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Gao Q, Li D, Wang Y, Zhao C, Li M, Xiao J, Kang Y, Lin H, Wang N. Analysis of intestinal flora and cognitive function in maintenance hemodialysis patients using combined 16S ribosome DNA and shotgun metagenome sequencing. Aging Clin Exp Res 2024; 36:28. [PMID: 38334873 PMCID: PMC10857965 DOI: 10.1007/s40520-023-02645-y] [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: 08/16/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
BACKGROUND Cognitive impairment is widely prevalent in maintenance hemodialysis (MHD) patients, and seriously affects their quality of life. The intestinal flora likely regulates cognitive function, but studies on cognitive impairment and intestinal flora in MHD patients are lacking. METHODS MHD patients (36) and healthy volunteers (18) were evaluated using the Montreal Cognitive Function Scale, basic clinical data, and 16S ribosome DNA (rDNA) sequencing. Twenty MHD patients and ten healthy volunteers were randomly selected for shotgun metagenomic analysis to explore potential metabolic pathways of intestinal flora. Both16S rDNA sequencing and shotgun metagenomic sequencing were conducted on fecal samples. RESULTS Roseburia were significantly reduced in the MHD group based on both 16S rDNA and shotgun metagenomic sequencing analyses. Faecalibacterium, Megamonas, Bifidobacterium, Parabacteroides, Collinsella, Tyzzerella, and Phascolarctobacterium were positively correlated with cognitive function or cognitive domains. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included oxidative phosphorylation, photosynthesis, retrograde endocannabinoid signaling, flagellar assembly, and riboflavin metabolism. CONCLUSION Among the microbiota, Roseburia may be important in MHD patients. We demonstrated a correlation between bacterial genera and cognitive function, and propose possible mechanisms.
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Affiliation(s)
- Qiuyi Gao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dianshi Li
- Centre for Empirical Legal Studies, Faculty of Law, University of Macau, Macau, China
| | - Yue Wang
- Department of Nephrology, Binzhou Medical University Affiliated Shengli Oilfield Central Hospital, Binzhou, China
| | - Chunhui Zhao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Mingshuai Li
- School of Graduate, Dalian Medical University, Dalian, China
| | - Jingwen Xiao
- School of Graduate, Dalian Medical University, Dalian, China
| | - Yan Kang
- School of Graduate, Dalian Medical University, Dalian, China
| | - Hongli Lin
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Nan Wang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
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Liu L, Yang J, Chen H, Jiang L, Tang Z, Zeng X. Characterization of the physicochemical Properties, bacterial community and non-volatile profiles of fermented Yu jiangsuan by Weissella cibaria and Lactobacillus plantarum. Food Chem X 2023; 20:100951. [PMID: 38144833 PMCID: PMC10740052 DOI: 10.1016/j.fochx.2023.100951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/26/2023] Open
Abstract
Yu jiangsuan (YJS) is a unique traditional fermented condiment in China. Physicochemical, bacterial communities, and non-volatile properties were examined in inoculation Autochthonous Weissella cibaria and Lactobacillus plantarum. The results indicated that inoculation samples did well in shortening fermentation time; amino acid nitrogen (AN) and TCA-soluble peptide contents of fermented YJS were 10.8% and 17.4% higher than those of naturally fermented YJS, respectively. However, its total volatile base nitrogen (TVB-N), thiobarbituric acid (TBARS), and nitrite were only 74.3%, 87.2% and 83.6% of those of naturally fermented YJS. In addition, the dominant bacterial genera were Lactobacillus, Weissella and Pectobacterium, whose contributions were 41.2%, 20.3% and 5.5%, respectively. Moreover, 26 significantly differential metabolites were identified, and involved in 10 metabolic pathways. The decomposition of substrates and the formation of differential metabolites in YJS were primarily centered on the TCA cycle and the metabolism of carbohydrates. Therefore, this study is conducive to discovering the bacterial community structure and metabolite composition of probiotic inoculated YJS fermentation, as well as the potential value of core functional bacteria genera in controlling YJS production in industry.
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Affiliation(s)
- Lu Liu
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
- Bureau of Agriculture and Rural Affairs of Majiang County, Guizhou Province, China
| | - Jintao Yang
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Hongyan Chen
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Lu Jiang
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Zhongyue Tang
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Xuefeng Zeng
- College of Life Sciences, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
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3
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Siddiqui SA, Erol Z, Rugji J, Taşçı F, Kahraman HA, Toppi V, Musa L, Di Giacinto G, Bahmid NA, Mehdizadeh M, Castro-Muñoz R. An overview of fermentation in the food industry - looking back from a new perspective. BIORESOUR BIOPROCESS 2023; 10:85. [PMID: 38647968 PMCID: PMC10991178 DOI: 10.1186/s40643-023-00702-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 04/25/2024] Open
Abstract
Fermentation is thought to be born in the Fertile Crescent, and since then, almost every culture has integrated fermented foods into their dietary habits. Originally used to preserve foods, fermentation is now applied to improve their physicochemical, sensory, nutritional, and safety attributes. Fermented dairy, alcoholic beverages like wine and beer, fermented vegetables, fruits, and meats are all highly valuable due to their increased storage stability, reduced risk of food poisoning, and enhanced flavor. Over the years, scientific research has associated the consumption of fermented products with improved health status. The fermentation process helps to break down compounds into more easily digestible forms. It also helps to reduce the amount of toxins and pathogens in food. Additionally, fermented foods contain probiotics, which are beneficial bacteria that help the body to digest food and absorb nutrients. In today's world, non-communicable diseases such as cardiovascular disease, type 2 diabetes, cancer, and allergies have increased. In this regard, scientific investigations have demonstrated that shifting to a diet that contains fermented foods can reduce the risk of non-communicable diseases. Moreover, in the last decade, there has been a growing interest in fermentation technology to valorize food waste into valuable by-products. Fermentation of various food wastes has resulted in the successful production of valuable by-products, including enzymes, pigments, and biofuels.
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Affiliation(s)
- Shahida Anusha Siddiqui
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Essigberg 3, 94315, Straubing, Germany.
- German Institute of Food Technologies (DIL E.V.), Prof.-Von-Klitzing Str. 7, 49610, Quakenbrück, Germany.
| | - Zeki Erol
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, İstiklal Campus, 15030, Burdur, Turkey
| | - Jerina Rugji
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, İstiklal Campus, 15030, Burdur, Turkey
| | - Fulya Taşçı
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, İstiklal Campus, 15030, Burdur, Turkey
| | - Hatice Ahu Kahraman
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, İstiklal Campus, 15030, Burdur, Turkey
| | - Valeria Toppi
- Department of Veterinary Medicine, University of Perugia, 06126, Perugia, Italy
| | - Laura Musa
- Department of Veterinary Medicine and Animal Sciences, University of Milan, 26900, Lodi, Italy
| | - Giacomo Di Giacinto
- Department of Veterinary Medicine, University of Perugia, 06126, Perugia, Italy
| | - Nur Alim Bahmid
- Research Center for Food Technology and Processing, National Research and Innovation Agency (BRIN), Gading, Playen, Gunungkidul, 55861, Yogyakarta, Indonesia
| | - Mohammad Mehdizadeh
- Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
- Ilam Science and Technology Park, Ilam, Iran
| | - Roberto Castro-Muñoz
- Tecnologico de Monterrey, Campus Toluca, Av. Eduardo Monroy Cárdenas 2000, San Antonio Buenavista, 50110, Toluca de Lerdo, Mexico.
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza St. 11/12, 80-233, Gdansk, Poland.
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4
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Olmo R, Wetzels SU, Berg G, Cocolin L, Hartmann M, Hugas M, Kostic T, Rattei T, Ruthsatz M, Rybakova D, Sessitsch A, Shortt C, Timmis K, Selberherr E, Wagner M. Food systems microbiome-related educational needs. Microb Biotechnol 2023; 16:1412-1422. [PMID: 37338855 DOI: 10.1111/1751-7915.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 06/21/2023] Open
Abstract
Within the European-funded Coordination and Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), the Workshop 'Education in Food Systems Microbiome Related Sciences: Needs for Universities, Industry and Public Health Systems' brought together over 70 researchers, public health and industry partners from all over the world to work on elaborating microbiome-related educational needs in food systems. This publication provides a summary of discussions held during and after the workshop and the resulting recommendations.
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Affiliation(s)
- Rocío Olmo
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie Urimare Wetzels
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Moritz Hartmann
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Marta Hugas
- European Food Safety Authority (EFSA), EU, Parma, Italy
| | - Tanja Kostic
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Evelyne Selberherr
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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5
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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; 64:8367-8383. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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6
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Garbacz K. Anticancer activity of lactic acid bacteria. Semin Cancer Biol 2022; 86:356-366. [PMID: 34995799 DOI: 10.1016/j.semcancer.2021.12.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023]
Abstract
Lactic acid bacteria (LAB), a group of Gram-positive microorganisms naturally occurring in fermented food products and used as probiotics, have been gaining the interest of researchers for years. LAB are potent, albeit still not wholly understood, source of bioactive compounds with various functions and activity. Metabolites of LAB, among others, short-chain fatty acids, exopolysaccharides and bacteriocins have promising anticancer potential. Research on the interactions between the bioactive metabolites of LAB and immune mechanisms demonstrated that these substances could exert a strong immunomodulatory effect, which would explain their vast therapeutic potential. The anticancer activity of LAB was confirmed both in vitro and in animal models against cancer cells from various malignancies. LAB inhibit tumor growth through various mechanisms, including antiproliferative activity, induction of apoptosis, cell cycle arrest, as well as through antimutagenic, antiangiogenic and anti-inflammatory effects. The aim of this review was to summarize the most recent data about the anticancer activity of LAB, with particular emphasis on the most promising bioactive compounds with potential clinical application.
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Affiliation(s)
- Katarzyna Garbacz
- Department of Oral Microbiology, Medical Faculty, Medical University of Gdansk, 25 Dębowa Str., 80-204, Gdansk, Poland.
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7
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Elucidating the mechanism underlying volatile and non-volatile compound development related to microbial amino acid metabolism during golden pomfret (Trachinotus ovatus) fermentation. Food Res Int 2022; 162:112095. [DOI: 10.1016/j.foodres.2022.112095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
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8
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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9
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Tanui CK, Benefo EO, Karanth S, Pradhan AK. A Machine Learning Model for Food Source Attribution of Listeria monocytogenes. Pathogens 2022; 11:pathogens11060691. [PMID: 35745545 PMCID: PMC9230378 DOI: 10.3390/pathogens11060691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 12/07/2022] Open
Abstract
Despite its low morbidity, listeriosis has a high mortality rate due to the severity of its clinical manifestations. The source of human listeriosis is often unclear. In this study, we investigate the ability of machine learning to predict the food source from which clinical Listeria monocytogenes isolates originated. Four machine learning classification algorithms were trained on core genome multilocus sequence typing data of 1212 L. monocytogenes isolates from various food sources. The average accuracies of random forest, support vector machine radial kernel, stochastic gradient boosting, and logit boost were found to be 0.72, 0.61, 0.7, and 0.73, respectively. Logit boost showed the best performance and was used in model testing on 154 L. monocytogenes clinical isolates. The model attributed 17.5 % of human clinical cases to dairy, 32.5% to fruits, 14.3% to leafy greens, 9.7% to meat, 4.6% to poultry, and 18.8% to vegetables. The final model also provided us with genetic features that were predictive of specific sources. Thus, this combination of genomic data and machine learning-based models can greatly enhance our ability to track L. monocytogenes from different food sources.
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Affiliation(s)
- Collins K. Tanui
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
- Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Edmund O. Benefo
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
| | - Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
| | - Abani K. Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; (C.K.T.); (E.O.B.); (S.K.)
- Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
- Correspondence:
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10
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Chelliah R, Banan-MwineDaliri E, Khan I, Wei S, Elahi F, Yeon SJ, Selvakumar V, Ofosu FK, Rubab M, Ju HH, Rallabandi HR, Madar IH, Sultan G, Oh DH. A review on the application of bioinformatics tools in food microbiome studies. Brief Bioinform 2022; 23:6533500. [PMID: 35189636 DOI: 10.1093/bib/bbac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Eric Banan-MwineDaliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Imran Khan
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Department of Biotechnology, University of Malakand, Khyber Pakhtunkhwa Pakistan
| | - Shuai Wei
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Vijayalakshmi Selvakumar
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Hum Hun Ju
- Department of Biological Environment, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Harikrishna Reddy Rallabandi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Inamul Hasan Madar
- Department of Biochemistry, School of Life Science, Bharathidasan, University, Thiruchirappalli, Tamilnadu, India
| | - Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Deog Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
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11
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Antimicrobial Bacillus: Metabolites and Their Mode of Action. Antibiotics (Basel) 2022; 11:antibiotics11010088. [PMID: 35052965 PMCID: PMC8772736 DOI: 10.3390/antibiotics11010088] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.
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12
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Wang Y, Zhang C, Liu F, Jin Z, Xia X. Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods. Crit Rev Food Sci Nutr 2022; 63:5841-5855. [PMID: 35014569 DOI: 10.1080/10408398.2021.2025035] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fermented foods are important parts of traditional food culture with a long history worldwide. Abundant nutritional materials and open fermentation contribute to the diversity of microorganisms, resulting in unique product quality and flavor. Lactic acid bacteria (LAB), as important part of traditional fermented foods, play a decisive role in the quality and safety of fermented foods. Reproduction and metabolic of microorganisms drive the food fermentation, and microbial interaction plays a major role in the fermentation process. Nowadays, LAB have attracted considerable interest due to their potentialities to add functional properties to certain foods or as supplements along with the research of gut microbiome. This review focuses on the characteristics of diversity and variability of LAB in traditional fermented foods, and describes the principal mechanisms involved in the flavor formation dominated by LAB. Moreover, microbial interactions and their mechanisms in fermented foods are presented. They provide a theoretical basis for exploiting LAB in fermented foods and improving the quality of traditional fermented foods. The traditional fermented food industry should face the challenge of equipment automation, green manufacturing, and quality control and safety in the production.
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Affiliation(s)
- Yingyu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | | | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
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13
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Karanth S, Tanui CK, Meng J, Pradhan AK. Exploring the predictive capability of advanced machine learning in identifying severe disease phenotype in Salmonella enterica. Food Res Int 2022; 151:110817. [PMID: 34980422 DOI: 10.1016/j.foodres.2021.110817] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
The past few years have seen a significant increase in availability of whole genome sequencing information, allowing for its incorporation in predictive modeling for foodborne pathogens to account for inter- and intra-species differences in their virulence. However, this is hindered by the inability of traditional statistical methods to analyze such large amounts of data compared to the number of observations/isolates. In this study, we have explored the applicability of machine learning (ML) models to predict the disease outcome, while identifying features that exert a significant effect on the prediction. This study was conducted on Salmonella enterica, a major foodborne pathogen with considerable inter- and intra-serovar variation. WGS of isolates obtained from various sources (i.e., human, chicken, and swine) were used as input in four machine learning models (logistic regression with ridge, random forest, support vector machine, and AdaBoost) to classify isolates based on disease severity (extraintestinal vs. gastrointestinal) in the host. The predictive performances of all models were tested with and without Elastic Net regularization to combat dimensionality issues. Elastic Net-regularized logistic regression model showed the best area under the receiver operating characteristic curve (AUC-ROC; 0.86) and outcome prediction accuracy (0.76). Additionally, genes coding for transcriptional regulation, acidic, oxidative, and anaerobic stress response, and antibiotic resistance were found to be significant predictors of disease severity. These genes, which were significantly associated with each outcome, could possibly be input in amended, gene-expression-specific predictive models to estimate virulence pattern-specific effect of Salmonella and other foodborne pathogens on human health.
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Affiliation(s)
- Shraddha Karanth
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Collins K Tanui
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20742, USA
| | - Abani K Pradhan
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA.
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14
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Tanui CK, Karanth S, Njage PM, Meng J, Pradhan AK. Machine learning-based predictive modeling to identify genotypic traits associated with Salmonella enterica disease endpoints in isolates from ground chicken. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112701] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Mokoena MP, Omatola CA, Olaniran AO. Applications of Lactic Acid Bacteria and Their Bacteriocins against Food Spoilage Microorganisms and Foodborne Pathogens. Molecules 2021; 26:7055. [PMID: 34834145 PMCID: PMC8622874 DOI: 10.3390/molecules26227055] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Lactic acid bacteria (LAB) are Gram-positive and catalase-negative microorganisms used to produce fermented foods. They appear morphologically as cocci or rods and they do not form spores. LAB used in food fermentation are from the Lactobacillus and Bifidobacterium genera and are useful in controlling spoilage and pathogenic microbes, due to the bacteriocins and acids that they produce. Consequently, LAB and their bacteriocins have emerged as viable alternatives to chemical food preservatives, curtesy of their qualified presumption of safety (QPS) status. There is growing interest regarding updated literature on the applications of LAB and their products in food safety, inhibition of the proliferation of food spoilage microbes and foodborne pathogens, and the mitigation of viral infections associated with food, as well as in the development of creative food packaging materials. Therefore, this review explores empirical studies, documenting applications and the extent to which LAB isolates and their bacteriocins have been used in the food industry against food spoilage microorganisms and foodborne pathogens including viruses; as well as to highlight the prospects of their numerous novel applications as components of hurdle technology to provide safe and quality food products.
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Affiliation(s)
- Mduduzi P. Mokoena
- Department of Biotechnology and Food Science, Durban University of Technology (Steve Biko Campus), P.O. Box 1334, Durban 4000, South Africa
| | - Cornelius A. Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa; (C.A.O.); (A.O.O.)
| | - Ademola O. Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa; (C.A.O.); (A.O.O.)
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16
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Effect of Daily Oral Lactobacillus plantarum PS128 on Exercise Capacity Recovery after a Half-Marathon. Nutrients 2021; 13:nu13114023. [PMID: 34836278 PMCID: PMC8619570 DOI: 10.3390/nu13114023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
A half-marathon (HM) is a vigorous high-intensity exercise, which could induce lower extremity musculoskeletal injury risks for recreational runners. They usually consume nonsteroidal anti-inflammatory drugs (NSAIDs) in order to shorten their return to play but ignore the side effects, such as peptic ulcers and renal and vascular disorders. Lactobacillus plantarum PS128 (PS128) could improve inflammation and oxidative stress by modulating the gut microbiota, thus potentially improving muscle damage and recovery. However, few studies have addressed the PS128 exercise capacity recovery 96 h after HM. Thus, this study aimed to investigate the effect of PS128 on exercise capacity and physiological adaptation after HM. A double-blind, randomized, placebo-controlled, counterbalanced, crossover trial was used for the experiment. HM was conducted at the beginning and end of the 4-week nutritional supplement administration. Eight recreational runners took two capsules (3 × 1010 CFU/capsule) of PS128 each morning and evening before meals for 4 weeks as the PS128 treatment (LT), or they took two capsules of placebo for 4 weeks as the placebo treatment (PT). In both treatments, an exercise capacity test (lower extremity muscle strength, anaerobic power, lower extremity explosive force, and aerobic capacity) and blood test (muscle fatigue, muscle damage, oxidative stress, and renal injury) were performed before the administration of the nutritional supplement (baseline), 48 h before HM (pre), and 0 h (0 h post), 3 h (3 h post), 24 h (24 h post), 48 h (48 h post), 72 h (72 h post), and 96 h (96 h post) after HM. There was no significant difference in the total duration of HM between PT and LT, but PT was found to be significantly higher than LT at Stage 4 (15,751–21,000 m) of HM (3394 ± 727 s vs. 2778 ± 551 s, p = 0.02). The lower extremity muscle strength measured using an isokinetic dynamometer in PT was significantly lower than that in LT at 72 h after HM. The lower extremity explosive force from the countermovement jump (CMJ) in PT was significantly decreased compared to 24 h prior. There was no significant difference between anaerobic power and aerobic capacity between the two treatments after HM. After HM, LT had lower muscle damage indices, such as myoglobin (3 h post-PT vs. -LT: 190.6 ± 118 ng/mL vs. 91.7 ± 68.6 ng/mL, p < 0.0001) and creatine phosphokinase (24 h post-PT vs. -LT: 875.8 ± 572.3 IU/L vs. 401 ± 295.7 IU/L, p < 0.0001). Blood urea nitrogen recovered in 24 h (24 h pre- vs. post-LT, p > 0.05) and higher superoxide dismutase was found in LT (96 h post-PT vs. -LT: 0.267 ± 0.088 U/mL vs. 0.462 ± 0.122 U/mL, p < 0.0001). In conclusion, PS128 supplementation was associated with an improvement in muscle damage, renal damage, and oxidative stress caused by HM through microbiota modulation and related metabolites but not in exercise capacity.
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17
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Che H, Yu J, Sun J, Lu K, Xie W. Bacterial composition changes and volatile compounds during the fermentation of shrimp paste: Dynamic changes of microbial communities and flavor composition. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Franco-Frías E, Mercado-Guajardo V, Merino-Mascorro A, Pérez-Garza J, Heredia N, León JS, Jaykus LA, Dávila-Aviña J, García S. Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment. MICROBIAL ECOLOGY 2021; 82:613-622. [PMID: 33570667 DOI: 10.1007/s00248-021-01709-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.
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Affiliation(s)
- Eduardo Franco-Frías
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Victor Mercado-Guajardo
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Angel Merino-Mascorro
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Janeth Pérez-Garza
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Norma Heredia
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Juan S León
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, NC, USA
| | - Jorge Dávila-Aviña
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Santos García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México.
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19
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Teng TS, Chin YL, Chai KF, Chen WN. Fermentation for future food systems: Precision fermentation can complement the scope and applications of traditional fermentation. EMBO Rep 2021; 22:e52680. [PMID: 33908143 DOI: 10.15252/embr.202152680] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
Modern biotechnology holds great potential for expanding the scope of fermentation to create novel foods and improve the sustainability of food production.
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Affiliation(s)
- Ting Shien Teng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore City, Singapore.,Food Science and Technology Programme, Nanyang Technological University, Singapore City, Singapore
| | - Yi Ling Chin
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore City, Singapore.,Food Science and Technology Programme, Nanyang Technological University, Singapore City, Singapore
| | - Kong Fei Chai
- Food Science and Technology Programme, Nanyang Technological University, Singapore City, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore City, Singapore.,Food Science and Technology Programme, Nanyang Technological University, Singapore City, Singapore
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20
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Vieira KCDO, Silva HRAD, Rocha IPM, Barboza E, Eller LKW. Foodborne pathogens in the omics era. Crit Rev Food Sci Nutr 2021; 62:6726-6741. [PMID: 33783282 DOI: 10.1080/10408398.2021.1905603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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21
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Tang J, Wu X, Mou M, Wang C, Wang L, Li F, Guo M, Yin J, Xie W, Wang X, Wang Y, Ding Y, Xue W, Zhu F. GIMICA: host genetic and immune factors shaping human microbiota. Nucleic Acids Res 2021; 49:D715-D722. [PMID: 33045729 PMCID: PMC7779047 DOI: 10.1093/nar/gkaa851] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/09/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023] Open
Abstract
Besides the environmental factors having tremendous impacts on the composition of microbial community, the host factors have recently gained extensive attentions on their roles in shaping human microbiota. There are two major types of host factors: host genetic factors (HGFs) and host immune factors (HIFs). These factors of each type are essential for defining the chemical and physical landscapes inhabited by microbiota, and the collective consideration of both types have great implication to serve comprehensive health management. However, no database was available to provide the comprehensive factors of both types. Herein, a database entitled 'Host Genetic and Immune Factors Shaping Human Microbiota (GIMICA)' was constructed. Based on the 4257 microbes confirmed to inhabit nine sites of human body, 2851 HGFs (1368 single nucleotide polymorphisms (SNPs), 186 copy number variations (CNVs), and 1297 non-coding ribonucleic acids (RNAs)) modulating the expression of 370 microbes were collected, and 549 HIFs (126 lymphocytes and phagocytes, 387 immune proteins, and 36 immune pathways) regulating the abundance of 455 microbes were also provided. All in all, GIMICA enabled the collective consideration not only between different types of host factor but also between the host and environmental ones, which is freely accessible without login requirement at: https://idrblab.org/gimica/.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xianglu Wu
- Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuan Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lidan Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Maiyuan Guo
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenqin Xie
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaona Wang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yingxiong Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.,Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yubin Ding
- Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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22
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Comin M, Di Camillo B, Pizzi C, Vandin F. Comparison of microbiome samples: methods and computational challenges. Brief Bioinform 2020; 22:88-95. [PMID: 32577746 DOI: 10.1093/bib/bbaa121] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/09/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
The study of microbial communities crucially relies on the comparison of metagenomic next-generation sequencing data sets, for which several methods have been designed in recent years. Here, we review three key challenges in the comparison of such data sets: species identification and quantification, the efficient computation of distances between metagenomic samples and the identification of metagenomic features associated with a phenotype such as disease status. We present current solutions for such challenges, considering both reference-based methods relying on a database of reference genomes and reference-free methods working directly on all sequencing reads from the samples.
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23
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Adebo OA. African Sorghum-Based Fermented Foods: Past, Current and Future Prospects. Nutrients 2020; 12:E1111. [PMID: 32316319 PMCID: PMC7231209 DOI: 10.3390/nu12041111] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 11/26/2022] Open
Abstract
Sorghum (Sorghum bicolor) is a well-known drought and climate resistant crop with vast food use for the inhabitants of Africa and other developing countries. The importance of this crop is well reflected in its embedded benefits and use as a staple food, with fermentation playing a significant role in transforming this crop into an edible form. Although the majority of these fermented food products evolve from ethnic groups and rural communities, industrialization and the application of improved food processing techniques have led to the commercial success and viability of derived products. While some of these sorghum-based fermented food products still continue to bask in this success, much more still needs to be done to further explore evolving techniques, technologies and processes. The addition of other affordable nutrient sources in sorghum-based fermented foods is equally important, as this will effectively augment the intake of a nutritionally balanced product.
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Affiliation(s)
- Oluwafemi Ayodeji Adebo
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg (Doornfontein Campus), P.O. Box 17011 Johannesburg, Gauteng 2028, South Africa
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24
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Capozzi V, Fragasso M, Russo P. Microbiological Safety and the Management of Microbial Resources in Artisanal Foods and Beverages: The Need for a Transdisciplinary Assessment to Conciliate Actual Trends and Risks Avoidance. Microorganisms 2020; 8:E306. [PMID: 32098373 PMCID: PMC7074853 DOI: 10.3390/microorganisms8020306] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
Current social and environmental trends explain the rising popularity of artisanal fermented foods and beverages. In contrast with their marketing success, several studies underline a lack of regulations necessary to claim differences occurred from the farm to the fork and to certify high quality and safety standards. Microbial-based fermentative processes represent the crucial phase in the production of fermented foods and beverages. Nevertheless, what are the effects of the application of the "artisanal" category to the management of food fermentations? This opinion paper is built up on this issue by analyzing microbial aspects, instances of innovation, safety issues, and possible solutions. Evidence indicates: (i) a global curiosity to exploit food fermentations as drivers of innovation in artisanal contexts and (ii) an increasing interest of the artisanal producers into management of fermentation that relies on native microbial consortia. Unfortunately, this kind of revamp of "artisanal food microbiology," rather than re-establishing artisanal content, can restore the scarce hygienic conditions that characterized underdeveloped food systems. We highlight that in the scientific literature, it is possible to underline existing approaches that, surpassing the dichotomy between relying on spontaneous fermentation and the use of commercial starter cultures, depict a "third way" to conjugate interest in enhancing the artisanal attributes with the need for correct management of microbial-related risks in the final products.
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Affiliation(s)
- Vittorio Capozzi
- Institute of Sciences of Food Production, National Research Council (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Mariagiovanna Fragasso
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (M.F.); (P.R.)
| | - Pasquale Russo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (M.F.); (P.R.)
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25
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Tremblay J, Yergeau E. Systematic processing of ribosomal RNA gene amplicon sequencing data. Gigascience 2019; 8:giz146. [PMID: 31816087 PMCID: PMC6901069 DOI: 10.1093/gigascience/giz146] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/07/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND With the advent of high-throughput sequencing, microbiology is becoming increasingly data-intensive. Because of its low cost, robust databases, and established bioinformatic workflows, sequencing of 16S/18S/ITS ribosomal RNA (rRNA) gene amplicons, which provides a marker of choice for phylogenetic studies, has become ubiquitous. Many established end-to-end bioinformatic pipelines are available to perform short amplicon sequence data analysis. These pipelines suit a general audience, but few options exist for more specialized users who are experienced in code scripting, Linux-based systems, and high-performance computing (HPC) environments. For such an audience, existing pipelines can be limiting to fully leverage modern HPC capabilities and perform tweaking and optimization operations. Moreover, a wealth of stand-alone software packages that perform specific targeted bioinformatic tasks are increasingly accessible, and finding a way to easily integrate these applications in a pipeline is critical to the evolution of bioinformatic methodologies. RESULTS Here we describe AmpliconTagger, a short rRNA marker gene amplicon pipeline coded in a Python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. It is designed to work within an HPC environment, supporting a complex network of job dependencies with a smart-restart mechanism in case of job failure or parameter modifications. As proof of concept, we present end results obtained with AmpliconTagger using 16S, 18S, ITS rRNA short gene amplicons and Pacific Biosciences long-read amplicon data types as input. CONCLUSIONS Using a selection of published algorithms for generating operational taxonomic units and amplicon sequence variants and for computing downstream taxonomic summaries and diversity metrics, we demonstrate the performance and versatility of our pipeline for systematic analyses of amplicon sequence data.
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Affiliation(s)
- Julien Tremblay
- Energy Mining and Environment, National Research Council Canada, Montreal, QC H4P-2R2, Canada
| | - Etienne Yergeau
- Centre INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, 531ad Boul. des Prairies, Laval, QC H7V-1B7, Canada
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Vilne B, Meistere I, Grantiņa-Ieviņa L, Ķibilds J. Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks. Front Microbiol 2019; 10:1722. [PMID: 31447800 PMCID: PMC6691741 DOI: 10.3389/fmicb.2019.01722] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/12/2019] [Indexed: 12/14/2022] Open
Abstract
Foodborne diseases (FBDs) are infections of the gastrointestinal tract caused by foodborne pathogens (FBPs) such as bacteria [Salmonella, Listeria monocytogenes and Shiga toxin-producing E. coli (STEC)] and several viruses, but also parasites and some fungi. Artificial intelligence (AI) and its sub-discipline machine learning (ML) are re-emerging and gaining an ever increasing popularity in the scientific community and industry, and could lead to actionable knowledge in diverse ranges of sectors including epidemiological investigations of FBD outbreaks and antimicrobial resistance (AMR). As genotyping using whole-genome sequencing (WGS) is becoming more accessible and affordable, it is increasingly used as a routine tool for the detection of pathogens, and has the potential to differentiate between outbreak strains that are closely related, identify virulence/resistance genes and provide improved understanding of transmission events within hours to days. In most cases, the computational pipeline of WGS data analysis can be divided into four (though, not necessarily consecutive) major steps: de novo genome assembly, genome characterization, comparative genomics, and inference of phylogeny or phylogenomics. In each step, ML could be used to increase the speed and potentially the accuracy (provided increasing amounts of high-quality input data) of identification of the source of ongoing outbreaks, leading to more efficient treatment and prevention of additional cases. In this review, we explore whether ML or any other form of AI algorithms have already been proposed for the respective tasks and compare those with mechanistic model-based approaches.
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Affiliation(s)
- Baiba Vilne
- Institute of Food Safety, Animal Health and Environment—“BIOR”, Riga, Latvia
- SIA net-OMICS, Riga, Latvia
| | - Irēna Meistere
- Institute of Food Safety, Animal Health and Environment—“BIOR”, Riga, Latvia
| | | | - Juris Ķibilds
- Institute of Food Safety, Animal Health and Environment—“BIOR”, Riga, Latvia
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Kelleher P, Mahony J, Bottacini F, Lugli GA, Ventura M, van Sinderen D. The Lactococcus lactis Pan-Plasmidome. Front Microbiol 2019; 10:707. [PMID: 31019500 PMCID: PMC6458302 DOI: 10.3389/fmicb.2019.00707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 01/01/2023] Open
Abstract
Plasmids are autonomous, self-replicating, extrachromosomal genetic elements that are typically not essential for growth of their host. They may encode metabolic capabilities, which promote the maintenance of these genetic elements, and may allow adaption to specific ecological niches and consequently enhance survival. Genome sequencing of 16 Lactococcus lactis strains revealed the presence of 83 plasmids, including two megaplasmids. The limitations of Pacific Biosciences SMRT sequencing in detecting the total plasmid complement of lactococcal strains is examined, while a combined Illumina/SMRT sequencing approach is proposed to combat these issues. Comparative genome analysis of these plasmid sequences combined with other publicly available plasmid sequence data allowed the definition of the lactococcal plasmidome, and facilitated an investigation into (bio) technologically important plasmid-encoded traits such as conjugation, bacteriocin production, exopolysaccharide (EPS) production, and (bacterio) phage resistance.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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29
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Inglin RC, Delbrück AI, Fässler B, Siebenmann KE, Lacroix C, Stevens MJA, Meile L. An approach to selectLactobacillusisolates as protective cultures for food fermentations. J Food Saf 2018. [DOI: 10.1111/jfs.12483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Raffael C. Inglin
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
| | - Alessia I. Delbrück
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
| | - Benjamin Fässler
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
| | - Katharina E. Siebenmann
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
| | - Marc J. A. Stevens
- Institute for Food Safety and Food Hygienic, University of Zurich; Zurich Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Department of Health Science and Technology; Institute of Food, Nutrition and Health, ETH Zurich; Zurich Switzerland
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Zang J, Xu Y, Xia W, Yu D, Gao P, Jiang Q, Yang F. Dynamics and diversity of microbial community succession during fermentation of Suan yu, a Chinese traditional fermented fish, determined by high throughput sequencing. Food Res Int 2018; 111:565-573. [PMID: 30007719 DOI: 10.1016/j.foodres.2018.05.076] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 01/10/2023]
Abstract
The main goal of this study was to investigate the dynamics, diversity and succession of microbial community present during the preparation of Suan yu (fermented fish), with and without starter cultures by high-throughput sequencing of 16S rRNA and ITS1 genes. Firmicutes and Ascomycota were the predominant phyla of bacteria and fungi, respectively, in all samples. At the genus level, Lactobacillus, Macrococcus and Staphylococcus were the predominating bacteria throughout the fermentation process, regardless of the inclusion of starter cultures. Saccharomyces was the predominating fungal genus in the early-fermentation stage of samples that inoculated starter cultures (MS), while the final product was dominated by Candida and Wickerhamomyces. Compared with naturally-fermented samples (NS; no starter cultures), Lactococcus, Leuconostoc, Enterococcus, Vibrio, Fusicolla and Torulaspora were inhibited and Aureobasidium emerged in samples inoculated with starter cultures (P < .05). Unweighted pair-group and principal component analyses of bacterial and fungal compositions revealed that microbiota structures differed between NS and MS samples. Redundancy analysis indicated that water content and pH might be important factors influencing the dominant bacterial and fungal community. Results indicated that microbial community were dynamic during fermentation process and the inoculation of mixed starter culture inhibited the growth of many organisms associated with food spoilage and contributed to the improvement of the quality of Suan yu products.
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Affiliation(s)
- Jinhong Zang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yanshun Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Wenshui Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Dawei Yu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Pei Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Qixing Jiang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Fang Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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31
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Precision food safety: A systems approach to food safety facilitated by genomics tools. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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Safety Assessment of Lactobacillus helveticus KLDS1.8701 Based on Whole Genome Sequencing and Oral Toxicity Studies. Toxins (Basel) 2017; 9:toxins9100301. [PMID: 28946645 PMCID: PMC5666348 DOI: 10.3390/toxins9100301] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/04/2017] [Accepted: 09/20/2017] [Indexed: 01/19/2023] Open
Abstract
Lactobacillus helveticus KLDS1.8701 isolated from Chinese traditional fermented dairy product has been shown earlier to possess probiotic potentials but it is important to evaluate its safety in view of its possible use as a probiotic. The aim of the present study is to critically assess the safety of L. helveticus KLDS1.8701 through multiple perspectives. The complete genome of L. helveticus KLDS1.8701 was sequenced to mine for safety-associated genes. The minimum inhibitory concentrations of 15 antimicrobials and the adverse metabolites were determined. Standard acute oral and subacute toxicity studies were conducted in rats. The results in silico disclosed that the genome of L. helveticus KLDS1.8701 carries no transferable antibiotic resistance genes, no virulence factors and only 3 genes related to adverse metabolites. In vitro results showed that L. helveticus KLDS1.8701 was resistant against 6 antimicrobials and did not raise safety concerns about biogenic amine, D-lactic acid and nitroreductase. The results in vivo revealed that no adverse effects on experimental rats were observed in the oral toxicity tests. Overall, findings from this study suggest that L. helveticus KLDS1.8701 is safe and can be used as a potential probiotic for human consumption.
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33
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Mokoena MP. Lactic Acid Bacteria and Their Bacteriocins: Classification, Biosynthesis and Applications against Uropathogens: A Mini-Review. Molecules 2017; 22:molecules22081255. [PMID: 28933759 PMCID: PMC6152299 DOI: 10.3390/molecules22081255] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/15/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022] Open
Abstract
Several lactic acid bacteria (LAB) isolates from the Lactobacillus genera have been applied in food preservation, partly due to their antimicrobial properties. Their application in the control of human pathogens holds promise provided appropriate strains are scientifically chosen and a suitable mode of delivery is utilized. Urinary tract infection (UTI) is a global problem, affecting mainly diabetic patients and women. Many uropathogens are developing resistance to commonly used antibiotics. There is a need for more research on the ability of LAB to inhibit uropathogens, with a view to apply them in clinical settings, while adhering to strict selection guidelines in the choice of candidate LAB. While several studies have indicated the ability of LAB to elicit inhibitory activities against uropathogens in vitro, more in vivo and clinical trials are essential to validate the efficacy of LAB in the treatment and prevention of UTI. The emerging applications of LAB such as in adjuvant therapy, oral vaccine development, and as purveyors of bioprotective agents, are relevant in infection prevention and amelioration. Therefore, this review explores the potential of LAB isolates and their bacteriocins to control uropathogens, with a view to limit clinical use of antibiotics.
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Affiliation(s)
- Mduduzi Paul Mokoena
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa.
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Walsh AM, Crispie F, Claesson MJ, Cotter PD. Translating Omics to Food Microbiology. Annu Rev Food Sci Technol 2017; 8:113-134. [DOI: 10.1146/annurev-food-030216-025729] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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35
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John MN, Joseph WM, Zacchaeus ON, Moses BS. Spontaneously fermented kenyan milk products: A review of the current state and future perspectives. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajfs2016.1516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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36
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Lima-Ojeda JM, Rupprecht R, Baghai TC. "I Am I and My Bacterial Circumstances": Linking Gut Microbiome, Neurodevelopment, and Depression. Front Psychiatry 2017; 8:153. [PMID: 28878696 PMCID: PMC5572414 DOI: 10.3389/fpsyt.2017.00153] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/02/2017] [Indexed: 01/01/2023] Open
Abstract
Recently, there has been renewed interest in the role played by microbiome in both human health and human disease. A correct equilibrium between the human host and their microorganisms is important for an appropriate physiological function. Extensive research has shown that microbes that inhabit the gastrointestinal tract-or gut microbiota-are involved not only in both nutritive and digestive activities but also in immunological processes. Moreover, the gut microbiome influences both central nervous system and energy homeostasis. An altered gut microbiome has been associated with the pathophysiology of different diseases, including neuropsychiatric disorders. Apparently, both environmental-diet, exposition to antibiotics, and infections-and host-genetic factors have a strong influence on gut microbiome, modulating the risk for neuropsychiatric illness. Also, early life disruption of the microbiome-gut-brain (MGB) axis has been associated with an increased risk of developing depression later in life, suggesting a link between gut microbiome, neurodevelopment, and depression. This review aims to contribute to this growing area of research by exploring the role played by the gut microbiome in neurodevelopment and in the etiology of the depressive syndrome, including nutritional, immunological, and energy homeostasis approaches.
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Affiliation(s)
- Juan M Lima-Ojeda
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Rainer Rupprecht
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
| | - Thomas C Baghai
- Department of Psychiatry and Psychotherapy, University of Regensburg, Regensburg, Germany
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37
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Berendsen EM, Koning RA, Boekhorst J, de Jong A, Kuipers OP, Wells-Bennik MHJ. High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn 1546 Transposon. Front Microbiol 2016; 7:1912. [PMID: 27994575 PMCID: PMC5133452 DOI: 10.3389/fmicb.2016.01912] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/15/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial endospore formers can produce spores that are resistant to many food processing conditions, including heat. Some spores may survive heating processes aimed at production of commercially sterile foods. Recently, it was shown that a spoVA operon, designated spoVA2mob, present on a Tn1546 transposon in Bacillus subtilis, leads to profoundly increased wet heat resistance of B. subtilis spores. Such Tn1546 transposon elements including the spoVA2mob operon were also found in several strains of Bacillus amyloliquefaciens and Bacillus licheniformis, and these strains were shown to produce spores with significantly higher resistances to wet heat than their counterparts lacking this transposon. In this study, the locations and compositions of Tn1546 transposons encompassing the spoVA2mob operons in B. amyloliquefaciens and B. licheniformis were analyzed. Introduction of these spoVA2mob operons into B. subtilis 168 (producing spores that are not highly heat resistant) rendered mutant 168 strains that produced high-level heat resistant spores, demonstrating that these elements in B. amyloliquefaciens and B. licheniformis are responsible for high level heat resistance of spores. Assessment of growth of the nine strains of each species between 5.2°C and 57.7°C showed some differences between strains, especially at lower temperatures, but all strains were able to grow at 57.7°C. Strains of B. amyloliquefaciens and B. licheniformis that contain the Tn1546 elements (and produce high-level heat resistant spores) grew at temperatures similar to those of their Tn1546-negative counterparts that produce low-level heat resistant spores. The findings presented in this study allow for detection of B. amyloliquefaciens and B. licheniformis strains that produce highly heat resistant spores in the food chain.
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Affiliation(s)
- Erwin M Berendsen
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Rosella A Koning
- Top Institute Food and NutritionWageningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Jos Boekhorst
- Top Institute Food and NutritionWageningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Anne de Jong
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands
| | - Oscar P Kuipers
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands
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Ruiz-Rodríguez L, Bleckwedel J, Eugenia Ortiz M, Pescuma M, Mozzi F. Lactic Acid Bacteria. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luciana Ruiz-Rodríguez
- Centro de Referencia para Lactobacilos (CERELA)-CONICET; Chacabuco 145. San Miguel de Tucumán 4000 Argentina
| | - Juliana Bleckwedel
- Centro de Referencia para Lactobacilos (CERELA)-CONICET; Chacabuco 145. San Miguel de Tucumán 4000 Argentina
| | - Maria Eugenia Ortiz
- Centro de Referencia para Lactobacilos (CERELA)-CONICET; Chacabuco 145. San Miguel de Tucumán 4000 Argentina
| | - Micaela Pescuma
- Centro de Referencia para Lactobacilos (CERELA)-CONICET; Chacabuco 145. San Miguel de Tucumán 4000 Argentina
| | - Fernanda Mozzi
- Centro de Referencia para Lactobacilos (CERELA)-CONICET; Chacabuco 145. San Miguel de Tucumán 4000 Argentina
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39
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Prospects for improved control of dairy-relevant sporeformers using -omics technologies. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Abriouel H, Lerma LL, Casado Muñoz MDC, Montoro BP, Kabisch J, Pichner R, Cho GS, Neve H, Fusco V, Franz CMAP, Gálvez A, Benomar N. The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health. Front Microbiol 2015; 6:1197. [PMID: 26579103 PMCID: PMC4621295 DOI: 10.3389/fmicb.2015.01197] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/15/2015] [Indexed: 11/21/2022] Open
Abstract
Despite the use of several Weissella (W.) strains for biotechnological and probiotic purposes, certain species of this genus were found to act as opportunistic pathogens, while strains of W. ceti were recognized to be pathogenic for farmed rainbow trout. Herein, we investigated the pathogenic potential of weissellas based on in silico analyses of the 13 whole genome sequences available to date in the NCBI database. Our screening allowed us to find several virulence determinants such as collagen adhesins, aggregation substances, mucus-binding proteins, and hemolysins in some species. Moreover, we detected several antibiotic resistance-encoding genes, whose presence could increase the potential pathogenicity of some strains, but should not be regarded as an excluding trait for beneficial weissellas, as long as these genes are not present on mobile genetic elements. Thus, selection of weissellas intended to be used as starters or for biotechnological or probiotic purposes should be investigated regarding their safety aspects on a strain to strain basis, preferably also by genome sequencing, since nucleotide sequence heterogeneity in virulence and antibiotic resistance genes makes PCR-based screening unreliable for safety assessments. In this sense, the application of W. confusa and W. cibaria strains as starter cultures or as probiotics should be approached with caution, by carefully selecting strains that lack pathogenic potential.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
| | - María Del Carmen Casado Muñoz
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
| | - Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
| | - Jan Kabisch
- Department of Microbiology and Biotechnology, Federal Research Institute of Nutrition and Food, Max Rubner-Institut , Kiel, Germany
| | - Rohtraud Pichner
- Department of Microbiology and Biotechnology, Federal Research Institute of Nutrition and Food, Max Rubner-Institut , Kiel, Germany
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Federal Research Institute of Nutrition and Food, Max Rubner-Institut , Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Federal Research Institute of Nutrition and Food, Max Rubner-Institut , Kiel, Germany
| | - Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy , Bari, Italy
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Federal Research Institute of Nutrition and Food, Max Rubner-Institut , Kiel, Germany
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén , Jaén, Spain
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