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Qiu Y, Yan F, Yu H, Li H, Xia S, Zhang J, Zhu J. The protective effects of Kefir extract (KE) on intestinal damage in larval zebrafish induced by Oxytetracycline: Insights into intestinal function, morphology, and molecular mechanisms. Food Res Int 2024; 190:114642. [PMID: 38945628 DOI: 10.1016/j.foodres.2024.114642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024]
Abstract
The antibiotic oxytetracycline (OTC) can be detected in contemporary natural aquatic environments and has been implicated in causing intestinal damage in humans exposed to OTC-contaminated food or water. The irreversible damage caused by high concentrations of OTC to the intestine suggests that treatment through dietary means could still be necessary. This study proved the effectiveness of kefir extract (KE) in reversing intestinal damage caused by oxytetracycline (OTC) exposure. Following a 24-hour KE treatment subsequent to OTC exposure from 3 to 8 days post-fertilization of zebrafish larvae, molecular-level and microbiomic assessments revealed significant improvements. These included reduced expression of proinflammatory factors (IL-8 and IL-1β), increased antioxidant levels, and reversed unhealthy distribution of intestinal microbiota. Furthermore, KE supplementation showed potential in enhancing intestinal motility in the experiment of Nile red staining and fluorescent microbead transit. However, histological analysis showed that this short-term treatment with KE only partially reversed the intestinal morphological changes induced by OTC, suggesting that a longer treatment period might be necessary for complete restoration.
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Affiliation(s)
- Yang Qiu
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Fujie Yan
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Huilin Yu
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Honghao Li
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Shengyao Xia
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhang
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jiajin Zhu
- College of Biosystems Engineering & Food Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Engineering Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China; Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo 315100, China.
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2
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Sadurski J, Polak-Berecka M, Staniszewski A, Waśko A. Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review. Foods 2024; 13:2216. [PMID: 39063300 PMCID: PMC11276190 DOI: 10.3390/foods13142216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
This review article offers a comprehensive overview of the current understanding of using metagenomic tools in food microbiome research. It covers the scientific foundation and practical application of genetic analysis techniques for microbial material from food, including bioinformatic analysis and data interpretation. The method discussed in the article for analyzing microorganisms in food without traditional culture methods is known as food metagenomics. This approach, along with other omics technologies such as nutrigenomics, proteomics, metabolomics, and transcriptomics, collectively forms the field of foodomics. Food metagenomics allows swift and thorough examination of bacteria and potential metabolic pathways by utilizing foodomic databases. Despite its established scientific basis and available bioinformatics resources, the research approach of food metagenomics outlined in the article is not yet widely implemented in industry. The authors believe that the integration of next-generation sequencing (NGS) with rapidly advancing digital technologies such as artificial intelligence (AI), the Internet of Things (IoT), and big data will facilitate the widespread adoption of this research strategy in microbial analysis for the food industry. This adoption is expected to enhance food safety and product quality in the near future.
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Affiliation(s)
- Jan Sadurski
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 20-704 Lublin, Poland; (M.P.-B.); (A.S.); (A.W.)
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Michielsen S, Vercelli GT, Cordero OX, Bachmann H. Spatially structured microbial consortia and their role in food fermentations. Curr Opin Biotechnol 2024; 87:103102. [PMID: 38461750 DOI: 10.1016/j.copbio.2024.103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.
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Affiliation(s)
- Sabine Michielsen
- Systems Biology Lab, A-LIFE/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands
| | - Gabriel T Vercelli
- Department of Civil and Environmental Engineering, 15 Vassar St, Cambridge, MA 02139, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, 15 Vassar St, Cambridge, MA 02139, USA
| | - Herwig Bachmann
- Systems Biology Lab, A-LIFE/AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, the Netherlands; Microbiology Department, NIZO Food Research, Ede, the Netherlands.
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Zhang T, Chang M, Zhou Y, Wang M, Yan M, Hou X, Liu R, Yuan Y, Yue T. Dynamic alterations of flavor, functional nutrients, and microbial community during fermentation of different animal milk kefirs. Food Res Int 2024; 186:114305. [PMID: 38729687 DOI: 10.1016/j.foodres.2024.114305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
Kefir is a traditional dairy beverage, usually made from cow or goat milk fermented with kefir grains, and has many health benefits. To elucidate the fermentation patterns of animal milk kefirs during the fermentation process and find the optimal milk types, cow, camel, goat, and donkey milk were fermented with kefir grains for 0, 1, 3, 5, and 7 days. Volatile and non-volatile metabolites and microbial changes were dynamically monitored. The results showed that volatile flavor substances were massively elevated in four kefirs on days 1-3. Lipids and carbohydrates gradually decreased, while amino acids, small peptides, and tryptophan derivatives accumulated during fermentation in four kefirs. Besides, four kefirs had similar alterations in Lactobacillus and Acetobacter, while some distinctions existed in low-abundance bacteria. Association analysis of microorganisms and volatile and non-volatile metabolites also revealed the underlying fermentation mechanism. This study found that appropriately extending the fermentation time contributed to the accumulation of some functional nutrients. Furthermore, goat and donkey milk could be the better matrices for kefir fermentation.
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Affiliation(s)
- Ting Zhang
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Min Chang
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Ye Zhou
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Meng Wang
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Min Yan
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Xiaohui Hou
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Ruixin Liu
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China
| | - Yahong Yuan
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China.
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an 710069, Shaanxi, China; Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an 710069, Shaanxi, China; Research Center of Food Safety Risk Assessment and Control, Xi'an 710069, Shaanxi, China.
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Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. ADVANCES IN GENETICS 2024; 111:237-310. [PMID: 38908901 DOI: 10.1016/bs.adgen.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.
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Affiliation(s)
- Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñaki Odriozola
- Health Department of Basque Government, Donostia-San Sebastián, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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Walsh LH, Breselge S, Martin JGP, Coakley M, Ferguson E, Stapleton A, Crispie F, O'Toole PW, Cotter PD. Kefir4All, a citizen science initiative to raise awareness of the roles that microbes play in food fermentation. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0015523. [PMID: 38661415 PMCID: PMC11044645 DOI: 10.1128/jmbe.00155-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/21/2023] [Indexed: 04/26/2024]
Abstract
Microorganisms are ubiquitous in nature and are central to human, animal, environmental, and planetary health. They play a particularly important role in the food chain and the production of high-quality, safe, and health-promoting foods, especially fermented foods. This important role is not always apparent to members of the public. Here, we describe Kefir4All, a citizen science project designed to provide the general public with an opportunity to expand their awareness, knowledge, and practical skills relating to microbiology, introduced through the medium of producing fermented food, i.e., milk kefir or water kefir. During the course of Kefir4All, 123 citizen scientists, from second-level school and non-school settings, participated in a study to track changes in the microbial composition of kefirs, by performing and recording details of milk kefir or water kefir fermentations they performed in their homes or schools over the 21-week project. At the start of the study, the citizen scientists were provided with milk or water kefir grains to initiate the fermentations. Both types of kefir grain are semi-solid, gelatinous-like substances, composed of exopolysaccharides and proteins, containing a symbiotic community of bacteria and yeast. The experimental component of the project was complemented by a number of education and outreach events, including career talks and a site visit to our research center (Kefir Day). At the end of the study, a report was provided to each citizen scientist, in which individualized results of their fermenting activities were detailed. A number of approaches were taken to obtain feedback and other insights from the citizen scientists. Evaluations took place before and after the Kefir4All project to gauge the citizen scientist's self-reported awareness, knowledge, and interest in microbiology and fermented foods. Further insights into the level of citizen science participation were gained through assessing the number of samples returned for analysis and the level of participation of the citizen scientists throughout the project. Notably, the survey results revealed a self-reported, increased interest in, and general knowledge of, science among the Kefir4All citizen scientists after undertaking the project and a willingness to take part in further citizen science projects. Ultimately, Kefir4All represents an example of the successful integration of citizen science into existing education and research systems.
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Affiliation(s)
- Liam H. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Cork, Ireland
| | - José Guilherme Prado Martin
- Department of Microbiology, Microbiology of Fermented Products Laboratory (FERMICRO), Universidade Federal de Viçosa, Viçosa, Brazil
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Eimear Ferguson
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
| | - Aimee Stapleton
- APC Microbiome Ireland SFI Research Centre, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W. O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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Elcheninov AG, Zayulina KS, Klyukina AA, Kremneva MK, Kublanov IV, Kochetkova TV. Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Microorganisms 2023; 12:16. [PMID: 38276185 PMCID: PMC10819033 DOI: 10.3390/microorganisms12010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Kseniya S. Zayulina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Mariia K. Kremneva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia;
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
| | - Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia; (K.S.Z.); (A.A.K.); (I.V.K.); (T.V.K.)
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