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Chinnadurai V, Govindasamy C. L-Asparaginase producing ability of Aspergillus species isolated from tapioca root soil and optimized ideal growth parameters for L-Asparaginase production. ENVIRONMENTAL RESEARCH 2024; 259:119543. [PMID: 38964574 DOI: 10.1016/j.envres.2024.119543] [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: 04/12/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
This research was designed to isolate the predominant L-asparaginase-producing fungus from rhizosphere soil of tapioca field and assess the suitable growth conditions required to produce maximum L-asparaginase activity. The Aspergillus tubingensis was identified as a predominant L-asparaginase producing fungal isolate from 15 isolates, and it was characterized by 18S rRNA sequencing. The L-asparaginase-producing activity was confirmed by pink color zone formation around the colonies in modified Czapek Dox agar plate supplemented with 1% L-Asparagine. The optimal growth conditions required for the L-asparaginase production by A. tubingensis were optimized as pH 6.0, temperature 30 °C, glucose as carbon source, 1.5% of L-Asparagine, ammonium sulphate as nitrogen source, rice husk as natural L-Asparagine enriched source, and 8 days of the incubation period. The L-Asparaginase activity from A. tubingensis was excellent under these optimal growth conditions. It significantly used rice husk as an alternative to synthetic L-Asparagine. As a result, this may be considered a sustainable method of converting organic waste into valuable raw material for microbial enzyme production.
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Affiliation(s)
- Vajjiram Chinnadurai
- Department of Botany, Sri Vidya Mandir Arts and Science (Autonomous), Katteri, Uthangarai, 636902, Krishnagiri, Tamil Nadu, India.
| | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh - 11433, Saudi Arabia
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Benyamini P. The Comparative Characterization of a Hypervirulent Acinetobacter baumannii Bacteremia Clinical Isolate Reveals a Novel Mechanism of Pathogenesis. Int J Mol Sci 2024; 25:9780. [PMID: 39337268 PMCID: PMC11432228 DOI: 10.3390/ijms25189780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen with exquisite survival capabilities under various environmental conditions and displays widespread resistance to common antibiotics. A. baumannii is a leading cause of nosocomial infections that result in high morbidity and mortality rates. Accordingly, when multidrug resistance rates surpass threshold levels, the percentage of A. baumannii clinical isolates surges. Research into A. baumannii has increased in the past decade, and multiple mechanisms of pathogenesis have been identified, including mechanisms underlying biofilm development, quorum sensing, exotoxin production, secretion system utilization, and more. To date, the two gold-standard strains used to investigate different aspects of A. baumannii pathogenesis include ATCC 17978 and ATCC 19606. Here, we report a comparative characterization study of three additional A. baumannii clinical isolates obtained from different infection types and derived from different anatomical regions of infected patients. The comparison of three clinical isolates in addition to the ATCC strains revealed that the hypervirulent bacteremia clinical isolate, known as HUMC1, employs a completely different mechanism of pathogenesis when compared to all its counterparts. In stark contrast to the other genetic variants, the hypervirulent HUMC1 isolate does not form biofilms, is antibiotic-susceptible, and has the capacity to reach higher levels of quorum compared to the other clinically relevant strains. Our data also reveal that HUMC1 does not shed endotoxin into the extracellular milieu, rather secretes the evolutionarily conserved, host-mimicking, Zonula occludens toxin (Zot). Taken together, our hypothesis that HUMC1 cells have the ability to reach higher levels of quorum and lack biofilm production and endotoxin shedding, accompanied by the substantial elaboration of Zot, suggests a novel mechanism of pathogenesis that appears to afford the hypervirulent pathogen with stealth-like capabilities when disseminating through the circulatory system in a state of bacteremia.
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Affiliation(s)
- Payam Benyamini
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
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3
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Diniz GDFD, Figueiredo JEF, Canuto KM, Cota LV, Souza ASDQ, Simeone MLF, Tinoco SMDS, Ribeiro PRV, Ferreira LVS, Marins MS, de Oliveira-Paiva CA, Dos Santos VL. Chemical and genetic characterization of lipopeptides from Bacillus velezensis and Paenibacillus ottowii with activity against Fusarium verticillioides. Front Microbiol 2024; 15:1443327. [PMID: 39252841 PMCID: PMC11381237 DOI: 10.3389/fmicb.2024.1443327] [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: 06/03/2024] [Accepted: 08/02/2024] [Indexed: 09/11/2024] Open
Abstract
Introduction The fungus Fusarium verticillioides significantly threatens maize crops in tropical soils. In light of this, biological control has emerged as a promising strategy to reduce fungicide costs and environmental risks. In this study, we aimed to test the antifungal activity of cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04) against F. verticillioides, thereby contributing to the development of effective biocontrol measures. Methods The research employed a comprehensive approach. The antifungal activity of the bacterial strains was tested using cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04). The UPLC-MS evaluated the CFS to identify the main bioactive molecules involved in the inhibitory effect on F. verticillioides. Scanning electron microscopy (SEM) was used to assess the impact of CFS on spores and hyphae, and genome sequencing was conducted to identify the genes involved in biological control. These robust methodologies ensure the reliability and validate our findings. Results The CFS of the four strains demonstrated significant inhibition of fungal growth. The UPLC-MS analysis revealed the presence of lipopeptides with antifungal activity, including surfactin and fengycins A and B expressed by the three strains of Bacillus velezensis and iturin A expressed by strains LIS05 and IM14. For Paenibacillus ottowii, fusaricidins, ABCDE, and five previously unreported lipopeptides were detected. Scanning electron microscopy (SEM) showed that treatments with CFS led to significant distortion and breakage of the F. verticillioides hyphae, in addition to the formation of cavities in the membrane. Genome mining confirmed the presence of genes coding for the lipopeptides identified by UPLC-MS, including the gene for iturin in CTO2. Genomic sequencing revealed that CT02, IM14, and LIS05 belong to different strains of Bacillus velezensis, and LIS04 belongs to Paenibacillus ottowii, a species recently described. Discussion The four bacterial strains, including three novel strains identified as Bacillus velezensis and one as the recently described species Paenibacillus ottowii, demonstrate significant potential as biocontrol agents for managing fungal disease. This finding underscores the novelty and potential impact of our research.
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Affiliation(s)
| | | | - Kirley Marques Canuto
- Multiuser Laboratory of Chemistry of Natural Products (LMQPN), Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | - Luciano Viana Cota
- Phytopathology Laboratory, Embrapa Maize and Sorghum, Sete Lagoas, MG, Brazil
| | - Ana Sheila de Queiroz Souza
- Multiuser Laboratory of Chemistry of Natural Products (LMQPN), Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | | | - Sylvia Morais de Sousa Tinoco
- Molecular Biology Laboratory, Embrapa Maize and Sorghum, Sete Lagoas, MG, Brazil
- Federal University of São João del-Rei, São João del Rei, MG, Brazil
| | | | | | - Mikaely Sousa Marins
- Department of Agricultural Microbiology, Federal University of Lavras, Lavras, MG, Brazil
| | | | - Vera Lúcia Dos Santos
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Zhao Y, Wang J, Xiao Q, Liu G, Li Y, Zha X, He Z, Kang J. New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes. Genomics 2024; 116:110925. [PMID: 39178998 DOI: 10.1016/j.ygeno.2024.110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.
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Affiliation(s)
- Yan Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Jiankang Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Qing Xiao
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Guihua Liu
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Yongjie Li
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xingping Zha
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Zhangjiang He
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
| | - Jichuan Kang
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
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Chunduru J, LaRoe N, Garza J, Hamood AN, Paré PW. Nosocomial Bacteria Inhibition with Polymyxin B: In Silico Gene Mining and In Vitro Analysis. Antibiotics (Basel) 2024; 13:745. [PMID: 39200045 PMCID: PMC11350920 DOI: 10.3390/antibiotics13080745] [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: 07/11/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/01/2024] Open
Abstract
Multidrug-resistant bacteria present a significant public health challenge; such pathogens exhibit reduced susceptibility to conventional antibiotics, limiting current treatment options. Cationic non-ribosomal peptides (CNRPs) such as brevicidine and polymyxins have emerged as promising candidates to block Gram-negative bacteria. To investigate the capability of bacteria to biosynthesize CNRPs, and specifically polymyxins, over 11,000 bacterial genomes were mined in silico. Paenibacillus polymyxa was identified as having a robust biosynthetic capacity, based on multiple polymyxin gene clusters. P. polymyxa biosynthetic competence was confirmed by metabolite characterization via HPLC purification and MALDI TOF/TOF analysis. When grown in a selected medium, the metabolite yield was 4 mg/L with a 20-fold specific activity increase. Polymyxin B (PMB) was assayed with select nosocomial pathogens, including Pseudomonas aeruginosa, Klebsiella pneumonia, and Acinetobacter baumaii, which exhibited minimum inhibitory concentrations of 4, 1, and 1 µg/mL, respectively.
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Affiliation(s)
- Jayendra Chunduru
- Chemistry & Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Nicholas LaRoe
- Chemistry & Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
| | - Jeremy Garza
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA (A.N.H.)
| | - Abdul N. Hamood
- Department of Immunology & Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA (A.N.H.)
| | - Paul W. Paré
- Chemistry & Biochemistry Department, Texas Tech University, Lubbock, TX 79409, USA
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Li W, Fu Y, Jiang Y, Hu J, Wei Y, Li H, Li J, Yang H, Wu Y. Synergistic Biocontrol and Growth Promotion in Strawberries by Co-Cultured Trichoderma harzianum TW21990 and Burkholderia vietnamiensis B418. J Fungi (Basel) 2024; 10:551. [PMID: 39194877 DOI: 10.3390/jof10080551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
This study aimed to investigate the efficiency of the secondary metabolites (SMs) produced by a co-culture of Trichoderma harzianum TW21990 and Burkholderia vietnamiensis B418 in the control of Colletotrichum siamense CM9. A fermentation filtrate of B418 + TW21990 co-culture (BT21) produced a notable increase in the inhibition rate of CM9 compared to those of TW21990 and B418 monocultures, which reached 91.40% and 80.46% on PDA plates and strawberry leaves, respectively. The BT21 fermentation broth exhibited high control efficiency on strawberry root rot of 68.95% in a pot experiment, which was higher than that in the monocultures and fluazinam treatment. In addition, BT21 treatment promoted strawberry root development, improved antioxidative enzyme activities in the leaves and roots, and enhanced the total chlorophyll content of the strawberry leaves. UHPLC-MS/MS analysis of fermentation filtrates was performed to elucidate SM variations, revealing 478 and 795 metabolites in BT21 co-culture in positive and negative ion modes, respectively. The metabolomic profiles suggested abundant SMs with antagonistic capabilities and growth-promoting effects: 3-(propan-2-yl)-octahydropyrrolo [1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Val)), 3-[(4-hydroxyphenyl)methyl]-octahydropyrrolo[1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Tyr)), 3-indoleacetic acid (IAA), 2-hydroxycinnamic acid, 4-aminobutyric acid (GABA), bafilomycin B1, and DL-indole-3-lactic acid (ILA) were significantly enhanced in the co-culture. Overall, this study demonstrates that a co-culture strategy is efficient for inducing bioactive SMs in T. harzianum and B. vietnamiensis, which could be exploited as a novel approach for developing biocontrol consortia.
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Affiliation(s)
- Wenzhe Li
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Yiting Fu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Yanqing Jiang
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Hongmei Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
| | - Yuanzheng Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250103, China
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Krysenko S, Wohlleben W. Role of Carbon, Nitrogen, Phosphate and Sulfur Metabolism in Secondary Metabolism Precursor Supply in Streptomyces spp. Microorganisms 2024; 12:1571. [PMID: 39203413 PMCID: PMC11356490 DOI: 10.3390/microorganisms12081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds.
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Affiliation(s)
- Sergii Krysenko
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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Mazumdar R, Thakur D. Antibacterial activity and biosynthetic potential of Streptomyces sp. PBR19, isolated from forest rhizosphere soil of Assam. Braz J Microbiol 2024:10.1007/s42770-024-01454-3. [PMID: 38985434 DOI: 10.1007/s42770-024-01454-3] [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: 03/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
An Actinomycetia isolate, designated as PBR19, was derived from the rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate, identified as Streptomyces sp., shares a sequence similarity of 93.96% with its nearest type strain, Streptomyces atrovirens. This finding indicates the potential classification of PBR19 as a new taxon within the Actinomycetota phylum. PBR19 displayed notable antibacterial action against some ESKAPE pathogens. The ethyl acetate extract of PBR19 (EtAc-PBR19) showed the lowest minimum inhibitory concentration (MIC) of ≥ 0.195 µg/mL against Acinetobacter baumannii ATCC BAA-1705. A lower MIC indicates higher potency against the tested pathogen. Scanning electron microscope (SEM) findings revealed significant changes in the cytoplasmic membrane structure of the pathogen. This suggests that the antibacterial activity may be linked to the disruption of the microbial membrane. The predominant chemical compound detected in the EtAc-PBR19 was identified as phenol, 3,5-bis(1,1-dimethylethyl), comprising 48.59% of the area percentage. Additionally, PBR19 was found to contain the type II polyketide synthases (PKS type II) gene associated with antibiotic synthesis. The predicted gene product of PKSII was identified as the macrolide antibiotic Megalomicin A. The taxonomic distinctiveness, potent antibacterial effects, and the presence of a gene associated with antibiotic synthesis suggest that PBR19 could be a valuable candidate for further exploration in drug development and synthetic biology. The study contributes to the broader understanding of microbial diversity and the potential for discovering bioactive compounds in less-explored environments.
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Affiliation(s)
- Rajkumari Mazumdar
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Debajit Thakur
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India.
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Boukouvala S, Kontomina E, Olbasalis I, Patriarcheas D, Tzimotoudis D, Arvaniti K, Manolias A, Tsatiri MA, Basdani D, Zekkas S. Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism. Sci Rep 2024; 14:14905. [PMID: 38942826 PMCID: PMC11213898 DOI: 10.1038/s41598-024-65342-4] [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: 01/14/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.
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Affiliation(s)
- Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece.
| | - Evanthia Kontomina
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Ioannis Olbasalis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dionysios Patriarcheas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimosthenis Tzimotoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Konstantina Arvaniti
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Aggelos Manolias
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Maria-Aggeliki Tsatiri
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimitra Basdani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Sokratis Zekkas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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Peng T, Guo J, Tong X. Advances in biosynthesis and metabolic engineering strategies of cordycepin. Front Microbiol 2024; 15:1386855. [PMID: 38903790 PMCID: PMC11188397 DOI: 10.3389/fmicb.2024.1386855] [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: 02/16/2024] [Accepted: 04/26/2024] [Indexed: 06/22/2024] Open
Abstract
Cordyceps militaris, also called as bei-chong-cao, is an insect-pathogenic fungus from the Ascomycota phylum and the Clavicipitaceae family. It is a valuable filamentous fungus with medicinal and edible properties that has been utilized in traditional Chinese medicine (TCM) and as a nutritious food. Cordycepin is the bioactive compound firstly isolated from C. militaris and has a variety of nutraceutical and health-promoting properties, making it widely employed in nutraceutical and pharmaceutical fields. Due to the low composition and paucity of wild resources, its availability from natural sources is limited. With the elucidation of the cordycepin biosynthetic pathway and the advent of synthetic biology, a green cordycepin biosynthesis in Saccharomyces cerevisiae and Metarhizium robertsii has been developed, indicating a potential sustainable production method of cordycepin. Given that, this review primarily focused on the metabolic engineering and heterologous biosynthesis strategies of cordycepin.
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Affiliation(s)
| | - Jinlin Guo
- The Ministry of Education Key Laboratory of Standardization of Chinese Medicine, Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China, Resources Breeding Base of Co-Founded, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinxin Tong
- The Ministry of Education Key Laboratory of Standardization of Chinese Medicine, Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China, Resources Breeding Base of Co-Founded, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Khunnonkwao P, Thitiprasert S, Jaiaue P, Khumrangsee K, Cheirsilp B, Thongchul N. The outlooks and key challenges in renewable biomass feedstock utilization for value-added platform chemical via bioprocesses. Heliyon 2024; 10:e30830. [PMID: 38770303 PMCID: PMC11103475 DOI: 10.1016/j.heliyon.2024.e30830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
The conversion of renewable biomass feedstock into value-added products via bioprocessing platforms has become attractive because of environmental and health concerns. Process performance and cost competitiveness are major factors in the bioprocess design to produce desirable products from biomass feedstock. Proper pretreatment allows delignification and hemicellulose removal from the liquid fraction, allowing cellulose to be readily hydrolyzed to monomeric sugars. Several industrial products are produced via sugar fermentation using either naturally isolated or genetically modified microbes. Microbial platforms play an important role in the synthesis of several products, including drop-in chemicals, as-in products, and novel compounds. The key elements in developing a fermentation platform are medium formulation, sterilization, and active cells for inoculation. Downstream bioproduct recovery may seem like a straightforward chemical process, but is more complex, wherein cost competitiveness versus recovery performance becomes a challenge. This review summarizes the prospects for utilizing renewable biomass for bioprocessing.
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Affiliation(s)
- Panwana Khunnonkwao
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Sitanan Thitiprasert
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Phetcharat Jaiaue
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Katsaya Khumrangsee
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
| | - Benjamas Cheirsilp
- Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Nuttha Thongchul
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand
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Tlou M, Ndou B, Mabona N, Khwathisi A, Ateba C, Madala N, Serepa-Dlamini MH. Next generation sequencing-aided screening, isolation, molecular identification, and antimicrobial potential for bacterial endophytes from the medicinal plant, Elephantorrhiza elephantina. Front Microbiol 2024; 15:1383854. [PMID: 38855763 PMCID: PMC11160484 DOI: 10.3389/fmicb.2024.1383854] [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: 02/08/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Elephantorrhiza elephantina, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African Plants. To date, there have been no reports on bacterial endophytes from this plant, their classes of secondary metabolites, and potential medicinal properties. This study presents (i) taxonomic characterization of bacterial endophytes in leaf and root tissues using 16S rRNA, (ii) bacterial isolation, morphological, and phylogenetic characterization, (iii) bacterial growth, metabolite extraction, and LC-MS-based metabolite fingerprinting, and (iv) antimicrobial testing of bacterial crude extracts. Next-generation sequencing yielded 693 and 2,459 DNA read counts for the rhizomes and leaves, respectively, detecting phyla including Proteobacteria, Bacteroidota, Gemmatimonadota, Actinobacteriota, Verrucomicrobiota, Dependentiae, Firmicutes, and Armatimonodata. At the genus level, Novosphingobium, Mesorhizobium, Methylobacterium, and Ralstonia were the most dominant in both leaves and rhizomes. From root tissues, four bacterial isolates were selected, and 16S rRNA-based phylogenetic characterization identified two closely related Pseudomonas sp. (strain BNWU4 and 5), Microbacterium oxydans BNWU2, and Stenotrophomonas maltophilia BNWU1. The ethyl acetate:chloroform (1:1 v/v) organic extract from each isolate exhibited antimicrobial activity against all selected bacterial pathogens. Strain BNWU5 displayed the highest activity, with minimum inhibitory concentrations ranging from 62.5 μg/mL to 250 μg/mL against diarrhoeagenic Escherichia coli, Escherichia coli O157:H7, Salmonella enterica, antibiotic-resistant Vibrio cholerae, Staphylococcus aureus, Bacillus cereus, and Enterococcus durans. LC-MS analysis of the crude extract revealed common antimicrobial metabolites produced by all isolates, including Phenoxomethylpenicilloyl (penicilloyl V), cis-11-Eicosenamide, 3-Hydroxy-3-phenacyloxindole, and 9-Octadecenamide.
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Affiliation(s)
- Matsobane Tlou
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Benedict Ndou
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Nokufa Mabona
- Department of Biochemistry, School of Physical and Chemical Sciences, North-West University, Mmabatho, South Africa
| | - Adivhaho Khwathisi
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Collins Ateba
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, School of Biological Sciences, North-West University, Mmabatho, South Africa
| | - Ntakadzeni Madala
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, Johannesburg, South Africa
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Shatri AMN. Biochemical characterization of actinomycete from Namibia rocky crest mountainous soil and analyzing their bioactive metabolites for antagonistic effect against human respiratory pathogens. Pan Afr Med J 2024; 48:12. [PMID: 39184844 PMCID: PMC11343499 DOI: 10.11604/pamj.2024.48.12.33596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/20/2023] [Indexed: 08/27/2024] Open
Abstract
Introduction the present study aimed at isolating and characterizing actinomycete from unexplored Windhoek rocky crest mountainous soil and extracting bioactive metabolites as possible therapeutics against common life-threatening Streptococcus pneumonia (S. pneumonia) and Stachybotrys chartarum (S. chartarum). Methods chemotaxonomy and biochemical methods were used to identify the isolates. The solvent extraction method was used to extract bioactive compounds. Agar overlay and disc diffusion methods were used to determine the antimicrobial activity of isolates and extracted bioactive metabolites against S. pneumonia and S. chartarum. The antioxidant activity of the extracted bioactive metabolites was determined using 2.2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method with ascorbic acid as a positive control. Comparison between groups was done using a Two-way ANOVA, followed by Bonferroni post-test. Results three distinct isolates from 3 soil samples were identified on starch casein agar and distinguished using biochemical tests. All three isolates showed strong inhibitory activity against S. pneumonia with average growth inhibition zones between 18.0±1.00 and 27±0.00 mm p< 0.005. All isolates showed potent inhibitory activity against S. chartarum with the average inhibition zones ranging between 42.0±1.00 and 48±0.00 mm, p< 0.005. The chloroform extracts showed potent DPPH activity of up to 73± 1.41%. Conclusion growth conditions and extraction solvents can influence the antimicrobial and antioxidant properties of bioactive metabolites.
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Affiliation(s)
- Albertina Mariina Ndinelao Shatri
- Department of Human, Biological and Translational Medical Sciences, University of Namibia, Private Bag 13301, Mandume Ndemufayo Avenue, Pionierspark, Windhoek, Namibia
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Gonzales M, Jacquet P, Gaucher F, Chabrière É, Plener L, Daudé D. AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria. JOURNAL OF NATURAL PRODUCTS 2024; 87:1268-1284. [PMID: 38390739 DOI: 10.1021/acs.jnatprod.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.
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Affiliation(s)
- Mélanie Gonzales
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
- Gene&GreenTK, Marseille 13005, France
| | | | | | - Éric Chabrière
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
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16
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Sahoo A, Dwivedi K, Almalki WH, Mandal AK, Alhamyani A, Afzal O, Alfawaz Altamimi AS, Alruwaili NK, Yadav PK, Barkat MA, Singh T, Rahman M. Secondary metabolites in topical infectious diseases and nanomedicine applications. Nanomedicine (Lond) 2024; 19:1191-1215. [PMID: 38651634 PMCID: PMC11418228 DOI: 10.2217/nnm-2024-0017] [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: 01/20/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Topical infection affects nearly one-third of the world's population; it may result from poor sanitation, hygienic conditions and crowded living and working conditions that accelerate the spread of topical infectious diseases. The problems associated with the anti-infective agents are drug resistance and long-term therapy. Secondary metabolites are obtained from plants, microorganisms and animals, but they are metabolized inside the human body. The integration of nanotechnology into secondary metabolites is gaining attention due to their interaction at the subatomic and skin-tissue levels. Hydrogel, liposomes, lipidic nanoparticles, polymeric nanoparticles and metallic nanoparticles are the most suitable carriers for secondary metabolite delivery. Therefore, the present review article extensively discusses the topical applications of nanomedicines for the effective delivery of secondary metabolites.
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Affiliation(s)
- Ankit Sahoo
- College of Pharmacy, J.S. University, Shikohabad, Firozabad, Utta Pradesh, 283135, India
| | - Khusbu Dwivedi
- Department of Pharmaceutics, Shambhunath Institute of Pharmacy, Jhalwa, Prayagraj, 211015, Uttar Pradesh, India
| | - Waleed H Almalki
- Department of Pharmacology & Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ashok Kumar Mandal
- Department of Pharmacology, Faculty of Medicine, University Malaya, Kuala Lumpur, 50603, Malaysia
| | - Abdurrahman Alhamyani
- Pharmaceuticals Chemistry Department, Faculty of Clinical Pharmacy, Al-Baha University, Alaqiq, 65779-7738, Saudi Arabia
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | | | - Nabil K Alruwaili
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakakah, Saudi Arabia
| | - Pradip Kumar Yadav
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Md Abul Barkat
- Department of Pharmaceutics, College of Pharmacy, University of Hafr Al Batin, Al-Batin, 39524, Saudi Arabia
| | - Tanuja Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India
| | - Mahfoozur Rahman
- Department of Pharmaceutical Sciences, Shalom Institute of Health & Allied Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad, 211007, Uttar Pradesh, India
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Tao C, Wang Q, Ji J, Zhou Z, Yue B, Zhang R, Jiang S, Yuan T. Utilization of carbon catabolite repression for efficiently biotransformation of anthraquinone O-glucuronides by Streptomyces coeruleorubidus DM. Front Microbiol 2024; 15:1393073. [PMID: 38690368 PMCID: PMC11058961 DOI: 10.3389/fmicb.2024.1393073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Carbon catabolite repression (CCR) is a highly conserved mechanism that regulates carbon source utilization in Streptomyces. CCR has a negative impact on secondary metabolite fermentation, both in industrial and research settings. In this study, CCR was observed in the daunorubicin (DNR)-producing strain Streptomyces coeruleorubidus DM, which was cultivated in high concentration of carbohydrates. Unexpectedly, DM exhibited a high ability for anthraquinone glucuronidation biotransformation under CCR conditions with a maximum bioconversion rate of 95% achieved at pH 6, 30°C for 24 h. The co-utilization of glucose and sucrose resulted in the highest biotransformation rate compared to other carbon source combinations. Three novel anthraquinone glucuronides were obtained, with purpurin-O-glucuronide showing significantly improved water solubility, antioxidant activity, and antibacterial bioactivity. Comparative transcript analysis revealed that glucose and sucrose utilization were significantly upregulated as DM cultivated under CCR condition, which strongly enhance the biosynthetic pathway of the precursors Uridine diphosphate glucuronic acid (UDPGA). Meanwhile, the carbon metabolic flux has significantly enhanced the fatty acid biosynthesis, the exhaust of acetyl coenzyme A may lead to the complete repression of the biosynthesis of DNR, Additionally, the efflux transporter genes were simultaneously downregulated, which may contribute to the anthraquinones intracellular glucuronidation. Overall, our findings demonstrate that utilizing CCR can be a valuable strategy for enhancing the biotransformation efficiency of anthraquinone O-glucuronides by DM. This approach has the potential to improve the bioavailability and therapeutic potential of these compounds, opening up new possibilities for their pharmaceutical applications.
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Affiliation(s)
- Chen Tao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Quyi Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junyang Ji
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ziyue Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bingjie Yue
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ran Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medical Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tianjie Yuan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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Rampelli S, Gallois S, D’Amico F, Turroni S, Fabbrini M, Scicchitano D, Candela M, Henry A. The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. iScience 2024; 27:109211. [PMID: 38433907 PMCID: PMC10904984 DOI: 10.1016/j.isci.2024.109211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Sandrine Gallois
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
- Institute of Environmental Science and Technology, ST, 08193 Bellaterra, Spain
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Amanda Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
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19
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Hye Baek J, Min Han D, Gyu Choi D, Ok Jeon C. Unraveling the carbohydrate metabolic characteristics of Leuconostoc mesenteroides J18 through metabolite and transcriptome analyses. Food Chem 2024; 435:137594. [PMID: 37804726 DOI: 10.1016/j.foodchem.2023.137594] [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: 04/09/2023] [Revised: 07/27/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023]
Abstract
The metabolic characteristics of Leuconostoc mesenteroides subsp. mesenteroides J18, which is mainly responsible for kimchi fermentation, on various carbon sources were investigated through carbon utilization, metabolite, and transcriptome analyses at different culture conditions (10 and 30 °C with/without 2.5% NaCl). The metabolic features of strain J18 were relatively similar across the four culture conditions. However, the metabolic characteristics of strain J18 showed significant variations depending on the carbon source. These distinct metabolic traits of strain J18 on various carbon sources were validated through transcriptomic analyses and the reconstruction of metabolic pathways. The transcriptional expression of the metabolic pathways in response to each carbon source consistently correlated with the production profiles of metabolites, including ethanol, acetoin, diacetyl, and riboflavin, in each carbon source. Our findings suggests that the abundance of Leu. mesenteroides during fermentation and the taste and flavor of fermented food products can be controlled by altering the carbon sources.
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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20
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B S A, Suresh V, S M, Sivaperumal P. Isolation of Secondary Metabolites From Marine Actinobacterium of Microbispora sp.T3S11 and Their Antibacterial Activities. Cureus 2024; 16:e56680. [PMID: 38646316 PMCID: PMC11032500 DOI: 10.7759/cureus.56680] [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: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction Marine actinobacteria are promising sources of novel bioactive compounds due to their distinct ecological niches and diverse secondary metabolite production capabilities. Among these, Microbispora sp. T3S11 is notable for its unique spore chain structure, which allows for both morphological and genetic identification. Despite its potential, little is understood about the secondary metabolites produced by this strain. In this study, we hope to fill this gap by extracting and analyzing the antibacterial activities of secondary metabolites from Microbispora sp. T3S11, which will be the first time its bioactive compound profile is investigated. Aim To evaluate the antibacterial activity of secondary metabolites isolated from the marine actinobacterium Microbispora sp. T3S11. Materials and methods The antibacterial assays were carried out on agar plates containing the appropriate media for each pathogen. Sterile filter paper disks were impregnated with secondary metabolites extracted from Microbispora sp. T3S11 and placed on the surface of agar plates inoculated with the appropriate pathogens. Similarly, disks containing tetracycline were used as a positive control. The plates were then incubated at the appropriate temperature for each pathogen, and the zones of inhibition around the disks were measured to determine the extracted metabolites' antibacterial activity. Result Secondary metabolites had antimicrobial activity against Streptococcus mutans, Klebsiella pneumonia, and methicillin-resistant Staphylococcus aureus (MRSA). The inhibition of S. mutans was 7.5 mm and 8.5 mm at 75 μg/mL and 100 μg/mL, respectively. Klebsiella pneumonia zones measured 7 mm and 7.5 mm, while MRSA zones measured 7.6 mm and 8.5 mm at the same concentrations. Tetracycline, the standard antibiotic, had larger inhibition zones: 22 mm for S. mutans and Klebsiella pneumonia and 16 mm for MRSA, indicating variable susceptibility. Conclusion We conclude that the secondary metabolites extracted from Microbispora sp. T3S11 exhibits high antibacterial activity. This could be attributed to the presence of various active compounds.
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Affiliation(s)
- Aardra B S
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vasugi Suresh
- Medical Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Menaka S
- Medical Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Pitchiah Sivaperumal
- Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, chennai, IND
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21
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Liu S, Zhang K, Yu Y, Lian X, Jiang L, Meng F, Wang Y, Zhu X, Duan Y. Influence of medium modifications (optimization) on high nematicidal activity of the fermentation broth of Clostridium beijerinckii. Front Bioeng Biotechnol 2024; 11:1283112. [PMID: 38239919 PMCID: PMC10795176 DOI: 10.3389/fbioe.2023.1283112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction: The nematode species Meloidogyne incognita has been responsible for significant financial losses within the agricultural sector. Nematophagous bacteria, characterised by their extensive distribution and broad spectrum of hosts, exhibit remarkable efficacy as natural antagonists against nematodes. Sneb518 (Clostridium beijerinckii) fermentation broth displayed substantial biocontrol activity against M. incognita in previous research. Optimizing fermentation conditions is a fundamental technique for dramatically enhancing end product performance. There has been no such study conducted yet on enhancing the nematicidal activities of Sneb518 (Clostridium beijerinckii) fermentation using response surface methodology (RSM). Methods: The influence of strain Sneb518 fermentation media and conditions on nematicidal activity was examined using the three-factor technique and a Plackett-Burman design, and the interaction between various fermentation factors was examined using a Box-Behnken design. The present study employed response surface methodology (RSM) to examine and enhance the nematicidal activity of Sneb518 culture filtrates by identifying and optimising the influential components. Results: Glucose, peanut cake flour, and potassium chloride as carbon, nitrogen, and inorganic salts displayed considerably increased nematicidal potential in the present study. Furthermore, the corrected mortality of J2 ranged from 52.24% to 91.15% when utilizing the Box-Behnken design. These findings clearly support the application of RSM for medium optimization. Moreover, the outcomes of the validation experiment corresponded to the model predictions. Discussion: This research has enhanced the biocontrol ability of C. beijerinckii to control M. incognita and this research has led to the advancement of new biocontrol agents.
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Affiliation(s)
- Shuang Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Kejun Zhang
- Tianjin Vocational College of Bioengineering, Tianjin, China
| | - Yun Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xinglong Lian
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Lanyuwen Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Fanqi Meng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang, China
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22
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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23
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Zhou L, Wang Q, Shen J, Li Y, Zhang H, Zhang X, Yang S, Jiang Z, Wang M, Li J, Wang Y, Liu H, Zhou Z. Metabolic engineering of glycolysis in Escherichia coli for efficient production of patchoulol and τ-cadinol. BIORESOURCE TECHNOLOGY 2024; 391:130004. [PMID: 37952591 DOI: 10.1016/j.biortech.2023.130004] [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: 10/09/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Glucose metabolism suppresses the microbial synthesis of sesquiterpenes with a syndrome of "too much of a good thing can be bad". Here, patchoulol production in Escherichia coli was increased 2.02 times by engineering patchoulol synthase to obtain an initial strain. Knocking out the synthetic pathway for cyclic adenosine monophosphate relieved glucose repression and improved patchoulol titer and yield by 27.7 % and 43.1 %, respectively. A glycolysis regulation device mediated by pyruvate sensing was constructed which effectively alleviated overflow metabolism in a high-glucose environment with 10.2 % greater patchoulol titer in strain 070QA. Without fine-tuning the glucose-feeding rate, patchoulol titer further increased to 1675.1 mg/L in a 5-L bioreactor experiment, which was the highest level reported in E. coli. Using strain 070QA as a chassis, the τ-cadinol titer reached 15.2 g/L, representing the first report for microbial production of τ-cadinol. These findings will aid in the industrial production of sesquiterpene.
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Affiliation(s)
- Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Qin Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Jiawen Shen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Yunyan Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Hui Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Xinrui Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Shiyi Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Ziyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Mengxuan Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Jun Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Yuxi Wang
- Food Micro-manufacturing Engineering and Safety Research Laboratory, Department of Food Science and Nutrition, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, People's Republic of China
| | - Haili Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China.
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24
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Yusuf D, Kholifaturrohmah R, Nurcholis M, Setiarto RHB, Anggadhania L, Sulistiani. Potential of White Jack Bean ( Canavalia ensiformis L. DC) Kefir as a Microencapsulated Antioxidant. Prev Nutr Food Sci 2023; 28:453-462. [PMID: 38188079 PMCID: PMC10764231 DOI: 10.3746/pnf.2023.28.4.453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024] Open
Abstract
Oxidative stress plays a major role in the pathogenesis and progression of noncommunicable diseases. Kefir is a fermented food that has been reported to repress oxidative stress. This study aimed to assess the antioxidant activity, bioactive composition, and encapsulation efficiency of white jack bean (WJB) kefir. The following procedures were conducted: WJB was prepared and converted into juice using water solvent. The sterilized WJB juice was then fermented with kefir grain (10%) for 24∼72 h. Every 24 h, the kefir was evaluated for antioxidant activity, and the dominant bioactive component suspected to be the source of the antioxidant activity was identified. The final stage was the encapsulation process. WJB kefir showed high antioxidant activity, inhibiting DPPH radicals by 90.51±4.73% and ABTS radicals by 86.63±2.34% after 72 h of fermentation. WJB kefir contained 0.35±0.01 mg GAE/g total phenolics and 0.08 mg/g total flavonoids. The LC/MS identification suggested that the bioactive antioxidant components of the WJB kefir were from the alkaloid, saponin, phenolic, and flavonoid groups. The encapsulation with maltodextrin using freeze drying resulted in microencapsulation of WJB kefir with a particle size of 6.42±0.13 μm. The encapsulation efficiency was 79.61%, and the IC50 value was 32.62 ppm. The encapsulation method was able to maintain the antioxidant stability of the kefir and extend its shelf life. WJB kefir, a nondairy, lactose-free kefir, can be used as an antioxidant functional food.
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Affiliation(s)
- Dandy Yusuf
- Research Center for Applied Microbiology, National Research and Innovation Agency the Republic of Indonesia, Cibinong 16911, Indonesia
- Research Collaboration Center for Traditional Fermentation, Surakarta 57126, Indonesia
| | - Risa Kholifaturrohmah
- Department of Food Science and Biotechnology, Faculty of Agricultural Technology, Brawijaya University, Malang 65145, Indonesia
| | - Mochamad Nurcholis
- Department of Food Science and Biotechnology, Faculty of Agricultural Technology, Brawijaya University, Malang 65145, Indonesia
| | - R. Haryo Bimo Setiarto
- Research Center for Applied Microbiology, National Research and Innovation Agency the Republic of Indonesia, Cibinong 16911, Indonesia
- Research Collaboration Center for Traditional Fermentation, Surakarta 57126, Indonesia
| | - Lutfi Anggadhania
- Research Center for Applied Microbiology, National Research and Innovation Agency the Republic of Indonesia, Cibinong 16911, Indonesia
| | - Sulistiani
- Research Center for Applied Microbiology, National Research and Innovation Agency the Republic of Indonesia, Cibinong 16911, Indonesia
- Research Collaboration Center for Traditional Fermentation, Surakarta 57126, Indonesia
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25
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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26
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Radjasa OK, Steven R, Humaira Z, Dwivany FM, Nugrahapraja H, Trinugroho JP, Kristianti T, Chahyadi A, Natanael Y, Priharto N, Kamarisima, Sembiring FAPB, Dwijayanti A, Kusmita L, Moeis MR, Suhardi VSH. Biosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites. Sci Rep 2023; 13:19273. [PMID: 37935710 PMCID: PMC10630419 DOI: 10.1038/s41598-023-44603-8] [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: 02/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.
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Affiliation(s)
- Ocky Karna Radjasa
- Research Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation Agency, Jakarta, 14430, Indonesia.
| | - Ray Steven
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Zalfa Humaira
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Fenny Martha Dwivany
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia.
| | - Husna Nugrahapraja
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Joko Pebrianto Trinugroho
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Tati Kristianti
- Institut Pendidikan Indonesia, Garut, West Java, 44151, Indonesia
| | - Agus Chahyadi
- University Center of Excellence for Nutraceuticals, Bioscience and Biotechnology Research Center, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Yosua Natanael
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Neil Priharto
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Kamarisima
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | | | - Ari Dwijayanti
- CNRS@CREATE Ltd., 1 Create Way, #08-01 Create Tower, Singapore, 138602, Singapore
| | - Lia Kusmita
- STIFAR Yayasan Pharmasi Semarang, Semarang, Central Java, 50124, Indonesia
| | - Maelita R Moeis
- Department of Biotechnology, Faculty of Science and Technology, Universitas Muhammadiyah Bandung, Bandung, West Java, 40262, Indonesia
| | - V Sri Harjati Suhardi
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
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27
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Mazucato VDS, Vieira PC. Exploring the chemical diversity of phytopathogenic fungi infecting edible fruits. Nat Prod Res 2023; 37:3947-3955. [PMID: 36597649 DOI: 10.1080/14786419.2022.2163482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
Two fungi, Fusarium guttiforme and Colletotrichum horii, were cultured under different conditions to obtain fourteen compounds. The axenic cultures of F. guttiforme and C. horii in potato dextrose broth (PDB) medium yielded fusaric acid (1), 9,10-dehydrofusaric acid (2), and tyrosol, whereas their co-cultivation produced fusarinol (5), a fusaric acid complex with magnesium (3), 9,10-dehydrofusaric acid complex with magnesium (4), and 5-butyl-5-(hydroxymethyl) dihydrofuranone (9). Upon changing the medium from PDB to Czapek, different compounds (uracil, p-hydroxy acetophenone, and cyclo(L-Leu-L-Pro) were obtained. Fusaric acid (1) was biotransformed into fusarinol (5) by C. horii, suggesting a detoxification process, and three other compounds were obtained: 7-hydroxyfusarinol (7), 9,10-dehydrofusarinol (6), and fusarinyl acetate (8). Epigenetic modulation of suberohydroxamic acid against F. guttiforme afforded gibepyrone B (10). These compounds were subjected to a papain inhibition enzymatic assay; the highest inhibitory activity was displayed by the two magnesium complexes, at 56 and 54% inhibition, respectively.
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Affiliation(s)
- Vitor de S Mazucato
- Departament of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Paulo C Vieira
- Departament of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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28
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Chávez-Hernández M, Ortiz-Álvarez J, Morales-Jiménez J, Villa-Tanaca L, Hernández-Rodríguez C. Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria. Microorganisms 2023; 11:2551. [PMID: 37894209 PMCID: PMC10608816 DOI: 10.3390/microorganisms11102551] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.
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Affiliation(s)
- Michelle Chávez-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - Jossue Ortiz-Álvarez
- Programa “Investigadoras e Investigadores por México”. Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT). Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México 03940, Mexico;
| | - Jesús Morales-Jiménez
- Departamento el Hombre y su Ambiente, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Villa Quietud, Coyoacán, Ciudad de México 04960, Mexico;
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
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29
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Kizilay HK, Küçükçetin A, Demir M. Optimization of carotenoid production by Umbelopsis ramanniana. Biotechnol Prog 2023; 39:e3369. [PMID: 37343233 DOI: 10.1002/btpr.3369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 06/23/2023]
Abstract
Umbelopsis ramanniana was investigated to increase carotenoid production. Nine different carbon sources and six different nitrogen sources were evaluated for the maximum carotenoid production. The most effective nitrogen and carbon sources were KNO3 and lactose, respectively. Then, the optimization of medium components for enhancement of carotenoid production by Umbelopsis ramanniana was achieved using Plackett-Burman design. Box-Behnken response surface methodology was applied to further optimize carotenoid and biomass production. Carbon to nitrogen ratio, lactose concentration, and shaking speed were studied as variables in Box-Behnken design. The optimum conditions for carotenoid and biomass production were determined as 32.42 g/L of lactose concentration, 20:1 of carbon to nitrogen ratio, and shaking speed of 130 rpm. The maximum carotenoid and biomass production under optimized conditions were 1141 μg/L (β-carotene-Eq) and 13.14 g/L, respectively. When compared to the control fermentation, carotenoid, and biomass production were increased by about 2 and 1.3 folds, respectively.
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Affiliation(s)
- Hatice Kübra Kizilay
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Ahmet Küçükçetin
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Muammer Demir
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
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30
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Brown JL, Gierke T, Butkovich LV, Swift CL, Singan V, Daum C, Barry K, Grigoriev IV, O’Malley MA. High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1171100. [PMID: 37746117 PMCID: PMC10512310 DOI: 10.3389/ffunb.2023.1171100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.
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Affiliation(s)
- Jennifer L. Brown
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Taylor Gierke
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Kong C, Duan C, Zhang S, Liu R, Sun Y, Zhou S. Effects of Co-Modification by Extrusion and Enzymatic Hydrolysis on Physicochemical Properties of Black Wheat Bran and Its Prebiotic Potential. Foods 2023; 12:2367. [PMID: 37372578 PMCID: PMC10297338 DOI: 10.3390/foods12122367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Black wheat bran (BWB) is an important source of dietary fiber (DF) and phenolic compounds and has stronger nutritional advantages than ordinary WB. However, the low content of soluble dietary fiber (SDF) negatively influences its physicochemical properties and nutritive functions. To obtain a higher content of SDF in BWB, we evaluated the impact of co-modification by extrusion and enzymes (cellulase, xylanase, high-temperature α-amylase, and acid protease) on water extractable arabinoxylan (WEAX) in BWB. An optimized co-modification method was obtained through single-factor and orthogonal experiments. The prebiotic potential of co-modified BWB was also evaluated using pooled fecal microbiota from young, healthy volunteers. The commonly investigated inulin served as a positive control. After co-modification, WEAX content was dramatically increased from 0.31 g/100 g to 3.03 g/100 g (p < 0.05). The water holding capacity, oil holding capacity, and cholesterol adsorption capacity (pH = 2.0 and pH = 7.0) of BWB were increased by 100%, 71%, 131%, and 133%, respectively (p < 0.05). Scanning electron microscopy demonstrated a looser and more porous microstructure for co-modified BWB granules. Through in vitro anerobic fermentation, co-modified BWB achieved a higher content of Bifidobacterium and Lactobacillus than inulin fermentation. In addition, co-modified BWB induced the highest butyric acid production, indicating high potential as prebiotics. The results may contribute to improving technologies for developing high-fiber-content cereal products.
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Affiliation(s)
- Chunli Kong
- School of Food and Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (C.K.)
| | - Caiping Duan
- School of Food and Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (C.K.)
| | - Shunzhi Zhang
- Department of Life Sciences, Yuncheng University, Yuncheng 044000, China
| | - Rui Liu
- Department of Life Sciences, Yuncheng University, Yuncheng 044000, China
- Shanxi Technology Innovation Center of High Value-Added Echelon Utilization of Premium Agro-Products, Yuncheng University, Yuncheng 044000, China
| | - Yuanlin Sun
- Department of Life Sciences, Yuncheng University, Yuncheng 044000, China
- Shanxi Technology Innovation Center of High Value-Added Echelon Utilization of Premium Agro-Products, Yuncheng University, Yuncheng 044000, China
| | - Sumei Zhou
- School of Food and Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (C.K.)
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32
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Al-Theyab N, Alrasheed O, Abuelizz HA, Liang M. Draft genome sequence of potato crop bacterial isolates and nanoparticles-intervention for the induction of secondary metabolites biosynthesis. Saudi Pharm J 2023; 31:783-794. [PMID: 37228327 PMCID: PMC10203779 DOI: 10.1016/j.jsps.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction Insights about the effects of gold nanoparticles (AuNPs) on the biosynthetic manipulation of unknown microbe secondary metabolites could be a promising technique for prospective research on nano-biotechnology. Aim In this research, we aimed to isolate a fresh, non-domesticated unknown bacterium strain from a common scab of potato crop located in Saudi Arabia and study the metabolic profile. Methodology This was achieved through genomic DNA (gDNA) sequencing using Oxford Nanopore Technology. The genomic data were subjected to several bioinformatics tools, including canu-1.9 software, Prokka, DFAST, Geneious Prime, and AntiSMASH. We exposed the culture of the bacterial isolate with different concentrations of AuNPs and investigated the effects of AuNPs on secondary metabolites biosynthesis using several analytical techniques. Furthermore, Tandem-mass spectrometric (MS/MS) technique was optimized for the characterization of several significant sub-classes. Results The genomic draft sequence assembly, alignment, and annotation have verified the bacterial isolate as Priestia megaterium. This bacterium has secondary metabolites related to different biosynthetic gene clusters. AuNPs intervention showed an increase in the production of compounds with the molecular weights of 254 and 270 Da in a direct-dependent manner with the increase of the AuNPs concentrations. Conclusion The increase in the yields of compound 1 and 2 concomitantly with the increase in the concentration of the added AuNPs provide evidences about the effects of nanoparticles on the biosynthesis of the secondary metabolites. It contributes to the discovery of genes involved in different biosynthetic gene clusters (BGCs) and prediction of the structures of the natural products.
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Affiliation(s)
- Nada Al-Theyab
- School of Biomedical Science and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar Alrasheed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hatem A. Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mingtao Liang
- School of Biomedical Science and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
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Pérez Matos AE, Bacci G, Borruso L, Landolfi M, Petrocchi D, Renzi S, Perito B. Characterization of the Bacterial Communities Inhabiting Tropical Propolis of Puerto Rico. Microorganisms 2023; 11:1130. [PMID: 37317104 DOI: 10.3390/microorganisms11051130] [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: 03/25/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Propolis is a resinous material produced by honeybees from different plant sources and used in the hive as a building material and to protect the colony from parasites and pathogens. Despite its antimicrobial properties, recent studies showed that propolis hosts diverse microbial strains, some with great antimicrobial potential. In this study, the first description of the bacterial community of propolis produced by the gentle Africanized honeybee was reported. Propolis was sampled from hives of two different geographic areas of Puerto Rico (PR, USA), and the associated microbiota investigated by both cultivation and metataxonomic approaches. Metabarcoding analysis showed appreciable bacterial diversity in both areas and statistically significant dissimilarity in the taxa composition of the two areas, probably due to the different climatic conditions. Both metabarcoding and cultivation data revealed the presence of taxa already detected in other hive components and compatible with the bee's foraging environment. Isolated bacteria and propolis extracts showed antimicrobial activity against Gram-positive and Gram-negative bacterial tester strains. These results support the hypothesis that the propolis microbiota could contribute to propolis' antimicrobial properties.
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Affiliation(s)
- Ana E Pérez Matos
- Biotechnology and Agrobiotechnology Research and Learning Center, Department of Natural Sciences, Pontifical Catholic University of Puerto Rico, Ponce 00717, Puerto Rico
| | - Giovanni Bacci
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, 39100 Bolzano, Italy
| | - Maria Landolfi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Faculty of Science and Technology, Free University of Bozen/Bolzano, 39100 Bolzano, Italy
| | - Dominique Petrocchi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Scientific Laboratory of Opificio delle Pietre Dure, Viale F. Strozzi 1, 50129 Firenze, Italy
| | - Sonia Renzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Brunella Perito
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
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Nagar S, Bharti M, Negi RK. Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 2023; 107:3273-3289. [PMID: 37052633 DOI: 10.1007/s00253-023-12503-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/18/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023]
Abstract
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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Jiang W, Sun J, Gao H, Tang Y, Wang C, Jiang Y, Zhang W, Xin F, Jiang M. Carotenoids production and genome analysis of a novel carotenoid producing Rhodococcus aetherivorans N1. Enzyme Microb Technol 2023; 164:110190. [PMID: 36603321 DOI: 10.1016/j.enzmictec.2022.110190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Carotenoids are a series of natural pigments with unique structure and physiological functions. In this study, a novel Rhodococcus aetherivorans strain N1 was discovered, which can produce 6.4 mg/g carotenoids including β-carotene, zeaxanthin and isorenieratene from glucose. Moreover, strain N1 can directly produce 3.0 mg/g carotenoids from the undetoxified straw hydrolysate, representing the highest carotenoids production from the undetoxified lignocellulosic hydrolysate. The crude carotenoid extracts of strain N1 showed efficient free radical scavenging activity and stability. Strain N1 has complete methylerythritol 4-phosphate (MEP) pathway and related genes for carotenoid synthesis, especially the rare aromatic carotenoid of isorenieratene. Genomic comparison between strain N1 and other carotenoid producing Rhodococcus sp. strains showed the conservatism and universality of carotenoids synthesis gene. These results proved that R. aetherivorans strain N1 can serve as a promising producer for the industrialization of carotenoid production.
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Affiliation(s)
- Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Jingxiang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Haiyan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yunhan Tang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Chao Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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36
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Recent Advances in Chitin Biosynthesis Associated with the Morphology and Secondary Metabolite Synthesis of Filamentous Fungi in Submerged Fermentation. J Fungi (Basel) 2023; 9:jof9020205. [PMID: 36836319 PMCID: PMC9967639 DOI: 10.3390/jof9020205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Metabolites produced by filamentous fungi are used extensively in the food and drug industries. With the development of the morphological engineering of filamentous fungi, numerous biotechnologies have been applied to alter the morphology of fungal mycelia and enhance the yields and productivity of target metabolites during submerged fermentation. Disruption of chitin biosynthesis can modify the cell growth and mycelial morphology of filamentous fungi and regulate the biosynthesis of metabolites during submerged fermentation. In this review, we present a comprehensive coverage of the categories and structures of the enzyme chitin synthase, chitin biosynthetic pathways, and the association between chitin biosynthesis and cell growth and metabolism in filamentous fungi. Through this review, we hope to increase awareness of the metabolic engineering of filamentous fungal morphology, provide insights into the molecular mechanisms of morphological control via chitin biosynthesis, and describe strategies for the application of morphological engineering to enhance the production of target metabolites in filamentous fungi during submerged fermentation.
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37
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Zhu H, Bierla K, Tan J, Szpunar J, Chen D, Lobinski R. Effects of the fermentation process on the selenite metabolism and selenium incorporation and speciation in a probiotic Bifidobacterium longum. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2023; 15:6965834. [PMID: 36583695 DOI: 10.1093/mtomcs/mfac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022]
Abstract
The influence of the fermentation process on selenite metabolism by a probiotic Bifidobacterium longum DD98 and its consequent enrichment in selenium (Se) were studied. The effects of sodium selenite (Na2SeO3) concentration (18-400 μg/ml), feeding time (12, 16, and 24 h), and fermentation stage (secondary and tertiary fermentation) were evaluated by measuring (i) the total Se content and its distribution between the water-soluble metabolome fraction and the water-insoluble fraction; (ii) the total concentrations of the two principal Se compounds produced: selenomethionine (SeMet) and γ-glutamyl-selenomethionine (γ-Glu-SeMet), and (iii) the speciation of Se in the metabolite fraction. The results revealed that the fermentation process notably changed the Se incorporation into metabolites (γ-Glu-SeMet and free SeMet) and proteins (bound-SeMet) in B. longum DD98. In particular, the production of SeMet was negatively correlated to that of γ-Glu-SeMet when no red precipitate was seen in the bacteria. The study offers a tool for the control of the optimization of the fermentation process towards the desired molecular speciation of the incorporated Se and hence contributes to the production of Se-enriched probiotics with good qualities and bioactivities.
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Affiliation(s)
- Hui Zhu
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Minhang District, Shanghai 200240, China.,Universite de Pau et des Pays de l'Adour, CNRS, E2S, Institute of Analytical and Physical Chemistry for the Environment and Materials, IPREM-UMR5254, Hélioparc, 64053 Pau, France
| | - Katarzyna Bierla
- Universite de Pau et des Pays de l'Adour, CNRS, E2S, Institute of Analytical and Physical Chemistry for the Environment and Materials, IPREM-UMR5254, Hélioparc, 64053 Pau, France
| | - Jun Tan
- China State Institute of Pharmaceutical Industry, No. 285 Gebaini Road, Pudong New Area, Shanghai 200120, China
| | - Joanna Szpunar
- Universite de Pau et des Pays de l'Adour, CNRS, E2S, Institute of Analytical and Physical Chemistry for the Environment and Materials, IPREM-UMR5254, Hélioparc, 64053 Pau, France
| | - Daijie Chen
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Ryszard Lobinski
- Universite de Pau et des Pays de l'Adour, CNRS, E2S, Institute of Analytical and Physical Chemistry for the Environment and Materials, IPREM-UMR5254, Hélioparc, 64053 Pau, France.,Chair of Analytical Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
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38
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Maimone NM, Junior MCP, de Oliveira LFP, Rojas-Villalta D, de Lira SP, Barrientos L, Núñez-Montero K. Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani. Front Microbiol 2023; 14:1187321. [PMID: 37213498 PMCID: PMC10192879 DOI: 10.3389/fmicb.2023.1187321] [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: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Phytopathogenic fungi are a considerable concern for agriculture, as they can threaten the productivity of several crops worldwide. Meanwhile, natural microbial products are acknowledged to play an important role in modern agriculture as they comprehend a safer alternative to synthetic pesticides. Bacterial strains from underexplored environments are a promising source of bioactive metabolites. Methods We applied the OSMAC (One Strain, Many Compounds) cultivation approach, in vitro bioassays, and metabolo-genomics analyses to investigate the biochemical potential of Pseudomonas sp. So3.2b, a strain isolated from Antarctica. Crude extracts from OSMAC were analyzed through HPLC-QTOF-MS/MS, molecular networking, and annotation. The antifungal potential of the extracts was confirmed against Rhizoctonia solani strains. Moreover, the whole-genome sequence was studied for biosynthetic gene clusters (BGCs) identification and phylogenetic comparison. Results and Discussion Molecular networking revealed that metabolite synthesis has growth media specificity, and it was reflected in bioassays results against R. solani. Bananamides, rhamnolipids, and butenolides-like molecules were annotated from the metabolome, and chemical novelty was also suggested by several unidentified compounds. Additionally, genome mining confirmed a wide variety of BGCs present in this strain, with low to no similarity with known molecules. An NRPS-encoding BGC was identified as responsible for producing the banamides-like molecules, while phylogenetic analysis demonstrated a close relationship with other rhizosphere bacteria. Therefore, by combining -omics approaches and in vitro bioassays, our study demonstrates that Pseudomonas sp. So3.2b has potential application to agriculture as a source of bioactive metabolites.
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Affiliation(s)
- Naydja Moralles Maimone
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Mario Cezar Pozza Junior
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Lucianne Ferreira Paes de Oliveira
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dorian Rojas-Villalta
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Simone Possedente de Lira
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
- *Correspondence: Leticia Barrientos, ; Kattia Núñez-Montero,
| | - Kattia Núñez-Montero
- Facultad Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco, Chile
- *Correspondence: Leticia Barrientos, ; Kattia Núñez-Montero,
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Barik K, Arya PK, Singh AK, Kumar A. Potential therapeutic targets for combating Mycoplasma genitalium. 3 Biotech 2023; 13:9. [PMID: 36532859 PMCID: PMC9755450 DOI: 10.1007/s13205-022-03423-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Mycoplasma genitalium (M. genitalium) has emerged as a sexually transmitted infection (STI) all over the world in the last three decades. It has been identified as a cause of male urethritis, and there is now evidence that it also causes cervicitis and pelvic inflammatory disease in women. However, the precise role of M. genitalium in diseases such as pelvic inflammatory disease, and infertility is unknown, and more research is required. It is a slow-growing organism, and with the advent of the nucleic acid amplification test (NAAT), more studies are being conducted and knowledge about the pathogenicity of this organism is being elucidated. The accumulation of data has improved our understanding of the pathogen and its role in disease transmission. Despite the widespread use of single-dose azithromycin in the sexual health field, M. genitalium is known to rapidly develop antibiotic resistance. As a result, the media frequently refer to this pathogen as the "new STI superbug." Despite their rarity, antibiotics available today have serious side effects. As the cure rates for first-line antimicrobials have decreased, it is now a challenge to determine the effective antimicrobial therapy. In this review, we summarise recent M. genitalium research and investigate potential therapeutic targets for combating this pathogen.
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Affiliation(s)
- Krishnendu Barik
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Praffulla Kumar Arya
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Ajay Kumar Singh
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Anil Kumar
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
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40
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Paudel L, Ghimire N, Han SR, Park H, Jung SH, Oh TJ. Complete genome of Nakamurella sp. PAMC28650: genomic insights into its environmental adaptation and biotechnological potential. Funct Integr Genomics 2022; 23:18. [PMID: 36564681 PMCID: PMC9789016 DOI: 10.1007/s10142-022-00937-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
The mechanisms underlying the survival of bacteria in low temperature and high radiation are not yet fully understood. Nakamurella sp. PAMC28650 was isolated from a glacier of Rwenzori Mountain, Uganda, which species belonged to Nakamurella genus based on 16S rRNA phylogeny, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis among Frankineae suborder. We conducted the whole genome sequencing and comparative genomics of Nakamurella sp. PAMC28650, to understand the genomic features pertaining to survival in cold environment, along with high UV (ultraviolet) radiation. This study highlights the role of polysaccharide in cold adaptation, mining of the UV protection-related secondary metabolites and other related to cold adaptation mechanism through different bioinformatics tools, and providing a brief overview of the genes present in DNA repair systems. Nakamurella sp. PAMC28650 contained glycogen and cellulose metabolism pathways, mycosporine-like amino acids and isorenieratene-synthesizing gene cluster, and a number of DNA repair systems. Also, the genome analysis showed osmoregulation-related genes and cold shock proteins. We infer these genomic features are linked to bacterial survival in cold and UV radiation.
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Affiliation(s)
- Lakshan Paudel
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - Nisha Ghimire
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, 25521, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun-Moon University, Asan, 31460, Korea. .,Genome-Based Bio-IT Convergence Institute, Asan, 31460, Korea. .,Department of Pharmaceutical Engineering and Biotechnology, Sun-Moon University, Asan, 31460, Korea.
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Styczynski M, Rogowska A, Nyabayo C, Decewicz P, Romaniuk F, Pączkowski C, Szakiel A, Suessmuth R, Dziewit L. Heterologous production and characterization of a pyomelanin of Antarctic Pseudomonas sp. ANT_H4: a metabolite protecting against UV and free radicals, interacting with iron from minerals and exhibiting priming properties toward plant hairy roots. Microb Cell Fact 2022; 21:261. [PMID: 36527127 PMCID: PMC9756463 DOI: 10.1186/s12934-022-01990-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Antarctica has one of the most extreme environments in the world. This region is inhabited by specifically adapted microorganisms that produce various unique secondary metabolites (e.g. pigments) enabling their survival under the harsh environmental conditions. It was already shown that these natural, biologically active molecules may find application in various fields of biotechnology. RESULTS In this study, a cold-active brown-pigment-producing Pseudomonas sp. ANT_H4 strain was characterized. In-depth genomic analysis combined with the application of a fosmid expression system revealed two different pathways of melanin-like compounds biosynthesis by the ANT_H4 strain. The chromatographic behavior and Fourier-transform infrared spectroscopic analyses allowed for the identification of the extracted melanin-like compound as a pyomelanin. Furthermore, optimization of the production and thorough functional analyses of the pyomelanin were performed to test its usability in biotechnology. It was confirmed that ANT_H4-derived pyomelanin increases the sun protection factor, enables scavenging of free radicals, and interacts with the iron from minerals. Moreover, it was shown for the first time that pyomelanin exhibits priming properties toward Calendula officinalis hairy roots in in vitro cultures. CONCLUSIONS Results of the study indicate the significant biotechnological potential of ANT_H4-derived pyomelanin and open opportunities for future applications. Taking into account protective features of analyzed pyomelanin it may be potentially used in medical biotechnology and cosmetology. Especially interesting was showing that pyomelanin exhibits priming properties toward hairy roots, which creates a perspective for its usage for the development of novel and sustainable agrotechnical solutions.
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Affiliation(s)
- Michal Styczynski
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agata Rogowska
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Christine Nyabayo
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Przemyslaw Decewicz
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Filip Romaniuk
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cezary Pączkowski
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Szakiel
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roderich Suessmuth
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Lukasz Dziewit
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Yusfi LA, Tjong DH, Chaniago I, Salsabilla A, Jamsari J. Growth Phase Influence the Gene Expression and Metabolite Production Related to Indole-3-Acetic Acid (IAA) Biosynthesis by Serratia plymuthica UBCF_13. Pak J Biol Sci 2022; 25:1047-1057. [PMID: 36978272 DOI: 10.3923/pjbs.2022.1047.1057] [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: 01/05/2023]
Abstract
<b>Background and Objective:</b> The optimization of the indole-3-acetic acid (IAA) producing capability of <i>Serratia plymuthica</i> UBCF_13 has been intensively studied. This work tried to reveal the effect of growth phases on IAA production, gene expression and metabolite synthesis related to the IAA biosynthesis pathway. <b>Materials and Methods:</b> The growth curve and IAA production were measured every 3 hrs. The putative IAA biosynthesis pathway was investigated based on the UBCF_13 genome. To identify the possible pathway of IAA biosynthesis in UBCF_13, we applied the Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and High-Performance Liquid Chromatography (HPLC) analysis to measure the transcript levels of each gene and indole metabolite production based on tryptophan treatment at different times of incubation. <b>Results:</b> The optimal IAA production on colorimetric assay was at 9 hrs of incubation (initial stationary phase). The level expression of <i>puuC</i>, <i>DDC</i>, <i>oxdA</i>, <i>amiE</i>, <i>nthA</i> and <i>nthB</i> have been upregulated maximum in 3 hrs of culture time (lag phase), except <i>tyrB</i> and <i>ipdC</i>. The highest transcript level of the genes was found in nitrile hydratase genes (<i>nthA</i> and <i>nthB</i>) and indole-3- acetamide (IAM) has been detected as the only intermediate in the crude extract of UBCF_13 thus the IAM pathway may be used to produce IAA. The maximum IAA production on HPLC analysis was found at 21 hrs of incubation (late stationary phase). <b>Conclusion:</b> This study gives a new insight that the best time to measure gene expression and intermediates related to the IAA biosynthetic pathway in bacteria was found at a specific growth phase.
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Santamaria G, Liao C, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J, Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife 2022; 11:e76119. [PMID: 36409069 PMCID: PMC9708071 DOI: 10.7554/elife.76119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations.
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Affiliation(s)
- Guillem Santamaria
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Zhe Wang
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francisco Rodrigues Pinto
- BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of LisboaLisboaPortugal
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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Le Han H, Jiang L, Thu Tran TN, Muhammad N, Kim SG, Tran Pham VP, Ng YJ, Khoo KS, Chew KW, Phuong Nguyen TD. Whole-genome analysis and secondary metabolites production of a new strain Brevibacillus halotolerans 7WMA2: A potential biocontrol agent against fungal pathogens. CHEMOSPHERE 2022; 307:136004. [PMID: 35970213 DOI: 10.1016/j.chemosphere.2022.136004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/05/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
The extensive usage of synthetic fungicides against fungal diseases has caused adverse impacts on both human and agricultural crops. Therefore, the current study aims to establish a new bacterium 7WMA2, as a biocontrol agent to achieve better antifungal results. The strain 7WMA2 was isolated from marine sediment, displayed a broad spectrum of several fungi that includes Alternaria alternata, Cladosporium sp., Candida albicans, Fusarium oxysporum, Trichosporon pullulans, and Trichophyton rubrum. The 16S rRNA phylogeny inferred that strain 7WMA2 was a member of Brevibacillus. The phylogenetic and biochemical analyses revealed that the strain 7WMA2 belongs to the species of Brevibacillus halotolerans. The complete genome sequence of Brevibacillus halotolerans 7WMA2 consists of a circular chromosome of 5,351,077 bp length with a GC content of 41.39 mol %, including 4433 CDS, 111 tRNA genes, and 36 rRNA genes. The genomic analysis showed 23 putative biosynthetic secondary metabolite gene clusters responsible for non-ribosomal peptides, polyketides and siderophores. The antifungal compounds concentrated from cell-free fermentation broth demonstrated strong inhibition of fungi, and the compounds are considerably thermal stable and adaptable to pH range 2-12. This complete genome sequence has provided insight for further exploration of antagonistic ability and its secondary metabolite compounds indicated feasibility as biological control agents against fungal infections.
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Affiliation(s)
- Ho Le Han
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea; Scientific Management Department, Dong A University, Da Nang City, Viet Nam
| | - Lingmin Jiang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Thi Ngoc Thu Tran
- The University of Danang, University of Technology and Education, Danang City 550000, Viet Nam
| | - Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea; University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea; University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | | | - Yan Jer Ng
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Kuan Shiong Khoo
- Faculty of Applied Sciences, UCSI University, UCSI Heights, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Kit Wayne Chew
- School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900, Sepang, Selangor Darul Ehsan, Malaysia.
| | - Thi Dong Phuong Nguyen
- The University of Danang, University of Technology and Education, Danang City 550000, Viet Nam.
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Insecticidal characteristics and structural identification of the potential active compounds from Streptomyces sp. KR0006: Strain improvement through mutagenesis. PLoS One 2022; 17:e0274766. [PMID: 36155980 PMCID: PMC9512179 DOI: 10.1371/journal.pone.0274766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/19/2022] Open
Abstract
Pest control by biological means is an effective, eco-friendly, and promising method that typically involves compounds naturally derived from actinomycetes. Thus, the present study aimed to screen, characterize, and identify the structure of insecticidal compounds from Streptomyces sp. KR0006 and increase the activity through mutagenesis. In the examination of the insecticidal activity level of the isolates, Streptomyces sp. KR0006 metabolite showed significant activity against larvae and moths of Plutella xylostella. Taxonomic analyses of the 16S rRNA gene sequences revealed that the isolated KR0006 strain tended to be 99% consistent with Streptomyces cinereoruber strain NBRC 12756. Three active compounds isolated from the culture filtrate of KR0006 were purified by solvent partition, mid-pressure liquid chromatography (MPLC), Sephadex LH20 column chromatography, and high-performance liquid chromatography (HPLC). By performing 1H-NMR, 13C-NMR, and 2D-NMR experiments, and high-resolution electrospray ionization mass spectrometry analysis, the 316-HP2, 316-HP3, and 316-HP5 compounds were inferred as antimycin A3a (MW, 519.; C26H36N2O9), antimycin A8a (MW, 534; C27H38N2O9), and antimycin A1a (MW, 548; C28H40N2O9) respectively. Mutant U67 obtained from exposure to ultraviolet (UV) irradiation (254 nm, height 17 cm) for 70 seconds resulted in a 70% more larval mortality than that of the initial wild culture. The second mutation of the culture broth enhanced insecticidal activity by 80 and 100% compared with the first mutation and initial medium, respectively. Our study found that Streptomyces sp. KR0006 strain produces insecticidal active compounds and could be used for practical pest management.
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Zahroh EW, Ningsih F, Sjamsuridzal W. DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH. BIOLINK (JURNAL BIOLOGI LINGKUNGAN INDUSTRI KESEHATAN) 2022. [DOI: 10.31289/biolink.v9i1.6438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.
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Wei S, Hu C, Nie P, Zhai H, Zhang S, Li N, Lv Y, Hu Y. Insights into the Underlying Mechanism of Ochratoxin A Production in Aspergillus niger CBS 513.88 Using Different Carbon Sources. Toxins (Basel) 2022; 14:toxins14080551. [PMID: 36006213 PMCID: PMC9415321 DOI: 10.3390/toxins14080551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022] Open
Abstract
Aspergillus niger produces carcinogenic ochratoxin A (OTA), a serious food safety and human health concern. Here, the ability of A. niger CBS 513.88 to produce OTA using different carbon sources was investigated and the underlying regulatory mechanism was elucidated. The results indicated that 6% sucrose, glucose, and arabinose could trigger OTA biosynthesis and that 1586 differentially expressed genes (DEGs) overlapped compared to a non-inducing nutritional source, peptone. The genes that participated in OTA and its precursor phenylalanine biosynthesis, including pks, p450, nrps, hal, and bzip, were up-regulated, while the genes involved in oxidant detoxification, such as cat and pod, were down-regulated. Correspondingly, the activities of catalase and peroxidase were also decreased. Notably, the novel Gal4-like transcription factor An12g00840 (AnGal4), which is vital in regulating OTA biosynthesis, was identified. Deletion of AnGal4 elevated the OTA yields by 47.65%, 54.60%, and 309.23% using sucrose, glucose, and arabinose as carbon sources, respectively. Additionally, deletion of AnGal4 increased the superoxide anion and H2O2 contents, as well as the sensitivity to H2O2, using the three carbon sources. These results suggest that these three carbon sources repressed AnGal4, leading to the up-regulation of the OTA biosynthetic genes and alteration of cellular redox homeostasis, ultimately triggering OTA biosynthesis in A. niger.
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Affiliation(s)
- Shan Wei
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Chaojiang Hu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Ping Nie
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Huanchen Zhai
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Na Li
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
| | - Yangyong Lv
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
- Correspondence: (Y.L.); (Y.H.)
| | - Yuansen Hu
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
- Henan Provincial Key Laboratory of Biological Processing and Nutritional Function of Wheat, Zhengzhou 450001, China
- Correspondence: (Y.L.); (Y.H.)
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Glycerol promotes biomass accumulation of Klebsiella pneumoniae by activating dha regulon. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mycelial Growth-promoting Potential of Extracellular Metabolites of Paraburkholderia spp. Isolated from Rhizopogon roseolus Sporocarp. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to investigate the effect of potential metabolite(s) produced by Paraburkholderia spp. isolated from the Rhizopogon roseolus (shouro mushroom) sporocarp on the mycelial growth of R. roseolus. For this purpose, we selected two molecularly identified bacteria: P. fungorum GIB024 and P. caledonica KN1. Direct confrontation assay at three different distances, a pour plate method that sampled bacterial spent broth either with and without agitation at 25 °C, and an indirect confrontation assay was carried out in order to assess the R. roseolus growth-promoting ability of Paraburkholderia spp. These assessments were carried out in a 1:5 diluted Melin-Norkran-modified medium with glucose (hs-dMMN) and without glucose (ls-dMMN). GIB024 promoted the growth of R. roseolus in ls-dMMN in short distance, whereas KN1 inhibited the growth of the fungus in that condition. In hs-dMMN, both bacteria have neutral or slightly promotion effect toward R. roseolus. We determined from the spent broth analysis that Paraburkholderia spp. that grew axenically under static conditions had a more pronounced mycelial growth-promoting effect on R. roseolus than under agitation conditions. We also found that high concentration of spent broth resulted in a decrease in mycelial growth-promoting ability. Volatile metabolite(s) produced by both bacteria did not promote the mycelial growth of R. roseolus. In conclusion, Paraburkholderia spp. exhibited a species- and nutrient (sugar)-dependent ability to promote the mycelial growth of R. roseolus, and the bacterial soluble metabolite(s) play a crucial role in their growth-promoting ability.
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Zong G, Cao G, Fu J, Zhang P, Chen X, Yan W, Xin L, Zhang W, Xu Y, Zhang R. MacRS Controls Morphological Differentiation and Natamycin Biosynthesis in Streptomyces gilvosporeus F607. Microbiol Res 2022; 262:127077. [DOI: 10.1016/j.micres.2022.127077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/10/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
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