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Wani AK, Chopra C, Ansari MA, Dar MA, Américo-Pinheiro JHP, Singh R. Characterization of thermostable carboxypeptidase from high-altitude hot spring metagenome. Int J Biol Macromol 2024; 276:133974. [PMID: 39029824 DOI: 10.1016/j.ijbiomac.2024.133974] [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: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn+2 ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
| | - Mushtaq Ahmad Ansari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mudasir A Dar
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, 212013, China
| | - Juliana Heloisa Pinê Américo-Pinheiro
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Department of Forest Science, Soils and Environment, Ave. Universitária, 3780, Botucatu, SP 18610-034, Brazil; Graduate Program in Environmental Sciences, Brazil University, Street Carolina Fonseca, 584, São Paulo, SP 08230-030, Brazil.
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India.
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Anu K, Kumari S, Choudhary G, Devi S. Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India. Braz J Microbiol 2024; 55:1545-1555. [PMID: 38421596 PMCID: PMC11153464 DOI: 10.1007/s42770-024-01284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.
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Affiliation(s)
- Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Sutar AA, Dashpute RS, Shinde YD, Mukherjee S, Chowdhury C. A Systemic Review on Fitness and Survival of Salmonella in Dynamic Environment and Conceivable Ways of Its Mitigation. Indian J Microbiol 2024; 64:267-286. [PMID: 39011015 PMCID: PMC11246371 DOI: 10.1007/s12088-023-01176-4] [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: 06/01/2023] [Accepted: 12/05/2023] [Indexed: 07/17/2024] Open
Abstract
Gastroenteritis caused by non-typhoidal Salmonella still prevails resulting in several recent outbreaks affecting many people worldwide. The presence of invasive non-typhoidal Salmonella is exemplified by several characteristic symptoms and their severity relies on prominent risk factors. The persistence of this pathogen can be attributed to its broad host range, complex pathogenicity and virulence and adeptness in survival under challenging conditions inside the host. Moreover, a peculiar aid of the ever-changing climatic conditions grants this organism with remarkable potential to survive within the environment. Abusive use of antibiotics for the treatment of gastroenteritis has led to the emergence of multiple drug resistance, making the infections difficult to treat. This review emphasizes the importance of early detection of Salmonella, along with strategies for accomplishing it, as well as exploring alternative treatment approaches. The exceptional characteristics exhibited by Salmonella, like strategies of infection, persistence, and survival parallelly with multiple drug resistance, make this pathogen a prominent concern to human health.
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Affiliation(s)
- Ajit A Sutar
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rohit S Dashpute
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Yashodhara D Shinde
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
| | - Srestha Mukherjee
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Rafiee Z, Jalili Tabaii M, Moradi M, Harirchi S. Unveiling Antibacterial Potential and Physiological Characteristics of Thermophilic Bacteria Isolated from a Hot Spring in Iran. Microorganisms 2024; 12:834. [PMID: 38674778 PMCID: PMC11051818 DOI: 10.3390/microorganisms12040834] [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: 02/20/2024] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The increasing worldwide demand for antimicrobial agents has significantly contributed to the alarming rise of antimicrobial resistance, posing a grave threat to human life. Consequently, there is a pressing need to explore uncharted environments, seeking out novel antimicrobial compounds that display exceptionally efficient capabilities. Hot springs harbor microorganisms possessing remarkable properties, rendering them an invaluable resource for uncovering groundbreaking antimicrobial compounds. In this study, thermophilic bacteria were isolated from Mahallat Hot Spring, Iran. Out of the 30 isolates examined, 3 strains exhibited the most significant antibacterial activities against Escherichia coli and Staphylococcus aureus. Furthermore, the supernatants of the isolated strains exhibited remarkable antibacterial activity, displaying notable resistance to temperatures as high as 75 °C for 30 min. It was determined that the two strains showed high similarity to the Bacillus genus, while strain Kh3 was classified as Saccharomonospora azurea. All three strains exhibited tolerance to NaCl. Bacillus strains demonstrated optimal growth at pH 5 and 40 °C, whereas S. azurea exhibited optimal growth at pH 9 and 45 °C. Accordingly, hot springs present promising natural reservoirs for the isolation of resilient strains possessing antibacterial properties, which can be utilized in disease treatment or within the food industry.
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Affiliation(s)
- Zeinab Rafiee
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan 81799-49999, Iran; (Z.R.); (M.M.)
| | - Maryam Jalili Tabaii
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan 81799-49999, Iran; (Z.R.); (M.M.)
| | - Maryam Moradi
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan 81799-49999, Iran; (Z.R.); (M.M.)
| | - Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran P.O. Box 3353-5111, Iran
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Yahiaoui B, Bounabi H, Boukerb AM, Gasmi M. Insights into Genomic Features and Potential Biotechnological Applications of Bacillus halotolerans Strain HGR5. Pol J Microbiol 2023; 72:477-490. [PMID: 38103009 PMCID: PMC10725166 DOI: 10.33073/pjm-2023-045] [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: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Algeria is one of the wealthiest countries in terms of hydrothermal sources, with more than two hundred hot springs. However, diverse and little-described microbial communities colonize these habitats, making them an intriguing research subject. This work reports the isolation of bacteria from two hot springs water samples in northeastern Algeria, evaluating their enzymatic activities and effect on plant pathogens. Out of the obtained 72 bacterial isolates and based on the 16S rRNA gene sequence analysis, the strain HGR5 belonging to Bacillus halotolerans had the most interesting activity profile. Interestingly, HGR5 was substantially active against Fusarium graminearum, Phytophthora infestans, and Alternaria alternata. Furthermore, this strain presented a high ability to degrade casein, Tween 80, starch, chitin, cellulose, and xylan. The genome sequence of HGR5 allowed taxonomic validation and screening of specific genetic traits, determining its antagonistic and enzymatic activities. Genome mining revealed that strain HGR5 encloses several secondary metabolite biosynthetic gene clusters (SM-BGCs) involved in metabolite production with antimicrobial properties. Thus, antimicrobial metabolites included bacillaene, fengycin, laterocidine, bacilysin, subtilosin, bacillibactin, surfactin, myxovirescin, dumulmycin, and elansolid A1. HGR5 strain genome was also mined for CAZymes associated with antifungal activity. Finally, the HGR5 strain exhibited the capacity to degrade polycaprolactone (PCL), a model substrate for polyester biodegradation. Overall, these results suggest that this strain may be a promising novel biocontrol agent with interesting plastic-degradation capability, opening the possibilities of its use in various biotechnological applications.
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Affiliation(s)
- Bilal Yahiaoui
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, Setif, Algeria
| | - Hadjira Bounabi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
| | - Amine M. Boukerb
- Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, CBSA UR 4312, Rouen, France
| | - Meriem Gasmi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
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Liu L, Liu Y, Liu S, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang B, Zhang D, Li F, Sun C. Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1247001. [PMID: 37886074 PMCID: PMC10599150 DOI: 10.3389/fmicb.2023.1247001] [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: 06/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied. Method Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively. Results A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics. Discussion Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.
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Affiliation(s)
- Lifang Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuyu Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Ngamcharungchit C, Chaimusik N, Panbangred W, Euanorasetr J, Intra B. Bioactive Metabolites from Terrestrial and Marine Actinomycetes. Molecules 2023; 28:5915. [PMID: 37570885 PMCID: PMC10421486 DOI: 10.3390/molecules28155915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Actinomycetes inhabit both terrestrial and marine ecosystems and are highly proficient in producing a wide range of natural products with diverse biological functions, including antitumor, immunosuppressive, antimicrobial, and antiviral activities. In this review, we delve into the life cycle, ecology, taxonomy, and classification of actinomycetes, as well as their varied bioactive metabolites recently discovered between 2015 and 2023. Additionally, we explore promising strategies to unveil and investigate new bioactive metabolites, encompassing genome mining, activation of silent genes through signal molecules, and co-cultivation approaches. By presenting this comprehensive and up-to-date review, we hope to offer a potential solution to uncover novel bioactive compounds with essential activities.
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Affiliation(s)
- Chananan Ngamcharungchit
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Nutsuda Chaimusik
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Watanalai Panbangred
- Research, Innovation and Partnerships Office, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Jirayut Euanorasetr
- Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
- Laboratory of Biotechnological Research for Energy and Bioactive Compounds, Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Khet Thung Khru, Bangkok 10140, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Pipite A, Siro G, Subramani R, Srinivasan S. Microbiological analysis, antimicrobial activity, heavy-metals content and physico-chemical properties of Fijian mud pool samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158725. [PMID: 36108855 DOI: 10.1016/j.scitotenv.2022.158725] [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: 06/22/2022] [Revised: 08/28/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
The hot springs are home to a rich bacterial diversity which could be the source of enzymes, antibiotics and many other commercially important products. Most of the hot springs present in Fiji are unexplored and their analysis of microbial diversity could be of great interest in facilitating various industrial, agricultural and medicinal applications. This study is an attempt to evaluate the heavy metal concentration and to analyze the comprehensive bacterial diversity of two Fijian thermal mud pools, namely Sabeto and Tifajek. The two hot springs have a pH of 7.28 to 7.19 and a temperature of 32.2 to 38.8 °C, respectively. Mean metal concentrations of the studied mud samples ranged from 4.758 to 6.870 mg/kg and followed a decreasing sequence as Fe > Mn > Zn > Na > Ni > Cd > Ca > Cr > Cu. Levels of Fe, Na, Mn, Zn, Ni, Cd, Ca, Cr, Cu in the mud pool samples were within World Health Organisation (WHO) limits, while Cd was above regulatory limits. The heavy metals analysis results showed that both mud pools had high values for Cd, above the WHO limit of 3 mg/kg. In addition, 8 strains of actinomycetes were successfully identified for the first time in the Sabeto mud pool, where most of them showed antibacterial activity. The genetic identification of most isolates was determined in BLASTn analyses of their 16S rRNA sequences. Isolates were identified as that of Streptomyces, Nocardia and Rhodococcus genus. Further, AntiSMASH results of the closest relatives of cultured actinobacteria have shown to produce antibiotics, natural pesticides and other compounds of various usage. This study also found no fecal coliforms and supports existing knowledge and practice of using Fijian thermal mud pools for their therapeutic properties. Overall, the presented work indicated that the studied mud pools have therapeutic properties, harboring wealth of bacteria with antibiotic profiles and were risk free from health-related issues of heavy metals and disease-causing pathogens. It provides great insight into the studied mud pools which serves as a baseline from which further heavy metal monitoring or mitigation programs and microbial researches can be conducted.
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Affiliation(s)
- Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji
| | - Galana Siro
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea.
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Abd-El-Kareem F, Elshahawy IE, Abd-Elgawad MMM. Native bacteria for field biocontrol of black root rot in Egyptian strawberry. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:82. [DOI: 10.1186/s42269-022-00775-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/20/2022] [Indexed: 09/01/2023]
Abstract
Abstract
Background
Increasing cultivation of strawberry in Egypt has boosted efforts to increase its yield. Biocontrol agents (BCAs) may avoid side effects and health risks caused by chemical fungicides used to control black root rot disease in strawberry. Some BCAs control the disease and augment strawberry yield, but additional research is needed to fit BCAs into emerging control strategies. The impact of six bacterial isolates of Paenibacillus polymyxa and Bacillus brevis on this disease and on berry yield is reported and compared to a common chemical fungicide.
Results
The bacterial isolates reduced the growth of the black root rot causal agents Fusarium solani, Rhizoctonia solani, and Macrophomina phaseolina, in dual culture bioassays. The greatest fungal inhibition was caused by P. polymyxa isolates 1 and 2 and B. brevis isolate 2. They suppressed the growth of F. solani, R. solani, and M. phaseolina by more than 74, 76, and 79%, respectively. Disease severity and incidence were significantly reduced on naturally infected strawberry plants in the field by the six isolates. The best results were obtained by the superior bioassay isolates which suppressed the disease incidence by 73, 77, and 71%, and its severity by 72, 78, and 70%, respectively. Disease suppression by bacteria was comparable to that by fungicide Actamyl. Bacteria surpassed Actamyl with regard to strawberry yield and enhancement of peroxidase and chitinase activities in the leaves.
Conclusions
These isolates are potential benign alternatives to fungicides used against black root rot in strawberry in Egypt. More studies are needed to examine their economic use on a wider scale.
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12
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The Use of Baikal Psychrophilic Actinobacteria for Synthesis of Biologically Active Natural Products from Sawdust Waste. FERMENTATION 2022. [DOI: 10.3390/fermentation8050213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
One of the relevant areas in microbiology and biotechnology is the study of microorganisms that induce the destruction of different materials, buildings, and machines and lead to negative effects. At the same time, the positive ecological effects of degradation can be explained by the detoxication of industrial and agricultural wastes, chemical substances, petroleum products, xenobiotics, pesticides, and other chemical pollutants. Many of these industrial wastes include hard-to-degrade components, such as lignocellulose or plastics. The biosynthesis of natural products based on the transformation of lignocellulosic wastes is of particular interest. One of the world’s unique ecosystems is presented by Lake Baikal. This ecosystem is characterized by the highest level of biodiversity, low temperatures, and a high purity of the water. Here, we studied the ability of several psychrophilic representatives of Baikal Actinobacteria to grow on sawdust wastes and transform them into bioactive natural products. Different strains of both widely spread genus of Actinobacteria and rare genera of Actinobacteria were tested. We used the LC-MS methods to show that Actinobacteria living in sawmill wastes can produce both known and novel natural products with antibiotic activity. We demonstrated that the type of sawmill wastes and their concentration influence the Actinobacteria biosynthetic potential. We have shown for the first time that the use of Baikal psychrophilic microorganisms as a factory for biodegradation is applicable for the transformation of lignocellulosic wastes. Thus, the development of techniques for screening novel natural products leads to an elaboration on the active ingredients for novel drugs.
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Alaidaroos BA. Rare Actinomycetes from Undiscovered Sources as a Source of Novel Antimicrobial Agents to Control Multidrug-Resistant Bacteria. INTERNATIONAL JOURNAL OF PHARMACEUTICAL RESEARCH AND ALLIED SCIENCES 2022. [DOI: 10.51847/dpfaj9fiep] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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14
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Wang X, Pecoraro L. Diversity and Co-Occurrence Patterns of Fungal and Bacterial Communities from Alkaline Sediments and Water of Julong High-Altitude Hot Springs at Tianchi Volcano, Northeast China. BIOLOGY 2021; 10:894. [PMID: 34571771 PMCID: PMC8464750 DOI: 10.3390/biology10090894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/28/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022]
Abstract
The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure and networks in sediments and water from the Julong hot springs using a combination of culture-based methods and metabarcoding. A total of 65 fungal and 21 bacterial strains were isolated. Fungal genera Trichoderma and Cladosporium were dominant in sediments, while the most abundant fungi in hot spring water were Aspergillus and Alternaria. Bacterial communities in sediments and water were dominated by the genera Chryseobacterium and Pseudomonas, respectively. Metabarcoding analysis revealed significant differences in the microorganism communities from the two hot springs. Results suggested a strong influence of pH on the analyzed microbial diversity, at least when the environmental conditions became clearly alkaline. Our analyses indicated that mutualistic interactions may play an essential role in shaping stable microbial networks in the studied hot springs. The much more complicated bacterial than fungal networks described in our study may suggest that the more flexible trophic strategies of bacteria are beneficial for their survival and fitness under extreme conditions.
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Affiliation(s)
- Xiao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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15
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Ruiz-Domínguez M, Fuentes J, Mendiola J, Cerezal-Mezquita P, Morales J, Vílchez C, Ibáñez E. Bioprospecting of cyanobacterium in Chilean coastal desert, Geitlerinema sp. molecular identification and pressurized liquid extraction of bioactive compounds. FOOD AND BIOPRODUCTS PROCESSING 2021. [DOI: 10.1016/j.fbp.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Identification of Multi-Potent Protein Subtilisin A from halophilic bacterium Bacillus firmus VE2. Microb Pathog 2021; 157:105007. [PMID: 34044052 DOI: 10.1016/j.micpath.2021.105007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022]
Abstract
Screening of halophiles with antimicrobial activity in saltpan soil samples from Nagapattinam district, Tamil Nadu, revealed isolate VE-2 as the most potent, identified as Bacillus firmus strain VE-2 through 16s rRNA gene sequencing. It had an optimum growth condition (OD 3.1) and antimicrobial protein (AMP) production (450 μg/mL) at 37 °C, pH 8, 25% NaCl, and 36 h incubation. SDS-PAGE analysis of the purified AMP showed the molecular weight of 36 kDa. HPLC analysis of the purified AMP showed different amino acids, such as asparagines, alanine, lysine, proline, threonine, glycine, cysteine, serine, aspartic acid leucine, and valine. Further characterization and identification using FT-IR, 2D-PAGE, MALDI-TOF, and in-silico analysis showed that the isolated AMP had the highest similarity to Subtilisin-A. It showed antibacterial activity against clinical bacterial pathogens like S. aureus, S. pyogenes, C. diphtheria, E. coli, and P. aeruginosa with the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration of 2.5 μg/mL and 20 μg/mL and also against various fungal pathogens such as A. niger, A. flavus, C. albicans, C. tropicalis and C. parapsilosis with the MIC and minimum fungicidal concentrations of 1.25-80 μg/mL. The purified AMP had excellent antioxidant potential, showed a scavenging effect against DPPH and Nitric oxide radicals, and displayed anticancer activity against HeLa cell lines with the IC50 values 53 μg/mL. Hence, the purified bioactive antimicrobial peptides (AMP) could also be used in anticancer therapies.
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17
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Ojha P, Kar NP, Nayak S, Patra AK, Sahoo KK. Isolation of a broad spectrum antimicrobial producing thermophilic Bacillus and characterization of its antimicrobial protein. Arch Microbiol 2021; 203:2059-2073. [PMID: 33575852 DOI: 10.1007/s00203-020-02162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
The hot spring water of Atri in India was believed to have disease curing property. An antibacterial producing organism was isolated and identified as Bacillus paralicheniformis by morphology, microscopy, and 16S-rRNA. Its secretion inhibited bacteria, yeast, and fungus in well-diffusion-method. The secreted antimicrobial was a 16.74 kDa protein homologous of chicken-lysozyme-C. The novel lysozyme's activities were recorded under different parameters. It was active from pH 5-9 and endured up to 60 °C for 120 min. Complete cell wall lysis of S. flexneri and P. aeruginosa was observed under a microscope at 4500× with a minimum inhibitory concentration of 7.8 µg/ml, while others required a higher dose, i.e., 13 µg/ml, and 20 µg/ml for E.coli and S. typhimurium, respectively. The discovered lysozyme has the extraordinary potential to lyse Gram-positive bacteria, yeast, fungus, and more efficiently lyse chick-lysozyme-C resistant lipopolysaccharide rich Gram-negative bacteria's outer cell wall.
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Affiliation(s)
- Purusottam Ojha
- Department of Botany and Biotechnology, Ravenshaw University, Cuttack, Odisha, India, 753003.,Imgenex India Pvt. Ltd, E5 Infocity, Chandka Industrial Estate, KIIT Post Office, Bhubaneswar, Odisha, India, 751024
| | | | - Shreenath Nayak
- Imgenex India Pvt. Ltd, E5 Infocity, Chandka Industrial Estate, KIIT Post Office, Bhubaneswar, Odisha, India, 751024
| | - Ashok Kumar Patra
- Imgenex India Pvt. Ltd, E5 Infocity, Chandka Industrial Estate, KIIT Post Office, Bhubaneswar, Odisha, India, 751024
| | - Khirod Kumar Sahoo
- Department of Botany and Biotechnology, Ravenshaw University, Cuttack, Odisha, India, 753003.
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18
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Arafat HH, Abu-Tahon MA, Isaac GS. Production of antibiotic carbomycin from Streptomyces graminofaciens with high lipid content mutation. Arch Microbiol 2020; 203:901-911. [PMID: 33078270 DOI: 10.1007/s00203-020-02085-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 09/27/2020] [Accepted: 10/06/2020] [Indexed: 11/24/2022]
Abstract
The most important tools in killing and overcoming on the microbes and pathogens that cause diseases in medicine and/or in agriculture are the antibiotics. The discovery and synthesis of the microbial natural products or antibiotics has greatly developed genetically and biotechnologically quickly in the last decades. It is necessary to access this great genetic diversity by finding ways to increase the level of expression of these biosynthetic pathways. In this study, we carried out an improvement in the antibiotic production of weak Streptomyces graminofaciens strain NBR9 that has high lipid content; using Ultra-Violet irradiation mutagenesis. This strain was isolated from the Northern Region in the kingdom of Saudi Arabia and identified biochemically and confirmed genetically by sequencing of the 16S rRNA gene as Streptomyces graminofaciens NBR9; Accession No. (MN640578). The resultant mutant strain showed increasing in their antimicrobial activities. The methods and techniques used for the antibiotic extraction, purification, characterization and identification proved that the obtained antibiotic is same with antibiotic Carbomycin.
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Affiliation(s)
- Hussam Hassan Arafat
- Department of Biology, Faculty of Science and Arts, Northern Border University, Rafha, Saudi Arabia. .,Department of Botany and Microbiology, Faculty of Science, Minia University, Minia City, 61519, Egypt.
| | - Medhat Ahmed Abu-Tahon
- Department of Biology, Faculty of Science and Arts, Northern Border University, Rafha, Saudi Arabia.,Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Roxy, Heliopolis, P.C.11757, Cairo, Egypt
| | - George Saad Isaac
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Roxy, Heliopolis, P.C.11757, Cairo, Egypt
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19
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Benammar L, İnan Bektaş K, Menasria T, Beldüz AO, Güler HI, Bedaida IK, Gonzalez JM, Ayachi A. Diversity and enzymatic potential of thermophilic bacteria associated with terrestrial hot springs in Algeria. Braz J Microbiol 2020; 51:1987-2007. [PMID: 32959204 DOI: 10.1007/s42770-020-00376-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/03/2020] [Indexed: 11/30/2022] Open
Abstract
This study aims to determine the diversity of culturable thermophilic bacteria isolated from eight terrestrial hot springs in Northeastern of Algeria using the conventional methods, SDS-PAGE fingerprinting of whole-cell proteins and 16S rRNA gene sequencing. In addition, their hydrolytic enzyme activities were also investigated. A total of 293 strains were isolated from the hot springs' water and sediment using different culture media. Overall, five distinct bacterial groups were characterized by whole-cell protein pattern analysis. Based on the 16S rRNA gene sequencing of 100 selected strains, the isolates were assigned to the following three major phyla: Firmicutes (93%), Deinococcus-Thermus (5%), and Actinobacteria (2%), which included 27 distinct species belonging to 12 different phylotypes, Aeribacillus, Aneurinibacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Laceyella, Meiothermus, Saccharomonospora, Thermoactinomyces, Thermobifida, and Thermus. The screening for nine extracellular enzymes showed that 65.87% of the isolates presented at least five types of enzyme activities, and 6.48% of strains combined all tested enzymes (amylase, cellulase, pectinase, esculinase, protease, gelatinase, lipase, lecithinase, and nuclease). It was found that Bacillus, Anoxybacillus, Aeribacillus, and Aneurinibacillus were the genera showing the highest activities. Likewise, the study showed an abundant and diverse thermophilic community with novel taxa presenting a promising source of thermozymes with important biotechnological applications. This study showed that a combined identification method using SDS-PAGE profiles of whole-cell proteins and subsequent 16S rRNA gene sequence analysis could successfully differentiate thermophilic bacteria from Algerian hot springs.
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Affiliation(s)
- L Benammar
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, 05078, Batna, Algeria.
- Molecular Biology Research Laboratory, Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey.
- Bacteriology Laboratory, Veterinary and Agricultural Sciences Institute, Department of Veterinary Sciences, University of Batna 1, 05000, Batna, Algeria.
| | - K İnan Bektaş
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - T Menasria
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, 12002, Tebessa, Algeria.
| | - A O Beldüz
- Molecular Biology Research Laboratory, Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - H I Güler
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - I K Bedaida
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences, University of Batna 2, 05078, Batna, Algeria
| | - J M Gonzalez
- Spanish National Research Council Seville (CSIC), Institute of Natural Resources and Agrobiology of Seville (IRNAS), Seville, Spain
| | - A Ayachi
- Bacteriology Laboratory, Veterinary and Agricultural Sciences Institute, Department of Veterinary Sciences, University of Batna 1, 05000, Batna, Algeria
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20
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Sharma N, Kumar J, Abedin MM, Sahoo D, Pandey A, Rai AK, Singh SP. Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya. BMC Microbiol 2020; 20:246. [PMID: 32778049 PMCID: PMC7418396 DOI: 10.1186/s12866-020-01923-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limited information is available in terms of molecular insights into the microbiome, including the uncultured microbes, of the Himalayan habitat. Hence, a vast majority of genomic resources are still under-explored from this region. Metagenome analysis has simplified the extensive in-depth exploration of diverse habitats. In the present study, the culture-independent whole metagenome sequencing methodology was employed for microbial diversity exploration and identification of genes involved in various metabolic pathways in two geothermal springs located at different altitudes in the Sikkim Himalaya. RESULTS The two hot springs, Polok and Reshi, have distinct abiotic conditions. The average temperature of Polok and Reshi was recorded to be 62 °C and 43 °C, respectively. Both the aquatic habitats have alkaline geochemistry with pH in the range of 7-8. Community profile analysis revealed genomic evidence of plentiful bacteria, with a minute fraction of the archaeal population in hot water reservoirs of Polok and Reshi hot spring. Mesophilic microbes belonging to Proteobacteria and Firmicutes phyla were predominant at both the sites. Polok exhibited an extravagant representation of Chloroflexi, Deinococcus-Thermus, Aquificae, and Thermotogae. Metabolic potential analysis depicted orthologous genes associated with sulfur, nitrogen, and methane metabolism, contributed by the microflora in the hydrothermal system. The genomic information of many novel carbohydrate-transforming enzymes was deciphered in the metagenomic description. Further, the genomic capacity of antimicrobial biomolecules and antibiotic resistance were discerned. CONCLUSION The study provided comprehensive molecular information about the microbial treasury as well as the metabolic features of the two geothermal sites. The thermal aquatic niches were found a potential bioresource of biocatalyst systems for biomass-processing. Overall, this study provides the whole metagenome based insights into the taxonomic and functional profiles of Polok and Reshi hot springs of the Sikkim Himalaya. The study generated a wealth of genomic data that can be explored for the discovery and characterization of novel genes encoding proteins of industrial importance.
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Affiliation(s)
- Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Jitesh Kumar
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Mohali, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong, Gangtok, India
| | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong, Gangtok, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong, Gangtok, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), SAS Nagar, Mohali, India.
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21
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Garber B, Glauser J. Recent Developments in Infectious Disease Chemotherapy: Review for Emergency Department Practitioners 2020. CURRENT EMERGENCY AND HOSPITAL MEDICINE REPORTS 2020; 8:116-121. [PMID: 32837804 PMCID: PMC7296288 DOI: 10.1007/s40138-020-00218-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Purpose of Review We discuss and review new antimicrobials for treatment of bacterial, viral, fungal, and parasitic infections with indications, contraindications, and side effects for each. We will also review new information and indications on older agents that are relevant to clinical practice. Many of them may be unfamiliar to Emergency Physicians given their newness and at times hospital restrictions on their use. We also review some new promising agents that are not yet in the clinical pipeline. Recent Findings As new antibiotics become available for clinicians to use, new information becomes available with respect to the drugs' indications, efficacy, pathogen resistance, drug-drug interactions, and side effects. Summary This article provides Emergency Department clinicians with a useful summary with new information on antibiotic use and recent research into agents which may become available.
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Affiliation(s)
- Boris Garber
- MetroHealth Medical Center, Case Western Reserve School of Medicine, Cleveland, OH USA
| | - Jonathan Glauser
- MetroHealth Medical Center, Case Western Reserve School of Medicine, Cleveland, OH USA
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22
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Cushnie TPT, Cushnie B, Echeverría J, Fowsantear W, Thammawat S, Dodgson JLA, Law S, Clow SM. Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls. Pharm Res 2020; 37:125. [PMID: 32529587 DOI: 10.1007/s11095-020-02849-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022]
Abstract
Bioprospecting is the exploration, extraction and screening of biological material and sometimes indigenous knowledge to discover and develop new drugs and other products. Most antibiotics in current clinical use (eg. β-lactams, aminoglycosides, tetracyclines, macrolides) were discovered using this approach, and there are strong arguments to reprioritize bioprospecting over other strategies in the search for new antibacterial drugs. Academic institutions should be well positioned to lead the early stages of these efforts given their many thousands of locations globally and because they are not constrained by the same commercial considerations as industry. University groups can lack the full complement of knowledge and skills needed though (eg. how to tailor screening strategy to biological source material). In this article, we review three key aspects of the bioprospecting literature (source material and in vitro antibacterial and toxicity testing) and present an integrated multidisciplinary perspective on (a) source material selection, (b) legal, taxonomic and other issues related to source material, (c) cultivation methods, (d) bioassay selection, (e) technical standards available, (f) extract/compound dissolution, (g) use of minimum inhibitory concentration and selectivity index values to identify progressible extracts and compounds, and (h) avoidable pitfalls. The review closes with recommendations for future study design and information on subsequent steps in the bioprospecting process.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand.
| | - Benjamart Cushnie
- Faculty of Pharmacy, Mahasarakham University, Kantarawichai, Thailand
| | - Javier Echeverría
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Winita Fowsantear
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | - Sutthiwan Thammawat
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | | | - Samantha Law
- National Collection of Industrial, Food and Marine Bacteria (NCIMB) Ltd, Aberdeen, UK
| | - Simon M Clow
- PMI BioPharma Solutions LLC, Nashville, Tennessee, USA
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23
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Thøgersen MS, Christensen SJ, Jepsen M, Pedersen LH, Stougaard P. Transglycosylating β-d-galactosidase and α-l-fucosidase from Paenibacillus sp. 3179 from a hot spring in East Greenland. Microbiologyopen 2020; 9:e980. [PMID: 31868312 PMCID: PMC7066462 DOI: 10.1002/mbo3.980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023] Open
Abstract
Thermal springs are excellent locations for discovery of thermostable microorganisms and enzymes. In this study, we identify a novel thermotolerant bacterial strain related to Paenibacillus dendritiformis, denoted Paenibacillus sp. 3179, which was isolated from a thermal spring in East Greenland. A functional expression library of the strain was constructed, and the library screened for β-d-galactosidase and α-l-fucosidase activities on chromogenic substrates. This identified two genes encoding a β-d-galactosidase and an α-l-fucosidase, respectively. The enzymes were recombinantly expressed, purified, and characterized using oNPG (2-nitrophenyl-β-d-galactopyranoside) and pNP-fucose (4-nitrophenyl-α-l-fucopyranoside), respectively. The enzymes were shown to have optimal activity at 50°C and pH 7-8, and they were able to hydrolyze as well as transglycosylate natural carbohydrates. The transglycosylation activities were investigated using TLC and HPLC, and the β-d-galactosidase was shown to produce the galactooligosaccharides (GOS) 6'-O-galactosyllactose and 3'-O-galactosyllactose using lactose as substrate, whereas the α-l-fucosidase was able to transfer the fucose moiety from pNP-fuc to lactose, thereby forming 2'-O-fucosyllactose. Since enzymes that are able to transglycosylate carbohydrates at elevated temperature are desirable in many industrial processes, including food and dairy production, we foresee the potential use of enzymes from Paenibacillus sp. 3179 in the production of, for example, instant formula.
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Affiliation(s)
- Mariane S. Thøgersen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Aarhus UniversityRoskildeDenmark
| | - Stefan J. Christensen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Roskilde UniversityRoskildeDenmark
| | - Morten Jepsen
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Novo Nordisk A/SBagsværdDenmark
| | | | - Peter Stougaard
- University of CopenhagenFrederiksberg CDenmark
- Present address:
Aarhus UniversityRoskildeDenmark
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Abstract
The marine environment encompasses a huge biological diversity and can be considered as an underexplored location for prospecting bioactive molecules. In this review, the current state of art about antimicrobial molecules from marine bacteria has been summarized considering the main phylum and sources evolved in a marine environment. Considering the last two decades, we have found as most studied group of bacteria producers of substances with antimicrobial activity is the Firmicutes phylum, in particular strains of the Bacillus genus. The reason for that can be attributed to the difficult cultivation of typical Actinobacteria from a marine sediment, whose members are the major producers of antimicrobial substances in land environments. However, a reversed trend has been observed in recent years with an increasing number of reports settling on Actinobacteria. Great diversity of chemical structures have been identified, such as fijimicyns and lynamicyns from Actinomycetes and macrolactins produced by Bacillus.
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Affiliation(s)
- Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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25
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Altaany Z, Alkaraki A, Abu-Siniyeh A, Al Momani W, Taani O. Evaluation of antioxidant status and oxidative stress markers in thermal sulfurous springs residents. Heliyon 2019; 5:e02885. [PMID: 31844754 PMCID: PMC6895573 DOI: 10.1016/j.heliyon.2019.e02885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/10/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Sulfurous springs have been traditionally used in medical treatment for different purposes. These beneficial effects of sulfurous water have been attributed to the presence of sulfurous compounds mainly in the form of hydrogen sulfide (H2S). The purpose of the present study is to explore the effects of long-term exposure to sulfurous springs on oxidative stress and antioxidant biomarkers responses in individuals who lived nearby the sulfurous springs. The studied area was Al- Hammah sulfurous springs, which is located in the northern part of the Jordan Rift Valley and host many sulfurous springs. Residents in sulfurous springs area are continuously exposed to water and gases emission more than the overall population. We have found that the sulphate levels were 7 times higher in sulfurous springs water samples than control water samples. The majority of the volunteers involved in the present study were more than ten years long residence and lived in range distance between one to five kilometers (less than 3 miles) away from main sulfurous spring, and visited the sulfurous spring at least once a month. We did not find any noticeable symptoms in sulfur spring residents such as headaches, nausea, breathing problems. The total oxidative stress (TOS) and oxidative stress index (OSI) in sulfurous spring residents were lower than control individuals. The total antioxidant capacity (TAC) and total nitric oxide (NOX) levels were higher in sulfurous spring residents compared to control group. Furthermore, we have highlighted that living nearby the sulfurous springs does not affect oxygen saturation levels (SPO2) or heart pulse rate . These findings suggest that long-term exposure to sulfurous springs boost the antioxidant capacity and reduce oxidative stress levels in the human body. Hence, visiting sulfurous springs can act as natural remedies to diminish oxidative stress as they show promising potential in several-oxidative stress-related diseases treatment.
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Affiliation(s)
- Zaid Altaany
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, 21163, Jordan
| | - Almuthanna Alkaraki
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid, 21163, Jordan
| | - Ahmed Abu-Siniyeh
- Department of Medical Laboratory Sciences, Faculty of science, Al-Balqa' Applied University, Jordan
| | - Waleed Al Momani
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, 21163, Jordan
| | - Omar Taani
- King Abdulla University Hospital, Irbid, 22110, Jordan
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Demain AL, Gómez-Ortiz B, Ruiz-Villafán B, Rodríguez-Sanoja R, Sánchez S. Recent findings of molecules with anti-infective activity: screening of non-conventional sources. Curr Opin Pharmacol 2019; 48:40-47. [DOI: 10.1016/j.coph.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 10/26/2022]
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Rubiano-Labrador C, Díaz-Cárdenas C, López G, Gómez J, Baena S. Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes. Extremophiles 2019; 23:793-808. [PMID: 31555903 DOI: 10.1007/s00792-019-01132-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/13/2019] [Indexed: 11/25/2022]
Abstract
Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean volcanic belt, in the eastern and central mountain ranges of the Colombian Andes were used as inocula for the growth and isolation of thermophilic microorganisms using substrates such as starch, gelatin, xylan, cellulose, Tween 80, olive oil, peptone and casamino acids. These springs differed in temperature (50-70 °C) and pH (6.5-7.5). The predominant ion in eastern mountain range thermal springs was sulphate, whereas that in central mountain range springs was bicarbonate. A total of 40 anaerobic thermophilic bacterial strains that belonged to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium were isolated. To investigate the metabolic potential of these isolates, selected strains were analysed for enzymatic activities to identify strains than can produce hydrolytic enzymes. We demonstrated that these thermal springs contained diverse microbial populations of anaerobic thermophilic comprising different metabolic groups of bacteria including strains belonging to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium with amylases, proteases, lipases, esterases, xylanases and pectinases; therefore, the strains represent a promising source of enzymes with biotechnological potential.
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Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
- Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Cartagena de Indias D.T. y C., Colombia
| | - Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia.
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Javier Gómez
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
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Exploring the Determinants of Hot Spring Tourism Customer Satisfaction: Causal Relationships Analysis Using ISM. SUSTAINABILITY 2019. [DOI: 10.3390/su11092613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To stand out in the hot spring tourism industry, customer satisfaction has become the crucial issue for competitiveness. A company cannot implement several customer satisfaction improvement practices altogether with limited resources. Researchers advocate that companies should evaluate the relationships among success factors and explore determinants for their improvement implementation. However, such a relationship evaluation has not yet been adequately performed. This paper intends to explore the determinants for improving hot spring customer satisfaction. Adopting grounded theory (GT) and using data collected from websites, Ctrip and Qunar, the first 12 key factors for customer satisfaction were identified. Then, their interrelationships were assessed by 15 experts, and interpretive structural modeling (ISM) was employed to analyze the interrelationships and the driving and dependence power among key factors. The results show that “Environment Quality”, “Special Resource”, “Convenience”, “Food”, Service Quality”, and “Facilities” were the decisive factors affecting customer satisfaction. The findings offer important implications for hot spring management and practice. The contribution of this study is using a novel approach to establish a hierarchical structural model for comprehensive understanding of factor relationships that influence hot spring tourists’ satisfaction and to explore decisive factors which can help hot spring practitioners to better plan and design effective improvement strategies to attract potential new consumers and retain their current consumers, especially with limited resources.
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Elyasifar B, Jafari S, Hallaj-Nezhadi S, Chapeland-leclerc F, Ruprich-Robert G, Dilmaghani A. Isolation and Identification of Antibiotic-Producing Halophilic Bacteria from Dagh Biarjmand and Haj Aligholi Salt Deserts, Iran. PHARMACEUTICAL SCIENCES 2019. [DOI: 10.15171/ps.2019.11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background: Halophilic bacteria are potent organisms in production of novel bioactive antimicrobial compounds which might be considered in drug innovation and control of plant pathogens. Salt deserts in Semnan province are of the most permanent hypersaline areas in the North of Iran. Despite the importance of these areas, there is no scientific report regarding the biodiversity and potency of their halophilic bacteria. Thus, aforementioned areas were selected to detect the halophilic bacteria. Methods: Here, seven strains were isolated and cultured on their molecular and biochemical properties were characterized. To determine the antibiotic potency of the isolates, agar well diffusion method was conducted. Phylogenetic analysis was done to reveal the isolates relationship with previously known strains. Results: As a result, growth of the strains in the medium containing 5 to 20% (w/v) NaCl determined that the majority of the isolates were moderately halophile. Catalase activity of all strains was positive. The results represented that D6A, Dar and D8B have antimicrobial effects against different plant and human pathogens. Phylogenic tree analysis also showed that two strains of D6A and Dar are belonged to Bacillus subtilis and D8B is belonged to Virgibacillus olivae. The bacteria extracts were evaluated for their antifungal and antibacterial activities on human and Plant pathogenic strains. The MIC of the extract B. subtilis against was found active against human pathogenic fungi and Plant pathogenic bacteria and fungi, ranging from 12.5 to 25 µg/mL. Conclusion: This study highlights the therapeutic and prophylactic potential of B. subtilis extracts as antibacterial and antifungal agents.
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Affiliation(s)
- Babak Elyasifar
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sevda Jafari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Somayeh Hallaj-Nezhadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Florence Chapeland-leclerc
- Univ Paris Descartes, Sorbonne Paris Cité, Institut des Energies de Demain (IED), UMR 8236, F-75205 Paris, France
| | - Gwenaël Ruprich-Robert
- Univ Paris Descartes, Sorbonne Paris Cité, Institut des Energies de Demain (IED), UMR 8236, F-75205 Paris, France
| | - Azita Dilmaghani
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Nishiyama E, Higashi K, Mori H, Suda K, Nakamura H, Omori S, Maruyama S, Hongoh Y, Kurokawa K. The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan. Front Bioeng Biotechnol 2018; 6:202. [PMID: 30619848 PMCID: PMC6306410 DOI: 10.3389/fbioe.2018.00202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022] Open
Abstract
Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.
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Affiliation(s)
- Eri Nishiyama
- Biotechnological Research Support Division, FASMAC Co. Ltd, Kanagawa, Japan.,Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Koichi Higashi
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Konomi Suda
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hitomi Nakamura
- Department of Solid Earth Geochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Soichi Omori
- Faculty of Liberal Arts, The Open University of Japan, Chiba, Japan
| | - Shigenori Maruyama
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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Prieto-Barajas CM, Valencia-Cantero E, Santoyo G. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Panda AK, Bisht SS, Kaushal BR, De Mandal S, Kumar NS, Basistha BC. Bacterial diversity analysis of Yumthang hot spring, North Sikkim, India by Illumina sequencing. BIG DATA ANALYTICS 2017. [DOI: 10.1186/s41044-017-0022-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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The amazing world of antibiotics. Biochem Pharmacol 2017; 133:1-3. [PMID: 28288822 DOI: 10.1016/j.bcp.2017.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/08/2017] [Indexed: 11/20/2022]
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