approach is presented using a microfluidic Evolution on a Chip (EVoc) design which progressively drives microbial cells from areas of lower H2O2 concentration to areas of higher concentration. Prolonged exposure, up to 72 h, revealed the survival of adaptive strains of Lacticaseibacillus rhamnosus GG, a beneficial probiotic often included in food products. After performing ALE on this microfluidic platform, the bacteria persisted under high H2O2 concentrations in repeated trials. After two progressive exposures, the ability of L. rhamnosus to grow in the presence of H2O2 increased from 1 mm H2O2 after a lag time of 31 h to 1 mm after 21 h, 2 mm after 28 h, and 3 mm after 42 h. The adaptive strains have different morphology, and gene expression compared to wild type, and genome sequencing revealed a potentially meaningful single nucleotide mutation in the protein omega-amidase.
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Affiliation(s)
- Ann V Nguyen
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Mohammad Yaghoobi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Peilong Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Qike Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Gianna P Ahnrud
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Genevieve Flock
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Patrick Marek
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
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Wang Y, Dong W, Chu L, Zhao H, He L, Sheng X. A combination of proteomics, genetics, and physiology provides insights into the acid-tolerance phenotype of Pseudomonas pergaminensis F77. Microbiol Res 2024; 278:127545. [PMID: 37952350 DOI: 10.1016/j.micres.2023.127545] [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: 09/13/2023] [Revised: 10/29/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023]
Abstract
Acid tolerance is crucial for the effective and persistent mineral weathering by acid-producing bacteria. Here, the molecular basis of the acid tolerance of mineral-weathering Pseudomonas pergaminensis F77 was identified using proteomics analysis of the strain under acid stress. Then, the acid tolerance of strain F77 and its mutants with deletion of the acid tolerance-related genes orf03767, mcp, resR, nueR, yegD, and fxsA, which are involved in the two-component systems, DNA repair, nucleotide binding, and membrane parts, were compared. Finally, the acid tolerance-related physiological mechanisms of strain F77 and its mutants F77ΔnueR and F77ΔresR under acidic conditions were characterized. The significantly upregulated proteins in the acid-adapted and acid-challenged strain F77 included the proteins involved in metabolic pathways associated with ATPase, membrane components, organic acid transmembrane transporters, response to stimulus, nucleotide binding, ABC transporters, and two-component systems. The cell numbers decreased by 24-100% at pH ≤ 4.50, while the membrane fluidity increased by 22-61% at pH ≤ 5.50 for the mutants F77ΔnueR and F77ΔresR, compared with that of strain F77. The intracellular H+-ATPase activities decreased by 29-33% for the mutant F77ΔnueR at pH ≤ 4.50% and 33-79% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00); meanwhile, the ratios of intracellular NAD+/NADH decreased by 71-91% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00), compared with that of strain F77. Furthermore, the intracellular putrescine concentrations were reduced by 40-70% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00) compared with that of strain F77. Our findings suggested that multiple proteins and metabolic pathways were associated with bacterial acid tolerance and revealed that nueR and resR were involved in acid tolerance based on their modulation of multiple acid tolerance-related physiological functions in strain F77.
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Affiliation(s)
- Yuanli Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, China
| | - Wen Dong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lingfeng Chu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hui Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Linyan He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Xiafang Sheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
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Deng Y, Pan J, Yang X, Yang S, Chi H, Yang X, Qu X, Sun S, You L, Hou C. Dual roles of nanocrystalline cellulose extracted from jute ( Corchorus olitorius L.) leaves in resisting antibiotics and protecting probiotics. NANOSCALE ADVANCES 2023; 5:6435-6448. [PMID: 38024324 PMCID: PMC10662138 DOI: 10.1039/d3na00345k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/14/2023] [Indexed: 12/01/2023]
Abstract
Antibiotics can cure diseases caused by bacterial infections, but their widespread use can have some side effects, such as probiotic reduction. There is an urgent need for such agents that can not only alleviate the damage caused by antibiotics, but also maintain the balance of the gut microbiota. In this study, we first characterized the nanocrystalline cellulose (NCC) extracted from plant jute (Corchorus olitorius L.) leaves. Next, we evaluated the protective effect of jute NCC and cellulose on human model gut bacteria (Lacticaseibacillus rhamnosus and Escherichia coli) under antibiotic stress by measuring bacterial growth and colony forming units. We found that NCC is more effective than cellulose in adsorbing antibiotics and defending the gut bacteria E. coli. Interestingly, the low-dose jute NCC clearly maintained the balance of key gut bacteria like Snodgrassella alvi and Lactobacillus Firm-4 in bees treated with tetracycline and reduced the toxicity caused by antibiotics. It also showed a more significant protective effect on human gut bacteria, especially L. rhamnosus, than cellulose. This study first demonstrated that low-dose NCC performed satisfactorily as a specific probiotic to mitigate the adverse effects of antibiotics on gut bacteria.
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Affiliation(s)
- Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Jiangpeng Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences Beijing 100093 P. R. China
- Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081 P. R. China
| | - Haiyang Chi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiushi Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Xiaoxin Qu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Shitao Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
| | - Linfeng You
- Department of Food and Biotechnology Engineering, Chongqing Technology and Business University Chongqing 400067 P. R. China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences Changsha 410205 P. R. China
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