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Wen L, Yang L, Chen C, Li J, Fu J, Liu G, Kan Q, Ho CT, Huang Q, Lan Y, Cao Y. Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods. Crit Rev Food Sci Nutr 2023:1-17. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.
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Affiliation(s)
- Linfeng Wen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lixin Yang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Cong Chen
- Guangdong Eco-engineering Polytechnic, Guangzhou, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Jiangyan Fu
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Guo Liu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qixin Kan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Yaqi Lan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
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Bacali C, Vulturar R, Buduru S, Cozma A, Fodor A, Chiș A, Lucaciu O, Damian L, Moldovan ML. Oral Microbiome: Getting to Know and Befriend Neighbors, a Biological Approach. Biomedicines 2022; 10:biomedicines10030671. [PMID: 35327473 PMCID: PMC8945538 DOI: 10.3390/biomedicines10030671] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The oral microbiome, forming a biofilm that covers the oral structures, contains a high number of microorganisms. Biofilm formation starts from the salivary pellicle that allows bacterial adhesion–colonization–proliferation, co-aggregation and biofilm maturation in a complex microbial community. There is a constant bidirectional crosstalk between human host and its oral microbiome. The paper presents the fundamentals regarding the oral microbiome and its relationship to modulator factors, oral and systemic health. The modern studies of oral microorganisms and relationships with the host benefits are based on genomics, transcriptomics, proteomics and metabolomics. Pharmaceuticals such as antimicrobials, prebiotics, probiotics, surface active or abrasive agents and plant-derived ingredients may influence the oral microbiome. Many studies found associations between oral dysbiosis and systemic disorders, including autoimmune diseases, cardiovascular, diabetes, cancers and neurodegenerative disorders. We outline the general and individual factors influencing the host–microbial balance and the possibility to use the analysis of the oral microbiome in prevention, diagnosis and treatment in personalized medicine. Future therapies should take in account the restoration of the normal symbiotic relation with the oral microbiome.
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Affiliation(s)
- Cecilia Bacali
- Department of Prosthodontics and Dental Materials, “Iuliu Hatieganu” University of Medicine and Pharmacy, 32 Clinicilor St., 400006 Cluj-Napoca, Romania; (C.B.); (S.B.)
| | - Romana Vulturar
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 6 Pasteur St., 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Correspondence:
| | - Smaranda Buduru
- Department of Prosthodontics and Dental Materials, “Iuliu Hatieganu” University of Medicine and Pharmacy, 32 Clinicilor St., 400006 Cluj-Napoca, Romania; (C.B.); (S.B.)
| | - Angela Cozma
- 4th Medical Department, University of Medicine and Pharmacy “Iuliu Hatieganu” Cluj-Napoca, 18 Republicii St., 400015 Cluj-Napoca, Romania;
| | - Adriana Fodor
- Clinical Center of Diabetes, Nutrition and Metabolic Diseases, “Iuliu Hatieganu” University of Medicine and Pharmacy, 2-4 Clinicilor St., 400012 Cluj-Napoca, Romania;
| | - Adina Chiș
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 6 Pasteur St., 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Ondine Lucaciu
- Department of Oral Health, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania;
| | - Laura Damian
- Department of Rheumatology, Emergency Clinical County Hospital Cluj, Centre for Rare Autoimmune and Autoinflammatory Diseases, 2-4 Clinicilor St., 400006 Cluj-Napoca, Romania;
- CMI Reumatologie Dr. Damian, 6-8 Petru Maior St., 400002 Cluj-Napoca, Romania
| | - Mirela Liliana Moldovan
- Department of Dermopharmacy and Cosmetics, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 12, I. Creanga St., 400010 Cluj-Napoca, Romania;
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Purohit HJ, Kapley A, Khardenavis A, Qureshi A, Dafale NA. Insights in Waste Management Bioprocesses Using Genomic Tools. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:121-170. [PMID: 27926430 DOI: 10.1016/bs.aambs.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
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Affiliation(s)
- H J Purohit
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Kapley
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Khardenavis
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Qureshi
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - N A Dafale
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
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Zarco MF, Vess TJ, Ginsburg GS. The oral microbiome in health and disease and the potential impact on personalized dental medicine. Oral Dis 2011; 18:109-20. [PMID: 21902769 DOI: 10.1111/j.1601-0825.2011.01851.x] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The oral microbiome is particularly imperative to health because it can cause both oral and systemic disease. The oral microbiome rests within biofilms throughout the oral cavity, forming an ecosystem that maintains health when in equilibrium. However, certain ecological shifts in the microbiome allow pathogens to manifest and cause disease. Severe forms of oral disease may result in systemic disease at different body sites. Microbiomics and metagenomics are two fields of research that have emerged to identify the presence of specific microbes in the body and understand the nature of the microbiome activity during both health and disease. The analysis of the microbiome and its genomes will pave the way for more effective therapeutic and diagnostic techniques and, ultimately, contribute to the development of personalized medicine and personalized dental medicine.
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Affiliation(s)
- M F Zarco
- Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA
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