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Chukwudulue UM, Barger N, Dubovis M, Luzzatto Knaan T. Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae. Mar Drugs 2023; 21:569. [PMID: 37999393 PMCID: PMC10672036 DOI: 10.3390/md21110569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.
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Affiliation(s)
| | | | | | - Tal Luzzatto Knaan
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa 103301, Israel; (U.M.C.); (N.B.); (M.D.)
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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Marine macroalga-associated heterotrophic Bacillus velezensis: a novel antimicrobial agent with siderophore mode of action against drug-resistant nosocomial pathogens. Arch Microbiol 2021; 203:5561-5575. [PMID: 34436634 DOI: 10.1007/s00203-021-02513-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022]
Abstract
Increased prevalence of microbial resistance and development of drug-resistant pathogens have triggered an urge among researchers to discover potential antimicrobial compounds, particularly from the marine habitat. The present study highlights the cultivable diversity and bioactivities of heterotrophic bacteria associated with marine macroalgae of southeast Indian coastal region. Culture-dependent isolation method resulted in 40 isolates, in which greater part of the isolates represented Gammaproteobacteria (62%) followed by that comprised of the phylum Firmicutes. One of the most active strains isolated from a macroalga, Laurencia papillosa, was characterized based on the integrated phenotypic and genotypic analysis as Bacillus velezensis MBTDLP1 MTCC 13048, with an inhibition zone of about 35 mm against methicillin-resistant Staphylococcus aureus (MRSA), was selected for bioprospecting studies. Type-I pks gene (MT394492) of 700 bp could be amplified from the heterotrophic B. velezensis. The bacterium exhibited siderophore production and possessed genes implicated in the biosynthesis of siderophore type of metabolites exhibiting 99% similarity with other GenBank sequences in BLAST search. B. velezensis exhibited promising anti-infective properties against methicillin-resistant Staphylococcus aureus (minimum inhibitory concentration 15 µg/mL), and the activities were positively correlated (r2 > 0.9) with iron-chelating activities. Chemical investigation of the organic extract of B. velezensis MBTDLP1 characterized a macrocyclic polyketide exhibiting prospective antibacterial potential against methicillin-resistant S. aureus (MIC 0.38 µg/mL), than that exhibited by positive control chloramphenicol (6.25 µg/mL). Significant antibacterial activity against drug-resistant bacteria combined with the presence of genes coding for bioactive secondary metabolites revealed that this marine symbiotic bacterium could be used against emerging antibiotic resistance.
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Liu J, Yu R, Jia J, Gu W, Zhang H. Assignment of Absolute Configurations of Two Promising Anti- Helicobacter pylori Agents from the Marine Sponge-Derived Fungus Aspergillus niger L14. Molecules 2021; 26:molecules26165061. [PMID: 34443650 PMCID: PMC8399357 DOI: 10.3390/molecules26165061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
A chemical investigation into endozoic fungus Aspergillus niger L14 derived from the marine sponge of Reniera japonica collected off Xinghai Bay (China) resulted in the isolation of two dimeric naphtho-γ-pyrones, fonsecinone A (1) and isoaurasperone A (2). Through a combination of ECD spectra and X-ray diffraction analysis, the chiral axes of compounds 1 and 2 were unambiguously determined as Rα-configurations. Bioassay results indicated that these substances exhibited remarkably inhibitory effects on human pathogens Helicobacter pylori G27 and 159 with MIC values of ≤4 μg/mL, which are similar to those of the positive control, ampicillin sodium. To the best of our knowledge, this is the first report on absolute configuration of 1 and crystallographic data of 2, as well as their potent anti-H. pylori activities.
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Affiliation(s)
- Jia Liu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (J.L.); (R.Y.)
| | - Ronglu Yu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (J.L.); (R.Y.)
| | - Jia Jia
- Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology, Nanjing Medical University, Nanjing 211166, China;
| | - Wen Gu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China;
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (J.L.); (R.Y.)
- Correspondence: ; Tel.: +86-571-8832-0913
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Gavriilidou A, Mackenzie TA, Sánchez P, Tormo JR, Ingham C, Smidt H, Sipkema D. Bioactivity Screening and Gene-Trait Matching across Marine Sponge-Associated Bacteria. Mar Drugs 2021; 19:75. [PMID: 33573261 PMCID: PMC7912018 DOI: 10.3390/md19020075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022] Open
Abstract
Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Thomas Andrew Mackenzie
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - Pilar Sánchez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - José Ruben Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
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Indraningrat AAG, Micheller S, Runderkamp M, Sauerland I, Becking LE, Smidt H, Sipkema D. Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths. Mar Drugs 2019; 17:E578. [PMID: 31614540 PMCID: PMC6836257 DOI: 10.3390/md17100578] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/23/2019] [Accepted: 10/05/2019] [Indexed: 01/15/2023] Open
Abstract
Sponge-associated bacteria have been mostly cultured from shallow water (≤30 m) sponges, whereas only few studies targeted specimens from below 30 m. This study assessed the cultivability of bacteria from two marine sponges Xestospongia muta and Agelas sventres collected from shallow (<30 m), upper mesophotic (30-60 m), and lower mesophotic (60-90 m) reefs. Sponge-associated bacteria were cultivated on six different media, and replicate plates were used to pick individual colonies or to recover the entire biomass. Prokaryotic community analysis was conducted using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 144 bacterial isolates were picked following a colony morphology coding scheme and subsequently identified by 16S rRNA gene sequence analysis. Sponge individuals at each depth-range harboured specific cultivable bacteria that were not retrieved from specimens collected at other depths. However, there were substantial differences in the number of colonies obtained for replicate sponges of the same species. In addition, source of inoculum and cultivation medium had more impact on the cultured prokaryotic community than sample collection depth. This suggests that the "plate count anomaly" is larger than differences in sponge-associated prokaryotic community composition related to depth.
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Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
- Faculty of Medicine and Health Science, Warmadewa University, Jln Terompong 24, Denpasar 80239, Bali, Indonesia.
| | - Sebastian Micheller
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Mandy Runderkamp
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Ina Sauerland
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
- Wageningen Marine Research, Wageningen University & Research, Ankerpark 27, 1781 AG Den Helder, The Netherlands.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. ACTA ACUST UNITED AC 2019; 46:1381-1400. [DOI: 10.1007/s10295-019-02198-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
Abstract
Natural products (NPs) produced by bacteria and fungi are often used as therapeutic agents due to their complex structures and wide range of bioactivities. Enzymes that build NPs are encoded by co-localized biosynthetic gene clusters (BGCs), and genome sequencing has recently revealed that many BGCs are “silent” under standard laboratory conditions. There are numerous methods used to activate “silent” BGCs that rely either upon altering culture conditions or genetic modification. In this review, we discuss several recent microbial cultivation methods that have been used to expand the scope of NPs accessible in the laboratory. These approaches are divided into three categories: addition of a physical scaffold, addition of small molecule elicitors, and co-cultivation with another microbe.
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Mehbub MF, Tanner JE, Barnett SJ, Bekker J, Franco CMM, Zhang W. A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens. Sci Rep 2018; 8:11801. [PMID: 30087404 PMCID: PMC6081443 DOI: 10.1038/s41598-018-30295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/23/2018] [Indexed: 11/09/2022] Open
Abstract
Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.
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Affiliation(s)
- Mohammad F Mehbub
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Jason E Tanner
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- SARDI Aquatic Sciences, 2 Hamra Avenue, West Beach, SA, 5024, Adelaide, Australia
| | - Stephen J Barnett
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Jan Bekker
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
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Marine Invertebrates: Underexplored Sources of Bacteria Producing Biologically Active Molecules. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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