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Kothe CI, Carøe C, Mazel F, Zilber D, Cruz-Morales P, Mohellibi N, Evans JD. Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation. Food Res Int 2024; 189:114490. [PMID: 38876584 DOI: 10.1016/j.foodres.2024.114490] [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: 02/28/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 06/16/2024]
Abstract
Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.
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Affiliation(s)
- Caroline Isabel Kothe
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | | | - Florent Mazel
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - David Zilber
- Novonesis, Hørsholm, Denmark; Restaurant Noma, Copenhagen, Denmark
| | - Pablo Cruz-Morales
- Yeast Natural Products, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Nacer Mohellibi
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, France
| | - Joshua D Evans
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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Ucak S. Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy. Chem Biodivers 2024; 21:e202302120. [PMID: 38613509 DOI: 10.1002/cbdv.202302120] [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: 01/02/2024] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 04/15/2024]
Abstract
One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.
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Affiliation(s)
- Samet Ucak
- Department of Medical Biology and Genetics, Faculty of Medicine, Istanbul Aydın University, Istanbul, 34295, Türkiye
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Aung T, Kim MJ. Wheat and Wheat-Derived Beverages: A Comprehensive Review of Technology, Sensory, Biological Activity, and Sustainability. Prev Nutr Food Sci 2023; 28:401-410. [PMID: 38188081 PMCID: PMC10764229 DOI: 10.3746/pnf.2023.28.4.401] [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: 06/15/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 01/09/2024] Open
Abstract
At present there is heightened demand for beverages that functionally improve human well-being. Wheat and wheat derivatives are excellent sources of nutrients and bioactive phytochemicals including phenolic compounds, dietary fiber, gamma amino butyric acid, and amino acids. Generally, wheat flour has been used extensively in baking and confectionery production, and wheat germ, and bran are byproducts that can be used to fortify some foods. However, limited attention has been paid to the use of wheat and wheat derivatives for beverage production. Our study therefore aimed to fill this gap by comprehensively exploring various aspects of wheat beverages. This review scrutinizes the use of wheat and wheat derivatives in beverage preparation, including processing methods, sensory perception, and biological properties, and also sheds light on the challenges and future perspectives of the wheat beverage industry. Our study offers valuable insight into the use of wheat for the design of functional, nonalcoholic plant-based beverages.
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Affiliation(s)
- Thinzar Aung
- Department of Food and Nutrition, Changwon National University, Gyeongnam 51140, Korea
| | - Mi Jeong Kim
- Department of Food and Nutrition, Changwon National University, Gyeongnam 51140, Korea
- Interdisciplinary Program in Senior Human Ecology, Changwon National University, Gyeongnam 51140, Korea
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Carole Sanya AK, Madode YE, Schoustra SE, Smid EJ, Linnemann AR. Technological variations, microbial diversity and quality characteristics of maize ogi used for akpan production in Benin. Food Res Int 2023; 170:113038. [PMID: 37316091 DOI: 10.1016/j.foodres.2023.113038] [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: 02/04/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
Fermented maize starch, called ogi in Benin, is used for preparing akpan, a traditional yoghurt-like food that contributes to the food and nutrition security of its consumers. Current ogi processing technologies used by two socio-cultural groups of Benin, namely the Fon and the Goun, and aspects of the quality of the fermented starches were studied to assess the current state-of-the-art, explore changes in key product characteristics over time and identify priorities for follow-up research to increase product quality and shelf life. A survey on processing technologies was conducted in five municipalities in south Benin and samples of maize starch were collected, which were analysed after the fermentation required to obtain ogi. Four processing technologies were identified, two from the Goun (G1, G2) and two from the Fon (F1, F2). The main difference between the four processing technologies was the steeping procedure used for the maize grains. The pH of the ogi samples ranged between 3.1 and 4.2, with the highest values for G1 samples, which also contained relatively higher concentrations of sucrose (0.05-0.3 g/L) than F1 samples (0.02-0.08 g/L), and lower citrate and lactate concentrations (0.2-0.3 and 5.6-16.9 g/L, respectively) than F2 samples (0.4-0.5 and 14-27.7 g/L, respectively). Fon samples collected in Abomey were particularly rich in volatile organic compounds and free essential amino acids. Members of the genera Lactobacillus (8.6-69.3%), Limosilactobacillus (5.4-79.1%), Streptococcus (0.6-59.3%) and Weissella (2.6-51.2%) dominated the bacterial microbiota of ogi with a significant abundance of Lactobacillus spp. in Goun samples. Sordariomycetes (10.6-81.9%) and Saccharomycetes (6.2-81.4%) dominated the fungal microbiota. The yeast community of ogi samples mainly consisted of the genera Diutina, Pichia, Kluyveromyces, Lachancea and unclassified members of the Dipodascaceae family. Hierarchical clustering of metabolic data showed similarities between samples from different technologies at a default threshold of 0.05. No obvious trend in the composition of the samples' microbial communities reflected the clusters observed for the metabolic characteristics. The results indicate that beyond the general impact of the use of Fon or Goun technologies on fermented maize starch, the individual contribution of processing practices warrants study, under controlled conditions, to determine the drivers of difference or similarity between maize ogi samples to further contribute to improving product quality and shelf life.
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Affiliation(s)
- A K Carole Sanya
- Food Quality and Design (FQD), Wageningen University and Research, The Netherlands, 6700 HB Wageningen, the Netherlands; Laboratoire des Sciences des Aliments (LSA), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Calavi, Benin.
| | - Yann E Madode
- Laboratoire des Sciences des Aliments (LSA), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Calavi, Benin.
| | - Sijmen E Schoustra
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, the Netherlands; Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia.
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, the Netherlands.
| | - Anita R Linnemann
- Food Quality and Design (FQD), Wageningen University and Research, The Netherlands, 6700 HB Wageningen, the Netherlands.
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Aydin A, Sudagidan M, Mamatova Z, Yurt MNZ, Ozalp VC, Zornu J, Tavornpanich S, Brun E. Bacterial Skin Microbiota of Seabass from Aegean Fish Farms and Antibiotic Susceptibility of Psychrotrophic Pseudomonas. Foods 2023; 12:foods12101956. [PMID: 37238774 DOI: 10.3390/foods12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023] Open
Abstract
Farming seabass (Dicentrarchus labrax) is an essential activity in the Mediterranean basin including the Aegean Sea. The main seabass producer is Turkey accounting for 155,151 tons of production in 2021. In this study, skin swabs of seabass farmed in the Aegean Sea were analysed with regard to the isolation and identification of Pseudomonas. Bacterial microbiota of skin samples (n = 96) from 12 fish farms were investigated using next-generation sequencing (NGS) and metabarcoding analysis. The results demonstrated that Proteobacteria was the dominant bacterial phylum in all samples. At the species level, Pseudomonas lundensis was identified in all samples. Pseudomonas, Shewanella, and Flavobacterium were identified using conventional methods and a total of 46 viable (48% of all NGS+) Pseudomonas were isolated in seabass swab samples. Additionally, antibiotic susceptibility was determined according to standards of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) in psychrotrophic Pseudomonas. Pseudomonas strains were tested for susceptibility to 11 antibiotics (piperacillin-tazobactam, gentamicin, tobramycin, amikacin, doripenem, meropenem, imipenem, levofloxacin, ciprofloxacin, norfloxacin, and tetracycline) from five different groups of antibiotics (penicillins, aminoglycosides, carbapenems, fluoroquinolones, and tetracyclines). The antibiotics chosen were not specifically linked to usage by the aquaculture industry. According to the EUCAST and CLSI, three and two Pseudomonas strains were found to be resistant to doripenem and imipenem (E-test), respectively. All strains were susceptible to piperacillin-tazobactam, amikacin, levofloxacin, and tetracycline. Our data provide insight into different bacteria that are prevalent in the skin microbiota of seabass sampled from the Aegean Sea in Turkey, and into the antibiotic resistance of psychrotrophic Pseudomonas spp.
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Affiliation(s)
- Ali Aydin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, Istanbul 34320, Turkey
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, Konya 42080, Turkey
| | - Zhanylbubu Mamatova
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, Istanbul 34320, Turkey
| | - Mediha Nur Zafer Yurt
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, Konya 42080, Turkey
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Medical School, Atilim University, Golbasi, Ankara 06830, Turkey
| | - Jacob Zornu
- Norwegian Veterinary Institute, 1433 Ås, Norway
| | | | - Edgar Brun
- Norwegian Veterinary Institute, 1433 Ås, Norway
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N'zi FAJA, Kouakou-Kouamé CA, N'guessan FK, Poss C, Teyssier C, Durand N, Montet D. Occurrence of mycotoxins and microbial communities in artisanal infant flours marketed in Côte d'Ivoire. World J Microbiol Biotechnol 2023; 39:128. [PMID: 36943491 DOI: 10.1007/s11274-023-03577-5] [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: 10/27/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
Abstract
The aim of this study was to determine the microbial diversity and mycotoxin profile of artisanal infant flours commonly vended in public healthcare centres and retail markets in Côte d'Ivoire. Thus, maize, millet, sorghum, soya and multigrain (mix of different cereals) flour samples collected from different localities were first, analysed for nutritional composition, then for microbial communities using high-throughput sequencing and for mycotoxins through UHPLC-MS/MS method. Firmicutes was the most abundant bacterial phylum and the dominant genera were Weissella, Staphylococcus, Pediococcus. Potential pathogenic genera such as Bacillus, Enterobacter, Acinetobacter and Burkholderia were also found. The fungal community was composed of two dominant phyla (Ascomycota and Basidiomycota) and 31 genera with > 0.1% relative abundance. In samples from public healthcare centres, Candida, Hyphopichia, Trichosporon, and Cyberlindnera were the most dominant genera according to the flour type while in samples from retail markets, they were Cyberlindnera, Clavispora, Nakaseomyces, Aureobasidium and Candida. Possible toxigenic genera Fusarium and Aspergillus were also detected. Aflatoxin B1 (AFB1), Ochractoxin (OTA), Fumonisin B1 (FB1) and B2 (FB2) were the mycotoxins found in the analysed flours. AFB1 was detected in 100% of maize (range 1.2-120.5 µg/kg; mean: 44.2 µg/kg) and 50-83.3% of millet flours (range 0.2-31.5 µg/kg; mean: 31.5 µg/kg). Its level in all maize and rice flour samples exceeded EU standard (0.1 µg/kg). For OTA and fumonisins, millet and maize flours showed the highest levels of sample exceeding the EU standard. Thus, artisanal infant flours marketed in Côte d'Ivoire, mainly maize and rice flours, although containing potentially beneficial bacteria, represent potential health risks for children.
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Affiliation(s)
- Fabienne Anne-Julie A N'zi
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire.
| | - Clémentine A Kouakou-Kouamé
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Florent K N'guessan
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui Abrogoua, 02 BP 801, Abidjan, 02, Côte d'Ivoire
| | - Charlie Poss
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Corinne Teyssier
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Noel Durand
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Didier Montet
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
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Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
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