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Somerville V, Thierer N, Schmidt RS, Roetschi A, Braillard L, Haueter M, Berthoud H, Shani N, von Ah U, Mazel F, Engel P. Genomic and phenotypic imprints of microbial domestication on cheese starter cultures. Nat Commun 2024; 15:8642. [PMID: 39366947 PMCID: PMC11452379 DOI: 10.1038/s41467-024-52687-7] [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: 03/29/2024] [Accepted: 09/16/2024] [Indexed: 10/06/2024] Open
Abstract
Domestication - the artificial selection of wild species to obtain variants with traits of human interest - was integral to the rise of complex societies. The oversupply of food was probably associated with the formalization of food preservation strategies through microbial fermentation. While considerable literature exists on the antiquity of fermented food, only few eukaryotic microbes have been studied so far for signs of domestication, less is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and maintained stable phenotypic traits. Molecular clock dating further suggests that the evolutionary origin of the bacteria approximately coincided with the first archaeological records of cheese making. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Liebefeld, Switzerland.
- Université Laval, Quebec, Canada.
- McGill, Montréal, Canada.
| | | | | | | | | | | | | | | | | | - Florent Mazel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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2
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Anelli P, Dall'Asta C, Cozzi G, Epifani F, Carella D, Scarpetta D, Brasca M, Moretti A, Susca A. Analysis of composition and molecular characterization of mycobiota occurring on surface of cheese ripened in Dossena's mine. Food Microbiol 2024; 123:104587. [PMID: 39038900 DOI: 10.1016/j.fm.2024.104587] [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: 03/28/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024]
Abstract
Accurate identification of the fungal community spontaneously colonizing food products, aged in natural and not controlled environments, provides information about potential mycotoxin risk associated with its consumption. Autochthonous mycobiota colonizing cheese aging in Dossena mines, was investigated and characterized by two approaches: microbial isolations and metabarcoding. Microbial isolations and metabarcoding analysis were conducted on cheese samples, obtained by four batches, produced in four different seasons of the year, aged for 90 and 180 days, by five dairy farms. The two approaches, with different taxonomical resolution power, highlighted Penicillium biforme among filamentous fungi, collected from 58 out of 68 cheeses, and Debaryomyces hansenii among yeasts, as the most abundant species (31 ÷ 65%), none representing a health risk for human cheese consumption. Shannon index showed that the richness of mycobiota increases after 180 days of maturation. Beta diversity analysis highlighted significant differences in composition of mycobiota of cheese produced by different dairy farms and aged for different durations. Weak negative growth interaction between P. biforme and Aspergillus westerdijkiae by in vitro analysis was observed leading to hypothesize that a reciprocal control is possible, also affected by natural environmental conditions, possibly disadvantageous for the last species.
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Affiliation(s)
- Pamela Anelli
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Parco Area delle Scienze, 17/A, 43121 Parma, Italy
| | - Giuseppe Cozzi
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy
| | - Filomena Epifani
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy
| | - Daria Carella
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy
| | - Davide Scarpetta
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Celoria 2, 20133 Milan, Italy
| | - Milena Brasca
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Celoria 2, 20133 Milan, Italy
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy
| | - Antonia Susca
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), via Amendola 122/0, 70126 Bari, Italy.
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3
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Bigey F, Menatong Tene X, Wessner M, Pradal M, Aury JM, Cruaud C, Neuvéglise C. Differential adaptation of the yeast Candida anglica to fermented food. Food Microbiol 2024; 123:104584. [PMID: 39038890 DOI: 10.1016/j.fm.2024.104584] [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: 03/03/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
A single strain of Candida anglica, isolated from cider, is available in international yeast collections. We present here seven new strains isolated from French PDO cheeses. For one of the cheese strains, we achieved a high-quality genome assembly of 13.7 Mb with eight near-complete telomere-to-telomere chromosomes. The genomes of two additional cheese strains and of the cider strain were also assembled and annotated, resulting in a core genome of 5966 coding sequences. Phylogenetic analysis showed that the seven cheese strains clustered together, away from the cider strain. Mating-type locus analysis revealed the presence of a MATa locus in the cider strain but a MATalpha locus in all cheese strains. The presence of LINE retrotransposons at identical genome position in the cheese strains, and two different karyotypic profiles resulting from chromosomal rearrangements were observed. Together, these findings are consistent with clonal propagation of the cheese strains. Phenotypic trait variations were observed within the cheese population under stress conditions whereas the cider strain was found to have a much greater capacity for growth in all conditions tested.
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Affiliation(s)
- Frédéric Bigey
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, 91057, France
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4
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Maini Rekdal V, Villalobos-Escobedo JM, Rodriguez-Valeron N, Olaizola Garcia M, Prado Vásquez D, Rosales A, Sörensen PM, Baidoo EEK, Calheiros de Carvalho A, Riley R, Lipzen A, He G, Yan M, Haridas S, Daum C, Yoshinaga Y, Ng V, Grigoriev IV, Munk R, Wijaya CH, Nuraida L, Damayanti I, Cruz-Morales P, Keasling JD. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nat Microbiol 2024; 9:2666-2683. [PMID: 39209985 PMCID: PMC11445060 DOI: 10.1038/s41564-024-01799-3] [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: 08/07/2023] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - José Manuel Villalobos-Escobedo
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Tecnológico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo León, Mexico
| | - Nabila Rodriguez-Valeron
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
- Basque Culinary Center, Mondragon Universitatea, Donostia, Gipuzkoa, Spain
| | | | - Diego Prado Vásquez
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Alexander Rosales
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Pia M Sörensen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Calheiros de Carvalho
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rasmus Munk
- ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark
| | - Christofora Hanny Wijaya
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Lilis Nuraida
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Isty Damayanti
- Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
- California Institute of Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
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5
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Luciano-Rosario D, Jurick WM, Gottschalk C. The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen. J Fungi (Basel) 2024; 10:430. [PMID: 38921416 PMCID: PMC11204653 DOI: 10.3390/jof10060430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.
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Affiliation(s)
- Dianiris Luciano-Rosario
- Food Quality Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
- ORISE Postdoctoral Research Fellow, Oak Ridge, TN 37830, USA
| | - Wayne M. Jurick
- Food Quality Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
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6
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Zhang C, Cheng Y, Qin Y, Wang C, Wang H, Ablimit A, Sun Q, Dong H, Wang B, Wang C. Occurrence, Risk Implications, Prevention and Control of CIT in Monascus Cheese: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9567-9580. [PMID: 38627202 DOI: 10.1021/acs.jafc.4c00588] [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: 05/02/2024]
Abstract
Monascus is a filamentous fungus that has been used in the food and pharmaceutical industries. When used as an auxiliary fermenting agent in the manufacturing of cheese, Monascus cheese is obtained. Citrinin (CIT) is a well-known hepatorenal toxin produced by Monascus that can harm the kidneys structurally and functionally and is frequently found in foods. However, CIT contamination in Monascus cheese is exacerbated by the metabolic ability of Monascus to product CIT, which is not lost during fermentation, and by the threat of contamination by Penicillium spp. that may be introduced during production and processing. Considering the safety of consumption and subsequent industrial development, the CIT contamination of Monascus cheese products needs to be addressed. This review aimed to examine its occurrence in Monascus cheese, risk implications, traditional control strategies, and new research advances in prevention and control to guide the application of biotechnology in the control of CIT contamination, providing more possibilities for the application of Monascus in the cheese industry.
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Affiliation(s)
- Chan Zhang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), No. 11 Fucheng Road, Haidian District, Beijing 100048, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Green Manufacturing and Biosynthesis of Food Bioactive Substances, China General Chamber of Commerce, Beijing 100048, China
| | - Ying Cheng
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Yuhui Qin
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Congcong Wang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Haijiao Wang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Arzugul Ablimit
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Qing Sun
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Huijun Dong
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Bei Wang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), No. 11 Fucheng Road, Haidian District, Beijing 100048, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Chengtao Wang
- School of Food and Health, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), No. 11 Fucheng Road, Haidian District, Beijing 100048, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
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7
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Maini Rekdal V, van der Luijt CRB, Chen Y, Kakumanu R, Baidoo EEK, Petzold CJ, Cruz-Morales P, Keasling JD. Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit. Nat Commun 2024; 15:2099. [PMID: 38485948 PMCID: PMC10940619 DOI: 10.1038/s41467-024-46314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Casper R B van der Luijt
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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8
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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9
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Visagie C, Yilmaz N, Kocsubé S, Frisvad J, Hubka V, Samson R, Houbraken J. A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Stud Mycol 2024; 107:1-66. [PMID: 38600958 PMCID: PMC11003441 DOI: 10.3114/sim.2024.107.01] [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: 07/21/2023] [Accepted: 11/13/2023] [Indexed: 04/12/2024] Open
Abstract
The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé & Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki & B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki & B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu & Mont.) Visagie, Malloch, L. Kriegsteiner, Samson & Houbraken; Xerochrysium coryli (Crous & Decock) Visagie & Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.
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Affiliation(s)
- C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S. Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
- ELKH-SZTE Pathomechanisms of Fungal Infections Research Group, University of Szeged, 6726 Szeged, Hungary
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Søltofts Plads, Building 221, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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10
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Pontes A, Paraíso F, Liu YC, Limtong S, Jindamorakot S, Jespersen L, Gonçalves C, Rosa CA, Tsai IJ, Rokas A, Hittinger CT, Gonçalves P, Sampaio JP. Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. iScience 2024; 27:108987. [PMID: 38333711 PMCID: PMC10850751 DOI: 10.1016/j.isci.2024.108987] [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: 09/05/2023] [Revised: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Savitree Limtong
- Department of Microbiology Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
| | - Sasitorn Jindamorakot
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
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11
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Cleere MM, Novodvorska M, Geib E, Whittaker J, Dalton H, Salih N, Hewitt S, Kokolski M, Brock M, Dyer PS. New colours for old in the blue-cheese fungus Penicillium roqueforti. NPJ Sci Food 2024; 8:3. [PMID: 38191473 PMCID: PMC10774375 DOI: 10.1038/s41538-023-00244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
Penicillium roqueforti is used worldwide in the production of blue-veined cheese. The blue-green colour derives from pigmented spores formed by fungal growth. Using a combination of bioinformatics, targeted gene deletions, and heterologous gene expression we discovered that pigment formation was due to a DHN-melanin biosynthesis pathway. Systematic deletion of pathway genes altered the arising spore colour, yielding white to yellow-green to red-pink-brown phenotypes, demonstrating the potential to generate new coloured strains. There was no consistent impact on mycophenolic acid production as a result of pathway interruption although levels of roquefortine C were altered in some deletants. Importantly, levels of methyl-ketones associated with blue-cheese flavour were not impacted. UV-induced colour mutants, allowed in food production, were then generated. A range of colours were obtained and certain phenotypes were successfully mapped to pathway gene mutations. Selected colour mutants were subsequently used in cheese production and generated expected new colourations with no elevated mycotoxins, offering the exciting prospect of use in future cheese manufacture.
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Affiliation(s)
- Matthew M Cleere
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- PhD Program in Biology, The Graduate Center; Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY10031, USA
| | - Michaela Novodvorska
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Elena Geib
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Jack Whittaker
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Heather Dalton
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Nadhira Salih
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Department of Biology, College of Education, University of Sulaimani, Sulaymaniyah, Iraq
| | - Sarah Hewitt
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthias Brock
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Paul S Dyer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
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12
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McTaggart AR, McLaughlin S, Slot JC, McKernan K, Appleyard C, Bartlett TL, Weinert M, Barlow C, Warne LN, Shuey LS, Drenth A, James TY. Domestication through clandestine cultivation constrained genetic diversity in magic mushrooms relative to naturalized populations. Curr Biol 2023; 33:5147-5159.e7. [PMID: 38052161 DOI: 10.1016/j.cub.2023.10.059] [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: 06/20/2023] [Revised: 09/04/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023]
Abstract
Fungi that are edible or fermentative were domesticated through selective cultivation of their desired traits. Domestication is often associated with inbreeding or selfing, which may fix traits other than those under selection, and causes an overall decrease in heterozygosity. A hallucinogenic mushroom, Psilocybe cubensis, was domesticated from its niche in livestock dung for production of psilocybin. It has caused accidental poisonings since the 1940s in Australia, which is a population hypothesized to be introduced from an unknown center of origin. We sequenced genomes of 38 isolates from Australia and compared them with 86 genomes of commercially available cultivars to determine (1) whether P. cubensis was introduced to Australia, and (2) how domestication has impacted commercial cultivars. Our analyses of genome-wide SNPs and single-copy orthologs showed that the Australian population is naturalized, having recovered its effective population size after a bottleneck when it was introduced, and it has maintained relatively high genetic diversity based on measures of nucleotide and allelic diversity. In contrast, domesticated cultivars generally have low effective population sizes and hallmarks of selfing and clonal propagation, including low genetic diversity, low heterozygosity, high linkage disequilibrium, and low allelic diversity of mating-compatibility genes. Analyses of kinship show that most cultivars are founded from related populations. Alleles in the psilocybin gene cluster are identical across most cultivars of P. cubensis with low diversity across coding sequence; however, unique allelic diversity in Australia and some cultivars may translate to differences in biosynthesis of psilocybin and its analogs.
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Affiliation(s)
- Alistair R McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; Funky Fungus, Burpengary, QLD 4505, Australia.
| | | | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin McKernan
- Research and Development, Medicinal Genomics, Beverly, MA 01915, USA
| | | | - Tia L Bartlett
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Matthew Weinert
- Entheogenesis Australis, PO Box 2046, Belgrave, 3160 VIC, Australia
| | - Caine Barlow
- Entheogenesis Australis, PO Box 2046, Belgrave, 3160 VIC, Australia
| | - Leon N Warne
- Little Green Pharma, West Perth, WA 6005, Australia
| | - Louise S Shuey
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - André Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48104, USA
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13
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Zadravec M, Lešić T, Brnić D, Pleadin J, Kraak B, Jakopović Ž, Perković I, Vahčić N, Tkalec VJ, Houbraken J. Regional distribution and diversity of Aspergillus and Penicillium species on Croatian traditional meat products. Int J Food Microbiol 2023; 406:110404. [PMID: 37778241 DOI: 10.1016/j.ijfoodmicro.2023.110404] [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: 05/17/2023] [Revised: 09/12/2023] [Accepted: 09/16/2023] [Indexed: 10/03/2023]
Abstract
Various factors, such as weather and production practices (e.g., environmental hygiene, process duration, raw material quality, ripening temperature, and relative humidity), in combination with the intrinsic product properties (e.g., pH, aw, salt content), significantly affect the growth of surface moulds. The aim of this study was to isolate and identify surface moulds retrieved from traditional meat products (TMPs) and correlate these data to the production region and production technology. The surface of 250 TMPs (dry-fermented sausages, n = 108; dry-cured meat products, n = 142) from five Croatian regions were sampled during a two-year period. Dry-fermented sausages had a significantly higher pH and a lower salt concentration when compared to dry-cured meat products. In total, 528 isolates were obtained, comprising 20 Penicillium and 17 Aspergillus species. The species most frequently isolated from the dry-fermented sausages were P. commune (32.4 %), A. proliferans (33 %), and P. solitum (14.8 %), while A. proliferans (52.1 %), P. commune (28.9 %) and P. citrinum (19.7 %) predominated in dry-cured meat products. Aspergillus predominated on the TMPs from southern Croatia, while Penicillium was prevalent on products from the other four regions, possibly due to differences in weather conditions. Seven potentially mycotoxigenic species (A. creber, A. flavus, A. niger, A. westerdijkiae, P. citrinum, P. commune, and P. nordicum) were isolated and identified. Regular monitoring of mould species and their toxigenic metabolites present on traditional meat products is of the utmost importance from the public health perspective, while the results of such a monitoring can prove beneficial for the tailoring of the production technology development.
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Affiliation(s)
- Manuela Zadravec
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia.
| | - Tina Lešić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia.
| | - Dragan Brnić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia.
| | - Jelka Pleadin
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia.
| | - Bart Kraak
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands.
| | - Željko Jakopović
- Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Irena Perković
- Croatian Veterinary Institute, Veterinary Department Vinkovci, J. Kozarca 24, 32100 Vinkovci, Croatia.
| | - Nada Vahčić
- Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Vesna Jaki Tkalec
- Croatian Veterinary Institute, Veterinary Department Križevci, Ivana Zakmardija Dijankovečkog 10, 48260 Križevci, Croatia.
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands.
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14
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Li L, Zhang H, Meng D, Yin H. Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions. Front Bioeng Biotechnol 2023; 11:1274020. [PMID: 37901845 PMCID: PMC10601642 DOI: 10.3389/fbioe.2023.1274020] [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: 08/09/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hetian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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15
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Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1. IMA Fungus 2023; 14:21. [PMID: 37803441 PMCID: PMC10559472 DOI: 10.1186/s43008-023-00121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 10/08/2023] Open
Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126, Bari, Italy
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126, Bari, Italy
| | - Felipe Balocchi
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ales Eichmeier
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071, Logroño, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071, Logroño, Spain
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Scott E Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- DOE Joint Bioenergy Institute, Emeryville, CA, 94608, USA
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via G. Amendola 165/a, 70126, Bari, Italy
| | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs, Lyngby, Denmark
| | - Eliska Hakalova
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44, Lednice, Czech Republic
| | - Richard D Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catarina Leal
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071, Logroño, Spain
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jakub Pecenka
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44, Lednice, Czech Republic
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126, Bari, Italy
| | - Anja Piso
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Milan Spetik
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44, Lednice, Czech Republic
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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16
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Valle M, Nguyen Van Long N, Jany JL, Koullen L, Rigalma K, Vasseur V, Huchet V, Coroller L. Impact of sodium chloride and carbon dioxide on conidial germination and radial growth of Penicillium camemberti. Food Microbiol 2023; 115:104309. [PMID: 37567615 DOI: 10.1016/j.fm.2023.104309] [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: 02/22/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 08/13/2023]
Abstract
Penicillium camemberti is a domesticated species adapted to the dairy environment, which is used as adjunct cultures to ripen soft cheeses. A recent population genomics analysis on P. camemberti revealed that P. camemberti is a clonal lineage with two varieties almost identical genetically but with contrasting phenotypes in terms of growth, color, mycotoxin production and inhibition of contaminants. P. camemberti variety camemberti is found on Camembert and Brie cheeses, and P. camemberti variety caseifulvum is mainly found on other cheeses like Saint-Marcellin and Rigotte de Condrieu. This study aimed to evaluate the impact of water activity (aw) reduced by sodium chloride (NaCl) and the increase of carbon dioxide (CO2) partial pressure, on conidial germination and growth of two varieties of P. camemberti: var. Camemberti and var. Caseifulvum. Mathematical models were used to describe the responses of P. camemberti strains to both abiotic factors. The results showed that these genetically distant strains had similar responses to increase in NaCl and CO2 partial pressure. The estimated cardinal values were very close between the strains although all estimated cardinal values were significantly different (Likelihood ratio tests, pvalue = 0.05%). These results suggest that intraspecific variability could be more exacerbated during fungal growth compared with conidial germination, especially in terms of macroscopic morphology. Indeed, var. Caseifulvum seemed to be more sensitive to an increase of CO2 partial pressure, as shown by the fungal morphology, with the occurrence of irregular outgrowths, while the morphology of var. Camemberti remains circular. These data could make it possible to improve the control of fungal development as a function of salt and carbon dioxide partial pressure. These abiotic factors could serve as technological barriers to prevent spoilage and increase the shelf life of cheeses. The present data will allow more precise predictions of fungal proliferation as a function of salt and carbon dioxide partial pressure, which are significant technological hurdles in cheese production.
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Affiliation(s)
- Marion Valle
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29000, Quimper, France; ADRIA Développement, UMT ACTIA 19.03 ALTER'IX, Quimper, France
| | | | - Jean-Luc Jany
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29280, Plouzané, France
| | - Loona Koullen
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29000, Quimper, France
| | - Karim Rigalma
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29280, Plouzané, France
| | - Valérie Vasseur
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29280, Plouzané, France
| | | | - Louis Coroller
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ACTIA 19.03 ALTER'IX, F-29000, Quimper, France.
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17
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Abstract
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Kasturi Lele
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Collin B Edwards
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
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18
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Lo Y, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evol Appl 2023; 16:1637-1660. [PMID: 37752962 PMCID: PMC10519415 DOI: 10.1111/eva.13591] [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: 07/04/2022] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
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Affiliation(s)
- Ying‐Chu Lo
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Jade Bruxaux
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - Samuel O'Donnell
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Alodie Snirc
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Stéphanie Le Prieur
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS‐MNHN, Muséum National d'Histoire NaturelleParis Cedex 05France
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity InstituteUtrechtThe Netherlands
| | - Robert Debuchy
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Tatiana Giraud
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Antoine Branca
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- IDEEV – Laboratoire Evolution, Génomes Comportement, EcologieCNRS Université Paris Saclay UMR 9191, IRD UMR 247Gif‐sur‐YvetteFrance
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19
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Crequer E, Ropars J, Jany J, Caron T, Coton M, Snirc A, Vernadet J, Branca A, Giraud T, Coton E. A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche. Evol Appl 2023; 16:1438-1457. [PMID: 37622099 PMCID: PMC10445096 DOI: 10.1111/eva.13578] [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: 01/24/2023] [Revised: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 08/26/2023] Open
Abstract
Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e., silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. The Termignon population indeed displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g., dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese-making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.
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Affiliation(s)
- Ewen Crequer
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Luc Jany
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Thibault Caron
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Monika Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Alodie Snirc
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Philippe Vernadet
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Antoine Branca
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Tatiana Giraud
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Emmanuel Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
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20
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Thorwall S, Trivedi V, Ottum E, Wheeldon I. Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis. Metab Eng 2023; 78:223-234. [PMID: 37369325 DOI: 10.1016/j.ymben.2023.06.008] [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: 02/22/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.
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Affiliation(s)
- Sarah Thorwall
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Eva Ottum
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA; Center for Industrial Biotechnology, University of California, Riverside, CA 92521, USA; Integrative Institute for Genome Biology, University of California, Riverside, CA 92521, USA.
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21
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Rodríguez J, Lobato C, Vázquez L, Mayo B, Flórez AB. Prodigiosin-Producing Serratia marcescens as the Causal Agent of a Red Colour Defect in a Blue Cheese. Foods 2023; 12:2388. [PMID: 37372599 DOI: 10.3390/foods12122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Technological defects in the organoleptic characteristics of cheese (odour, colour, texture, and flavour) reduce quality and consumer acceptance. A red colour defect in Cabrales cheese (a traditional, blue-veined, Spanish cheese made from raw milk) occurs infrequently but can have a notable economic impact on family-owned, artisanal cheesemaking businesses. This work reports the culture-based determination of Serratia marcescens as the microbe involved in the appearance of red spots on the surface and nearby inner areas of such cheese. Sequencing and analysis of the genome of one S. marcescens isolate, RO1, revealed a cluster of 16 genes involved in the production of prodigiosin, a tripyrrole red pigment. HPLC analysis confirmed the presence of prodigiosin in methanol extracts of S. marcescens RO1 cultures. The same was also observed in extracts from red areas of affected cheeses. The strain showed low survival rates under acidic conditions but was not affected by concentrations of up to 5% NaCl (the usual value for blue cheese). The optimal conditions for prodigiosin production by S. marscescens RO1 on agar plates were 32 °C and aerobic conditions. Prodigiosin has been reported to possess antimicrobial activity, which agrees with the here-observed inhibitory effect of RO1 supernatants on different bacteria, the inhibition of Enterobacteriaceae, and the delayed development of Penicillium roqueforti during cheesemaking. The association between S. marcescens and the red colour defect was strengthened by recreating the fault in experimental cheeses inoculated with RO1. The data gathered in this study point towards the starting milk as the origin of this bacterium in cheese. These findings should help in the development of strategies that minimize the incidence of pigmenting S. marcescens in milk, the red defect the bacterium causes in cheese, and its associated economic losses.
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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), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Cristina Lobato
- 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
| | - 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
- 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
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - 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
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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22
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Corbu VM, Gheorghe-Barbu I, Dumbravă AȘ, Vrâncianu CO, Șesan TE. Current Insights in Fungal Importance-A Comprehensive Review. Microorganisms 2023; 11:1384. [PMID: 37374886 DOI: 10.3390/microorganisms11061384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Besides plants and animals, the Fungi kingdom describes several species characterized by various forms and applications. They can be found in all habitats and play an essential role in the excellent functioning of the ecosystem, for example, as decomposers of plant material for the cycling of carbon and nutrients or as symbionts of plants. Furthermore, fungi have been used in many sectors for centuries, from producing food, beverages, and medications. Recently, they have gained significant recognition for protecting the environment, agriculture, and several industrial applications. The current article intends to review the beneficial roles of fungi used for a vast range of applications, such as the production of several enzymes and pigments, applications regarding food and pharmaceutical industries, the environment, and research domains, as well as the negative impacts of fungi (secondary metabolites production, etiological agents of diseases in plants, animals, and humans, as well as deteriogenic agents).
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Affiliation(s)
- Viorica Maria Corbu
- Genetics Department, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
- Research Institute of the University of Bucharest-ICUB, 91-95 Spl. Independentei, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Research Institute of the University of Bucharest-ICUB, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| | - Andreea Ștefania Dumbravă
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| | - Corneliu Ovidiu Vrâncianu
- Research Institute of the University of Bucharest-ICUB, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| | - Tatiana Eugenia Șesan
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
- Academy of Agricultural Sciences and Forestry, 61 Bd. Mărăşti, District 1, 011464 Bucharest, Romania
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23
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Zhang ZX, Li ZH, Li SM. Formation of the Fungal Indole Alkaloid Speradine F Implies Multiple Nonenzymatic Oxidation Steps. JOURNAL OF NATURAL PRODUCTS 2023; 86:1053-1060. [PMID: 37043818 DOI: 10.1021/acs.jnatprod.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The highly oxygenated indole alkaloid speradine F (4) with a 6/5/6/5/5/5 hexacyclic skeleton was isolated from a culture of Penicillium palitans, together with its precursors β-cyclopiazonic acid (β-CPA, 5) and cyclopiazonic acid (CPA, 1). Gene deletion and heterologous expression led to the identification of the responsible five-gene spe cluster for the speradine skeleton formation. Precursor supply experiments proved that 1 was enzymatically converted, via 2-oxoCPA (2), to speradine A (3), which subsequently undergoes multistep nonenzymatic hydroxylations to 4.
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Affiliation(s)
- Zheng-Xi Zhang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Zhang-Hai Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
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Martin JGP, Cotter PD. Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity? Heliyon 2023; 9:e15110. [PMID: 37151695 PMCID: PMC10161367 DOI: 10.1016/j.heliyon.2023.e15110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The microbial diversity of artisanal cheeses has been ever more extensively explored over recent years. Many new studies have been particularly focused on the detection and identification of fungi associated with cheese rinds. This is not surprising given that the composition and abundance of fungi on the cheese surface can significantly contribute to desirable sensory qualities, while also contributing to defects, particularly during ripening, and risks associated with the production of mycotoxins. Here we critically review the impact of fungi on the quality of artisanal cheeses, as well as the risks associated with the presence of particular species or strains with specific phenotypes. Ultimately, we address the question; should fungi be predominantly considered villains when it comes to artisanal cheese safety or could their presence be better exploited by producers in order to generate innovative products with greater added value? Such discussions will be increasingly important from the perspective of the future commercialization and regulation of artisanal cheeses that frequently contain a high abundance of moulds.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Corresponding author.
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Ireland
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25
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De Respinis S, Caminada A, Pianta E, Buetti-Dinh A, Riva Scettrini P, Petrini L, Tonolla M, Petrini O. Fungal communities on alpine cheese rinds in Southern Switzerland. BOTANICAL STUDIES 2023; 64:6. [PMID: 36905471 PMCID: PMC10008522 DOI: 10.1186/s40529-023-00371-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region. RESULTS Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars. CONCLUSIONS Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors.
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Affiliation(s)
- Sophie De Respinis
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - AnnaPaola Caminada
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Elisa Pianta
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Antoine Buetti-Dinh
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Patrizia Riva Scettrini
- Agriculture Advisory Service, Republic and Canton of Ticino, Viale Stefano Franscini 17, 6501, Bellinzona, Switzerland
| | | | - Mauro Tonolla
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Orlando Petrini
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland.
- POLE Pharma Consulting, Via Al Perato 15C, 6932, Breganzona, Switzerland.
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26
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Savary O, Coton E, Maillard MB, Gaucheron F, Le Meur C, Frisvad J, Thierry A, Jany JL, Coton M. Functional diversity of Bisifusarium domesticum and the newly described Nectriaceae cheese-associated species. Food Res Int 2023; 168:112691. [PMID: 37120186 DOI: 10.1016/j.foodres.2023.112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023]
Abstract
Bisifusarium domesticum is among the main molds used during cheese-making for its "anticollanti" property that prevents the sticky smear defect of some cheeses. Previously, numerous cheese rinds were sampled to create a working collection and not only did we isolate B. domesticum but we observed a completely unexpected diversity of "Fusarium-like" fungi belonging to the Nectriaceae family. Four novel cheese-associated species belonging to two genera were described: Bisifusarium allantoides, Bisifusarium penicilloides, Longinectria lagenoides, and Longinectria verticilliformis. In this study, we thus aimed at determining their potential functional impact during cheese-making by evaluating their lipolytic and proteolytic activities as well as their capacity to produce volatile (HS-Trap GC-MS) and non-volatile secondary metabolites (HPLC & LC-Q-TOF). While all isolates were proteolytic and lipolytic, higher activities were observed at 12 °C for several B. domesticum, B. penicilloides and L. lagenoides isolates, which is in agreement with typical cheese ripening conditions. Using volatilomics, we identified multiple cheese-related compounds, especially ketones and alcohols. B. domesticum and B. penicilloides isolates showed higher aromatic potential although compounds of interest were also produced by B. allantoides and L. lagenoides. These species were also lipid producers. Finally, an untargeted extrolite analysis suggested a safety status of these strains as no known mycotoxins were produced and revealed the production of potential novel secondary metabolites. Biopreservation tests performed with B. domesticum suggested that it may be an interesting candidate for biopreservation applications in the cheese industry in the future.
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27
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Friedrich A, Gounot JS, Tsouris A, Bleykasten C, Freel K, Caradec C, Schacherer J. Contrasting Genomic Evolution Between Domesticated and Wild Kluyveromyces lactis Yeast Populations. Genome Biol Evol 2023; 15:evad004. [PMID: 36634937 PMCID: PMC9897184 DOI: 10.1093/gbe/evad004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of Kluyveromyces lactis, a yeast species well known for its involvement in dairy processes and also present in natural environments. Using a combination of short- and long-read sequencing strategies, we investigated the genomic variability of 41 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10-2) compared with other species such as Saccharomyces cerevisiae (θw = 1.6 × 10-2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10-3), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation, and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.
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Affiliation(s)
- Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | | | - Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | | | - Kelle Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
- Institut Universitaire de France (IUF), Paris 75005, France
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Kliks J, Białobrzycka Z, Krzyszkowska M, Korycka-Korwek J, Ciepliński M, Kasprzak M. The Aroma Composition of Koryciński Cheese Ripened in Different Temperatures. Molecules 2022; 27:8745. [PMID: 36557877 PMCID: PMC9783123 DOI: 10.3390/molecules27248745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
As a regional product, Koryciński cheese is one of the most important cheeses in the Podlasie region of Poland. In this study, the influence of technological processes, such as ripening, on shaping the organoleptic characteristics of cheese was determined. Korycin-type cheeses are produced from cow's milk according to traditional technology. The ripening process lasted 466 h at 5 °C, 10 °C, and 15 °C. The aging temperature had a decisive influence on the number of esters and organic acids formed, which were analyzed by gas chromatography-mass spectrometry (GC/MS). The organoleptic properties of the cheeses were also related to the ripening temperature.
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Affiliation(s)
- Jarosław Kliks
- Faculty of Biological Sciences, University of Zielona Gora, Prof. Z. Szafrana 1 Street, 65-417 Zielona Gora, Poland
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29
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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30
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Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol 2022; 70:102236. [PMID: 36368125 DOI: 10.1016/j.mib.2022.102236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
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The Biotransformation of Lupine Seeds by Lactic Acid Bacteria and Penicillium camemberti into a Plant-Based Camembert Alternative, and Its Physicochemical Changes during 7 Weeks of Ripening. FERMENTATION 2022. [DOI: 10.3390/fermentation8090447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been increasing consumer interest and research into plant-based dairy alternatives, due to the increasingly negative impact of animal products on human health, animal welfare, and the environment. The purpose of this study was to investigate the physicochemical and microbiological changes in a Camembert alternative based on the seeds of sweet lupine (Lupinus angustifolius L cv. ‘Boregine’). After heat treatment and homogenization, the seeds were incubated with lactic acid bacteria (LAB) and Penicillium camemberti mold. After fermentation at room temperature, the samples were stored at 12 °C for 14 days, and then ripened until day 49 at 6 °C. Changes in microbial population, acidity, texture, content of polyphenols, flavonoids, reducing sugars, and free amino acids were monitored. In addition, the antioxidant capacity of the samples during ripening was determined. The results showed that LAB and fungi were able to grow well in the lupine matrix. Initially, a decrease in pH was observed, while in the further stages of ripening, alkalization of the product linked with progressive proteolysis associated with an increase in free amino acid content was noted. Hydrolysis of polysaccharides and an increase in antioxidant activity were observed. This indicates the potential of lupine seeds as a raw material for the development of a new group of plant-based ripened cheese alternatives.
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32
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Effects of Five Filamentous Fungi Used in Food Processes on In Vitro and In Vivo Gut Inflammation. J Fungi (Basel) 2022; 8:jof8090893. [PMID: 36135618 PMCID: PMC9504484 DOI: 10.3390/jof8090893] [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: 07/04/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
Food processes use different microorganisms, from bacteria to fungi. Yeast strains have been extensively studied, especially Saccharomyces cerevisiae. However, to date, very little is known about the potential beneficial effects of molds on gut health as part of gut microbiota. We undertook a comprehensive characterization of five mold strains, Penicillium camemberti, P. nalgiovense, P. roqueforti, Fusarium domesticum, and Geotrichum candidum used in food processes, on their ability to trigger or protect intestinal inflammation using in vitro human cell models and in vivo susceptibility to sodium dextran sulfate-induced colitis. Comparison of spore adhesion to epithelial cells showed a very wide disparity in results, with F. domesticum and P. roqueforti being the two extremes, with almost no adhesion and 20% adhesion, respectively. Interaction with human immune cells showed mild pro-inflammatory properties of all Penicillium strains and no effect of the others. However, the potential anti-inflammatory abilities detected for G. candidum in vitro were not confirmed in vivo after oral gavage to mice before and during induced colitis. According to the different series of experiments carried out in this study, the impact of the spores of these molds used in food production is limited, with no specific beneficial or harmful effect on the gut.
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33
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Tamang JP, Anupma A, Nakibapher Jones Shangpliang H. Ethno-microbiology of Tempe, an Indonesian fungal-fermented soybean food and Koji, a Japanese fungal starter culture. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wang R, Wu J, Jiang N, Lin H, An F, Wu C, Yue X, Shi H, Wu R. Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods. Crit Rev Food Sci Nutr 2022; 63:569-584. [PMID: 35647734 DOI: 10.1080/10408398.2022.2081127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Horizontal gene transfer (HGT) has contributed significantly to the adaptability of bacteria, yeast and mold in fermented foods, whose evidence has been found in several fermented foods. Although not every HGT has biological significance, it plays an important role in improving the quality of fermented foods. In this review, how HGT facilitated microbial domestication and adaptive evolution in fermented foods was discussed. HGT can assist in the industrial innovation of fermented foods, and this adaptive evolution strategy can improve the quality of fermented foods. Additionally, the mechanism underlying HGT in fermented foods were analyzed. Furthermore, the critical bottlenecks involved in optimizing HGT during the production of fermented foods and strategies for optimizing HGT were proposed. Finally, the prospect of HGT for promoting the industrial innovation of fermented foods was highlighted. The comprehensive report on HGT in fermented foods provides a new trend for domesticating preferable starters for food fermentation, thus optimizing the quality and improving the industrial production of fermented foods.
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Affiliation(s)
- Ruhong Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Nan Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Hao Lin
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Chen Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Haisu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
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Zha H, Li Q, Chang K, Xia J, Li S, Tang R, Li L. Characterising the Intestinal Bacterial and Fungal Microbiome Associated With Different Cytokine Profiles in Two Bifidobacterium strains Pre-Treated Rats With D-Galactosamine-Induced Liver Injury. Front Immunol 2022; 13:791152. [PMID: 35401547 PMCID: PMC8987000 DOI: 10.3389/fimmu.2022.791152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Multiple probiotics have protective effects against different types of liver injury. Different intestinal microbes could be beneficial to the protective effects of the probiotics on the treated cohorts in different aspects. The current study was designed to determine the intestinal bacterial and fungal microbiome associated with different cytokine profiles in the Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 pretreated rats with D-galactosamine-induced liver injury. In this study, partition around medoids clustering analysis determined two distinct cytokine profiles (i.e., CP1 and CP2) comprising the same 11 cytokines but with different levels among the LI09, LI10, positive control (PC), and negative control (NC) cohorts. All rats in PC and NC cohorts were determined with CP1 and CP2, respectively, while the rats with CP1 in LI09 and LI10 cohorts had more severe liver injury than those with CP2, suggesting that CP2 represented better immune status and was the “better cytokine profile” in this study. PERMANOVA analyses showed that the compositions of both bacterial and fungal microbiome were different in the LI10 cohorts with different cytokine profiles, while the same compositions were similar between LI09 cohorts with different cytokine profiles. The phylotype abundances of both bacteria and fungi were different in the rats with different cytokine profiles in LI09 or LI10 cohorts according to similarity percentage (SIMPER) analyses results. At the composition level, multiple microbes were associated with different cytokine profiles in LI09 or LI10 cohorts, among which Flavonifractor and Penicillium were the bacterium and fungus most associated with LI09 cohort with CP2, while Parabacteroides and Aspergillus were the bacterium and fungus most associated with LI10 cohort with CP2. These microbes were determined to influence the cytokine profiles of the corresponding cohorts. At the structure level, Corynebacterium and Cephalotrichiella were determined as the two most powerful gatekeepers in the microbiome networks of LI09 cohort CP2, while Pseudoflavonifractor was the most powerful gatekeeper in LI10 cohort with CP2. These identified intestinal microbes were likely to be beneficial to the effect of probiotic Bifidobacterium on the immunity improvement of the treated cohorts, and they could be potential microbial biomarkers assisting with the evaluation of immune status of probiotics-treated cohorts.
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Affiliation(s)
- Hua Zha
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kevin Chang
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengjie Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruiqi Tang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Lanjuan Li,
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37
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Curr Biol 2021; 31:5149-5162.e6. [PMID: 34648730 PMCID: PMC8660109 DOI: 10.1016/j.cub.2021.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy.
| | - Mohamed S Sarhan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy; CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander Schoenafinger
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy; Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Stefania Zingale
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Aitor Blanco-Míguez
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Jan Cemper-Kiesslich
- Interfaculty Department of Legal Medicine & Department of Classics, University of Salzburg, Ignaz-Harrer-Straße 79, 5020 Salzburg, Austria
| | - Wilfried Rosendahl
- Reiss-Engelhorn-Museen, Zeughaus C5, 68159 Mannheim, Germany; Curt-Egelhorn-Zentrum Archäomtrie, D6,3, 61859 Mannheim, Germany
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all'Adige (TN), Italy
| | - Thomas Rattei
- CUBE (Division of Computational Systems Biology), Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Klaus Oeggl
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Nicola Segata
- Department CIBIO, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Hans Reschreiter
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria
| | - Kerstin Kowarik
- Prehistoric Department, Museum of Natural History Vienna, Burgring 7, 1010 Vienna, Austria.
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Tamang JP. "Ethno-microbiology" of ethnic Indian fermented foods and alcoholic beverages. J Appl Microbiol 2021; 133:145-161. [PMID: 34821430 DOI: 10.1111/jam.15382] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/14/2021] [Accepted: 11/19/2021] [Indexed: 01/29/2023]
Abstract
The concept of "ethno-microbiology" is to understand the indigenous knowledge of the Indian people for production of culturally and organoleptically acceptable fermented foods by natural fermentation. About 1000 types of common, uncommon, rare, exotic and artisan fermented foods and beverages are prepared and consumed in different geographical regions by multi-ethnic communities in India. Indian fermented foods are mostly acidic and some are alkaline, along with various types of alcoholic beverages. A colossal diversity of microorganisms comprising bacteria mostly belongs to phylum Firmicutes, filamentous moulds and enzyme- and alcohol-producing yeasts under phyla Ascomycota and Mucoromycota, and few bacteriophages and archaea have been reported from Indian fermented foods. Some microorganisms associated with fermented foods have functionalities and health promoting benefits. "Ethno-microbiology" of ethnic Indian people has exhibited the proper utilisation of substrates either singly or in combination such as fermented cereal-legume mixture (idli, dosa and dhokla) in South and West India, sticky fermented soybean food (kinema and related foods), fermented perishable leafy vegetable (gundruk and related foods), fermented bamboo shoots (soibum and related foods) and fermented fish (ngari and others) in North East India, and fermented meat and sausage-like products in the Indian Himalayas, fermented coconut beverage (toddy) in coastal regions, and various types of naturally fermented milk products (dahi and related products) in different regions of India. This review has also highlighted the "ethno-microbiology" knowledge of the people involving the consortia of essential microorganisms in traditionally prepared amylolytic starters for production of cereal-based alcoholic beverages. The novelty of this review is the interpretation of ethno-microbiological knowledge innovated by ethnic Indian people on the use of beneficial microorganisms for food fermentation to obtain the desired fermented food products for consumption.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
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Biodeterioration of Salón de Reinos, Museo Nacional del Prado, Madrid, Spain. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198858] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Salón de Reinos, a remnant of the 17th century Palacio del Buen Retiro, was built as a recreational residence under the reign of Felipe IV between 1632 and 1640 and was the main room for the monarch’s receptions. This Salón owes its name to the fact that the coats of arms (shields) of the 24 kingdoms that formed Spain in Felipe IV’s time were painted on the vault, above the windows. In addition, the ceiling shows an original decorative composition. The painted ceiling and window vaults showed deterioration evidenced by fissures, water filtration, detachments of the paint layer, and black stains denoting fungal colonization related to humidity. Ten strains of bacteria and 14 strains of fungi were isolated from the deteriorated paintings. Their biodeteriorative profiles were detected through plate assays. The most frequent metabolic functions were proteolytic and lipolytic activities. Other activities, such as the solubilization of gypsum and calcite and the production of acids, were infrequent among the isolates.
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Chacón-Vargas K, McCarthy CO, Choi D, Wang L, Yu JH, Gibbons JG. Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism. Front Microbiol 2021; 12:691296. [PMID: 34326825 PMCID: PMC8313989 DOI: 10.3389/fmicb.2021.691296] [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: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.
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Affiliation(s)
- Katherine Chacón-Vargas
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Colin O McCarthy
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Dasol Choi
- Deapertment of Food Science, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jae-Hyuk Yu
- Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States.,Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - John G Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States.,Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
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Muñoz-Tebar N, González-Navarro EJ, López-Díaz TM, Santos JA, de Elguea-Culebras GO, García-Martínez MM, Molina A, Carmona M, Berruga MI. Biological Activity of Extracts from Aromatic Plants as Control Agents against Spoilage Molds Isolated from Sheep Cheese. Foods 2021; 10:1576. [PMID: 34359446 PMCID: PMC8303263 DOI: 10.3390/foods10071576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this work was to assess the antifungal and antioxidant activity of essential oils and ethanolic extracts from distilled solid by-products from aromatic plants (Artemisia dracunculus, Hyssopus officinalis, Lavandula stoechas, Origanum vulgare and Satureja montana) against 14 fungi strains isolated from sheep cheese and identified at species level using DNA barcoding based on β-tubulin sequence analysis. In addition, capacity of fungi to produce ochratoxin A, patulin, cyclopiazonic acid and sterigmatocystin was analyzed. Of the isolates, 85.7% belonged to Penicillium (P. commune/biforme, P. crustosum) and 14.3% to Aspergillus (A. puulaauensis and A. jensenii), the first time that these Aspergillus species have been found in sheep's cheese. All P. commune isolates were producers of cyclopiazonic acid, and the two Aspergillus strains produced sterigmatocystin, but the others did not produce any tested mycotoxin. Among the essential oils tested, oregano, savory and tarragon had a significant antifungal activity against all the isolated strains, but no ethanolic extract showed antifungal activity. By contrast, ethanolic extracts showed great potential as antioxidants. The identification of new molds in cheese will help the dairy industry to know more about those molds affecting the sector, and the use of aromatic plants in the control of fungal spoilage could be a suitable alternative to chemical preservatives used in the agri-food industry.
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Affiliation(s)
- Nuria Muñoz-Tebar
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Emilio J. González-Navarro
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Teresa María López-Díaz
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (T.M.L.-D.); (J.A.S.)
| | - Jesús A. Santos
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (T.M.L.-D.); (J.A.S.)
| | | | - M. Mercedes García-Martínez
- Catedra de Química Agrícola, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain;
| | - Ana Molina
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - Manuel Carmona
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
| | - María Isabel Berruga
- Food Quality Research Group, Institute for Regional Development (IDR), Universidad de Castilla-La Mancha, 02071 Albacete, Spain; (N.M.-T.); (E.J.G.-N.); (A.M.); (M.C.)
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43
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Draft Genome Sequences of Aspergillus and Penicillium Species Isolated from the International Space Station and Crew Resupply Vehicle Capsule. Microbiol Resour Announc 2021; 10:10/13/e01398-20. [PMID: 33795349 PMCID: PMC8104057 DOI: 10.1128/mra.01398-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The draft whole-genome sequences (WGS) of 30 fungal strains isolated from the International Space Station and belonging to the Penicillium and Aspergillus genera were assembled. The WGS will allow for detailed genomic characterization to determine the possible applications and importance for space and biotechnological industries.
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Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int J Food Microbiol 2021; 354:109174. [PMID: 34103155 DOI: 10.1016/j.ijfoodmicro.2021.109174] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023]
Abstract
Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.
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Affiliation(s)
- Thibault Caron
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France; Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France.
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Anne-Claire Péron
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Pascale Lieben
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sammy Brunel
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Michel Place
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Pascal Bonnarme
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Antoine Branca
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Sophie Landaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
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Ropars J, Caron T, Lo YC, Bennetot B, Giraud T. [The domestication of Penicillium cheese fungi]. C R Biol 2020; 343:155-176. [PMID: 33108120 DOI: 10.5802/crbiol.15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Domestication is the process of organism evolution under selection by humans, and as such has been a model for studying adaptation since Charles Darwin. Here we review recent studies on the genomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicillium roqueforti used for maturing blue cheeses, and the Penicillium camemberti species complex used for making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontal gene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiated populations with contrasted traits, several populations having independently been domesticated for cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial for cheese making in comparison to non-cheese populations, regarding color, spore production, growth rates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/or competitive ability. The cheese populations also show degeneration for some unused functions such as decreased ability of sexual reproduction or of growth under harsh conditions. These recent findings have fundamental importance for our understanding of adaptation and have applied interest for strain improvement.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Thibault Caron
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Ying-Chu Lo
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Bastien Bennetot
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
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