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Han DM, Baek JH, Choi DG, Jeon MS, Eyun SI, Jeon CO. Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity. Food Microbiol 2024; 119:104435. [PMID: 38225047 DOI: 10.1016/j.fm.2023.104435] [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: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 01/17/2024]
Abstract
Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.
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Affiliation(s)
- Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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2
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Baroncelli R, Cobo-Díaz JF, Benocci T, Peng M, Battaglia E, Haridas S, Andreopoulos W, LaButti K, Pangilinan J, Lipzen A, Koriabine M, Bauer D, Le Floch G, Mäkelä MR, Drula E, Henrissat B, Grigoriev IV, Crouch JA, de Vries RP, Sukno SA, Thon MR. Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi. Gigascience 2024; 13:giae036. [PMID: 38940768 PMCID: PMC11212070 DOI: 10.1093/gigascience/giae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/05/2024] [Accepted: 05/25/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes. RESULTS Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation. CONCLUSIONS These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.
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Affiliation(s)
- Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 40-50, 40127 Bologna, Italy
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, Campus Vegazana, 24007 León, Spain
| | - Tiziano Benocci
- Center for Health and Bioresources, Austrian Institute of Technology (AIT), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mao Peng
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sajeet Haridas
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - William Andreopoulos
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Kurt LaButti
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Jasmyn Pangilinan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Maxim Koriabine
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Diane Bauer
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
| | - Gaetan Le Floch
- Laboratory of Biodiversity and Microbial Ecology (LUBEM), IBSAM, ESIAB, EA 3882, University of Brest, Technopôle Brest-Iroise, Parv. Blaise Pascal, 29280 Plouzané, France
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Siltavuorenpenger 5, 00170 Helsinki, Finland
| | - Elodie Drula
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Bernard Henrissat
- UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS), University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- The French National Institute for Agricultural Research (INRA), USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23453 Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- Joint Genome Institute, Lawrence Berkeley National Laboratory, United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, MD 20705, Beltsville, USA
| | - Ronald P de Vries
- Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Serenella A Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
| | - Michael R Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
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3
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He S, Deng X, Han Y, Gong Z, Wang J, Tao X, Tong H, Chen Y. Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head". Food Chem 2023; 429:136992. [PMID: 37516054 DOI: 10.1016/j.foodchem.2023.136992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/17/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.
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Affiliation(s)
- Shiqiang He
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Xinyi Deng
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuxin Han
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Zhengli Gong
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Jian Wang
- Ice Island Mountain Tea Company, Mengku Town, Shuangjiang Autonomous County, Yunnan Province, China
| | - Xiaoqi Tao
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Huarong Tong
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China
| | - Yingjuan Chen
- Department of Tea Science, College of Food Science, Southwest University, Chongqing 400715, China.
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4
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Kun RS, Salazar-Cerezo S, Peng M, Zhang Y, Savage E, Lipzen A, Ng V, Grigoriev IV, de Vries RP, Garrigues S. The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. J Fungi (Basel) 2023; 9:jof9040438. [PMID: 37108893 PMCID: PMC10142829 DOI: 10.3390/jof9040438] [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: 02/17/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the knowledge about the storage polysaccharide regulators AmyR and InuR in Aspergillus niger. AmyR controls starch degradation, while InuR is involved in sucrose and inulin utilization. In our study, the phenotypes of A. niger parental, ΔamyR, ΔinuR and ΔamyRΔinuR strains were assessed in both solid and liquid media containing sucrose or inulin as carbon source to evaluate the roles of AmyR and InuR and the effect of culture conditions on their functions. In correlation with previous studies, our data showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active. In contrast, growth profiles and transcriptomic data showed that the deletion of amyR in the ΔinuR background strain resulted in more pronounced growth reduction on both substrates, mainly evidenced by data originating from solid cultures. Overall, our results show that submerged cultures do not always reflect the role of transcription factors in the natural growth condition, which is better represented on solid substrates. Importance: The type of growth has critical implications in enzyme production by filamentous fungi, a process that is controlled by transcription factors. Submerged cultures are the preferred setups in laboratory and industry and are often used for studying the physiology of fungi. In this study, we showed that the genetic response of A. niger to starch and inulin was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment did not fully match the behavior of the fungus in a solid environment. These results have direct implications in enzyme production and would help industry choose the best approaches to produce specific CAZymes for industrial purposes.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Emily Savage
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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5
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Bai Z, Zhang N, Jin Y, Chen L, Mao Y, Sun L, Fang F, Liu Y, Han M, Li G. Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks. Front Cell Infect Microbiol 2023; 12:919701. [PMID: 36683686 PMCID: PMC9846645 DOI: 10.3389/fcimb.2022.919701] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Faecalibacterium prausnitzii is a beneficial human gut microbe and a candidate for next-generation probiotics. With probiotics now being used in clinical treatments, concerns about their safety and side effects need to be considered. Therefore, it is essential to obtain a comprehensive understanding of the genetic diversity, functional characteristics, and potential risks of different F. prausnitzii strains. In this study, we collected the genetic information of 84 F . prausnitzii strains to conduct a pan-genome analysis with multiple perspectives. Based on single-copy genes and the sequences of 16S rRNA and the compositions of the pan-genome, different phylogenetic analyses of F. prausnitzii strains were performed, which showed the genetic diversity among them. Among the proteins of the pan-genome, we found that the accessory clusters made a greater contribution to the primary genetic functions of F. prausnitzii strains than the core and specific clusters. The functional annotations of F. prausnitzii showed that only a very small number of proteins were related to human diseases and there were no secondary metabolic gene clusters encoding harmful products. At the same time, complete fatty acid metabolism was detected in F. prausnitzii. In addition, we detected harmful elements, including antibiotic resistance genes, virulence factors, and pathogenic genes, and proposed the probiotic potential risk index (PPRI) and probiotic potential risk score (PPRS) to classify these 84 strains into low-, medium-, and high-risk groups. Finally, 15 strains were identified as low-risk strains and prioritized for clinical application. Undoubtedly, our results provide a comprehensive understanding and insight into F. prausnitzii, and PPRI and PPRS can be applied to evaluate the potential risks of probiotics in general and to guide the application of probiotics in clinical application.
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Affiliation(s)
- Zipeng Bai
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Na Zhang
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yu Jin
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Chen
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yujie Mao
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Lingna Sun
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Feifei Fang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Liu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Maozhen Han
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Gangping Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Król B, Słupczyńska M, Wilk M, Asghar M, Cwynar P. Anaerobic rumen fungi and fungal direct-fed microbials
in ruminant feeding. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/153961/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Buijs VA, Zuijdgeest XCL, Groenewald JZ, Crous PW, de Vries RP. Carbon utilization and growth-inhibition of citrus-colonizing Phyllosticta species. Fungal Biol 2021; 125:815-825. [PMID: 34537177 DOI: 10.1016/j.funbio.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/09/2021] [Accepted: 05/21/2021] [Indexed: 11/15/2022]
Abstract
The genus Phyllosticta includes both endophytic and phytopathogenic species that occur on a broad range of plant hosts, including Citrus. Some pathogenic species cause severe disease, such as Phyllosticta citricarpa, the causal agent of Citrus Black Spot (CBS). In contrast, other species, such as Phyllosticta capitalensis, have an endophytic lifestyle in numerous plant hosts. Carbon utilization capabilities are hypothesized to influence both host range and lifestyle, and are in part determined by the set of Carbohydrate Active Enzyme (CAZyme) encoding genes of a species. In this study, carbon utilization capabilities of five Phyllosticta species were determined, as well as the CAZyme repertoire (CAZome) encoded in their genomes. Little variation was found among species in terms of carbon utilization capabilities and CAZome. However, one of the tested carbon sources, sugar beet pulp (SBP), inhibited growth of the plant pathogens, also when combined with another carbon source, while endophytic species remained unaffected.
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Affiliation(s)
- Valerie A Buijs
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands; Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xander C L Zuijdgeest
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Johannes Z Groenewald
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Pedro W Crous
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands; Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
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8
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Cabral DJ, Wurster JI, Korry BJ, Penumutchu S, Belenky P. Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin. mSystems 2020; 5:e00317-20. [PMID: 32723789 PMCID: PMC7394352 DOI: 10.1128/msystems.00317-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dietary composition and antibiotic use have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption. Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome structure and transcriptional activity. We found that Western diet consumption dramatically increased Bacteroides abundances and shifted the community toward the metabolism of simple sugars and mucus glycoproteins. Mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. Transcriptionally, we found that ciprofloxacin reduced the abundance of tricarboxylic acid (TCA) cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this, we observed extensive diet-dependent differences in the impact of ciprofloxacin on microbiota function. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a role in determining the impacts of ciprofloxacin on microbiome composition and microbiome function.IMPORTANCE Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our "Western"-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Thus, we hypothesize that the Western diet will shift microbiota metabolism toward simple sugar and mucus degradation and away from polysaccharide utilization. Because of bacterial metabolism's critical role in antibiotic susceptibility, this change in baseline metabolism will impact how the structure and function of the microbiome are impacted by ciprofloxacin exposure. Understanding how diet modulates antibiotic-induced microbiome disruption will allow for the development of dietary interventions that can alleviate many of the microbiome-dependent complications of antibiotic treatment.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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9
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Ma Y, Ling TJ, Su XQ, Jiang B, Nian B, Chen LJ, Liu ML, Zhang ZY, Wang DP, Mu YY, Jiao WW, Liu QT, Pan YH, Zhao M. Integrated proteomics and metabolomics analysis of tea leaves fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus. Food Chem 2020; 334:127560. [PMID: 32711271 DOI: 10.1016/j.foodchem.2020.127560] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/22/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022]
Abstract
Post-fermented Pu-erh tea (PFPT) is a microbially-fermented tea with distinct sensory qualities and multiple health benefits. Aspergillus are the dominant fungi in the fermentation and the main contributors to the characteristics of PFPT, so their underlying functions warrant detailed study. Here, tea leaves were fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus, and resulting samples (designated as Asn, Ast and Asf, respectively) were analyzed by proteomic and metabolomic methods. Changes to the composition of flavonoids, glycerophospholipids, organo-oxygen compounds and fatty acids resulting from Aspergillus fermentation were observed. Carbohydrate-active enzymes, e.g., endoglucanases and cellulases, for degradation of cellulose, starch, lignin, pectin, xylan and xyloglucan were identified. Glycoside hydrolase, glycosyltransferases, tannase, laccases, vanillyl-alcohol oxidases and benzoquinone reductase were identified and hypothesized to catalyze hydrolysis, oxidation, polymerization and degradation of phenolic compounds. Together, functions of Aspergillius were demonstrated as production of enzymes to change concentrations and compositions of metabolites in tea leaves.
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Affiliation(s)
- Yan Ma
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Tie-Jun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 Anhui, China
| | - Xiao-Qin Su
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Hangzhou Tea Research Institute, CHINA COOP, Hangzhou 310016, China
| | - Bin Jiang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Bo Nian
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Li-Jiao Chen
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ming-Li Liu
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Zheng-Yan Zhang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Dao-Ping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong-Ying Mu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen-Wen Jiao
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qian-Ting Liu
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ying-Hong Pan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Ming Zhao
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China; State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China.
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10
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Wang Y, Shen Q, Zhong S, Chen Y, Yang Y. Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves. Microorganisms 2020; 8:microorganisms8070981. [PMID: 32629932 PMCID: PMC7409109 DOI: 10.3390/microorganisms8070981] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/20/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or sun-dried mulberry leaves (Group S) on changes in ruminal microbial communities, rumen fermentation parameters and serum biochemical indices. The control group (Group C) received a typical total mixed ration (TMR). 16S rRNA gene sequencing revealed 209 genera belonging to 19 bacterial phyla dominated by Firmicutes and Bacteroidetes. Only the relative abundances of Erysipelotrichaceae_UCG-009 were significantly different among the three groups (p < 0.05). Physiological and biochemical findings revealed that only the serum leptin concentrations were significantly decreased when mulberry leaves were added to the diets (p < 0.05). Correlation analysis revealed that Ruminococcus_2 were significantly positively correlated with the butyrate concentration. These findings suggested that supplementation with mulberry leaves only induced minor changes in the abovementioned indicators, implying that the rumen fermentation status was still stable after adding mulberry leaves to the diets.
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Affiliation(s)
- Yaoyue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Y.W.); (Q.S.); (S.Z.)
| | - Qingmiao Shen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Y.W.); (Q.S.); (S.Z.)
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Shu Zhong
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Y.W.); (Q.S.); (S.Z.)
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Y.W.); (Q.S.); (S.Z.)
- Correspondence: (Y.C.); (Y.Y.)
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Y.W.); (Q.S.); (S.Z.)
- Correspondence: (Y.C.); (Y.Y.)
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11
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Han M, Liu G, Chen Y, Wang D, Zhang Y. Comparative Genomics Uncovers the Genetic Diversity and Characters of Veillonella atypica and Provides Insights Into Its Potential Applications. Front Microbiol 2020; 11:1219. [PMID: 32655519 PMCID: PMC7324755 DOI: 10.3389/fmicb.2020.01219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/13/2020] [Indexed: 11/18/2022] Open
Abstract
Veillonella atypica is a bacterium that is present in the gut and the oral cavity of mammals and plays diverse roles in different niches. A recent study demonstrated that Veillonella is highly associated with marathon running and approved that V. atypica gavage improves treadmill run time in mice, revealing that V. atypica has a high biotechnological potential in improving athlete performance. However, a comprehensive analysis of the genetic diversity, function traits, and genome editing method of V. atypica remains elusive. In the present study, we conducted a systemically comparative analysis of the genetic datasets of nine V. atypica strains. The pan-genome of V. atypica consisted of 2,065 homologous clusters and exhibited an open pan-genome structure. A phylogenetic analysis of V. atypica with two different categories revealed that V. atypica OK5 was the most distant from the other eight V. atypica strains. A total of 43 orthologous genes were identified as CAZyme genes and grouped into 23 CAZyme families. The CAZyme components derived from accessory clusters contributed to the differences in the ability of the nine V. atypica strains to utilize carbohydrates. An integrated analysis of the metabolic pathways of V. atypica suggested that V. atypica strains harbored vancomycin resistance and were involved in several biosynthesis pathways of secondary metabolites. The V. atypica strains harbored four main Cas proteins, namely, CAS-Type IIIA, CAS-Type IIA, CAS-Type IIC, and CAS-Type IIID. This pilot study provides an in-depth understanding of and a fundamental knowledge about the biology of V. atypica that allow the possibility to increase the biotechnological potential of this bacterium.
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Affiliation(s)
- Maozhen Han
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Gang Liu
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Yajun Chen
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Dong Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
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12
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A comparative genomics study of 23 Aspergillus species from section Flavi. Nat Commun 2020; 11:1106. [PMID: 32107379 PMCID: PMC7046712 DOI: 10.1038/s41467-019-14051-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi. Aspergillus fungi classified within the section Flavi include harmful and beneficial species. Here, Kjærbølling et al. analyse the genomes of 23 Flavi species, showing high genetic diversity and potential for synthesis of over 13,700 CAZymes and 1600 secondary metabolites.
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13
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Zhang Y, Wang J, Yajun C, Zhou M, Wang W, Geng M, Xu D, Xu Z. Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes. MYCOBIOLOGY 2020; 48:104-114. [PMID: 32363038 PMCID: PMC7178859 DOI: 10.1080/12298093.2020.1725361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/02/2020] [Accepted: 01/22/2020] [Indexed: 05/27/2023]
Abstract
The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.
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Affiliation(s)
- Yan Zhang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Jingjing Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Chen Yajun
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei Wang
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Ming Geng
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Decong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Zhongdong Xu
- School of Life Sciences, Hefei Normal University, Hefei, China
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14
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Hautbergue T, Jamin EL, Costantino R, Tadrist S, Meneghetti L, Tabet JC, Debrauwer L, Oswald IP, Puel O. Combination of Isotope Labeling and Molecular Networking of Tandem Mass Spectrometry Data To Reveal 69 Unknown Metabolites Produced by Penicillium nordicum. Anal Chem 2019; 91:12191-12202. [PMID: 31464421 DOI: 10.1021/acs.analchem.9b01634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The secondary metabolome of Penicillium nordicum is poorly documented despite its frequent detection on contaminated food and its capacity to produce toxic metabolites such as ochratoxin A. To characterize metabolites produced by this fungi, we combined a full stable isotopes labeling with the dereplication of tandem mass spectrometry (MS/MS) data by molecular networking. First, the untargeted metabolomic analysis by high-resolution mass spectrometry of a double stable isotope labeling of P. nordicum enabled the specific detection of its metabolites and the unambiguous determination of their elemental composition. Analyses showed that infection of substrate by P. nordicum lead to the production of at least 92 metabolites and that 69 of them were completely unknown. Then, curated molecular networks of MS/MS data were generated with GNPS and MetGem, specifically on the features of interest, which allowed highlighting 13 fungisporin-related metabolites that had not previously been identified in this fungus and 8 that had never been observed in any fungus. The structures of the unknown compounds, namely, a native fungisporin and seven linear peptides, were characterized by tandem mass spectrometry experiments. The analysis of P. nordicum growing on its natural substrates, i.e. pork ham, turkey ham, and cheese, demonstrated that 10 of the known fungisporin-related metabolites and three of the new metabolites were also synthesized. Thus, the curation of data for molecular networking using a specific detection of metabolites of interest with stable isotopes labeling allowed the discovery of new metabolites produced by the food contaminant P. nordicum.
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Affiliation(s)
- Thaïs Hautbergue
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France.,Axiom platform, MetaToul-MetaboHUB , National Infrastructure for Metabolomics and Fluxomics , F-31027 Toulouse , France
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France.,Axiom platform, MetaToul-MetaboHUB , National Infrastructure for Metabolomics and Fluxomics , F-31027 Toulouse , France
| | - Robin Costantino
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France.,Axiom platform, MetaToul-MetaboHUB , National Infrastructure for Metabolomics and Fluxomics , F-31027 Toulouse , France
| | - Souria Tadrist
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France
| | - Lauriane Meneghetti
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France.,Axiom platform, MetaToul-MetaboHUB , National Infrastructure for Metabolomics and Fluxomics , F-31027 Toulouse , France
| | - Jean-Claude Tabet
- Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA , Université Paris Saclay, MetaboHUB , F-91191 Gif-sur-Yvette , France.,Sorbonne Universités , Campus Pierre et Marie Curie, IPCM , 4 place Jussieu , 75252 Paris Cedex 05, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France.,Axiom platform, MetaToul-MetaboHUB , National Infrastructure for Metabolomics and Fluxomics , F-31027 Toulouse , France
| | - Isabelle P Oswald
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology) , Université de Toulouse, INRA, ENVT, INP-Purpan , UPS , F-31027 Toulouse , France
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15
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Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A. Enzymes of early-diverging, zoosporic fungi. Appl Microbiol Biotechnol 2019; 103:6885-6902. [PMID: 31309267 PMCID: PMC6690862 DOI: 10.1007/s00253-019-09983-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/26/2022]
Abstract
The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism’s fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, and Cryptomycota represent the earliest diverging lineages of the Fungal Kingdom. The review describes the enzyme compositions of these zoosporic fungi, underscoring the enzymes involved in biomass degradation. The review connects the lifestyle and substrate affinities of the zoosporic fungi to the secretome composition by examining both classical phenotypic investigations and molecular/genomic-based studies. The carbohydrate-active enzyme profiles of 19 genome-sequenced species are summarized. Emphasis is given to recent advances in understanding the functional role of rumen fungi, the basis for the devastating chytridiomycosis, and the structure of fungal cellulosome. The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens, and saprotrophs. Early-diverging fungi digest most major types of biopolymers: cellulose, hemicellulose, pectin, chitin, and keratin. It is thus to be expected that early-diverging fungi in its entirety represents a rich and diverse pool of secreted, metabolic enzymes. The review presents the methods used for enzyme discovery, the diversity of enzymes found, the status and outlook for recombinant production, and the potential for applications. Comparative studies on the composition of secretome enzymes of early-diverging fungi would contribute to unraveling the basal lineages of fungi.
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Affiliation(s)
- Lene Lange
- Bioeconomy, Research & Advisory, Karensgade 5, Valby, DK-2500, Copenhagen, Denmark.
| | - Kristian Barrett
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Frank Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B1R6, Canada
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16
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Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vries RP. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Stud Mycol 2018; 91:61-78. [PMID: 30425417 PMCID: PMC6231085 DOI: 10.1016/j.simyco.2018.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.
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Affiliation(s)
- M V Aguilar-Pontes
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - J Brandl
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kongens Lyngby, Denmark
| | - E McDonnell
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | - K Strasser
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | - T T M Nguyen
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | - R Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - S Mondo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - A Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - J L Nybo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kongens Lyngby, Denmark
| | - T C Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kongens Lyngby, Denmark
| | - I V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - M R Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kongens Lyngby, Denmark
| | - A Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | - R P de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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