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Elsbaey M, Jomori T, Tanaka J, Oku N, Igarashi Y. Okichromanone, a new antiviral chromanone from a marine-derived Microbispora. J Antibiot (Tokyo) 2024; 77:389-392. [PMID: 38519549 DOI: 10.1038/s41429-024-00718-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
Okichromanone (1), a new chromanone, was isolated from the culture extract of a sponge-derived actinomycete Microbispora, along with known 1-hydroxyphenazine (2). Compound 1 was elucidated to exist as a mixture of two isomeric structures (1a and 1b) at a ratio of nearly 3:2. Compounds 1 and 2 showed anti HSV-I activity with IC50 values 40 and 86 μM, respectively, and anti HSV-II activity with IC50 values 59 and 123 μM, respectively.
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Affiliation(s)
- Marwa Elsbaey
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
| | - Takahiro Jomori
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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2
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [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: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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3
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Manikkam R, Murthy S, Palaniappan S, Kaari M, Sahu AK, Said M, Ganesan V, Kannan S, Ramasamy B, Thirugnanasambandan S, Dastager SG, Hanna LE, Kumar V. Antibacterial and Anti-HIV Metabolites from Marine Streptomyces albus MAB56 Isolated from Andaman and Nicobar Islands, India. Appl Biochem Biotechnol 2023; 195:7738-7754. [PMID: 37086378 DOI: 10.1007/s12010-023-04493-y] [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] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Marine-derived actinobacteria have tremendous potential to produce novel metabolites with diverse biological activities. The Andaman coast of India has a lot of microbial diversity, but it is still a relatively unknown ecology for isolating novel actinobacteria with beneficial bioactive compounds. We have isolated 568 actinobacterial strains from mangrove rhizosphere sediments and sponge samples. Crude extracts from 75 distinct strains were produced by agar surface fermentation and extracted using ethyl acetate. In the disc diffusion method, 25 actinobacterial strains showed antimicrobial activity; notably, the strain MAB56 demonstrated promising broad-spectrum activity. Strain MAB56 was identified as Streptomyces albus by cultural, microscopic, and molecular methods. Conditions for bioactive metabolites from MAB56 were optimized and produced in a lab-scale fermenter. Three active metabolites (C1, C2, and C3) that showed promising broad-spectrum antimicrobial activity were isolated through HPLC-based purification. Based on the UV, FT-IR, NMR, and LC-MS analysis, the chemical nature of the active compounds was confirmed as 12-methyltetradecanoic acid (C1), palmitic acid (C2), and tridecanoic acid (C3) with molecular formulae C14H28O2, C16H32O2, and C13H26O2, respectively. Interestingly, palmitic acid (C2) also exhibited anti-HIV activity with an IC50 value of < 1 µg/ml. Our findings reveal that the actinobacteria from the Andaman marine ecosystems are promising for isolating anti-infective metabolites.
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Affiliation(s)
- Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India.
| | - Sangeetha Murthy
- Department of Microbiology, Periyar University, Salem, 636011, Tamil Nadu, India
| | | | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - Amit Kumar Sahu
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Madhukar Said
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Vijayalakshmi Ganesan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - Sivakumar Kannan
- CAS in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | | | | | - Syed G Dastager
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis, Chennai, 600031, Tamil Nadu, India
| | - Vanaja Kumar
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
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4
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Ngema SS, Khumalo SH, Ojo MC, Pooe OJ, Malilehe TS, Basson AK, Madoroba E. Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli. Microorganisms 2023; 11:2539. [PMID: 37894198 PMCID: PMC10609338 DOI: 10.3390/microorganisms11102539] [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: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.
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Affiliation(s)
- Siyanda S. Ngema
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Solomuzi H. Khumalo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Michael C. Ojo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Tsolanku S. Malilehe
- Department of Water and Sanitation, University of Limpopo, Private Bag X1106, Polokwane 0727, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
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5
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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6
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González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom 2023; 9:mgen000921. [PMID: 36748531 PMCID: PMC9973853 DOI: 10.1099/mgen.0.000921] [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] [Indexed: 01/21/2023] Open
Abstract
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.
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Affiliation(s)
- Luz A González-Salazar
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Michelle Quezada
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorena Rodríguez-Orduña
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico.,Present address: Microbial Diversity and Specialized Metabolism Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Cuauhtémoc Licona-Cassani
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico.,Division of Integrative Biology, Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, Mexico
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7
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Balraj J, Murugesan T, Dhanapal AR, Kalieswaran V, Jairaman K, Archunan G, Jayaraman A. Bioconversion of lovastatin to simvastatin by Streptomyces carpaticus toward the inhibition of HMG-CoA activity. Biotechnol Appl Biochem 2022. [PMID: 36524308 DOI: 10.1002/bab.2429] [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: 08/29/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
The aim of this study was the modification of lovastatin by microbes to improve its potential. Actinobacteria exhibit staggering diversity in terms of their biosynthetic capability for specialized metabolites which has been traced back to the presence of specialized gene clusters. The objective of the study is to exploit the potential of Actinobacteria strain(s), which can biotransform lovastatin to simvastatin, which might be a more potent therapeutic agent than lovastatin. We have screened 40 Actinobacteria strains and assessed their biotransformation potential primarily through thin layer chromatography (TLC) analysis, followed by high performance thin layer chromatography and high performance liquid chromatography analysis. One strain C7 (CTL S12) has been identified as a potential Actinobacteria that favored the simvastatin biotransformation. The morphological and biochemical analysis together with 16S rRNA sequencing coupled with phylogenetic analysis confirmed the ideal strain (C7) as Streptomyces carpaticus. Successively, the purified simvastatin from S. carpaticus was characterized by liquid chromatography-mass spectrometry (LC-MS), infrared spectrometry, nuclear magnetic resonance, and HMG-CoA assay. In the LC-MS analysis, a peak at 419.24 m/z confirmed the elemental composition of simvastatin (C25 H39 O5 ). In HMG-CoA assay, the IC50 of simvastatin was 50 μg/ml, and the inhibitory potential was 1.36 times higher compared to that of lovastatin. Thus, the biotransformation of simvastatin from lovastatin by S. carpaticus is reported for the first time.
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Affiliation(s)
- Janani Balraj
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Thandeeswaran Murugesan
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India.,Bharathiar Cancer Theranostics Research Centre, RUSA2.0, 641046, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Anand Raj Dhanapal
- Centre for Plant Tissue Culture and Central Instrumentation Laboratory, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India.,Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Vidhya Kalieswaran
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Karunyadevi Jairaman
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Angayarkanni Jayaraman
- Department of Microbial Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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8
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Saadouli I, Marasco R, Mejri L, Hamden H, Guerfali MM, Stathopoulou P, Daffonchio D, Cherif A, Ouzari HI, Tsiamis G, Mosbah A. Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins. Front Microbiol 2022; 13:997832. [PMID: 36583041 PMCID: PMC9793712 DOI: 10.3389/fmicb.2022.997832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.
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Affiliation(s)
- Ilhem Saadouli
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lassaad Mejri
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Haytham Hamden
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Meriem M’saad Guerfali
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ameur Cherif
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia,*Correspondence: Hadda-Imene Ouzari,
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece,George Tsiamis,
| | - Amor Mosbah
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia,Amor Mosbah,
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9
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Schneider YK, Hagestad OC, Li C, Hansen EH, Andersen JH. Selective isolation of Arctic marine actinobacteria and a down-scaled fermentation and extraction strategy for identifying bioactive compounds. Front Microbiol 2022; 13:1005625. [DOI: 10.3389/fmicb.2022.1005625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
Actinobacteria are among the most prolific producers of bioactive secondary metabolites. In order to collect Arctic marine bacteria for the discovery of new bioactive metabolites, actinobacteria were selectively isolated during a research cruise in the Greenland Sea, Norwegian Sea and the Barents Sea. In the frame of the isolation campaign, it was investigated how different sample treatments, isolation media and sample-sources, such as animals and sediments, affected the yield of actinobacterial isolates to aid further isolation campaigns. Special attention was given to sediments, where we expected spores of spore forming bacteria to enrich. Beside actinobacteria a high share of bacilli was obtained which was not desired. An experimental protocol for down-scaled cultivation and extraction was tested and compared with an established low-throughput cultivation and extraction protocol. The heat-shock method proved suitable to enrich spore-, or endospore forming bacteria such as bacilli. Finally, a group bioactive compounds could be tentatively identified using UHPLC–MS/MS analysis of the active fractions.
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10
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John J A, Samuel MS, Govarthanan M, Selvarajan E. A comprehensive review on strategic study of cellulase producing marine actinobacteria for biofuel applications. ENVIRONMENTAL RESEARCH 2022; 214:114018. [PMID: 35961544 DOI: 10.1016/j.envres.2022.114018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/12/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Every year, 180 billion tonnes of cellulose are produced by plants as waste biomass after the cultivation of the desired product. One of the smart and effective ways to utilize this biomass rather than burn it is to utilize the biomass to adequately meet the energy needs with the help of microbial cellulase that can catalytically convert the cellulose into simple sugar units. Marine actinobacteria is one of the plentiful gram-positive bacteria known for its industrial application as it can produce multienzyme cellulase with high thermal tolerance, pH stability and high resistant towards metal ions and salt concentration, along with other antimicrobial properties. Highly stable cellulase obtained from marine actinobacteria will convert the cellulose biomass into glucose, which is the precursor for biofuel production. This review will provide a comprehensive outlook of various strategic applications of cellulase from marine actinobacteria which can facilitate the breakdown of lignocellulosic biomass to bioenergy with respect to its characteristics based on the location/environment that the organism was collected and its screening strategies followed by adopted methodologies to mine the novel cellulase genome and enhance the production, thereby increasing the activity of cellulase continued by effective immobilization on novel substrates for the multiple usage of cellulase along with the industrial applications.
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Affiliation(s)
- Ashwini John J
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India
| | - Melvin S Samuel
- Department of Material Science and Engineering, University of Winsconsin-Milwaukee, Milwaukee, WI, USA
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Departrment of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India
| | - Ethiraj Selvarajan
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India.
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11
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Zhu Y, Zheng G, Xin X, Ma J, Ju J, An F. Combinatorial strategies for production improvement of anti-tuberculosis antibiotics ilamycins E 1/E 2 from deep sea-derived Streptomyces atratus SCSIO ZH16 ΔilaR. BIORESOUR BIOPROCESS 2022; 9:111. [PMID: 38647771 PMCID: PMC10992044 DOI: 10.1186/s40643-022-00599-z] [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: 08/25/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Ilamycins E1/E2 are novel cyclic heptapeptides from Streptomyces atratus SCSIO ZH16, which have the MIC value of 9.8 nM against Mycobacterium tuberculosis H37Rv. However, the lower fermentative titer of ilamycins E1/E2 cut off further development for novel anti-TB lead drugs. In order to break the obstacle, the combinatorial strategy of medium optimization, fermentative parameters optimization, exogenous addition of metal ions, precursors, and surfactants was developed to promoted the production of ilamycins E1/E2. Addition of 1 mM ZnCl2 at 0 h, 1 g/L tyrosine at 96 h, and 2 g/L shikimic acid at 48 h increased the production of ilamycins E1/E2 from 13.51 to 762.50 ± 23.15, 721.39 ± 19.13, and 693.83 ± 16.86 mg/L, respectively. qRT-PCR results showed that the transcription levels of key genes in Embden-Meyerhof-Parnas pathway, hexose phosphate shunt pathway, and shikimic acid pathway were upregulated. In addition, the production of ilamycins E1/E2 reached 790.34 mg/L in a 5-L bioreactor by combinatorial strategy. Combinatorial strategies were used for improving ilamycins E1/E2 production in S. atratus ΔilaR and provided a sufficient basis on further clinic development.
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Affiliation(s)
- Yunfei Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Gaofan Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiujuan Xin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Faliang An
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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12
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Kalkan S. Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity. MARINE POLLUTION BULLETIN 2022; 183:114063. [PMID: 36057154 DOI: 10.1016/j.marpolbul.2022.114063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.
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Affiliation(s)
- Samet Kalkan
- Recep Tayyip Erdogan University, Faculty of Fisheries, Ataturk Street Fener District, 53100 Merkez, Rize, Turkey.
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13
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Azad MAK, Chunhacha P, Suriyachadkun C, Sripreechasak P, Tanasupawat S, Phongsopitanun W. Saccharothrix obliqua sp. nov., isolated from soil of Sichang Island, Thailand. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During an investigation of rare actinobacteria, isolate SC076T was isolated from a soil sample collected from Sichang Island, Chonburi Province, Thailand. The strain showed the highest 16S rRNA gene similarity to
Saccharothrix australiensis
DSM 43800T (98.6%) and
Saccharothrix espanaensis
DSM 44229T (98.6%). The zigzag morphology of the spore chain was observed on the aerial mycelia. meso-Diaminopimelic acid was detected in the peptidoglycan. Whole-cell sugars contained rhamnose, ribose, mannose glucose and galactose. Polar lipids were phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, unidentified ninhydrin-positive glycolipid, unidentified glycolipid and four unidentified lipids. The menaquinones were MK-9(H8), MK-9(H4), MK-9(H2) and MK-9(H0). The predominant fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The draft genome of SC076T was 8040245 bp with a G+C content of 72.5 mol%. The results of genomic analysis between strain SC076T and the related type strains showed that the digital DNA–DNA hybridization and average nucleotide identity values among the strains were 23.6-32.8% and 77.7–86.8 %, respectively, which are lower than the thresholds used to distinguish strains from others of the same species. Based on the taxonomic evidence, strain SC076T represents a novel species of the genus
Saccharothrix
for which the name Saccharothrix obliqua sp. nov. is proposed. The type strain is SC076T (=TBRC 14540T=NBRC 115117T).
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Affiliation(s)
- Md. Abul Kalam Azad
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Preedakorn Chunhacha
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani 12120, Thailand
| | - Paranee Sripreechasak
- Department of Biotechnology, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
- Pharmaceutical Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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14
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Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [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: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
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15
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Duhsaki L, Mukherjee S, Rani TS, Madhuprakash J. Genome analysis of Streptomyces sp. UH6 revealed the presence of potential chitinolytic machinery crucial for chitosan production. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:431-442. [PMID: 34192819 DOI: 10.1111/1758-2229.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Chitosan and its derivatives have numerous applications in wastewater treatment as bio-coagulants, flocculants and bio-adsorbents against both particulate and dissolved pollutants. Chitinolytic bacteria secrete an array of enzymes, which play crucial role in chitin to chitosan conversion. Consequently, there is a growing demand for identification and characterization of novel bacterial isolates with potential implications in chitosan production. We describe genomic features of the new isolate Streptomyces sp. UH6. Analysis of the 6.51 Mb genome revealed the GC content as 71.95% and presence of 6990 coding sequences of which 63% were functionally annotated. Further, we identified two possible chitin-utilization pathways, which employ secreted enzymes like lytic polysaccharide monooxygenases and family-18 glycoside hydrolases (GHs). More importantly, the genome has six family-4 polysaccharide deacetylases with probable role in chitin to chitosan conversion, as well as two chitosanases belonging to GH46 and GH75 families. In addition, the gene clusters, dasABC and ngcEFG coding for transporters, which mediate the uptake of N,N'-diacetylchitobiose and N-acetyl-d-glucosamine were identified. Several genes responsible for hydrolysis of other polysaccharides and fermentation of sugars were also identified. Taken together, the phylogenetic and genomic analyses suggest that the isolate Streptomyces sp. UH6 secretes potential chitin-active enzymes responsible for chitin to chitosan conversion.
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Affiliation(s)
- Lal Duhsaki
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | - Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
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16
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Microbiological Analysis and Metagenomic Profiling of the Bacterial Community of an Anthropogenic Soil Modified from Typic Haploxererts. LAND 2022. [DOI: 10.3390/land11050748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This work aimed to characterize the microbial communities of an anthropogenic soil originating from application of pedotechniques to Vertisols in a Mediterranean environment. Bare soil profiles were sampled at three depths (0–10 cm, 10–30 cm, and 30–50 cm) and compared with the original soil not transformed at the same depths. The anthropogenic soils were characterized by a higher CaCO3 concentration (360–640 g/kg) than control soil (190–200 g/kg), while an opposite trend was registered for clay, where control soil showed a higher concentration (465 g/kg on average) than anthropogenic soil (355 g/kg on average). Organic carbon content was much higher in the untransformed soil. All samples were microbiologically investigated using a combined culture-dependent and -independent approach. Each pedon displayed a generally decreasing level with soil depth for the several microbial groups investigated; in particular, filamentous fungi were below the detection limit at 30–50 cm. To isolate bacteria actively involved in soil particle aggregation, colonies with mucoid appearance were differentiated at the strain level and genetically identified: the major groups were represented by Bacillus and Pseudomonas. MiSeq Illumina analysis identified Actinobacteria and Firmicutes as the main groups. A high microbial variability was found in all the three anthropogenic pedons and the microorganisms constitute a mature community.
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17
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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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18
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Abid S, Farid A, Abid R, Rehman MU, Alsanie WF, Alhomrani M, Alamri AS, Asdaq SMB, Hefft DI, Saqib S, Muzammal M, Morshedy SA, Alruways MW, Ghazanfar S. Identification, Biochemical Characterization, and Safety Attributes of Locally Isolated Lactobacillus fermentum from Bubalus bubalis (buffalo) Milk as a Probiotic. Microorganisms 2022; 10:954. [PMID: 35630398 PMCID: PMC9144466 DOI: 10.3390/microorganisms10050954] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
The demand of functional foods is on the rise, and researchers are trying to develop nutritious dairy products by using well-characterized strains of bacteria. In this study, we identified locally isolated strains of Lactobacillus fermentum from Bubalus bubalis (Nilli Ravi buffalo) milk and evaluated their potential as probiotics in food products like fermented milk. Fifteen Lactobacillus strains were initially isolated, and only four strains (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were examined for morphological and biochemical characterizations due to their ability of gas production in Durham tubes. Moreover, these strains were selected for further probiotic characterizations due to their extreme morphological resemblance with lactic acid bacteria for their antimicrobial activity, enzymatic potential, autoaggregation capability, hydrophobicity, and acid and bile tolerance. All selected isolates showed significant probiotic potential. However, NMCC-14 and NMCC-17 strains showed maximum probiotic potential. The isolates (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were identified as Lactobacillus fermentum utilizing 16S rRNA gene sequencing. The in vivo safety study of NMCC-14 (dose: 1010 CFU/day/mice; 21 days, orally) showed no histological dysfunctions in a mouse model. Pathogenic bacterial enzymes reduced the beneficial bacterial load in the host gastrointestinal tract. These results suggest that the NMCC-14 strain is safe and can be potentially used as a probiotic. Moreover, fermented milk was prepared by using the NMCC-14 strain. The results revealed that NMCC-14 strain-based fermented milk had significantly (p < 0.05) higher protein content (4.4 ± 0.06), water-holding capacity (WHC), and dynamic viscosity as compared to non-fermented milk. The results suggest that L. fermentum NMCC-14 is safe and nontoxic; hence, it can be a beneficial supplement to be used for the development of dairy products to be subjected to further clinical testing.
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Affiliation(s)
- Sana Abid
- Department of Biology, Faculty of Science & Technology, Virtual University, Lahore 54000, Pakistan;
| | - Arshad Farid
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan 29050, Pakistan; (A.F.); (M.M.)
| | - Rameesha Abid
- Department of Biotechnology, University of Sialkot, Sialkot 51310, Pakistan;
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Mujeeb Ur Rehman
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45500, Pakistan;
| | - Walaa F. Alsanie
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | - Abdulhakeem S. Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University, Al Hawiyah 21944, Saudi Arabia; (W.F.A.); (M.A.); (A.S.A.)
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Al Hawiyah 21944, Saudi Arabia
| | | | - Daniel Ingo Hefft
- Reaseheath College, University Centre Reaseheath, Nantwich CW5 6DF, UK;
| | - Saddam Saqib
- Department of Biotechnology, Mohi- ud-Din Islamic University, Nerian Sharif 12080, Pakistan;
| | - Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan 29050, Pakistan; (A.F.); (M.M.)
| | - Sabrin Abdelrahman Morshedy
- Fish and Animal Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21526, Egypt;
| | - Mashael W. Alruways
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra 15273, Saudi Arabia;
| | - Shakira Ghazanfar
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
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19
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Sedeek AM, Ismail MM, Elsayed TR, Ramadan MA. Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated microorganisms. Lett Appl Microbiol 2022; 75:511-525. [PMID: 35485872 DOI: 10.1111/lam.13728] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Marine microorganisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation, and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies like in situ cultivation, dilution-to-extinction cultivation, and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling, and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine microorganism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.
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Affiliation(s)
- Abdelrahman M Sedeek
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismaillia, 41522, Egypt
| | - Maha M Ismail
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Egypt, Giza, 12613, Egypt
| | - Mohamed A Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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20
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Chakraborty B, Kumar RS, Almansour AI, Gunasekaran P, Nayaka S. Bioprospection and secondary metabolites profiling of marine Streptomyces levis strain KS46. Saudi J Biol Sci 2022; 29:667-679. [PMID: 35197732 PMCID: PMC8847965 DOI: 10.1016/j.sjbs.2021.11.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/09/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
The quest for novel broad spectrum bioactive compounds is needed continuously because of the rapid advent of pathogenic multi drug resistant organisms. Actinomycetes, isolated from unexplored habitats can be a solution of this problem. The motive of this research work was isolation of actinomycetes having potential antimicrobial activities from unexplored regions of Devbag and Tilmati beach. The isolated actinomycetes were screened against pathogenic microbes for antimicrobial activities through cross streak method. Enzyme production activity was checked for these actinomycetes for amylase, protease, cellulase and lipase enzymes. Further antimicrobial activity of ethyl acetate extract of the potent strain KS46 was performed. The strain KS46 was identified with 16S rRNA gene sequencing and secondary structure was analysed. Gas chromatography–Mass spectrometry (GC–MS) profiling was conducted to ascertain the presence of bioactive metabolites in the ethyl acetate extract. The collected samples were pre-treated and 70 actinomycetes were isolated. The Streptomyces sp. strain KS46 showed the best antimicrobial activity in primary screening. Ethyl acetate extract of the strain KS46 revealed antimicrobial activity against S. aureus, B. subtilis, B. cereus, E. faecalis, K. pneumoniae, E. coli, S. flexneri, C. albicans and C. glabrata. The 16S rRNA gene sequencing identified the strain KS46 as Streptomyces levis strain KS46. The GC–MS metabolite profiling of the ethyl acetate extract revealed the availability of 42 compounds including fatty acid esters, fatty acid anhydrides, alkanes, steroids, esters, alcohols, carboxylic ester, etc. having antibacterial, antifungal, antiproliferative, antioxidant activities. This study indicated that Devbag and Tilmati beaches being untapped habitats have enormous diversity of promising antimicrobial metabolite producing actinomycetes. Therefore, further exploration should be carried out to characterize the potential actinomycetes, which can be optimistic candidates for generation of novel antimicrobial drugs.
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21
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Zamora-Quintero AY, Torres-Beltrán M, Guillén Matus DG, Oroz-Parra I, Millán-Aguiñaga N. Rare actinobacteria isolated from the hypersaline Ojo de Liebre Lagoon as a source of novel bioactive compounds with biotechnological potential. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001144. [PMID: 35213299 PMCID: PMC8941997 DOI: 10.1099/mic.0.001144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022]
Abstract
The Ojo de Liebre Lagoon is a Marine Protected Area that lies within a UNESCO World Heritage Site and is a critical habitat for important migratory species such as the grey whale and bird species. Unique hypersaline environments, such as the Ojo de Liebre Lagoon, are underexplored in terms of their bacterial and chemical diversity, representing a potential source for new bioactive compounds with pharmacological properties. Actinobacteria are one of the most diverse and prolific taxonomic bacterial groups in terms of marine bioactive compounds. This study aimed to identify the culturable actinobacterial community inhabiting the Lagoon, as well as to test their potential as new sources of anticancer compounds with pharmacological potential. A selective isolation approach focused on spore-forming bacteria from 40 sediment samples generated a culture collection of 64 strains. The 16S rRNA gene analyses identified three phyla in this study, the Actinobacteria, Firmicutes and Proteobacteria, where the phylum Actinobacteria dominated (57%) the microbial community profiles. Within the Actinobacteria, nine different genera were isolated including the Actinomadura, Micromonospora, Nocardiopsis, Plantactinospora and Streptomyces sp. We observed seasonal differences on actinobacteria recovery. For instance, Micromonospora strains were recovered during the four sampling seasons, while Arthrobacter and Pseudokineococcus were only isolated in February 2018, and Blastococcus, Rhodococcus and Streptomyces were uniquely isolated in June 2018. Ethyl acetate crude extracts derived from actinobacterial cultures were generated and screened for cytotoxic activity against six cancer cell lines. Strains showed promising low percentages of viability on lung (H1299), cervical (SiHa), colon (Caco-2) and liver (HepG2) cancer lines. Molecular networking results suggest many of the metabolites produced by these strains are unknown and they might harbour novel chemistry. Our results showed the Ojo de Liebre Lagoon is a novel source for isolating diverse marine actinobacteria which produce promising bioactive compounds for potential biotechnological use as anticancer agents.
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Affiliation(s)
- Andrea Y. Zamora-Quintero
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Mónica Torres-Beltrán
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Dulce G. Guillén Matus
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Irasema Oroz-Parra
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Natalie Millán-Aguiñaga
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
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22
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Ouchene R, Intertaglia L, Zaatout N, Kecha M, Suzuki MT. Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment. J Appl Microbiol 2021; 132:2870-2882. [PMID: 34919313 DOI: 10.1111/jam.15415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
AIMS The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity. METHODS AND RESULTS Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown. CONCLUSION The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain. SIGNIFICANCE AND IMPACT OF THE STUDY This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.
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Affiliation(s)
- Rima Ouchene
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria.,Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Université, CNRS, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Observatoire Océanologique de Banyuls, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Nawel Zaatout
- Faculty of Natural and Life Sciences, University of Batna, Batna, Algeria
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Marcelino T Suzuki
- Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Université, CNRS, Observatoire Océanologique, Banyuls-sur-Mer, France
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Castejón P, Cabas I, Gómez V, Chaves-Pozo E, Cerezo-Ortega I, Moriñigo MÁ, Martínez-Manzanares E, Galindo-Villegas J, García-Ayala A. Vaccination of Gilthead Seabream After Continuous Xenoestrogen Oral Exposure Enhances the Gut Endobolome and Immune Status via GPER1. Front Immunol 2021; 12:742827. [PMID: 34721409 PMCID: PMC8551918 DOI: 10.3389/fimmu.2021.742827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
In fish culture settings, the exogenous input of steroids is a matter of concern. Recently, we unveiled that in the gilthead seabream (Sparus aurata), the G protein-coupled estrogen receptor agonist G-1 (G1) and the endocrine disruptor 17α-ethinylestradiol (EE2) are potent modulators in polyreactive antibody production. However, the integral role of the microbiota upon immunity and antibody processing in response to the effect of EE2 remains largely unexplored. Here, juvenile seabreams continuously exposed for 84 days to oral G1 or EE2 mixed in the fish food were intraperitoneally (i.p.) immune primed on day 42 with the model antigen keyhole limpet hemocyanin (KLH). A critical panel of systemic and mucosal immune markers, serum VTG, and humoral, enzymatic, and bacteriolytic activities were recorded and correlated with gut bacterial metagenomic analysis 1 day post-priming (dpp). Besides, at 15 dpp, animals received a boost to investigate the possible generation of specific anti-KLH antibodies at the systemic and mucosal interphases by the end of the trial. On day 43, EE2 but not G1 induced a significant shift in the serum VTG level of naive fish. Simultaneously, significant changes in some immune enzymatic activities in the serum and gut mucus of the EE2-treated group were recorded. In comparison, the vaccine priming immunization resulted in an attenuated profile of most enzymatic activities in the same group. The gut genes qPCR analysis exhibited a related pattern, only emphasized by a significant shift in the EE2 group's il1b expression. The gut bacterial microbiome status underwent 16S rRNA dynamic changes in alpha diversity indices, only with the exposure to oral G1, supporting functional alterations on cellular processes, signaling, and lipid metabolism in the microbiota. By the same token, the immunization elevated the relative abundance of Fusobacteria only in the control group, while this phylum was depleted in both the treated groups. Remarkably, the immunization also promoted changes in the bacterial class Betaproteobacteria and the estrogen-associated genus Novosphingobium. Furthermore, systemic and mucosal KLH-specific immunoglobulin (Ig)M and IgT levels in the fully vaccinated fish showed only slight changes 84 days post-estrogenic oral administration. In summary, our results highlight the intrinsic relationship among estrogens, their associated receptors, and immunization in the ubiquitous fish immune regulation and the subtle but significant crosstalk with the gut endobolome.
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Affiliation(s)
- Pablo Castejón
- Department of Cell Biology and Histology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Instituto Murciano de Investigacion Biosanitaria (IMIB), Centro de Investigacion Biomedica en Red Enfermedades Raras (CIBERER), Murcia, Spain
| | - Isabel Cabas
- Department of Cell Biology and Histology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Instituto Murciano de Investigacion Biosanitaria (IMIB), Centro de Investigacion Biomedica en Red Enfermedades Raras (CIBERER), Murcia, Spain
| | - Victoria Gómez
- Department of Cell Biology and Histology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Instituto Murciano de Investigacion Biosanitaria (IMIB), Centro de Investigacion Biomedica en Red Enfermedades Raras (CIBERER), Murcia, Spain
| | - Elena Chaves-Pozo
- Aquaculture Department, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Isabel Cerezo-Ortega
- Department of Microbiology, Faculty of Sciences, University of Malaga, Málaga, Spain
| | - Miguel Ángel Moriñigo
- Department of Microbiology, Faculty of Sciences, University of Malaga, Málaga, Spain
| | | | | | - Alfonsa García-Ayala
- Department of Cell Biology and Histology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Instituto Murciano de Investigacion Biosanitaria (IMIB), Centro de Investigacion Biomedica en Red Enfermedades Raras (CIBERER), Murcia, Spain
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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25
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Diketopiperazine derivative from marine actinomycetes Nocardiopsis sp. SCA30 with antimicrobial activity against MRSA. Arch Microbiol 2021; 203:6173-6181. [PMID: 34632524 DOI: 10.1007/s00203-021-02582-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
Actinobacteria isolated from marine sources are a potential source of novel natural products. In this study, we report isolation, biological activity and characterization of secondary metabolites from strain Nocardiopsis sp. SCA30, isolated from marine sediments of Havelock Islands, Andaman and Nicobar, India. The ethyl acetate extracts of the isolate on screening for biological activity demonstrated antibacterial potency and antiproliferative activity. The extracts showed anticancer activity in a panel of cell lines, including HCT 15, HT 29, MCF 7 and MDA-MB 468, at concentrations ranging from 62.5 to 1000 µg/ml. A dose-dependent reduction in cell viability was observed in all the tested cell lines. The extract at 15 µg/ml and 30 µg/ml inhibited growth of methicillin-resistant Staphylococcus aureus ATCC NR-46071 and NR-46171 with MIC's of 15.62 and 7.81 µg/ml, respectively. LC-MS and NMR studies revealed that the antibacterial and anticancer compound isolated from Nocardiopsis sp. SCA30 is 1-acetyl-4-4(hydroxyphenyl)piperazine.
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Deep-Sea Actinobacteria Mitigate Salinity Stress in Tomato Seedlings and Their Biosafety Testing. PLANTS 2021; 10:plants10081687. [PMID: 34451732 PMCID: PMC8401925 DOI: 10.3390/plants10081687] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022]
Abstract
Soil salinity is an enormous problem affecting global agricultural productivity. Deep-sea actinobacteria are interesting due to their salt tolerance mechanisms. In the present study, we aim to determine the ability of deep-sea Dermacoccus (D. barathri MT2.1T and D. profundi MT2.2T) to promote tomato seedlings under 150 mM NaCl compared with the terrestrial strain D. nishinomiyaensis DSM20448T. All strains exhibit in vitro plant growth-promoting traits of indole-3-acetic acid production, phosphate solubilization, and siderophore production. Tomato seedlings inoculated with D. barathri MT2.1T showed higher growth parameters (shoot and root length, dry weight, and chlorophyll content) than non-inoculated tomato and the terrestrial strain under 150 mM NaCl. In addition, hydrogen peroxide (H2O2) in leaves of tomatoes inoculated with deep-sea Dermacoccus was lower than the control seedlings. This observation suggested that deep-sea Dermacoccus mitigated salt stress by reducing oxidative stress caused by hydrogen peroxide. D. barathri MT2.1T showed no harmful effects on Caenorhabditis elegans, Daphnia magna, Eisenia foetida, and Escherichia coli MC4100 in biosafety tests. This evidence suggests that D. barathri MT2.1T would be safe for use in the environment. Our results highlight the potential of deep-sea Dermacoccus as a plant growth promoter for tomatoes under salinity stress.
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Chen RW, He YQ, Cui LQ, Li C, Shi SB, Long LJ, Tian XP. Diversity and Distribution of Uncultured and Cultured Gaiellales and Rubrobacterales in South China Sea Sediments. Front Microbiol 2021; 12:657072. [PMID: 34220745 PMCID: PMC8248818 DOI: 10.3389/fmicb.2021.657072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Actinobacteria are ubiquitous in marine ecosystems, and they are regarded as an important, underexplored, potential pharmaceutical resource. The orders Gaiellales and Rubrobacterales are deep taxonomic lineages of the phylum Actinobacteria, both are represented by a single genus and contain only a few species. Although they have been detected frequently by high-throughput sequencing, their functions and characteristics in marine habitats remain unknown due to the lack of indigenous phenotypes. Here, we investigated the status of the orders in South China Sea (SCS) sediments using culture-independent and culture-dependent methods. Gaiellales is the second-most abundant order of Actinobacteria and was widely distributed in SCS sediments at water depths of 42-4,280 m, and four novel marine representatives in this group were successfully cultured. Rubrobacterales was present at low abundance in energy-limited marine habitats. An isolation strategy for Rubrobacterales from marine samples was proposed, and a total of 138 mesophilic Rubrobacterales strains were isolated under conditions of light and culture time combined with high-salinity or low-nutrient media. Marine representatives recovered in this study formed branches with a complex evolutionary history in the phylogenetic tree. Overall, the data indicate that both Gaiellales and Rubrobacterales can adapt to and survive in extreme deep-sea environments. This study lays the groundwork for further analysis of the distribution and diversity of the orders Gaiellales and Rubrobacterales in the ocean and provides a specific culture strategy for each group. The results open a window for further research on the ecological roles of the two orders in marine ecosystems.
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Affiliation(s)
- Rou-Wen Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan-Qiu He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lin-Qing Cui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Song-Biao Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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28
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Li C, He YQ, Cui LQ, Albuquerque L, Chen RW, Long LJ, Tian XP. Miltoncostaea marina gen. nov. sp. nov., and Miltoncostaea oceani sp. nov., a novel deep branching phylogenetic lineage within the class Thermoleophilia isolated from marine environments, and proposal of Miltoncostaeaceae fam. nov. and Miltoncostaeales ord. nov. Syst Appl Microbiol 2021; 44:126216. [PMID: 34157594 DOI: 10.1016/j.syapm.2021.126216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
Two novel marine actinobacteria, designated as SCSIO 60955T and SCSIO 61214T, were isolated from deep-sea sediment samples collected from the South China Sea. The cells of these organisms stained Gram-negative and were rod shaped. These strains were aerobic, and catalase- and oxidase-positive. Optimal growth occurred at 28 °C and pH 7 over 14 days of cultivation. Both strains possessed phospholipids and phosphoglycolipids. The main menaquinone was MK-7. The major fatty acid was C16:0. The peptidoglycan structure was type A1γ' (meso-Dpm). Analysis of genome sequences revealed that the genome size of SCSIO 60955T was 3.37 Mbp with G + C content of 76.1%, while the genome size of SCSIO 61214T was 3.67 Mbp with a G + C content of 74.8%. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains were 73.4% and 97.7% and that with other recognized Thermoleophilia species were less than 69.1% and 87.8%, respectively. Phylogenetic analysis of the 16S rRNA gene sequences showed that strains SCSIO 60955T and SCSIO 61214T were separately clustered together and formed a well-separated phylogenetic branch distinct from their most related neighbor Gaiella occulta. Based on the data presented here, these two strains are proposed to represent two novel species of a novel genus, for which the name Miltoncostaea marina gen. nov., sp. nov., with the type strain SCSIO 60955T (=DSM 110281T =CGMCC 1.18757T), and Miltoncostaea oceani sp. nov., with the type strain SCSIO 61214T (=KCTC 49527T =CGMCC 1.18758T) are proposed. We also propose that these organisms represent a novel family named Miltoncostaeaceae fam. nov. of a novel order Miltoncostaeales ord. nov.
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Affiliation(s)
- Cun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Qiu He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Lin-Qing Cui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luciana Albuquerque
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Rou-Wen Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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Goel N, Fatima SW, Kumar S, Sinha R, Khare SK. Antimicrobial resistance in biofilms: Exploring marine actinobacteria as a potential source of antibiotics and biofilm inhibitors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00613. [PMID: 33996521 PMCID: PMC8105627 DOI: 10.1016/j.btre.2021.e00613] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is one of the serious global public health threats that require immediate action. With the emergence of new resistance mechanisms in infection-causing microorganisms such as bacteria, fungi, and viruses, AMR threatens the effective prevention and treatment of diseases caused by them. This has resulted in prolonged illness, disability, and death. It has been predicted that AMR will lead to over ten million deaths by 2050. The rapid spread of multidrug-resistant bacteria is also causing old antibiotics to become ineffective. Among the diverse factors contributing to AMR, intrinsic biofilm development has been highlighted as an essential contributing facet. Moreover, biofilm-derived antibiotic tolerance leads to serious recurrent chronic infections. Therefore, the discovery of novel bioactive molecules is a potential solution that can help combat AMR. To achieve this, sustained mining of novel antimicrobial leads from actinobacteria, particularly marine actinobacteria, can be a promising strategy. Given their vast diversity and different habitats, the extraordinary capacity of actinobacteria can be tapped to synthesize new antibiotics or bioactive molecules for biofilm inhibition. Advanced screening strategies and novel approaches in the field of modern biochemical and molecular biology can be used to detect such new compounds. In view of this, the present review focuses on understanding some of the recent strategies to inhibit biofilm formation and explores the potential role of marine actinobacteria as sources of novel antibiotics and biofilm inhibitor molecules.
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Affiliation(s)
- Nikky Goel
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sumit Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sunil K. Khare
- Department of Chemistry, Indian Institute of Technology Delhi, India
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30
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Kwon DH, Kim GY, Cha HJ, Kim S, Kim HS, Hwang HJ, Choi YH. Nargenicin A1 attenuates lipopolysaccharide-induced inflammatory and oxidative response by blocking the NF-κB signaling pathway. EXCLI JOURNAL 2021; 20:968-982. [PMID: 34267609 PMCID: PMC8278209 DOI: 10.17179/excli2021-3506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 12/04/2022]
Abstract
Inflammation caused by the excessive production of pro-inflammatory mediators and cytokines in abnormally activated macrophages promotes the initiation and progression of many diseases along with oxidative stress. Previous studies have suggested that nargenicin A1, an antibacterial macrolide isolated from Nocardia sp. may be a potential treatment for inflammatory responses and oxidative stress, but the detailed mechanisms are still not well studied. In this study, we investigated the inhibitory effect of nargenicin A1 on inflammatory and oxidative stress in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages and zebrafish (Danio rerio) models. Our results indicated that nargenicin A1 treatment significantly inhibited LPS-induced release of pro-inflammatory mediators including nitric oxide (NO) and prostaglandin E2, which was associated with decreased inducible NO synthase and cyclooxygenase-2 expression. In addition, nargenicin A1 attenuated the LPS-induced expression of pro-inflammatory cytokines, such as tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and monocyte chemotactic protein-1, reducing their extracellular secretion. Nargenicin A1 also suppressed LPS-induced generation of reactive oxygen species. Moreover, nargenicin A1 abolished the LPS-mediated nuclear translocation of nuclear factor-kappa B (NF-κB) and the degradation of inhibitor IκB-α, indicating that nargenicin A1 exhibited anti-inflammatory effects by inhibiting the NF-κB signaling pathway. Furthermore, nargenicin A1 showed strong protective effects against NO and ROS production in LPS-injected zebrafish larvae. In conclusion, our findings suggest that nargenicin A1 ameliorates LPS-induced anti-inflammatory and antioxidant effects by downregulating the NF-κB signaling pathway, and that nargenicin A1 can be a potential functional agent to prevent inflammatory- and oxidative-mediated damage.
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Affiliation(s)
- Da Hye Kwon
- Anti-Aging Research Center, Dong-eui University, Busan, Republic of Korea.,Department of Biochemistry, Dong-eui University College of Korean Medicine, Busan, Republic of Korea
| | - Gi-Young Kim
- Department of Marine Life Science, School of Marine Biomedical Sciences, Jeju National University, Jeju, Republic of Korea
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Hye-Jin Hwang
- Department of Food and Nutrition, College of Nursing, Healthcare Sciences & Human Ecology, Dong-eui University, Busan, Republic of Korea
| | - Yung Hyun Choi
- Anti-Aging Research Center, Dong-eui University, Busan, Republic of Korea.,Department of Biochemistry, Dong-eui University College of Korean Medicine, Busan, Republic of Korea
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31
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Aigle A, Bourgeois E, Marjolet L, Houot S, Patureau D, Doelsch E, Cournoyer B, Galia W. Relative Weight of Organic Waste Origin on Compost and Digestate 16S rRNA Gene Bacterial Profilings and Related Functional Inferences. Front Microbiol 2021; 12:667043. [PMID: 34054773 PMCID: PMC8160089 DOI: 10.3389/fmicb.2021.667043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products' bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.
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Affiliation(s)
- Axel Aigle
- Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France
| | - Emilie Bourgeois
- Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France
| | - Laurence Marjolet
- Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France
| | - Sabine Houot
- UMR ECOSYS, INRAE, AgroParisTech, Thiverval-Grignon, France
| | | | - Emmanuel Doelsch
- CIRAD, UPR Recyclage et risque, Montpellier, France.,Recyclage et Risque, Univ Montpellier, CIRAD, Montpellier, France
| | - Benoit Cournoyer
- Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France
| | - Wessam Galia
- Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France
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Albanese D, Coleine C, Rota-Stabelli O, Onofri S, Tringe SG, Stajich JE, Selbmann L, Donati C. Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. MICROBIOME 2021; 9:63. [PMID: 33741058 PMCID: PMC7980648 DOI: 10.1186/s40168-021-01021-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/02/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.). RESULTS A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The "Candidatus Jiangella antarctica" has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa. CONCLUSIONS Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract.
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Affiliation(s)
- Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720 USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Watkins Drive 3401, Riverside, Riverside, CA 92507 USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Via al Porto Antico, 16128 Genoa, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
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Tanveer F, Shehroz M, Ali M, Xie Y, Abbasi R, Shinwari ZK, Yasmin A. Genome sequence analysis and bioactivity profiling of marine-derived actinobacteria, Brevibacterium luteolum, and Cellulosimicrobium funkei. Arch Microbiol 2021; 203:2491-2500. [PMID: 33677635 DOI: 10.1007/s00203-021-02203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 11/25/2022]
Abstract
Genome analysis gives important insights into the biosynthetic potential of marine actinobacteria. The genomes of two marine actinomycetes Brevibacterium luteolum MOSEL-ME10a and Cellulosimicrobium funkei MOSEL-ME6 were sequenced to identify the biosynthetic gene clusters (BGCs). Additionally, anti-proliferative, antioxidant, and enzyme inhibitory activities were studied in vitro. We report a total genome size of 2.77 Mb with GC content of 67.8% and 6.81 Mb with GC content of 69% for Brevibacterium sp. MOSEL-ME10a and Cellulosimicrobium sp. MOSEL-ME6, respectively. Biosynthetic gene clusters (BGCs) encoding different classes of natural products were predicted including terpenes, peptides, siderophores, ectoines, and bacteriocins. The bioactivity potential of crude extracts derived from these strains was evaluated. Notable anti-proliferative activity was observed against HepG2 cell line (hepatocellular carcinoma) with an IC50 value of 182 µg/mL for Brevibacterium sp. MOSEL-ME10a. Furthermore, antioxidant activity was assessed with IC50 values of 48.91 µg/mL and 102.5 µg/mL for Brevibacterium sp. MOSEL-ME10a and Cellulosimicrobium sp. MOSEL-ME6, respectively. Protein kinase inhibition potential was observed only for Brevibacterium sp. MOSEL-ME10a. Our study also reports lower amylase enzyme inhibition potential for both strains. Moreover, both crude extracts showed only slight-to-no toxic effect on erythrocytes at 400 µg/mL and below, indicating erythrocyte membrane stability. Our data present the genomic features revealing biosynthetic potential of marine actinobacteria as well as biological activities found in vitro.
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Affiliation(s)
- Faouzia Tanveer
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Muhammad Shehroz
- Department of Biotechnology, Virtual University of Pakistan, Peshawar, 25000, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yunying Xie
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rashda Abbasi
- Institute of Biomedical and Genetic Engineering, G-9/1, Islamabad, 44000, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Azra Yasmin
- Microbiology and Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
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34
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Liem M, Regensburg-Tuïnk T, Henkel C, Jansen H, Spaink H. Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing. BMC Res Notes 2021; 14:42. [PMID: 33531031 PMCID: PMC7852107 DOI: 10.1186/s13104-021-05457-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 01/20/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. RESULTS With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.
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Affiliation(s)
- M Liem
- Institute Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - T Regensburg-Tuïnk
- Institute Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - C Henkel
- Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - H Jansen
- Future Genomics Technologies, Leiden, The Netherlands
| | - H Spaink
- Institute Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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35
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Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiol Res 2021; 246:126708. [PMID: 33529791 DOI: 10.1016/j.micres.2021.126708] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022]
Abstract
Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.
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Affiliation(s)
- Polpass Arul Jose
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.
| | - Anjisha Maharshi
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, India.
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36
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Choi Y, Kwon D, Park C, Lee H, Hong S, Kim GY, Cha HJ, Kim S, Kim HS, Hwang HJ. Ethanol extract of Chondracanthus tenellus (Harvey) Hommersand attenuates lipopolysaccharide-induced inflammatory and oxidative response by blocking the NF-κB, MAPKs, and PI3K/Akt signaling pathways. Asian Pac J Trop Biomed 2021. [DOI: 10.4103/2221-1691.326099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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37
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Jia P, Li M, Feng H, Ma M, Gai J, Yang Z. Actinobacterial Communities of Chosen Extreme Habitats in China. POLISH JOURNAL OF ECOLOGY 2020. [DOI: 10.3161/15052249pje2020.68.3.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Pengli Jia
- School of Earth Sciences and Resources, China University of Geosciences, 29 Xueyuan Road, Beijing 100083, China
| | - Miao Li
- School of Earth Sciences and Resources, China University of Geosciences, 29 Xueyuan Road, Beijing 100083, China
| | - Haiyan Feng
- School of Earth Sciences and Resources, China University of Geosciences, 29 Xueyuan Road, Beijing 100083, China
| | - Mutian Ma
- School of Earth Sciences and Resources, China University of Geosciences, 29 Xueyuan Road, Beijing 100083, China
| | - Jingping Gai
- College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Zhongfang Yang
- School of Earth Sciences and Resources, China University of Geosciences, 29 Xueyuan Road, Beijing 100083, China
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38
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Messaoudi O, Wink J, Bendahou M. Diversity of Actinobacteria Isolated from Date Palms Rhizosphere and Saline Environments: Isolation, Identification and Biological Activity Evaluation. Microorganisms 2020; 8:E1853. [PMID: 33255541 PMCID: PMC7760371 DOI: 10.3390/microorganisms8121853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/20/2023] Open
Abstract
The diversity of cultural Actinobacteria in two types of Algerian Sahara environments, including saline environments and date palms rhizosphere, was investigated. In this study, a total of 40 strains of actinomycetes was isolated from different soil samples, using a rehydration and centrifugation method. Molecular identification, based on 16S rRNA gene sequence analysis, revealed that these isolates were affiliated to six clusters corresponding to eight genera, including Streptomyces, Nocardiopsis, Saccharopolyspora, Actinomadura, Actinocorallia, Micromonospora, Couchioplanes, and Planomonospora. A taxonomic analysis, based on the morphological, physiological, biochemical, and molecular investigation, of selected strains, which belong to the rare Actinobacteria, was undertaken. Four strains (CG3, A111, A93, and A79) were found to form distinct phyletic lines and represent new actinobacterial taxa. An assessment of antimicrobial proprieties of the 40 obtained actinomycetes strains, showed moderate to strong antimicrobial activities against fungi and bacteria. This study demonstrated the richness of Algerian Sahara with rare Actinobacteria, which can provide novel bioactive metabolites, to solving some of the most challenging problems of the day, such as multi-drug resistance.
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Affiliation(s)
- Omar Messaoudi
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
- Department of Biology, Faculty of Science, University of Amar Telidji, 03000 Laghouat, Algeria
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Mourad Bendahou
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
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Isolation and structure determination of new linear azole-containing peptides spongiicolazolicins A and B from Streptomyces sp. CWH03. Appl Microbiol Biotechnol 2020; 105:93-104. [PMID: 33215256 DOI: 10.1007/s00253-020-11016-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Linear azole-containing peptides are a class of ribosomally synthesized and post-translationally modified peptides. We performed a chemical investigation on marine actinomycetes, and new linear azole-containing peptides named spongiicolazolicins A and B were found in the MeOH extracts of a newly isolated strain Streptomyces sp. CWH03 (NBRC 114659) and two strains of S. spongiicola (strain HNM0071T: DSM 103383T and strain 531S: NBRC 113560). The strain Streptomyces sp. CWH03 was indicated to be a new species closely related to S. spongiicola by phylogenetic analysis using the genome sequence. The new peptides named spongiicolazolicins A and B were isolated from the cell of Streptomyces sp. CWH03. The partial structure of spongiicolazolicin A was determined by 2D NMR experiments. Based on data of MS/MS experiments, the chemical structures of spongiicolazolicins A and B were proposed using the amino acid sequence deduced from the precursor-encoding gene, which was found from whole-genome sequence data of Streptomyces sp. CWH03. The biosynthetic gene cluster of spongiicolazolicins was proposed based on comparative analysis with that of a known linear azole peptide goadsporin. KEY POINTS: • Streptomyces sp. CWH03 was a new species isolated from marine sediment. • New linear azole-containing peptides named spongiicolazolicins A and B were isolated. • Biosynthetic pathway of spongiicolazolicins was proposed.
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40
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Lu S, Wang J, Sheng R, Fang Y, Guo R. Novel Bioactive Polyketides Isolated from Marine Actinomycetes: An Update Review from 2013 to 2019. Chem Biodivers 2020; 17:e2000562. [PMID: 33206470 DOI: 10.1002/cbdv.202000562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022]
Abstract
Marine organism-associated actinobacteria represent a valuable resource for marine drugs due to their abundant secondary metabolites. The special environments in the ocean, for instance, high salt, high pressure, low temperature and oligotrophy, not only adapt to survival of actinomycetes but also enhance molecular diversity of actinomycete secondary metabolites production, thus making marine actinomycetes important sources of marine-based bioactive compounds, especially polyketides. Herein, we summarized the structures and pharmacological activities of polyketides from actinobacteria associated with marine organisms from 2013 to 2019; moreover, the main source species of actinomycetes were discussed as well. We expected that this review would be helpful for future in-depth research and development of marine-based bioactive polyketides.
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Affiliation(s)
- Silei Lu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Jiangming Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Ruilong Sheng
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Portugal
| | - Yiwen Fang
- Department of Chemistry, College of Science, Shantou University, Shantou, 515063, P. R. China
| | - Ruihua Guo
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, 201306, P. R. China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, P. R. China
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41
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Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
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Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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42
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Muhamadali H, Simoens K, Xu Y, Nicolai B, Bernaerts K, Goodacre R. Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24. Metabolites 2020; 10:E379. [PMID: 32972026 PMCID: PMC7569812 DOI: 10.3390/metabo10090379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 01/11/2023] Open
Abstract
In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period.
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Affiliation(s)
- Howbeer Muhamadali
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Kenneth Simoens
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F Box 2424, 3001 Leuven, Belgium; (K.S.); (K.B.)
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven (University of Leuven), Willem de Croylaan 42 Box 2428, 3001 Leuven, Belgium;
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F Box 2424, 3001 Leuven, Belgium; (K.S.); (K.B.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, UK; (H.M.); (Y.X.)
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
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43
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Chen RW, Li C, He YQ, Cui LQ, Long LJ, Tian XP. Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea. Int J Syst Evol Microbiol 2020; 70:5576-5585. [PMID: 32941125 DOI: 10.1099/ijsem.0.004449] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-positive bacteria, designated as SCSIO 52909T and SCSIO 52915T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909T and SCSIO 52915T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909T (=KCTC 49412T=CGMCC 1.13853T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915T (=KCTC 49411T=CGMCC 1.13852T), are proposed.
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Affiliation(s)
- Rou-Wen Chen
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cun Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Yuan-Qiu He
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Lin-Qing Cui
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
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44
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Characterization of anti-BCG benz[α]anthraquinones and new siderophores from a Xinjiang desert-isolated rare actinomycete Nocardia sp. XJ31. Appl Microbiol Biotechnol 2020; 104:8267-8278. [PMID: 32830291 PMCID: PMC7443361 DOI: 10.1007/s00253-020-10842-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 02/05/2023]
Abstract
Abstract The current global demand for novel anti-TB drugs has drawn urgent attention on the discovery of natural product compounds with anti-TB activity. Lots of efforts have emphasized on environmental samples from unexplored or underexplored natural habits and identified numerous rare actinomycete taxa producing structurally diverse bioactive natural products. Herein, we report a survey of the rare actinobacteria diversity in Xinjiang region together with the discovery of anti-TB active natural products from these strains. We have collected 17 soil samples at different sites with different environmental conditions, from which 39 rare actinobacteria were identified by using a selective isolation strategy with 5 media variations. Among those isolated strains, XJ31 was identified as a new Nocardia sp. based on 16S rRNA gene analysis. Through one strain-many compounds (OSMAC) strategy combined with anti-Bacillus Calmette-Guérin bioassay-guided isolation, two groups of compounds were identified. They were twelve siderophores (nocardimicins, 1-12) and two anthraquinones (brasiliquinones, 13 and 14) and ten of them were identified as new compounds. The structures of the purified compounds were elucidated using HR-ESI-MS, 1D NMR, and 2D NMR techniques. The anti-TB bioassays revealed that the two benz[α]anthraquinones have potent activity against BCG (MICs = 25 μM), which can be used as a promising start point for further anti-TB drug development. Key points • Ten new natural products were identified from Nocardia sp. XJ31. • Brasiliquinones13and14showed moderate anti-BCG activity. Electronic supplementary material The online version of this article (10.1007/s00253-020-10842-2) contains supplementary material, which is available to authorized users.
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45
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Mitousis L, Thoma Y, Musiol-Kroll EM. An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds. Antibiotics (Basel) 2020; 9:E494. [PMID: 32784409 PMCID: PMC7460540 DOI: 10.3390/antibiotics9080494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
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Affiliation(s)
| | | | - Ewa M. Musiol-Kroll
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (L.M.); (Y.T.)
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46
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Hu D, Sun C, Jin T, Fan G, Mok KM, Li K, Lee SMY. Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis. Front Microbiol 2020; 11:1540. [PMID: 32922368 PMCID: PMC7375171 DOI: 10.3389/fmicb.2020.01540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022] Open
Abstract
Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Jin
- Beijing Genomics Institute, Shenzhen, China
| | | | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
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47
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de Siqueira GMV, Silva-Rocha R, Guazzaroni ME. Turning the Screw: Engineering Extreme pH Resistance in Escherichia coli through Combinatorial Synthetic Operons. ACS Synth Biol 2020; 9:1254-1262. [PMID: 32438805 DOI: 10.1021/acssynbio.0c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh conditions, usually very distant from those in which these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different industrial appplications. In this work, synthetic biology approaches were used to engineer enhanced acidic resistance in Escherichia coli through the characterization of a collection of unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for resistance in synthetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.
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Affiliation(s)
- Guilherme M. V. de Siqueira
- Departamento de Bioquı́mica, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - Rafael Silva-Rocha
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP 14049-900, Brasil
| | - María-Eugenia Guazzaroni
- Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP 14040-901, Brasil
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48
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Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans. Microorganisms 2020; 8:microorganisms8060900. [PMID: 32549367 PMCID: PMC7355893 DOI: 10.3390/microorganisms8060900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).
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49
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Nguyen CT, Dhakal D, Pham VTT, Nguyen HT, Sohng JK. Recent Advances in Strategies for Activation and Discovery/Characterization of Cryptic Biosynthetic Gene Clusters in Streptomyces. Microorganisms 2020; 8:E616. [PMID: 32344564 PMCID: PMC7232178 DOI: 10.3390/microorganisms8040616] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
Streptomyces spp. are prolific sources of valuable natural products (NPs) that are of great interest in pharmaceutical industries such as antibiotics, anticancer chemotherapeutics, immunosuppressants, etc. Approximately two-thirds of all known antibiotics are produced by actinomycetes, most predominantly by Streptomyces. Nevertheless, in recent years, the chances of the discovery of novel and bioactive compounds from Streptomyces have significantly declined. The major hindrance for obtaining such bioactive compounds from Streptomyces is that most of the compounds are not produced in significant titers, or the biosynthetic gene clusters (BGCs) are cryptic. The rapid development of genome sequencing has provided access to a tremendous number of NP-BGCs embedded in the microbial genomes. In addition, the studies of metabolomics provide a portfolio of entire metabolites produced from the strain of interest. Therefore, through the integrated approaches of different-omics techniques, the connection between gene expression and metabolism can be established. Hence, in this review we summarized recent advancements in strategies for activating cryptic BGCs in Streptomyces by utilizing diverse state-of-the-art techniques.
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Affiliation(s)
- Chung Thanh Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Jae-Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea
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50
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Paderog MJV, Suarez AFL, Sabido EM, Low ZJ, Saludes JP, Dalisay DS. Anthracycline Shunt Metabolites From Philippine Marine Sediment-Derived Streptomyces Destroy Cell Membrane Integrity of Multidrug-Resistant Staphylococcus aureus. Front Microbiol 2020; 11:743. [PMID: 32390983 PMCID: PMC7193051 DOI: 10.3389/fmicb.2020.00743] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/30/2020] [Indexed: 11/13/2022] Open
Abstract
The rise of antibiotic resistance (ABR) and the drying up of the pipeline for the development of new antibiotics demands an urgent search for new antibiotic leads. While the majority of clinically available antibiotics were discovered from terrestrial Streptomyces, related species from marine sediments as a source of antibiotics remain underexplored. Here, we utilized culture-dependent isolation of thirty-five marine sediment-derived actinobacterial isolates followed by a screening of their antibacterial activity against multidrug-resistant S. aureus ATCC BAA-44. Our results revealed that the crude extract of Streptomyces griseorubens strain DSD069 isolated from marine sediments collected in Romblon, Philippines displays the highest antibacterial activity, with 96.4% growth inhibition. The S. aureus ATCC BAA-44 cells treated with crude extract of Streptomyces griseorubens strain DSD069 showed cell membrane damage as demonstrated by (a) leakage and loss of vital cell constituents, including DNA and proteins, (b) irregular shrinkage of cells, and (c) increase membrane permeability. The antibiotic compounds were identified as Bisanhydroaklavinone and 1-Hydroxybisanhydroaklavinone with MIC value of 6.25 μg/mL and 50.00 μg/mL, respectively. Bisanhydroaklavinone and 1-Hydroxybisanhydroaklavinone are shunt metabolites in the biosynthesis of anticancer anthracycline derivatives namely doxorubicin, daunorubicin, and cinerubins. It is rare, however, that shunt metabolites are accumulated during fermentation of marine sediment-derived Streptomyces strain without genetic modification. Thus, our study provides evidence that natural bacterial strain can produce Bisanhydroaklavinone and 1-Hydroxybisanhydroaklavinone as antibiotic leads to combat ABR.
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Affiliation(s)
- Melissa June V Paderog
- Department of Pharmacy, College of Health and Allied Medical Professions, University of San Agustin, Iloilo City, Philippines.,Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City, Philippines
| | - Angelica Faith L Suarez
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City, Philippines
| | - Edna M Sabido
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City, Philippines
| | | | - Jonel P Saludes
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City, Philippines.,Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City, Philippines.,Balik Scientist Program, Philippine Council for Health Research and Development, Department of Science and Technology, Taguig, Philippines
| | - Doralyn S Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City, Philippines.,Balik Scientist Program, Philippine Council for Health Research and Development, Department of Science and Technology, Taguig, Philippines.,Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City, Philippines
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