1
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van Olst B, Nugroho A, Boeren S, Vervoort J, Bachmann H, Kleerebezem M. Bacterial proteome adaptation during fermentation in dairy environments. Food Microbiol 2024; 121:104514. [PMID: 38637076 DOI: 10.1016/j.fm.2024.104514] [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: 01/10/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
The enzymatic repertoire of starter cultures belonging to the Lactococcus genus determines various important characteristics of fermented dairy products but might change in response to the substantial environmental changes in the manufacturing process. Assessing bacterial proteome adaptation in dairy and other food environments is challenging due to the high matrix-protein concentration and is even further complicated in particularly cheese by the high fat concentrations, the semi-solid state of that matrix, and the non-growing state of the bacteria. Here, we present bacterial harvesting and processing procedures that enable reproducible, high-resolution proteome determination in lactococcal cultures harvested from laboratory media, milk, and miniature Gouda cheese. Comparative proteome analysis of Lactococcus cremoris NCDO712 grown in laboratory medium and milk revealed proteome adaptations that predominantly reflect the differential (micro-)nutrient availability in these two environments. Additionally, the drastic environmental changes during cheese manufacturing only elicited subtle changes in the L. cremoris NCDO712 proteome, including modified expression levels of enzymes involved in flavour formation. The technical advances we describe offer novel opportunities to evaluate bacterial proteomes in relation to their performance in complex, protein- and/or fat-rich food matrices and highlight the potential of steering starter culture performance by preculture condition adjustments.
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Affiliation(s)
- Berdien van Olst
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Avis Nugroho
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Microbiology Department, NIZO Food Research, Ede, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Jacques Vervoort
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Herwig Bachmann
- Microbiology Department, NIZO Food Research, Ede, the Netherlands; Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands; TI Food and Nutrition, Wageningen, the Netherlands.
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2
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Lutin J, Dufrene F, Guyot P, Palme R, Achilleos C, Bouton Y, Buchin S. Microbial composition and viability of natural whey starters used in PDO Comté cheese-making. Food Microbiol 2024; 121:104521. [PMID: 38637083 DOI: 10.1016/j.fm.2024.104521] [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: 12/21/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/20/2024]
Abstract
Natural whey starters (NWS) are cultures with undefined multiple-strains species commonly used to speed up the fermentation process of cheeses. The aim of this study was to explore the diversity and the viability of Comté cheese NWS microbiota. Culture-dependent methods, i.e. plate counting and genotypic characterization, and culture-independent methods, i.e. qPCR, viability-qPCR, fluorescence microscopy and DNA metabarcoding, were combined to analyze thirty-six NWS collected in six Comté cheese factories at two seasons. Our results highlighted that NWS were dominated by Streptococcus thermophilus (ST) and thermophilic lactobacilli. These species showed a diversity of strains based on Rep-PCR. The dominance of Lactobacillus helveticus (LH) over Lactobacillus delbrueckii (LD) varied depending on the factory and the season. This highlighted two types of NWS: the type-ST/LD (LD > LH) and the type-ST/LH (LD < LH). The microbial composition varied depending on cheese factory. One factory was distinguished by its level of culturable microbial groups (ST, enterococci and yeast) and its fungi diversity. The approaches used to estimate the viability showed that most NWS cells were viable. Further investigations are needed to understand the microbial diversity of these NWS.
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Affiliation(s)
- Jade Lutin
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Franck Dufrene
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Philippe Guyot
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Romain Palme
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Christine Achilleos
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Yvette Bouton
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France.
| | - Solange Buchin
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
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3
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Parlindungan E, Sadovskaya I, Vinogradov E, Lugli GA, Ventura M, van Sinderen D, Mahony J. Novel cell wall polysaccharide genotypes and structures of lactococcal strains isolated from milk and fermented foods. Int J Food Microbiol 2024; 424:110840. [PMID: 39126753 DOI: 10.1016/j.ijfoodmicro.2024.110840] [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: 04/05/2024] [Revised: 06/24/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
The biosynthetic machinery for cell wall polysaccharide (CWPS) formation in Lactococcus lactis and Lactococcus cremoris is encoded by the cwps locus. The CWPS of lactococci typically consists of a neutral rhamnan component, which is embedded in the peptidoglycan, and to which a surface-exposed side chain oligosaccharide or polysaccharide pellicle (PSP) component is attached. The rhamnan component has been shown for several lactococcal strains to consist of a repeating rhamnose trisaccharide subunit, while the side chain is diverse in glycan content, polymeric status and glycosidic linkage architecture. The observed structural diversity of the CWPS side chain among lactococcal strains is reflected in the genetic diversity within the variable 3' region of the corresponding cwps loci. To date, four distinct cwps genotypes (A, B, C, D) have been identified, while eight subtypes (C1 through to C8) have been recognized among C-genotype strains. In the present study, we report the identification of three novel subtypes of the lactococcal cwps C genotypes, named C9, C10 and C11. The CWPS of four isolates representing C7, C9, C10 and C11 genotypes were analysed using 2D NMR to reveal their unique CWPS structures. Through this analysis, the structure of one novel rhamnan, three distinct PSPs and three exopolysaccharides were elucidated. Results obtained in this study provide further insights into the complex nature and fascinating diversity of lactococcal CWPSs. This highlights the need for a holistic view of cell wall-associated glycan structures which may contribute to robustness of certain strains against infecting bacteriophages. This has clear implications for the fermented food industry that relies on the consistent application of lactococcal strains in mesophilic production systems.
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Affiliation(s)
- Elvina Parlindungan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Irina Sadovskaya
- Univ. Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, USC ANSES, INRAe, Univ. Artois, Univ. Lille, Univ. Picardie Jules Verne, Univ. Liège, Junia, F-62200 Boulogne-sur-Mer, France
| | - Evgeny Vinogradov
- National Research Council Canada, Institute for Biological Sciences, Ottawa, ON, Canada
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.
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4
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Paillet T, Lamy-Besnier Q, Figueroa C, Petit MA, Dugat-Bony E. Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years. mSystems 2024; 9:e0020124. [PMID: 38860825 PMCID: PMC11265279 DOI: 10.1128/msystems.00201-24] [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: 02/09/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.
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Affiliation(s)
- Thomas Paillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
| | - Quentin Lamy-Besnier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Clarisse Figueroa
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Eric Dugat-Bony
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Palaiseau, France
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5
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Gapp C, Dijamentiuk A, Mangavel C, Callon C, Theil S, Revol-Junelles AM, Chassard C, Borges F. Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization. mSystems 2024:e0044524. [PMID: 39041801 DOI: 10.1128/msystems.00445-24] [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: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. IMPORTANCE Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.
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Affiliation(s)
- Chloé Gapp
- Université de Lorraine, LIBio, Nancy, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | | | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
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6
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Luo Y, Liao H, Huang X, Zhang C, Gao L, Wang Z, Xia X. Unraveling the Metabolic Behavior and Interspecific Interaction Pattern of Lactic Acid Bacteria within Chinese Rice Wine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14899-14911. [PMID: 38913831 DOI: 10.1021/acs.jafc.4c02461] [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: 06/26/2024]
Abstract
The synthetic community of lactic acid bacteria (LAB) is commonly utilized in the food industry for manipulating product properties. However, the intermediate interactions and ecological stability resulting from metabolic differences among various LAB types remain poorly understood. We aimed to analyze the metabolic behavior of single and combined lactic acid bacteria in China rice wine based on microbial succession. Three-stage succession patterns with obligate heterofermentative LAB dominating prefermentation and homofermentative LAB prevailing in main fermentation were observed. Facultative heterofermentative LAB exhibited significant growth. Pairwise coculture interactions revealed 63.5% positive, 34.4% negative, and 2.1% neutral interactions, forming nontransitive and transitive competition modes. Nontransitive competitive combinations demonstrated stability over ∼200 generations through amino acid (mainly aspartic acid, glutamine, and serine) cross-feeding and lactic acid detoxification, which also showed potential for controlling biogenic amines and developing LAB starter cultures. Our findings offer insights into the mechanistic underpinnings of LAB interaction networks.
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Affiliation(s)
- Yi Luo
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Hui Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- Jiangsu Tanggou Liangxianghe Liquor Co., Ltd., Lianyungang, Jiangsu 222535, P. R. China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300000, P. R. China
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7
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da Silva Duarte V, de Paula Dias Moreira L, Skeie SB, Svalestad F, Øyaas J, Porcellato D. Database selection for shotgun metaproteomic of low-diversity dairy microbiomes. Int J Food Microbiol 2024; 418:110706. [PMID: 38696985 DOI: 10.1016/j.ijfoodmicro.2024.110706] [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: 02/15/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 05/04/2024]
Abstract
The metaproteomics field has recently gained more and more interest as a valuable tool for studying both the taxonomy and function of microbiomes, including those used in food fermentations. One crucial step in the metaproteomics pipeline is selecting a database to obtain high-quality taxonomical and functional information from microbial communities. One of the best strategies described for building protein databases is using sample-specific or study-specific protein databases obtained from metagenomic sequencing. While this is true for high-diversity microbiomes (such as gut and soil), there is still a lack of validation for different database construction strategies in low-diversity microbiomes, such as those found in fermented dairy products where starter cultures containing few species are used. In this study, we assessed the performance of various database construction strategies applied to metaproteomics on two low-diversity microbiomes obtained from cheese production using commercial starter cultures and analyzed by LC-MS/MS. Substantial differences were detected between the strategies, and the best performance in terms of the number of peptides and proteins identified from the spectra was achieved by metagenomic-derived databases. However, extensive databases constructed from a high number of available online genomes obtained a similar taxonomical and functional annotation of the metaproteome compared to the metagenomic-derived databases. Our results indicate that, in the case of low-diversity dairy microbiomes, the use of publically available genomes to construct protein databases can be considered as an alternative to metagenome-derived databases.
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Affiliation(s)
- Vinícius da Silva Duarte
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, P.O. Box 5003, N-1432 Ås, Norway
| | - Luiza de Paula Dias Moreira
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, P.O. Box 5003, N-1432 Ås, Norway
| | - Siv B Skeie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, P.O. Box 5003, N-1432 Ås, Norway
| | | | - Jorun Øyaas
- TINE SA, P.O. Box 7, Kalbakken, N-0902 Oslo, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NMBU, P.O. Box 5003, N-1432 Ås, Norway.
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8
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Qin X, Hou Q, Zhao H, Wang P, Yang S, Liao N, Huang J, Li X, He Q, Nethmini RT, Jiang G, He S, Chen Q, Dong K, Li N. Resource diversity disturbs marine Vibrio diversity and community stability, but loss of Vibrio diversity enhances community stability. Ecol Evol 2024; 14:e11234. [PMID: 38646003 PMCID: PMC11027015 DOI: 10.1002/ece3.11234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Vibrio is a salt-tolerant heterotrophic bacterium that occupies an important ecological niche in marine environments. However, little is known about the contribution of resource diversity to the marine Vibrio diversity and community stability. In this study, we investigated the association among resource diversity, taxonomic diversity, phylogenetic diversity, and community stability of marine Vibrio in the Beibu Gulf. V. campbellii and V. hangzhouensis were the dominant groups in seawater and sediments, respectively, in the Beibu Gulf. Higher alpha diversity was observed in the sediments than in the seawater. Marine Vibrio community assembly was dominated by deterministic processes. Pearson's correlation analysis showed that nitrite (NO 2 - -N), dissolved inorganic nitrogen (DIN), ammonium (NH 4 + -N), and pH were the main factors affecting marine Vibrio community stability in the surface, middle, and bottom layers of seawater and sediment, respectively. Partial least-squares path models (PLS-PM) demonstrated that resource diversity, water properties, nutrients, and geographical distance had important impacts on phylogenetic and taxonomic diversity. Regression analysis revealed that the impact of resource diversity on marine Vibrio diversity and community stability varied across different habitats, but loss of Vibrio diversity increases community stability. Overall, this study provided insights into the mechanisms underlying the maintenance of Vibrio diversity and community stability in marine environments.
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Affiliation(s)
- Xinyi Qin
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
- Key Laboratory of Environment Change and Resources use in Beibu Gulf, Ministry of EducationNanning Normal UniversityNanningChina
| | - Qinghua Hou
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
| | - Huaxian Zhao
- Key Laboratory of Environment Change and Resources use in Beibu Gulf, Ministry of EducationNanning Normal UniversityNanningChina
| | - Pengbin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of OceanographyMinistry of Natural Re‐SourcesHangzhouChina
| | - Shu Yang
- Key Laboratory of Environment Change and Resources use in Beibu Gulf, Ministry of EducationNanning Normal UniversityNanningChina
| | - Nengjian Liao
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
| | | | - Xiaoli Li
- School of AgricultureLudong UniversityYantaiChina
| | - Qing He
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
| | - Rajapakshalage Thashikala Nethmini
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
| | - Gonglingxia Jiang
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
| | - Shiying He
- Key Laboratory of Environment Change and Resources use in Beibu Gulf, Ministry of EducationNanning Normal UniversityNanningChina
| | - Qingxiang Chen
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
| | - Ke Dong
- Department of Biological SciencesKyonggi UniversitySuwon‐siGyeonggi‐doSouth Korea
| | - Nan Li
- Laboratory for Coastal Ocean Variation and Disaster Prediction, Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, College of Ocean and MeteorologyGuangdong Ocean UniversityZhanjiangChina
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9
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024:S0966-842X(24)00057-X. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [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: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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10
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White K, Eraclio G, McDonnell B, Bottacini F, Lugli GA, Ventura M, Volontè F, Dal Bello F, Mahony J, van Sinderen D. A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures. Appl Environ Microbiol 2024; 90:e0215223. [PMID: 38334291 PMCID: PMC10952461 DOI: 10.1128/aem.02152-23] [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: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024] Open
Abstract
The dairy fermentation industry relies on the activity of lactic acid bacteria in robust starter cultures to accomplish milk acidification. Maintenance of the composition of these starter cultures, whether defined or undefined, is essential to ensure consistent and high-quality fermentation end products. To date, limited information exists regarding the microbial composition of undefined starter culture systems. Here, we describe a culture-based analysis combined with a metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, we describe a qPCR-based genotype detection assay, which is capable of discerning nine distinct lactococcal genotypes to characterize these undefined starter cultures, and which can be applied to monitor compositional changes in an undefined starter culture during a fermentation. IMPORTANCE This study reports on the development of a combined culture-based analysis and metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, a novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes (based on lactococcal cell wall polysaccharide biosynthesis gene clusters), was used to monitor compositional changes in an undefined starter culture following phage attack. These analytical approaches facilitate a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important QC aspect due to the increasing demand for consistent and high-quality dairy products.
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Affiliation(s)
- Kelsey White
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Brian McDonnell
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | | | | | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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11
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Ndiaye A, Fliss I, Filteau M. High-throughput characterization of the effect of sodium chloride and potassium chloride on 31 lactic acid bacteria and their co-cultures. Front Microbiol 2024; 15:1328416. [PMID: 38435689 PMCID: PMC10904479 DOI: 10.3389/fmicb.2024.1328416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/26/2024] [Indexed: 03/05/2024] Open
Abstract
Salt (NaCl) is associated with a risk of hypertension and the development of coronary heart disease, so its consumption should be limited. However, salt plays a key role in the quality and safety of food by controlling undesirable microorganisms. Since studies have focused primarily on the effect of salts on the overall counts of the lactic acid bacteria (LAB) group, we have not yet understood how salt stress individually affects the strains and the interactions between them. In this study, we characterized the effect of sodium chloride (NaCl) and potassium chloride (KCl) on the growth and acidification of 31 LAB strains. In addition, we evaluated the effect of salts on a total of 93 random pairwise strain combinations. Strains and co-cultures were tested at 3% NaCl, 5% NaCl, and 3% KCl on solid medium using an automated approach and image analysis. The results showed that the growth of LAB was significantly reduced by up to 68% at 5% NaCl (p < 0.0001). For the co-cultures, a reduction of up to 57% was observed at 5% NaCl (p < 0.0001). However, acidification was less affected by salt stress, whether for monocultures or co-cultures. Furthermore, KCl had a lesser impact on both growth and acidification compared to NaCl. Indeed, some strains showed a significant increase in growth at 3% KCl, such as Lactococcus lactis subsp. lactis 74310 (23%, p = 0.01). More importantly, co-cultures appeared to be more resilient and had more varied responses to salt stress than the monocultures, as several cases of suppression of the significant effect of salts on acidification and growth were detected. Our results highlight that while salts can modulate microbial interactions, these latter can also attenuate the effect of salts on LAB.
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Affiliation(s)
- Amadou Ndiaye
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Ismail Fliss
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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12
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Decadt H, Weckx S, De Vuyst L. The microbial and metabolite composition of Gouda cheese made from pasteurized milk is determined by the processing chain. Int J Food Microbiol 2024; 412:110557. [PMID: 38237418 DOI: 10.1016/j.ijfoodmicro.2024.110557] [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: 08/17/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/28/2024]
Abstract
Gouda cheeses of different production batches and ripening times often differ in metabolite composition, which may be due to the starter culture mixture applied or the growth of non-starter lactic acid bacteria (NSLAB) upon maturation. Therefore, a single Gouda cheese production batch was systematically investigated from the thermized milk to the mature cheeses, ripened for up to 100 weeks, to identify the main bacterial species and metabolites and their dynamics during the whole production and ripening. As this seemed to be starter culture strain- and NSLAB-dependent, it requested a detailed, longitudinal, and quantitative investigation. Hereto, microbial colony enumeration, high-throughput full-length 16S rRNA gene sequencing, and a metabolomic approach were combined. Culture-dependently, Lactococcus lactis was the most abundant species from its addition as part of the starter culture up to the first two months of cheese ripening. Afterward, the NSLAB Lacticaseibacillus paracasei became the main species during ripening. The milk was a possible inoculation source for the latter species, despite pasteurization. Culture-independently, the starter LAB Lactococcus cremoris and Lc. lactis were the most abundant species in the cheese core throughout the whole fermentation and ripening phases up to 100 weeks. The cheese rind from 40 until 100 weeks of ripening was characterized by a high relative abundance of the NSLAB Tetragenococcus halophilus and Loigolactobacillus rennini, which both came from the brine. These species were linked with the production of the biogenic amines cadaverine and putrescine. The most abundant volatile organic compound was acetoin, an indicator of citrate and lactose fermentation during the production day, whereas the concentrations of free amino acids were an indicator of the ripening time.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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13
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Dijamentiuk A, Mangavel C, Gapp C, Elfassy A, Revol-Junelles AM, Borges F. Serial cultures in invert emulsion and monophase systems for microbial community shaping and propagation. Microb Cell Fact 2024; 23:50. [PMID: 38355580 PMCID: PMC10865683 DOI: 10.1186/s12934-024-02322-3] [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: 12/14/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Microbial communities harbor important biotechnological potential in diverse domains, however, the engineering and propagation of such communities still face both knowledge and know-how gaps. More specifically, culturing tools are needed to propagate and shape microbial communities, to obtain desired properties, and to exploit them. Previous work suggested that micro-confinement and segregation of microorganisms using invert (water-in-oil, w/o) emulsion broth can shape communities during propagation, by alleviating biotic interactions and inducing physiological changes in cultured bacteria. The present work aimed at evaluating invert emulsion and simple broth monophasic cultures for the propagation and shaping of bacterial communities derived from raw milk in a serial propagation design. RESULTS The monophasic setup resulted in stable community structures during serial propagation, whereas the invert emulsion system resulted in only transiently stable structures. In addition, different communities with different taxonomic compositions could be obtained from a single inoculum. Furthermore, the implementation of invert emulsion systems has allowed for the enrichment of less abundant microorganisms and consequently facilitated their isolation on culture agar plates. CONCLUSIONS The monophasic system enables communities to be propagated in a stable manner, whereas the invert emulsion system allowed for the isolation of less abundant microorganisms and the generation of diverse taxonomic compositions from a single inoculum.
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Affiliation(s)
- Alexis Dijamentiuk
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Chloé Gapp
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France
| | | | - Frédéric Borges
- Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine, Nancy, France.
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14
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van Nes EH, Pujoni DGF, Shetty SA, Straatsma G, de Vos WM, Scheffer M. A tiny fraction of all species forms most of nature: Rarity as a sticky state. Proc Natl Acad Sci U S A 2024; 121:e2221791120. [PMID: 38165929 PMCID: PMC10786311 DOI: 10.1073/pnas.2221791120] [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: 12/23/2022] [Accepted: 11/11/2023] [Indexed: 01/04/2024] Open
Abstract
Using data from a wide range of natural communities including the human microbiome, plants, fish, mushrooms, rodents, beetles, and trees, we show that universally just a few percent of the species account for most of the biomass. This is in line with the classical observation that the vast bulk of biodiversity is very rare. Attempts to find traits allowing the tiny fraction of abundant species to escape rarity have remained unsuccessful. Here, we argue that this might be explained by the fact that hyper-dominance can emerge through stochastic processes. We demonstrate that in neutrally competing groups of species, rarity tends to become a trap if environmental fluctuations result in gains and losses proportional to abundances. This counter-intuitive phenomenon arises because absolute change tends to zero for very small abundances, causing rarity to become a "sticky state", a pseudoattractor that can be revealed numerically in classical ball-in-cup landscapes. As a result, the vast majority of species spend most of their time in rarity leaving space for just a few others to dominate the neutral community. However, fates remain stochastic. Provided that there is some response diversity, roles occasionally shift as stochastic events or natural enemies bring an abundant species down allowing a rare species to rise to dominance. Microbial time series spanning thousands of generations support this prediction. Our results suggest that near-neutrality within niches may allow numerous rare species to persist in the wings of the dominant ones. Stand-ins may serve as insurance when former key species collapse.
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Affiliation(s)
- Egbert H. van Nes
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
| | - Diego G. F. Pujoni
- Federal University of Minas Gerais, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Laboratório de Limnologia, Ecotoxicologia e Ecologia Aquática, Belo HorizonteMG CEP31270-901, Brazil
| | - Sudarshan A. Shetty
- Laboratory of Microbiology, Wageningen University, WageningenNL-6700 EH, The Netherlands
| | - Gerben Straatsma
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, WageningenNL-6700 EH, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki00014, Finland
| | - Marten Scheffer
- Aquatic Ecology and Water Quality Management Group, Environmental Science Department, Wageningen University, WageningenNL-6700 AA, The Netherlands
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15
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White K, Eraclio G, Lugli GA, Ventura M, Mahony J, Bello FD, van Sinderen D. A Metagenomics Approach to Enumerate Bacteriophages in a Food Niche. Methods Mol Biol 2024; 2738:185-199. [PMID: 37966600 DOI: 10.1007/978-1-0716-3549-0_12] [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] [Indexed: 11/16/2023]
Abstract
Dairy fermentation relies on the activity of starter cultures composed primarily of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus strains to produce consistent, high-quality products. Bacteriophages are a constant threat to the industry, often causing slowed or failed fermentation resulting in significant economic losses. To ensure the continuation of reliable fermentation practices, it is important to detect and monitor the phage populations impacting different starter cultures. This has traditionally been done primarily through culture-dependent methods but has since expanded into viral metagenomics. Here we outline a protocol for a targeted virome extraction from a dairy whey sample, followed by subsequent sequencing and phageome analysis of the sample.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele Andrea 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
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
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16
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Zhao S, Dorau R, Tømmerholt L, Gu L, Tadesse BT, Zhao G, Solem C. Simple & better - Accelerated cheese ripening using a mesophilic starter based on a single strain with superior autolytic properties. Int J Food Microbiol 2023; 407:110398. [PMID: 37714070 DOI: 10.1016/j.ijfoodmicro.2023.110398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023]
Abstract
In the manufacture of rennet-coagulated cheese, autolysis is a rate-limiting step for ripening. Previously, a highly autolytic and thermotolerant Lactococcus lactis strain, RD07, was generated, which in preliminary laboratory cheese trials demonstrated great potential as a cheese ripening accelerant. RD07 is proteinase positive (Prt+) and capable of metabolizing citrate (Cit+). In this study, we obtained two derivatives of RD07: EC8 lacking the citrate plasmid, and EC2 lacking the proteinase plasmid. EC2 and EC8 retained the autolytic properties of RD07, and autolyzed 20 times faster than Flora Danica (FD) and SD96, where the latter is the parent of RD07. The three strains EC2, EC8 and RD07 were used in a ratio of 90:8:2, to create a simple starter termed ERC. ERC was less sensitive to cooking when cultured in milk and autolyzed well after entering the stationary phase upon facing sugar starvation. The ERC starter was benchmarked against FD and SD96 in laboratory cheese trials. The free amino acid content in cheese prepared using the ERC culture was 31 % and 34 % higher than in cheese prepared using FD and SD96, respectively. Overall, the ERC culture resulted in a more rapid release of free amino acids. A large-scale (5000 L) Gouda cheese trial at a Danish dairy demonstrated that the single strain ERC starter was comparable in performance to FD + an adjunct Lactobacillus helveticus culture. Furthermore, a large-scale Danbo cheese trial demonstrated that ERC could reduce the ripening period by 50 % for long-term ripened (25 weeks) cheese, resulting in better cheese.
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Affiliation(s)
- Shuangqing Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Robin Dorau
- Novozymes A/S, Biologiens vej 2, DK-2800 Kgs. Lyngby, Denmark
| | | | - Liuyan Gu
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Belay Tilahun Tadesse
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Ge Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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17
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [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] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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18
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Pfau M, Degregori S, Johnson G, Tennenbaum SR, Barber PH, Philson CS, Blumstein DT. The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231305. [PMID: 37830026 PMCID: PMC10565414 DOI: 10.1098/rsos.231305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.
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Affiliation(s)
- Madison Pfau
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Sam Degregori
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Gina Johnson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Stavi R. Tennenbaum
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Conner S. Philson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
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19
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Wu F, Xie X, Du T, Jiang X, Miao W, Wang T. Lactococcus lactis, a bacterium with probiotic functions and pathogenicity. World J Microbiol Biotechnol 2023; 39:325. [PMID: 37776350 DOI: 10.1007/s11274-023-03771-5] [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: 07/31/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Lactococcus lactis (L. lactis) is the primary organism for lactic acid bacteria (LAB) and is a globally recognized safe microorganism for the regulation of the intestinal micro-ecological balance of animals and improving the immune performance of the host. L. lactis is known to play a commercially important role in feed fortification, milk fermentation, and vaccine production, but pathogenic L. lactis has been isolated from many clinical cases in recent years, such as the brain of silver carp with Lactococcosis, the liver and spleen of diseased waterfowl, milk samples and padding materials with cow mastitis, and blood and urine from human patients with endocarditis. In dairy farming, where L. lactis has been used as a probiotic in the past, however, some studies have found that L. lactis can cause mastitis in cows, but the lack of understanding of the pathogenesis of mastitis in cows caused by L. lactis has become a new problem. The main objective of this review is to analyze the increasingly serious clinical mastitis caused by L. lactis and combined with the wide application of L. lactis as probiotics, to comprehensively discuss the characteristics and diversity of L. lactis.
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Affiliation(s)
- Fan Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinmei Xie
- Elanco (Shanghai)Animal Health Co, Ltd, No.1, Field Middle Road, Wusi Farm, Fengxian District, Shanghai, China
| | - Tao Du
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodan Jiang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wei Miao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tiancheng Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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20
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Spus M, Wardhana YR, Wolkers-Rooijackers JC, Abee T, Smid EJ. Lytic bacteriophages affect the population dynamics of multi-strain microbial communities. MICROBIOME RESEARCH REPORTS 2023; 2:33. [PMID: 38045922 PMCID: PMC10688827 DOI: 10.20517/mrr.2023.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/25/2023] [Accepted: 08/25/2023] [Indexed: 12/05/2023]
Abstract
Background: Lytic bacteriophages infect and lyse bacteria and, as a by-product, may affect diversity in microbial communities through selective predation on abundant bacterial strains. We used a complex dairy starter named Ur to investigate population dynamics of Lactococcus lactis, Lactococcus cremoris and Leuconostoc mesenteroides strains in terms of constant-diversity and periodic selection models. Methods: To mimic the starter Ur, we designed blends of 24 strains representing all eight previously identified genetic lineages in the starter culture. The blends were propagated by daily transfers in milk for over 500 generations in the presence or absence of a cocktail of lytic bacteriophages. The relative abundance of genetic lineages of L. lactis, L. cremoris and Lc. mesenteroides strains present in the complex blend, as well as phage presence, were monitored. Results: Control blends without phage predation showed decreased strain diversity, leading to a stable state due to the domination of the fittest strain(s) of a particular lineage according to periodic selection dynamics. However, in phage-challenged blends, predation caused a large shift in the microbial composition by killing the fittest and sensitive strains. Conclusion: It was demonstrated that phage-challenged blends maintained their diversity at the level of genetic lineages, thus providing experimental support for the constant-diversity dynamics model in a complex microbial community.
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Affiliation(s)
- Maciej Spus
- TI Food and Nutrition, Wageningen 6700 AA, the Netherlands
- Food Microbiology, Wageningen University, Wageningen 6700 AA, the Netherlands
| | | | - Judith C.M. Wolkers-Rooijackers
- TI Food and Nutrition, Wageningen 6700 AA, the Netherlands
- Food Microbiology, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Eddy J. Smid
- TI Food and Nutrition, Wageningen 6700 AA, the Netherlands
- Food Microbiology, Wageningen University, Wageningen 6700 AA, the Netherlands
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21
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Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Comput Biol 2023; 19:e1011363. [PMID: 37578975 PMCID: PMC10449394 DOI: 10.1371/journal.pcbi.1011363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
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Affiliation(s)
- William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
| | - Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany
| | - Djordje Bajić
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Almut Heinken
- Inserm U1256 Laboratoire nGERE, Université de Lorraine, Nancy, France
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
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22
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Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 2023; 391-393:110124. [PMID: 36841075 DOI: 10.1016/j.ijfoodmicro.2023.110124] [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: 09/18/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 02/23/2023]
Abstract
Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.
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23
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Xie L, Bi Y, Zhang Y, Guo N. Effect of Coal Mining on Soil Microorganisms from Stipa krylovii Rhizosphere in Typical Grassland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3689. [PMID: 36834383 PMCID: PMC9960647 DOI: 10.3390/ijerph20043689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The environmental changes caused by coal mining activities caused disturbances to the plant, soil, and microbial health in the mining area. Arbuscular mycorrhizal fungi (AMF) play an important role in the ecological restoration of mining areas. However, it is less understood how soil fungal communities with multiple functional groups respond to coal mining, and the quantitative impact and risk of mining disturbance. Therefore, in this study, the effect of coal mining on soil microorganisms' composition and diversity were analyzed near the edge of an opencast coal-mine dump in the Shengli mining area, Xilingol League, Inner Mongolia. The response strategy of soil fungi to coal mining and the stability of arbuscular mycorrhizal fungi (AMF) in the soil fungal community were determined. Our results showed that coal mining affected AMF and soil fungi in areas within 900 m from the coal mine. The abundance of endophytes increased with the distance between sampling sites and the mine dump, whereas the abundance of saprotroph decreased with the distance between sampling sites and the mine dump. Saprotroph was the dominant functional flora near the mining area. The nodes percentage of Septoglomus and Claroideoglomus and AMF phylogenetic diversity near the mining area were highest. AMF responded to the mining disturbance via the variety and evolution strategy of flora. Furthermore, AMF and soil fungal communities were significantly correlated with edaphic properties and parameters. Soil available phosphorus (AP) was the main influencer of soil AMF and fungal communities. These findings evaluated the risk range of coal mining on AMF and soil fungal communities and elucidated the microbial response strategy to mining disturbance.
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Affiliation(s)
- Linlin Xie
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Yinli Bi
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
- Institute of Ecological and Environmental Restoration in Mining Areas of West China, Xi’an University of Science and Technology, Xi’an 710054, China
| | - Yanxu Zhang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Nan Guo
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
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24
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Sanchez A, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC, Kuehn S. The community-function landscape of microbial consortia. Cell Syst 2023; 14:122-134. [PMID: 36796331 DOI: 10.1016/j.cels.2022.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.
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Affiliation(s)
- Alvaro Sanchez
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA; Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain.
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Abigail Skwara
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The Unviersity of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
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25
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Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation. Foods 2023; 12:foods12030673. [PMID: 36766201 PMCID: PMC9914028 DOI: 10.3390/foods12030673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.
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26
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Schaerer LG, Wu R, Putman LI, Pearce JM, Lu T, Shonnard DR, Ong RG, Techtmann SM. Killing two birds with one stone: chemical and biological upcycling of polyethylene terephthalate plastics into food. Trends Biotechnol 2023; 41:184-196. [PMID: 36058768 DOI: 10.1016/j.tibtech.2022.06.012] [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: 02/25/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 01/24/2023]
Abstract
Most polyethylene terephthalate (PET) plastic waste is landfilled or pollutes the environment. Additionally, global food production must increase to support the growing population. This article explores the feasibility of using microorganisms in an industrial system that upcycles PET into edible microbial protein powder to solve both problems simultaneously. Many microorganisms can utilize plastics as feedstock, and the resultant microbial biomass contains fats, nutrients, and proteins similar to those found in human diets. While microbial degradation of PET is promising, biological PET depolymerization is too slow to resolve the global plastic crisis and projected food shortages. Evidence reviewed here suggests that by coupling chemical depolymerization and biological degradation of PET, and using cooperative microbial communities, microbes can efficiently convert PET waste into food.
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Affiliation(s)
- Laura G Schaerer
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Ruochen Wu
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Lindsay I Putman
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Joshua M Pearce
- Department of Electrical and Computer Engineering, Western University, London, Ontario, Canada
| | - Ting Lu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - David R Shonnard
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Rebecca G Ong
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.
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27
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Dijamentiuk A, Mangavel C, Elfassy A, Michaux F, Burgain J, Rondags E, Delaunay S, Ferrigno S, Revol-Junelles AM, Borges F. Invert emulsions alleviate biotic interactions in bacterial mixed culture. Microb Cell Fact 2023; 22:16. [PMID: 36670385 PMCID: PMC9854087 DOI: 10.1186/s12934-022-02014-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The large application potential of microbiomes has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Confocal laser scanning microscopy revealed that this system allowed to segregate microorganisms in independent droplets. Granulomorphometric analysis showed that the invert emulsion remains stable during at least 24 h, and that the introduction of bacteria did not have a significant impact on the structure of the invert emulsion. A two-strain antagonistic model demonstrated that this invert emulsion system allows the propagation of two strains without the exclusion of the less-fit bacterium. The monitoring of single-strain cultures of bacteria representative of a cheese microbiota revealed that all but Brevibacterium linens were able to grow. A consortium consisting of Lactococcus lactis subsp. lactis biovar diacetylactis, Streptococcus thermophilus, Leuconostoc mesenteroides, Staphylococcus xylosus, Lactiplantibacillus plantarum and Carnobacterium maltaromaticum was successfully cultivated without detectable biotic interactions. Metabarcoding analysis revealed that the system allowed a better maintenance of alpha diversity and produced a propagated bacterial consortium characterized by a structure closer to the initial state compared to non-emulsified medium. This culture system could be an important tool in the field of microbial community engineering.
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Affiliation(s)
- Alexis Dijamentiuk
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Florentin Michaux
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Emmanuel Rondags
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Stéphane Delaunay
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Sandie Ferrigno
- grid.29172.3f0000 0001 2194 6418IECL, Equipe BIGS, INRIA Nancy, Université de Lorraine, Nancy, France
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28
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Decadt H, Weckx S, De Vuyst L. The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production. Front Microbiol 2023; 14:1128394. [PMID: 36876114 PMCID: PMC9978159 DOI: 10.3389/fmicb.2023.1128394] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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29
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Sola L, Quadu E, Bortolazzo E, Bertoldi L, Randazzo CL, Pizzamiglio V, Solieri L. Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait. Sci Rep 2022; 12:17322. [PMID: 36243881 PMCID: PMC9569347 DOI: 10.1038/s41598-022-22207-y] [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: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.
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Affiliation(s)
- Laura Sola
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Emanuele Quadu
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Elena Bortolazzo
- grid.423913.eCentro Ricerche Produzioni Animali, 42121 Reggio Emilia, Italy
| | | | - Cinzia L. Randazzo
- grid.8158.40000 0004 1757 1969Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy ,ProBioEtna Srl, 95123 Catania, Italy
| | - Valentina Pizzamiglio
- grid.433295.aConsorzio del Formaggio Parmigiano Reggiano, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy ,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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30
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Rodríguez J, Vázquez L, Flórez AB, Mayo B. Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk. Front Microbiol 2022; 13:1000683. [PMID: 36212860 PMCID: PMC9539746 DOI: 10.3389/fmicb.2022.1000683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
This work reports the characterization of three lactic acid bacteria (LAB) strains -Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30- existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted ("domesticated") to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.
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Affiliation(s)
- Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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31
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Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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32
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Paillet T, Lossouarn J, Figueroa C, Midoux C, Rué O, Petit MA, Dugat-Bony E. Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory. Viruses 2022; 14:v14081620. [PMID: 35893685 PMCID: PMC9331655 DOI: 10.3390/v14081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such this type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from the cheese rind were tested through a spot assay against a collection of bacteria isolated from the same cheese and identified by sequencing the full-length small subunit ribosomal RNA gene. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. A sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR, and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.
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Affiliation(s)
- Thomas Paillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Clarisse Figueroa
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, PROSE, 92761 Antony, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Eric Dugat-Bony
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
- Correspondence:
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Ma B, Liu Y, Lin H, Fan H, Lu C, Zhao K, Qi J. A pilot-scale study of the integrated floc-ultrafiltration membrane-based drinking water treatment process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154809. [PMID: 35341872 DOI: 10.1016/j.scitotenv.2022.154809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Although applications of the integrated ultrafiltration (UF) membrane have been investigated for years, most studies have been conducted at the lab scale. Here, a case study on the integrated Fe-based floc-UF process was presented. To enhance membrane performance, both pre-filtration (bag filter) and pre-oxidation were used as pretreatments to remove particles and inhibit the development of microorganisms. Results showed that the integrated process operated stably with pre-treatments, and the UF membrane fouling behavior could be divided into three different phases: slow increase rate (phase I), medium increase rate (phase II), and fast increase rate (phase III). In comparison to those in phases II and III, both natural organic matters and colloids were the main membrane fouling mechanisms during phase I, as the pollutants were not successfully removed by flocs initially. With the continuous injection of flocs, a loose cake layer became the main fouling mechanism during phase II, resulting in the deterioration of membrane fouling. During phase III, however, microorganisms (e.g., Proteobacteria) were inevitably nourished within the cake layer and played an important role in aggravating the degree of membrane fouling. During this integrated membrane-based process, several operating factors, including floc concentration, sludge discharge frequency, and the aeration rate during backwashing, played important roles in determining membrane performance. In addition, except for oxygen consumption, all the effluent quality parameters met the drinking water criteria followed in China (GB5749-2006).
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Affiliation(s)
- Baiwen Ma
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Lehrstuhl für Technische Chemie II, Universität Duisburg-Essen, Essen 45117, Germany.
| | - Yansong Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of New Energy and Environment, Jilin University, Changchun, 130021, Jilin, China
| | - Hui Lin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Fan
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chaojie Lu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Qi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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34
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Correlation analysis of normal and moldy beef jerky microbiota with Volatile compounds. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 2022; 368:109618. [DOI: 10.1016/j.ijfoodmicro.2022.109618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/21/2022] [Accepted: 03/06/2022] [Indexed: 12/15/2022]
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Castledine M, Sierocinski P, Inglis M, Kay S, Hayward A, Buckling A, Padfield D. Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution. Front Cell Infect Microbiol 2022; 12:834406. [PMID: 35310856 PMCID: PMC8931298 DOI: 10.3389/fcimb.2022.834406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and evolution. The dynamics of coevolution—notably whether host or parasite has an evolutionary advantage—is greatly affected by the relative amount of genetic variation in host resistance and parasite infectivity traits. While studies have manipulated genetic diversity during coevolution, such as by increasing mutation rates, it is unclear how starting genetic diversity affects host–parasite coevolution. Here, we (co)evolved the bacterium Pseudomonas fluorescens SBW25 and two bacteriophage genotypes of its lytic phage SBW25ɸ2 in isolation (one phage genotype) and together (two phage genotypes). Bacterial populations rapidly evolved phage resistance, and phage reciprocally increased their infectivity in response. When phage populations were evolved with bacteria in isolation, bacterial resistance and phage infectivity increased through time, indicative of arms-race coevolution. In contrast, when both phage genotypes were together, bacteria did not increase their resistance in response to increasing phage infectivity. This was likely due to bacteria being unable to evolve resistance to both phage via the same mutations. These results suggest that increasing initial parasite genotypic diversity can give parasites an evolutionary advantage that arrests long-term coevolution. This study has important implications for the applied use of phage in phage therapy and in understanding host–parasite dynamics in broader ecological and evolutionary theory.
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Lacorte GA, Cruvinel LA, de Paula Ávila M, Dias MF, de Abreu Pereira A, Nascimento AMA, de Melo Franco BDG. Investigating the influence of Food Safety Management Systems (FSMS) on microbial diversity of Canastra cheeses and their processing environments. Food Microbiol 2022; 105:104023. [DOI: 10.1016/j.fm.2022.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
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Moonga HB, Schoustra SE, Linnemann AR, Shindano J, Smid EJ. Towards valorisation of indigenous traditional fermented milk: mabisi as a model. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Liu Y, Tempelaars MH, Boeren S, Alexeeva S, Smid EJ, Abee T. Extracellular vesicle formation in Lactococcus lactis is stimulated by prophage-encoded holin-lysin system. Microb Biotechnol 2022; 15:1281-1295. [PMID: 35229476 PMCID: PMC8966010 DOI: 10.1111/1751-7915.13972] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022] Open
Abstract
Gram-positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how EVs are released through the cell walls in Gram-positive bacteria. In this study, we characterized underlying mechanisms of EV production and provide evidence for a role of prophage activation in EV release using the Gram-positive bacterium Lactococcus lactis as a model. By applying a standard EV isolation procedure, we observed the presence of EVs in the culture supernatant of a lysogenic L. lactis strain FM-YL11, for which the prophage-inducing condition led to an over 10-fold increase in EV production in comparison with the non-inducing condition. In contrast, the prophage-encoded holin-lysin knockout mutant YL11ΔHLH and the prophage-cured mutant FM-YL12 produced constantly low levels of EVs. Under the prophage-inducing condition, FM-YL11 did not show massive cell lysis. Defective phage particles were found to be released in and associated with holin-lysin-induced EVs from FM-YL11, as demonstrated by transmission electron microscopic images, flow cytometry and proteomics analysis. Findings from this study further generalized the EV-producing phenotype to Gram-positive L. lactis, and provide additional insights into the EV production mechanism involving prophage-encoded holin-lysin system. The knowledge on bacterial EV production can be applied to all Gram-positive bacteria and other lactic acid bacteria with important roles in fermentations and probiotic formulations, to enable desired release and delivery of cellular components with nutritional values or probiotic effects.
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Affiliation(s)
- Yue Liu
- Food Microbiology, Wageningen University and Research, P.O. Box 17, Wageningen, 6700 AA, the Netherlands
| | - Marcel H Tempelaars
- Food Microbiology, Wageningen University and Research, P.O. Box 17, Wageningen, 6700 AA, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Svetlana Alexeeva
- Food Microbiology, Wageningen University and Research, P.O. Box 17, Wageningen, 6700 AA, the Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, P.O. Box 17, Wageningen, 6700 AA, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, P.O. Box 17, Wageningen, 6700 AA, the Netherlands
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 PMCID: PMC8776748 DOI: 10.1038/s41396-021-01071-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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41
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 DOI: 10.1101/2021.01.14.426499v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/27/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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42
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Biolcati F, Ferrocino I, Bottero MT, Dalmasso A. The Bacterial and Fungal Microbiota of “Robiola di Roccaverano” Protected Designation of Origin Raw Milk Cheese. Front Microbiol 2022; 12:776862. [PMID: 35173686 PMCID: PMC8841559 DOI: 10.3389/fmicb.2021.776862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Robiola di Roccaverano is an artisanal Protected Designation of Origin (PDO) soft cheese made with raw goat’s milk and by the addition of Natural Milk Culture (NMC) to drive the fermentation process. Cheeses collected from five different dairy plants were analyzed for their bacterial and fungal microbiota diversity. Lactococcus lactis and Leuconostoc mesenteroides were the main bacterial population, while Galactomyces candidum and Kluyveromyces marxianus constituted the core mycobiota but many other minor taxa were observed, suggesting a high level of complexity in fungal composition by these cheeses compared to bacteria population.
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Affiliation(s)
- Federica Biolcati
- Dipartimento di Scienze Veterinarie, Università di Torino, Grugliasco, Italy
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
- *Correspondence: Federica Biolcati,
| | - Ilario Ferrocino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
| | | | - Alessandra Dalmasso
- Dipartimento di Scienze Veterinarie, Università di Torino, Grugliasco, Italy
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White K, Yu JH, Eraclio G, Dal Bello F, Nauta A, Mahony J, van Sinderen D. Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods. MICROBIOME RESEARCH REPORTS 2022; 1:3. [PMID: 38089066 PMCID: PMC10714293 DOI: 10.20517/mrr.2021.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 02/19/2024]
Abstract
Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Jun-Hyeok Yu
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Authors contributed equally
| | | | | | - Arjen Nauta
- FrieslandCampina, Amersfoort 3800 BN, The Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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Abstract
Lactococcus lactis strains residing in the microbial community of a complex dairy starter culture named “Ur” are hosts to prophages belonging to the family Siphoviridae. L. lactis strains (TIFN1 to TIFN7) showed detectable spontaneous phage production and release (109 to 1010 phage particles/ml) and up to 10-fold increases upon prophage induction, while in both cases we observed no obvious cell lysis typically described for the lytic life cycle of Siphoviridae phages. Intrigued by this phenomenon, we investigated the host-phage interaction using strain TIFN1 (harboring prophage proPhi1) as a representative. We confirmed that during the massive phage release, all bacterial cells remain viable. Further, by monitoring phage replication in vivo, using a green fluorescence protein reporter combined with flow cytometry, we demonstrated that the majority of the bacterial population (over 80%) is actively producing phage particles when induced with mitomycin C. The released tailless phage particles were found to be engulfed in lipid membranes, as evidenced by electron microscopy and lipid staining combined with chemical lipid analysis. Based on the collective observations, we propose a model of phage-host interaction in L. lactis TIFN1 where the phage particles are engulfed in membranes upon release, thereby leaving the producing host intact. Moreover, we discuss possible mechanisms of chronic, or nonlytic, release of LAB Siphoviridae phages and its impact on the bacterial host. IMPORTANCE In complex microbial consortia such as fermentation starters, bacteriophages can alter the dynamics and diversity of microbial communities. Bacteriophages infecting Lactococcus lactis are mostly studied for their detrimental impact on industrial dairy fermentation processes. In this study, we describe a novel form of phage-bacterium interaction in an L. lactis strain isolated from a complex dairy starter culture: when the prophages harbored in the L. lactis genome are activated, the phage particles are engulfed in lipid membranes upon release, leaving the producing host intact. Findings from this study provide additional insights into the diverse manners of phage-bacterium interactions and coevolution, which are essential for understanding the population dynamics in complex microbial communities like fermentation starters.
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Alekseeva AY, Groenenboom AE, Smid EJ, Schoustra SE. Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph181910093. [PMID: 34639397 PMCID: PMC8508538 DOI: 10.3390/ijerph181910093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.
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Affiliation(s)
- Anna Y. Alekseeva
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Correspondence:
| | - Anneloes E. Groenenboom
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Eddy J. Smid
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Sijmen E. Schoustra
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka 10101, Zambia
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Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome. Microorganisms 2021; 9:microorganisms9091843. [PMID: 34576739 PMCID: PMC8468716 DOI: 10.3390/microorganisms9091843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 01/04/2023] Open
Abstract
Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.
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48
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Aitzhanova A, Oleinikova Y, Mounier J, Hymery N, Leyva Salas M, Amangeldi A, Saubenova M, Alimzhanova M, Ashimuly K, Sadanov A. Dairy associations for the targeted control of opportunistic Candida. World J Microbiol Biotechnol 2021; 37:143. [PMID: 34328568 DOI: 10.1007/s11274-021-03096-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/18/2021] [Indexed: 01/15/2023]
Abstract
Antifungal and antibacterial activities of twenty-six combinations of lactic acid bacteria, propionibacteria, acetic acid bacteria and dairy yeasts inoculated in whey and milk were investigated. Associations including acetic acid bacteria were shown to suppress growth of the opportunistic yeast Candida albicans in well-diffusion assays. The protective effect of milk fermented with the two most promising consortia was confirmed in Caco-2 cell culture infected with C. albicans. Indeed, these fermented milks, after heat-treatment or not, suppressed lactate dehydrogenase release after 48 h while significant increase in LDH release was observed in the positive control (C. albicans alone) and with fermented milk obtained using commercial yogurt starter cultures. The analysis of volatile compounds in the cell-free supernatant using solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) showed accumulation of significant amount of acetic acid by the consortium composed of Lactobacillus delbrueckii 5, Lactobacillus gallinarum 1, Lentilactobacillus parabuchneri 3, Lacticaseibacillus paracasei 33-4, Acetobacter syzygii 2 and Kluyveromyces marxianus 19, which corresponded to the zone of partial inhibition of C. albicans growth during well-diffusion assays. Interestingly, another part of anti-Candida activity, yielding small and transparent inhibition zones, was linked with the consortium cell fraction. This study showed a correlation between anti-Candida activity and the presence of acetic acid bacteria in dairy associations as well as a significant effect of two dairy associations against C. albicans in a Caco-2 cell model. These two associations may be promising consortia for developing functional dairy products with antagonistic action against candidiasis agents.
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Affiliation(s)
- Aida Aitzhanova
- Al-Farabi Kazakh National University, Al-Farabi ave., 71, 050040, Almaty, Kazakhstan
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
| | - Yelena Oleinikova
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan.
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Univ Brest, 29280, Plouzané, France
| | - Nolwenn Hymery
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Univ Brest, 29280, Plouzané, France
| | - Marcia Leyva Salas
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Univ Brest, 29280, Plouzané, France
| | - Alma Amangeldi
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
| | - Margarita Saubenova
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
| | - Mereke Alimzhanova
- Al-Farabi Kazakh National University, Al-Farabi ave., 71, 050040, Almaty, Kazakhstan
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
| | - Kazhybek Ashimuly
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
| | - Amankeldy Sadanov
- Research and Production Center for Microbiology and Virology, Bogenbay Batyr str., 105, 050010, Almaty, Kazakhstan
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Flórez AB, Vázquez L, Rodríguez J, Mayo B. Directed Recovery and Molecular Characterization of Antibiotic Resistance Plasmids from Cheese Bacteria. Int J Mol Sci 2021; 22:7801. [PMID: 34360567 PMCID: PMC8346141 DOI: 10.3390/ijms22157801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to antimicrobials is a growing problem of worldwide concern. Plasmids are thought to be major drivers of antibiotic resistance spread. The present work reports a simple way to recover replicative plasmids conferring antibiotic resistance from the bacteria in cheese. Purified plasmid DNA from colonies grown in the presence of tetracycline and erythromycin was introduced into plasmid-free strains of Lactococcus lactis, Lactiplantibacillus plantarum and Lacticaseibacillus casei. Following antibiotic selection, the plasmids from resistant transformants were isolated, analyzed by restriction enzyme digestion, and sequenced. Seven patterns were obtained for the tetracycline-resistant colonies, five from L. lactis, and one each from the lactobacilli strains, as well as a single digestion profile for the erythromycin-resistant transformants obtained in L. lactis. Sequence analysis respectively identified tet(S) and ermB in the tetracycline- and erythromycin-resistance plasmids from L. lactis. No dedicated resistance genes were detected in plasmids conferring tetracycline resistance to L. casei and L. plantarum. The present results highlight the usefulness of the proposed methodology for isolating functional plasmids that confer antibiotic resistance to LAB species, widen our knowledge of antibiotic resistance in the bacteria that inhabit cheese, and emphasize the leading role of plasmids in the spread of resistance genes via the food chain.
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Affiliation(s)
- Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.V.); (J.R.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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50
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Contribution of traditional fermented foods to food systems transformation: value addition and inclusive entrepreneurship. Food Secur 2021. [DOI: 10.1007/s12571-021-01185-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractTo date, many efforts to eradicate hunger include increasing agricultural production, processing of raw materials and supplementation, and fortification of foods. Locally produced foods represent a significant part of Food Systems as they contribute to tackling hunger and malnutrition. However, few studies have investigated the processing of traditional fermented foods at household level as a means to improve nutrition and triggering inclusive entrepreneurship, two crucial dimensions Food Systems build on. Fermentation is an ancient processing technique that relies on transformation of raw materials by microbial activity and is mainly undertaken by women. This paper posits that upscaling small scale fermented food processing activities while enhancing functional food properties and fostering women entrepreneurship contributes to prevention of food losses, promotion of nutrition and health, and entrepreneurial opportunities for current processors. This is key for effective policy interventions to foster food security in challenging contexts.⨪.
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