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Lu YT, Wu YY, Li YN, Zheng WY, Liu WZ. Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis. Arch Microbiol 2024; 206:342. [PMID: 38967823 DOI: 10.1007/s00203-024-04069-2] [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: 01/08/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
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Affiliation(s)
- Yi-Ting Lu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Yi-Yi Wu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
| | - Ya-Nan Li
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China
- Department of Pharmaceutical Laboratory, Anhui Sunhere Pharmaceutical Excipients Co., Ltd, Huainan, Anhui Province, 232000, China
| | - Wei-Yi Zheng
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
| | - Wen-Zheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, PR China.
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Bandeira L, Faria C, Cavalcante F, Mesquita A, Martins C, Martins S. Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01184-x. [PMID: 38961050 DOI: 10.1007/s12223-024-01184-x] [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: 12/12/2023] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.
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Affiliation(s)
- Leonardo Bandeira
- Ecology and Natural Resources, Federal University of Ceará, Fortaleza, Brazil.
- Graduate Course of Ecology and Natural Resources, Department of Biology, Campus of Pici, Federal University of Ceará, Fortaleza, 60440-900, Brazil.
| | | | - Fernando Cavalcante
- Ecology and Natural Resources, Federal University of Ceará, Fortaleza, Brazil
| | - Ariel Mesquita
- Biotechnology of Natural Resources, Federal University of Ceará, Fortaleza, Brazil
| | - Claudia Martins
- Graduate Course of Ecology and Natural Resources, Department of Biology, Campus of Pici, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Suzana Martins
- Graduate Course of Ecology and Natural Resources, Department of Biology, Campus of Pici, Federal University of Ceará, Fortaleza, 60440-900, Brazil
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Nuhamunada M, Mohite OS, Phaneuf P, Palsson B, Weber T. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res 2024; 52:5478-5495. [PMID: 38686794 PMCID: PMC11162802 DOI: 10.1093/nar/gkae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.
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Affiliation(s)
- Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Patrick V Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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Zheng H, Wang M, Fan Y, Yang J, Zhao Z, Chen H, Ye Z, Zheng Z, Yu K. Reuse of composted food waste from rural China as vermicomposting substrate: effects on earthworms, associated microorganisms, and economic benefits. ENVIRONMENTAL TECHNOLOGY 2024; 45:2685-2697. [PMID: 36846968 DOI: 10.1080/09593330.2023.2184728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
ABSTRACTAerobic composting of food waste (FW) from rural China using a composting device results in a substantial financial burden on the government. This study aimed to assess the feasibility of mitigating this cost using vermicomposting of composted FW. The specific aims were to elucidate the effects of composted FW on earthworm growth and reproduction, reveal the changes in the physical and chemical properties of earthworm casts during vermicomposting, identify the microbial community structure associated with vermicomposting, and perform a financial analysis based on the yield of earthworms and earthworm casts. Mixing composted FW and mature cow dung in an equal ratio achieved the highest earthworm reproduction rate, where 100 adult earthworms produced 567 juvenile earthworms and 252 cocoons in 40 d. Earthworms reduce salt content of vermicomposting substrates by assimilating Na+ and promoting humification by transforming humin into humic and fulvic acid, thus producing earthworm casts with a high generation index > 80%. When composted FW was added to a vermicomposting substrate, a distinctive microbial community structure with alkaliphilic, halophilic, and lignocellulolytic microorganisms dominated the microflora. The dominant bacterial species was Saccharopolyspora rectivirgula, and the dominant fungal species changed from Kernia nitida to Coprinopsis scobicola. Furthermore, microbial genes for refractory organic matter and fat degradation were observed in Vibrio cholerae, Kernia nitida, and Coprinopsis scobicola. Financial analysis showed that vermicomposting has the potential to reduce the cost associated with FW disposal from $ 57 to $ 18/t.
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Affiliation(s)
- Huabao Zheng
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Min Wang
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Yueqin Fan
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Jian Yang
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Zhuoqun Zhao
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Hengyuan Chen
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
| | - Zhenwei Ye
- Office of Qingshanhu strict, Government of Linan district, Linan, People's Republic of China
| | - Zhanwang Zheng
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
- Zhejiang Sunda Public Environmental Protection Co. Ltd., Hangzhou, People's Republic of China
| | - Kefei Yu
- College of Environmental and Resource Science, Zhejiang A&F University, Linan, People's Republic of China
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Shao M, Xu F, Ke X, Huang M, Chu J. Enhancing erythromycin production in Saccharopolyspora erythraea through rational engineering and fermentation refinement: A Design-Build-Test-Learn approach. Biotechnol J 2024; 19:e2400039. [PMID: 38797723 DOI: 10.1002/biot.202400039] [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: 01/16/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Industrial production of bioactive compounds from actinobacteria, such as erythromycin and its derivatives, faces challenges in achieving optimal yields. To this end, the Design-Build-Test-Learn (DBTL) framework, a systematic metabolic engineering approach, was employed to enhance erythromycin production in Saccharopolyspora erythraea (S. erythraea) E3 strain. A genetically modified strain, S. erythraea E3-CymRP21-dcas9-sucC (S. erythraea CS), was developed by suppressing the sucC gene using an inducible promoter and dcas9 protein. The strain exhibited improved erythromycin synthesis, attributed to enhanced precursor synthesis and increased NADPH availability. Transcriptomic and metabolomic analyses revealed altered central carbon metabolism, amino acid metabolism, energy metabolism, and co-factor/vitamin metabolism in CS. Augmented amino acid metabolism led to nitrogen depletion, potentially causing cellular autolysis during later fermentation stages. By refining the fermentation process through ammonium sulfate supplementation, erythromycin yield reached 1125.66 mg L-1, a 43.5% increase. The results demonstrate the power of the DBTL methodology in optimizing erythromycin production, shedding light on its potential for revolutionizing antibiotic manufacturing in response to the global challenge of antibiotic resistance.
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Affiliation(s)
- Minghao Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Feng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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Suksaard P, Butdee W, Suriyachadkun C, Sirikesorn L, Duangmal K. Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils. Curr Microbiol 2024; 81:130. [PMID: 38589729 DOI: 10.1007/s00284-024-03661-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024]
Abstract
During the course of the isolation of actinobacteria from sweet potato field soils collected from Phra Nakhon Si Ayutthaya province of Thailand, strain TS4A08T was isolated and subjected to a polyphasic taxonomic approach. The 16S rRNA gene sequence analysis of strain TS4A08T revealed that it is closely related to the type strains of Saccharopolyspora aridisoli, and Saccharopolyspora endophytica with 98.7%, and 98.6% similarity, respectively. However, phylogenetic analyses using 16S rRNA gene and genome sequences indicated that strain TS4A08T clustered with Saccharopolyspora flava AS4.1520T (98.2% similarity), well-supported by bootstrap values, and formed distinct line from the two closest strains. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values between the genome sequences of strain TS4A08T and the closest type strains of S. aridisoli, S. endophytica, and S. flava, were 86.1-93.2% and 33.1-49.6%, respectively, which were less than the threshold for the species delineation. The genome size and the DNA G + C content of strain TS4A08T were 6.6 Mbp and 70.5%, respectively. The strain grew well at 25-37 °C, pH range of 7-9, and NaCl concentration of 0-5% (w/v). Whole-cell hydrolysates contained meso-diaminopimelic acid. The major fatty acids were iso-C16:0, anteiso-C17:0, and iso-C15:0. Strain TS4A08T exhibited phosphatidylcholine in its polar lipid profile, with MK-9(H4) being the predominant isoprenologue. The strain exhibits typical chemotaxonomic properties of the genus Saccharopolyspora, including arabinose, galactose, and ribose as whole-cell sugars. Strain TS4A08T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora ipomoeae sp. nov. is proposed. The type strain is TS4A08T (= TBRC 17271T = NBRC 115967T).
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Affiliation(s)
- Paweena Suksaard
- Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Huntra, Phra Nakhon Si Ayutthaya, 13000, Thailand.
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Laongsri Sirikesorn
- Department of Plant Science, Faculty of Agricultural Technology and Agro-Industry, Rajamangala University of Technology Suvarnabhumi, Huntra, Phra Nakhon Si Ayutthaya, 13000, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Biodiversity Center, Kasetsart University (BDCKU), Bangkok, 10900, Thailand
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Zou H, He J, Chu Y, Xu B, Li W, Huang S, Guan X, Liu F, Li H. Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133139. [PMID: 38056273 DOI: 10.1016/j.jhazmat.2023.133139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/31/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 μg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.
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Affiliation(s)
- Hua Zou
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Jiangtao He
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China.
| | - Yanjia Chu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Baoshi Xu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Wei Li
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Shiwen Huang
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Xiangyu Guan
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; School of Ocean Sciences, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing 100083, China; MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences, Beijing 100083, China
| | - Haiyan Li
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Giacomelli Ribeiro H, Teresinha Van Der Sand S. Exploring the Trends in Actinobacteria as Biological Control Agents of Phytopathogenic Fungi: A (Mini)-Review. Indian J Microbiol 2024; 64:70-81. [PMID: 38468744 PMCID: PMC10924869 DOI: 10.1007/s12088-023-01166-6] [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: 03/24/2023] [Accepted: 11/27/2023] [Indexed: 03/13/2024] Open
Abstract
Biological control has been considered a sustainable alternative to combat phytopathogens. The increase of studies in the past few years involving Actinobacteria as biological control agents of phytopathogenic fungi has motivated us to search for which Actinobacteria genus that have been studied in the last five years and explore their mechanisms of antifungal activity. The accesses were carried out on three multidisciplinary digital platforms: PubMED/MedLine, Web of Science and Scopus. Actinobacteria from genus Amycolatopsis, Curtobacterium, Kocuria, Nocardioides, Nocardiopsis, Saccharopolyspora, Streptoverticillium and especially Streptomyces showed a broad antifungal spectrum through several antibiosis mechanisms such as the production of natural antifungal compounds, siderophores, extracellular hydrolytic enzymes and activation of plant defense system. We observed the formation of a methodology based on antagonistic compounds bioactivity to select efficient Actinobacteria to be used as biological control agents against phytopathogenic fungi. The use of multifunctional Actinobacteria has been proven to be efficient, not only by its natural protective activity against phytopathogenic fungi but also because of their ability to act as plant growth-promoting bacteria.
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Affiliation(s)
- Heloísa Giacomelli Ribeiro
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos 2600, Porto Alegre, RS 90035-003 Brazil
| | - Sueli Teresinha Van Der Sand
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos 2600, Porto Alegre, RS 90035-003 Brazil
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El-Hawary SS, Hassan MHA, Hudhud AO, Al-Karmalawy AA, Mustafa M, Hamed EAE, Abdelmohsen UR, Mohammed R. LC-HRMS Profiling and Cytotoxic Potential of Actinomycetes Associated with the Red Sea Soft Coral Sarcophyton glaucum: In vitro and In silico Studies. Chem Biodivers 2024; 21:e202301617. [PMID: 38193652 DOI: 10.1002/cbdv.202301617] [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: 10/14/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
In the current study, the actinomycetes associated with the red sea-derived soft coral Sarcophyton glaucum were investigated in terms of biological and chemical diversity. Four different media, M1, ISP2, Marine Agar (MA), and Actinomycete isolation agar (AIA) were used for the isolation of three strains of actinomycetes that were identified as Streptomyces sp. UR 25, Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. LC-HRMS analysis was used to investigate the chemical diversity of the isolated actinobacteria. The LC-HRMS data were statistically processed using MetaboAnalyst 5.0 viz to differentiate the extract groups and determine the optimal growth culturing conditions. Multivariate data statistical analysis revealed that the Micromonospora sp. extract cultured on (MA) medium is the most distinctive extract in terms of chemical composition. While, the Streptomyces sp. UR 25 extracts are differ significantly from Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. Biological investigation using in vitro cytotoxic assay for actinobacteria extracts revealed the prominent potentiality of the Streptomyces sp. UR 25 cultured on oligotrophic medium against human hepatoma (HepG2), human breast adenocarcinoma (MCF-7) and human colon adenocarcinoma (CACO2) cell lines (IC50 =3.3, 4.2 and 6.8 μg/mL, respectively). SwissTarget Prediction speculated that among the identified compounds, 16-deethyl, indanomycin (8) could have reasonable affinity on HDM2 active site. In this respect, molecular docking study was performed for compound (8) to reveal a substantial affinity on HDM2 active site. In addition, molecular dynamics simulations were carried out at 200 ns for the most active compound (8) compared to the co-crystallized inhibitor DIZ giving deeper information regarding their thermodynamic and dynamic properties as well.
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Affiliation(s)
- Seham S El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11511, Egypt
| | - Marwa H A Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed O Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit University, Sohag, 82511, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, 12566, Egypt
| | - Muhamad Mustafa
- IBMM, CNRS, ENSCM, Université de Montpellier, Montpellier, 34095, France
- Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya University, Minia, 61111, Egypt
| | - Elsayed A E Hamed
- National institute of oceanography and Fisheries, Hurghada-Red Sea (NIOF), 84511, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia, 61111, Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
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Ma D, Liu S, Liu H, Zhang S, Xu Y, Mao J. Environmental factors drive microbial community succession in biofortified wheat Qu and its improvement on the quality of Chinese huangjiu. J Biosci Bioeng 2024; 137:124-133. [PMID: 38102024 DOI: 10.1016/j.jbiosc.2023.11.008] [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: 04/03/2023] [Revised: 11/04/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023]
Abstract
Wheat Qu plays the role of saccharification fermentation, providing microorganisms and flavor in the fermentation of huangjiu, and the use of functional microorganisms to fortify wheat Qu is becoming increasingly popular. Yet, the mechanisms promoting microbial successions of wheat Qu remain unclear. In this study, we first correlated microbial community succession with physicochemical factors (moisture, temperature, acidity, glucoamylase and amylase) in inoculated raw wheat Qu (IRWQ) with Saccharopolyspora rosea. The Mantel test was performed to investigate the significance and found that temperature (r = 0.759, P = 0.001), moisture (r = 0.732, P = 0.006), and acidity (r = 0.712, P = 0.017) correlated significantly with the bacterial community in phase 1 (0-40 h). Meanwhile, temperature correlated significantly with the fungal community in phases 1 and 2 (40-120 h). To confirm the effect of temperature on microbial communities, the artificial reduction of bio-heat (37°C) in IRWQ also reduced the relative abundance of heat-resistant microorganisms including Bacillus and Saccharopolyspora. A higher abundance of Saccharopolyspora (87%) in IRWQ was observed following biofortified inoculation of S. rosea, in which glucoamylase activity increased by 40% compared to non-inoculated raw wheat Qu (NIRWQ) (1086 U/g vs 776 U/g). Finally, the IRWQ was employed to mechanized huangjiu fermentation and it was found to reduce the bitter amino acid and higher alcohol content by 27% and 8%, respectively, improving the drinking comfort and quality of huangjiu.
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Affiliation(s)
- Donglin Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 312000, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China
| | - Haipo Liu
- China Alcoholic Drinks Association, Haidian, Beijing 100089, China
| | - Suyi Zhang
- Luzhou Laojiao Group Co. Ltd., Luzhou 646000, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 312000, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China.
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11
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Parra J, Beaton A, Seipke RF, Wilkinson B, Hutchings MI, Duncan KR. Antibiotics from rare actinomycetes, beyond the genus Streptomyces. Curr Opin Microbiol 2023; 76:102385. [PMID: 37804816 DOI: 10.1016/j.mib.2023.102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 10/09/2023]
Abstract
Throughout the golden age of antibiotic discovery, Streptomyces have been unsurpassed for their ability to produce bioactive metabolites. Yet, this success has been hampered by rediscovery. As we enter a new stage of biodiscovery, omics data and existing scientific repositories can enable informed choices on the biodiversity that may yield novel antibiotics. Here, we focus on the chemical potential of rare actinomycetes, defined as bacteria within the order Actinomycetales, but not belonging to the genus Streptomyces. They are named as such due to their less-frequent isolation under standard laboratory practices, yet there is increasing evidence to suggest these biologically diverse genera harbour considerable biosynthetic and chemical diversity. In this review, we focus on examples of successful isolation and genera that have been the focus of more concentrated biodiscovery efforts, we survey the representation of rare actinomycete taxa, compared with Streptomyces, across natural product data repositories in addition to its biosynthetic potential. This is followed by an overview of clinically useful drugs produced by rare actinomycetes and considerations for future biodiscovery efforts. There is much to learn about these underexplored taxa, and mounting evidence suggests that they are a fruitful avenue for the discovery of novel antimicrobials.
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Affiliation(s)
- Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José 11501-2060, Costa Rica; Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Ainsley Beaton
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryan F Seipke
- University of Leeds, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
| | - Barrie Wilkinson
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew I Hutchings
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow G4 0RE, UK.
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12
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Pan Y, Lv H, Feng X, Zhou S, Hu H, Chen S, Cheng Y, Fan F, Gong S, Chen P, Chu Q. Epigallocatechin gallate (EGCG) alleviates the inflammatory response and recovers oral microbiota in acetic acid-induced oral inflammation mice. Food Funct 2023; 14:10069-10082. [PMID: 37867423 DOI: 10.1039/d3fo03107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The oral microbiota, the second largest microbiome in the human body, plays an integral role in maintaining both the local oral and systemic health of the host. Oral microecological imbalances have been identified as a potential risk factor for numerous oral and systemic diseases. As a representative component of tea, epigallocatechin gallate (EGCG) has demonstrated inhibitory effects on most pathogens in single-microbial models. In this study, the regulatory effect of EGCG on more complex oral microbial systems was further explored through a mouse model of acetic acid-induced oral inflammation. Acetic acid induces histological damage in the cheek pouch, tongue, and throat, such as broken mucosa, submucosal edema, and muscular disorders. These detrimental effects were ameliorated significantly following EGCG treatment. Additionally, EGCG reduced the levels of the inflammatory cytokines interleukin-6 and tumor necrosis factor-α to alleviate the inflammation of the tongue, cheek pouch, and throat. According to the 16S rDNA gene sequencing data, EGCG treatment contributed to increased diversity of the oral microbiota and the reversal of oral microecological disorder. This study demonstrates the regulatory effect of EGCG on dysregulated oral microbiota, providing a potential option for the prevention and treatment of oral-microbiota-associated diseases.
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Affiliation(s)
- Yani Pan
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Helin Lv
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Xinyu Feng
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Su Zhou
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Hao Hu
- College of Food and Health, Zhejiang A & F University, Hangzhou 311300, China
| | - Shuxi Chen
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Yan Cheng
- Hangzhou Real Taste Tea Culture Development Co., Ltd., Hangzhou 311100, China
| | - Fangyuan Fan
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Shuying Gong
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Ping Chen
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
| | - Qiang Chu
- Tea Research Institute, Zhejiang University, Hangzhou 310058, China.
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13
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Wu-Chuang A, Hartmann D, Maitre A, Mateos-Hernández L, Frantová H, Urbanová V, Obregon D, Cabezas-Cruz A, Perner J. Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae. MICROBIAL ECOLOGY 2023; 86:2400-2413. [PMID: 37249591 DOI: 10.1007/s00248-023-02244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.
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Affiliation(s)
- Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - David Hartmann
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic
| | - Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), 20250, Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Helena Frantová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Urbanová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France.
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic.
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14
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [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: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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15
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Bertrand CDF, Martins R, Quintas-Nunes F, Reynolds-Brandão P, Crespo MTB, Nascimento FX. Saccharopolyspora sp. NFXS83 in Marine Biotechnological Applications: From Microalgae Growth Promotion to the Production of Secondary Metabolites. Microorganisms 2023; 11:microorganisms11040902. [PMID: 37110324 PMCID: PMC10145562 DOI: 10.3390/microorganisms11040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a potential source of these compounds. This study reports the characterization and genomic analysis of Saccharopolyspora sp. NFXS83, a marine bacterium isolated from seawater from the Sado estuary in Portugal. The NFXS83 strain produced multiple functional and stable extracellular enzymes under high-salt conditions, showed the ability to synthesize auxins such as indole-3-acetic acid, and produced diffusible secondary metabolites capable of inhibiting the growth of Staphylococcus aureus. Furthermore, when Phaeodactylum tricornutum was co-cultivated with strain NFXS83 a significant increase in microalgae cell count, cell size, auto-fluorescence, and fucoxanthin content was observed. Detailed analysis revealed the presence of clusters involved in the production of various secondary metabolites, including extracellular enzymes, antimicrobial compounds, terpenes, and carotenoids in the genome of strain NFXS83. Ultimately, these findings indicate that Saccharopolyspora sp. NFXS83 has a significant potential for a wide range of marine biotechnological applications.
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16
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Andrić S, Rigolet A, Argüelles Arias A, Steels S, Hoff G, Balleux G, Ongena L, Höfte M, Meyer T, Ongena M. Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor. THE ISME JOURNAL 2023; 17:263-275. [PMID: 36357782 PMCID: PMC9860033 DOI: 10.1038/s41396-022-01337-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022]
Abstract
Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.
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Affiliation(s)
- Sofija Andrić
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Augustin Rigolet
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sébastien Steels
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Grégory Hoff
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.5477.10000000120346234Present Address: Ecology and Biodiversity, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Guillaume Balleux
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Loïc Ongena
- grid.4861.b0000 0001 0805 7253Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Monica Höfte
- grid.5342.00000 0001 2069 7798Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thibault Meyer
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.7849.20000 0001 2150 7757Present Address: UMR Ecologie Microbienne, F-69622, University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Marc Ongena
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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17
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Li Y, Qiao H, Zhang R, Zhang W, Wen P. Microbial Diversity and Volatile Flavor Compounds in Tibetan Flavor Daqu. Foods 2023; 12:foods12020324. [PMID: 36673416 PMCID: PMC9858000 DOI: 10.3390/foods12020324] [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: 11/13/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
In this study, the microbial diversity in Tibetan flavor Daqu was analyzed based on single molecule real-time sequencing (SMRT). The volatile flavor compounds in Daqu were detected using the headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). In addition, the correlation between various microbes and volatile flavor compounds was explored. Our studies indicated that the dominant bacterial genera in Tibetan flavor Daqu were Oceanobacillus, Kroppenstedtia, Virgibacillus, Enterococcus, Pediococcus, Streptomyces, Saccharopolyspora, Leuconostoc, uncultured_bacterium_f_Lachnospiraceae and Lactobacillus. The dominant fungal genera were Wickerhamomyces, Monascus, Aspergillus and Rhizomucor. 101 volatile compounds were detected in the Daqu samples, including alcohols, acids, esters, aldehydes, hydrocarbons, ketones, ethers, aromatics and pyrazines, and 10 key flavor compounds were identified using the relative odor activity value (ROAV). The results of our correlation analysis showed that Enterococcus was mainly associated with the synthesis of aldehydes such as trans-2-octenal, and uncultured_bacterium_f_lachnospiraceae was associated with the synthesis of most aldehydes. This paper has systematically investigated the physicochemical indices, microbial community structure and flavor compounds of Tibetan flavor Daqu, which is helpful in gaining a deeper understanding of the characteristics of Tibetan flavor Daqu.
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Affiliation(s)
- Yaping Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Haijun Qiao
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Rui Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibing Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (W.Z.); (P.W.)
| | - Pengcheng Wen
- Functional Dairy Product Engineering Lab of Gansu Province, Yingmen Village, Anning, Lanzhou 730070, China
- Correspondence: (W.Z.); (P.W.)
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18
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Ma D, Liu S, Liu H, Nan M, Xu Y, Han X, Mao J. Developing an innovative raw wheat Qu inoculated with Saccharopolyspora and its application in Huangjiu. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:7301-7312. [PMID: 35757866 DOI: 10.1002/jsfa.12096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Mechanized Huangjiu is a stable product, is not subject to seasonal production restrictions, and markedly reduces labor intensity compared to traditional manual Huangjiu. However, the bitterness of mechanized Huangjiu impedes its further development. RESULTS Based on process optimization, when the fermentation temperature was 45 °C and the fermentation time was 122 h, the inoculation amount of Saccharopolyspora was 5%, the amount of added water was 26%, and the glucoamylase and amylase activities of wheat Qu increased by 27% and 40% respectively, compared with those before optimization. Huangjiu fermented by raw wheat Qu inoculated with Saccharopolyspora rosea F2014 showed a significant (P < 0.05) decrease in bitter amino acid content (1.24 vs. 2.86 g L-1 , a decrease of 56%), which attenuated its bitterness. CONCLUSION An innovative fermentation process of inoculating Saccharopolyspora into raw wheat Qu was developed for the first time. Such a process could be used to control bitterness based on raw wheat Qu inoculated with Saccharopolyspora rosea F2014, instead of traditional wheat Qu in Huangjiu fermentation. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Donglin Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Haipo Liu
- Famous Wine Collection Committee, China Alcoholic Drinks Association, Beijing, China
| | - Mujia Nan
- Basic Department, University of Tibetan Medicine, Lhasa, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Xiao Han
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co. Ltd, Zhejiang, China
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19
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What Are the Main Factors That Affect the Flavor of Sauce-Aroma Baijiu. Foods 2022; 11:foods11213534. [PMID: 36360147 PMCID: PMC9657106 DOI: 10.3390/foods11213534] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
Sauce-aroma Baijiu is a distilled Baijiu well-known in China, and features a unique sauce-aroma style formed by a complex producing process in a specific geographical environment. However, there are few comprehensive reviews of the factors influencing the formation of its flavor. To this end, reviews are hereby carried out over factors including different components in brewing raw materials, geographical environment of Baijiu production, brewing technology including the production of high-temperature Daqu and the brewing process, storage technology including the type of storage containers, storage time and storage temperature involved in the production of Sauce-aroma Baijiu. In addition, the effects of these factors on the flavor formation of Sauce-aroma Baijiu are also revealed, providing references and forging a foundation for stabilizing and improving the quality of Sauce-aroma Baijiu.
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20
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Ma D, Liu S, Han X, Nan M, Xu Y, Qian B, Wang L, Mao J. Complete genome sequence, metabolic model construction, and huangjiu application of Saccharopolyspora rosea A22, a thermophilic, high amylase and glucoamylase actinomycetes. Front Microbiol 2022; 13:995978. [PMID: 36246298 PMCID: PMC9554608 DOI: 10.3389/fmicb.2022.995978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Saccharopolyspora is an important microorganism in the fermentation process of wheat qu and huangjiu, yet the mechanisms by which it performs specific functions in huangjiu remain unclear. A strain with high amylase and glucoamylase activities was isolated from wheat qu and identified as Saccharopolyspora rosea (S. rosea) A22. We initially reported the whole genome sequence of S. rosea A22, which comprised a circular chromosome 6,562,638 bp in size with a GC content of 71.71%, and 6,118 protein-coding genes. A functional genomic analysis highlighted regulatory genes involved in adaptive mechanisms to harsh conditions, and in vitro experiments revealed that the growth of S. rosea A22 could be regulated in response to the stress condition. Based on whole-genome sequencing, the first genome-scale metabolic model of S. rosea A22 named iSR1310 was constructed to predict the growth ability on different media with 91% accuracy. Finally, S. rosea A22 was applied to huangjiu fermentation by inoculating raw wheat qu, and the results showed that the total higher alcohol content was reduced by 12.64% compared with the control group. This study has elucidated the tolerance mechanisms and enzyme-producing properties of S. rosea A22 at the genetic level, providing new insights into its application to huangjiu.
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Affiliation(s)
- Donglin Ma
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Shuangping Liu
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
- *Correspondence: Shuangping Liu,
| | - Xiao Han
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Mujia Nan
- Basic Department, University of Tibetan Medicine, Lhasa, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Bin Qian
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Lan Wang
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
| | - Jian Mao
- State Key Laboratory of Food Science and Technology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing Huangjiu Industry Innovation Service Complex, Shaoxing, China
- Jian Mao,
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21
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Succession of endophytic bacterial community and its contribution to cinnamon oil production during cinnamon shade-drying process. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100094. [PMID: 35415681 PMCID: PMC8991592 DOI: 10.1016/j.fochms.2022.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 11/20/2022]
Abstract
Shade-drying of cinnamon leaves makes great contribution to cinnamon oil production. Shade-drying process changed the composition of endophytic bacterial community in cinnamon leaves. The production of cinnamon oil and the evolution of endophytic bacterial community were positive correlated. Saccharopolyspora has application potential on the improvement of cinnamon oil content.
Cinnamon oil is a blend of secondary metabolites and is widely used as spice. Endophytic bacteria are always related to the secondary metabolites production. However, the potential of endophytic bacteria communities for cinnamon oil production during cinnamon shade-drying process is still not clear. In this study, we investigated the composition and metabolic function of endophytic bacterial community during 80-day shade-drying process. The temporal dynamics of essential oil content and its dominant constituents were analyzed. The succession of endophytic bacterial community from d0 to d80 was identified. The influence of endophytic bacterial community evolution on cinnamon oil is significant positive. Predictive functional analysis indicated that shade-drying process was rich in Saccharopolyspora that produce enzymes for the conversion of phenylalanine to cinnamaldehyde. These findings enhance our understanding of the functional bacterial genera and functional genes involved in the production of cinnamon oil during cinnamon shade-drying process.
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22
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Microbiological Aspects of Unique, Rare, and Unusual Fatty Acids Derived from Natural Amides and Their Pharmacological Profile. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13030030] [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 the proposed review, the pharmacological profile of unique, rare, and unusual fatty acids derived from natural amides is considered. These amides are produced by various microorganisms, lichens, and fungi. The biological activity of some natural fatty acid amides has been determined by their isolation from natural sources, but the biological activity of fatty acids has not been practically studied. According to QSAR data, the biological activity of fatty acids is shown, which demonstrated strong antifungal, antibacterial, antiviral, antineoplastic, anti-inflammatory activities. Moreover, some fatty acids have shown rare activities such as antidiabetic, anti-infective, anti-eczematic, antimutagenic, and anti-psoriatic activities. For some fatty acids that have pronounced biological properties, 3D graphs are shown that show a graphical representation of unique activities. These data are undoubtedly of both theoretical and practical interest for chemists, pharmacologists, as well as for the pharmaceutical industry, which is engaged in the synthesis of biologically active drugs.
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23
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Veyisoglu A, Tatar D, Saygin H, Cetin D, Guven K, Sahin N. Saccharopolyspora soli sp. nov., isolated from Northern Cyprus soil. Arch Microbiol 2022; 204:371. [PMID: 35670849 DOI: 10.1007/s00203-022-02994-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/02/2022]
Abstract
A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain K220T, was isolated from soil collected from Cape Andreas (Zafer Burnu), Northern Cyprus, and subjected to a polyphasic taxonomic approach. The organism was shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Saccharopolyspora. 16S rRNA gene sequence analysis of strain K220T showed that it is closely related to the type strains of Saccharopolyspora maritima 3SS5-12 T, Saccharopolyspora kobensis JCM 9109 T and Saccharopolyspora hirsuta ATCC 27875 T with 97.6, 97.5 and 97.0% sequence similarity, respectively. In silico DNA-DNA hybridization and average nucleotide identity values between strain K220T and type strains of the genus Saccharopolyspora with publicly available genomes were 22.1-31.2% and 76.0-83.16%, respectively. The DNA G + C content of strain K220T was 68.3 mol%. The genome of strain K220T has genes associated with 24 biosynthetic gene clusters. The strain contained MK-9(H4) and iso-C16: 0 as the predominant respiratory quinone and fatty acid, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine. Based on evidence collected from the genotypic, phenotypic and phylogenetic analyses, strain K220T is considered to represent a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora soli sp. nov. is proposed. The type strain is K220T (= JCM 33912T = KCTC 49395T).
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Affiliation(s)
- Aysel Veyisoglu
- Vocational School of Health Services, Department of Medical Laboratory Techniques, Sinop University, 57000, Sinop, Turkey.
| | - Demet Tatar
- Osmancık Ömer Derindere Vocational School, Department of Medical Services and Techniques, Hitit University, 19500, Çorum, Turkey
| | - Hayrettin Saygin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Demet Cetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi University, 06500, Ankara, Turkey
| | - Kiymet Guven
- Faculty of Science, Biology Department, Eskisehir Technical University, 26555, Eskişehir, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139, Samsun, Turkey
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24
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Gupta S, Li D, Ostrov DA, Nguyen CQ. Epitope Mapping of Pathogenic Autoantigens on Sjögren’s Syndrome-Susceptible Human Leukocyte Antigens Using In Silico Techniques. J Clin Med 2022; 11:jcm11061690. [PMID: 35330015 PMCID: PMC8953074 DOI: 10.3390/jcm11061690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/17/2022] Open
Abstract
Sjögren’s syndrome (SjS) is characterized by lymphocytic infiltration and the dysfunction of the salivary and lacrimal glands. The autoimmune response is driven by the effector T cells and their cytokines. The activation of the effector helper T cells is mediated by autoantigen presentation by human leukocyte antigen (HLA) class II molecules of antigen-presenting cells. Studies using familial aggregation, animal models, and genome-wide association demonstrate a significant genetic correlation between specific risk HLAs and SjS. One of the key HLA alleles is HLA-DRB1*0301; it is one of the most influential associations with primary SjS, having the highest odds ratio and occurrence across different ethnic groups. The specific autoantigens attributed to SjS remain elusive, especially the specific antigenic epitopes presented by HLA-DRB1*0301. This study applied a high throughput in silico mapping technique to identify antigenic epitopes of known SjS autoantigens presented by high-risk HLAs. Furthermore, we identified specific binding HLA-DRB1*0301 epitopes using structural modeling tools such as Immune Epitope Database and Analysis Resource IEDB, AutoDock Vina, and COOT. By deciphering the critical epitopes of autoantigens presented by HLA-DRB1*0301, we gain a better understanding of the origin of the antigens, determine the T cell receptor function, learn the mechanism of disease progression, and develop therapeutic applications.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA;
| | - Danmeng Li
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (D.L.); (D.A.O.)
| | - David A. Ostrov
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (D.L.); (D.A.O.)
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA;
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL 32611, USA
- Correspondence: ; Tel.: +1-352-294-4180; Fax: +1-352-392-9704
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25
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Zhang J, Liu S, Sun H, Jiang Z, Xu Y, Mao J, Qian B, Wang L, Mao J. Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu. Food Res Int 2022; 152:110707. [PMID: 35181108 DOI: 10.1016/j.foodres.2021.110707] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/13/2021] [Accepted: 09/05/2021] [Indexed: 12/11/2022]
Abstract
Daqu and wheat Qu are saccharification and fermenting agents in Chinese huangjiu and baijiu production. This study aimed to investigate the difference between Daqu and wheat Qu in physicochemical indices, microbial communities, functional genes, and the metabolic network of key microbes responsible for flavor synthesis by whole-metagenome sequencing and metabolite analysis. Herein, physicochemical indices indicated that compared with wheat Qu, Daqu exhibited higher protease and cellulase activity and acidity, and lower glucoamylase and amylase enzyme activity. Metagenomic sequencing reveals that although Daqu and wheat Qu community composition have significant differences at species level, they have similar functional genes. Daqu were enriched in Pediococcus pentosaceus, Weissella paramesenteroides, Rasamsonia emersonii and Byssochlamys spectabilis (22.48% of the total abundance), while wheat Qu harbored greater abundances of Saccharopolyspora (54.78%, Saccharopolyspora rectivirgula, Saccharopolyspora shandongensis, Saccharopolyspora hirsuta, Saccharopolyspora spinose, and Saccharopolyspora erythraea). From a functional perspective, the important functions of Daqu and wheat Qu are both amino acid metabolism and carbohydrate metabolism. Meanwhile, a combined analysis among microbiota, functional genes, and dominant flavors indicated S. shandongensis, S. rectivirgula, and S. spinose might be the main contributor to the synthesis of flavor compounds in wheat Qu, while R. emersonii, W. paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Weissella cibaria and P. pentosaceus may make the greatest contribution to flavor compounds synthesis in Daqu. This study reveals the microbial and functional dissimilarities of Daqu and wheat Qu, and helps elucidating different metabolic roles of microbes during flavor formation.
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Affiliation(s)
- Jing Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shuangping Liu
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 31200, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Hailong Sun
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengfei Jiang
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Jieqi Mao
- Department of Food Science and Technology, National University of Singapore, Science Drive 2, 117542, Singapore
| | - Bin Qian
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Lan Wang
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Jian Mao
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 31200, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China.
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26
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Li X, Ke X, Qiao L, Sui Y, Chu J. Comparative genomic and transcriptomic analysis guides to further enhance the biosynthesis of erythromycin by an overproducer. Biotechnol Bioeng 2022; 119:1624-1640. [PMID: 35150130 DOI: 10.1002/bit.28059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/12/2022]
Abstract
Omics approaches have been applied to understand the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from high-throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified fragment deletions inside 56 coding sequences and 255 single nucleotide polymorphisms over the genome of E3. A substantial number of genomic variations were observed in genes responsible for pathways which were interconnected to the biosynthesis of erythromycin by supplying precursors/cofactors or by signal transduction. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Through comparative transcriptomic analysis, L-glutamine/L-glutamate and 2-oxoglutarate were identified as reporter metabolites. Around the node of 2-oxoglutarate, genomic mutations were also observed. Based on the omics association analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 71% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhanced production of erythromycin by the overproducer. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Lijia Qiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Yufei Sui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
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27
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Saito S, Oku N, Igarashi Y. Mycetoindole, an N-acyl dehydrotryptophan with plant growth inhibitory activity from an actinomycete of the genus Actinomycetospora. J Antibiot (Tokyo) 2022; 75:44-47. [PMID: 34522026 DOI: 10.1038/s41429-021-00474-7] [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: 06/30/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/09/2022]
Abstract
A rare actinomycetal strain of the genus Actinomycetospora was found to produce a new tryptophan derivative, designated mycetoindole (1). The structure of 1 was determined to be N-3-methylcrotonoyl (Z)-dehydrotryptophan by NMR and MS analytical methods. Compound 1 reduced the root growth of lettuce Lactuca sativa seedlings at concentrations above 0.1 μM and almost completely inhibited seed germination at 10 μM.
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Affiliation(s)
- Shun Saito
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan.
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28
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Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov., Saccharopolyspora terrae sp. nov. and their biotechnological potential revealed by genome analysis. Syst Appl Microbiol 2021; 44:126270. [PMID: 34653842 DOI: 10.1016/j.syapm.2021.126270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022]
Abstract
Exploration of unexplored habitats for novel actinobacteria with high bioactivity potential holds great promise in the search for novel entities. During the course of isolation of actinobacteria from desert soils, four actinobacteria, designated as 5K548T, 7K502T, 16K309T and 16K404T, were isolated from the Karakum Desert and their bioactivity potential as well as taxonomic provenances were revealed by comprehensive genome analyses. Pairwise sequence analyses of the 16S rRNA genes indicated that the four strains are representatives of putatively novel taxa within the prolific actinobacterial genus Saccharopolyspora. The strains have typical chemotaxonomic characteristics of the genus Saccharopolyspora by having meso-diaminopimelic acid as diagnostic diaminoacid, arabinose, galactose and ribose as whole-cell sugars. Consistent with this assignment, all of the isolates contained phosphatidylcholine in their polar lipid profiles and MK-9(H4) as the predominant menaquinone. The sizes of the genomes of the isolates ranged from 6.0 to 10.2 Mb and the associated G + C contents from 69.6 to 69.7 %. Polyphasic characterizations including determination of overall genome relatedness indices revealed that the strains are representatives of four novel species in the genus Saccharopolyspora. Consequently, isolates 5K548T, 7K502T, 16K404T and 16K309T are proposed as novel Saccharopolyspora species for which the names of Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov. and Saccharopolyspora terrae sp. nov. are proposed, respectively. Comprehensive genome analysis for biosynthetic gene clusters showed that the strains have high potential for novel secondary metabolites. Moreover, the strains harbour many antimicrobial resistance genes providing more evidence for their potentiality for bioactive metabolites.
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29
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Peng J, Ma J, Wei X, Zhang C, Jia N, Wang X, Wang ET, Hu D, Wang Z. Accumulation of beneficial bacteria in the rhizosphere of maize (Zea mays L.) grown in a saline soil in responding to a consortium of plant growth promoting rhizobacteria. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01650-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Purpose
Salt stress reduces plant growth and is now becoming one of the most important factors restricting the agricultural productivity. Inoculation of plant growth-promoting rhizobacteria (PGPR) has been shown to confer plant tolerance against abiotic stress, but the detailed mechanisms of how this occurs remain unclear and the application effects in different reports are unstable. In order to obtain a favorite effect of PGPR inoculation and improve our knowledge about the related mechanism, we performed this study to analyze the mechanism of a PGPR consortium on improving the salt resistance of crops.
Methods
A region-specific (Saline land around Bohai Sea in China) PGPR consortium was selected that contains three strains (Pseudomonas sp. P8, Peribacillus sp. P10, and Streptomyces sp. X52) isolated from rhizosphere of Sonchus brachyotus DC. grown in a saline soil. By inoculation tests, their plant growth-promoting (PGP) traits and ability to improve the salt resistance of maize were investigated and shifting in rhizosphere bacterial community of the inoculated plants was analyzed using the high-throughput sequencing technology.
Results
The three selected strains were salt tolerant, presented several growth promoting properties, and inhibited several phytopathogenic fungi. The inoculation of this consortium promoted the growth of maize plant and enriched the beneficial bacteria in rhizosphere of maize in a saline soil, including the nitrogen fixing bacteria Azotobacter, Sinorhizobium, and Devosia, and the nitrification bacteria Candidatus Nitrososphaera, and Nitrosovibrio.
Conclusions
The bacterial consortium P8/P10/X52 could improve plant growth in a saline soil by both their PGP traits and regulating the rhizosphere bacterial community. The findings provided novel information about how the PGPR helped the plants in the view of microbiome.
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30
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Riahi HS, Heidarieh P, Fatahi-Bafghi M. Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology. J Appl Microbiol 2021; 132:890-906. [PMID: 34469043 DOI: 10.1111/jam.15271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.
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Affiliation(s)
- Hanieh Sadat Riahi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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31
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Ruiz-Villafán B, Cruz-Bautista R, Manzo-Ruiz M, Passari AK, Villarreal-Gómez K, Rodríguez-Sanoja R, Sánchez S. Carbon catabolite regulation of secondary metabolite formation, an old but not well-established regulatory system. Microb Biotechnol 2021; 15:1058-1072. [PMID: 33675560 PMCID: PMC8966007 DOI: 10.1111/1751-7915.13791] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/28/2022] Open
Abstract
Secondary microbial metabolites have various functions for the producer microorganisms, which allow them to interact and survive in adverse environments. In addition to these functions, other biological activities may have clinical relevance, as diverse as antimicrobial, anticancer and hypocholesterolaemic effects. These metabolites are usually formed during the idiophase of growth and have a wide diversity in their chemical structures. Their synthesis is under the impact of the type and concentration of the culture media nutrients. Some of the molecular mechanisms that affect the synthesis of secondary metabolites in bacteria (Gram‐positive and negative) and fungi are partially known. Moreover, all microorganisms have their peculiarities in the control mechanisms of carbon sources, even those belonging to the same genus. This regulatory knowledge is necessary to establish culture conditions and manipulation methods for genetic improvement and product fermentation. As the carbon source is one of the essential nutritional factors for antibiotic production, its study has been imperative both at the industrial and research levels. This review aims to draw the utmost recent advances performed to clarify the molecular mechanisms of the negative effect exerted by the carbon source on the secondary metabolite formation, emphasizing those found in Streptomyces, one of the genera most profitable antibiotic producers.
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Affiliation(s)
- Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Monserrat Manzo-Ruiz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Ajit Kumar Passari
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Karen Villarreal-Gómez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
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32
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Gamaleldin NM, Bakeer W, Sayed AM, Shamikh YI, El-Gendy AO, Hassan HM, Horn H, Abdelmohsen UR, Hozzein WN. Exploration of Chemical Diversity and Antitrypanosomal Activity of Some Red Sea-Derived Actinomycetes Using the OSMAC Approach Supported by LC-MS-Based Metabolomics and Molecular Modelling. Antibiotics (Basel) 2020; 9:E629. [PMID: 32971728 PMCID: PMC7558093 DOI: 10.3390/antibiotics9090629] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
In the present study, we investigated the actinomycetes associated with the Red Sea-derived soft coral Sarcophyton glaucum in terms of biological and chemical diversity. Three strains were cultivated and identified to be members of genera Micromonospora, Streptomyces, and Nocardiopsis; out of them, Micromonospora sp. UR17 was putatively characterized as a new species. In order to explore the chemical diversity of these actinobacteria as far as possible, they were subjected to a series of fermentation experiments under altering conditions, that is, solid and liquid fermentation along with co-fermentation with a mycolic acid-containing strain, namely Nocardia sp. UR23. Each treatment was found to affect these actinomycetes differently in terms of biological activity (i.e., antitrypanosomal activity) and chemical profiles evidenced by LC-HRES-MS-based metabolomics and multivariate analysis. Thereafter, orthogonal projections to latent structures discriminant analysis (OPLS-DA) suggested a number of metabolites to be associated with the antitrypanosomal activity of the active extracts. The subsequent in silico screenings (neural networking-based and docking-based) further supported the OPLS-DA results and prioritized desferrioxamine B (3), bafilomycin D (10), and bafilomycin A1 (11) as possible antitrypanosomal agents. Our approach in this study can be applied as a primary step in the exploration of bioactive natural products, particularly those from actinomycetes.
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Affiliation(s)
- Noha M. Gamaleldin
- Department of Microbiology, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo 11837, Egypt;
- Center for Drug Research and Development, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo 11837, Egypt
| | - Walid Bakeer
- Department of Microbiology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (W.B.); (A.O.E.-G.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
| | - Yara I. Shamikh
- Department of Microbiology & Immunology, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
- Virology Department, Egyptian Center for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Ahmed O. El-Gendy
- Department of Microbiology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (W.B.); (A.O.E.-G.)
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt;
| | - Hannes Horn
- Independent Researcher, 69126 Heidelberg, Germany;
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
| | - Wael N. Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62512, Egypt
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Hifnawy MS, Fouda MM, Sayed AM, Mohammed R, Hassan HM, AbouZid SF, Rateb ME, Keller A, Adamek M, Ziemert N, Abdelmohsen UR. The genus Micromonospora as a model microorganism for bioactive natural product discovery. RSC Adv 2020; 10:20939-20959. [PMID: 35517724 PMCID: PMC9054317 DOI: 10.1039/d0ra04025h] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 11/21/2022] Open
Abstract
This review covers the development of the genus Micromonospora as a model for natural product research and the timeline of discovery progress from the classical bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target specific products. It focuses on the reported chemical structures along with their biological activities and the synthetic and biosynthetic studies they have inspired. This survey summarizes the extraordinary biosynthetic diversity that can emerge from a widely distributed actinomycete genus and supports future efforts to explore under-explored species in the search for novel natural products. We explore the genus Micromonospora as a model for natural product research and the discovery progress from the classical bioassay-guided approaches through to the application of genome mining and genetic engineering techniques that target specific products.![]()
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