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Yan C, Owen JS, Seo EY, Jung D, He S. Microbial Interaction is Among the Key Factors for Isolation of Previous Uncultured Microbes. J Microbiol 2023; 61:655-662. [PMID: 37589838 PMCID: PMC10477116 DOI: 10.1007/s12275-023-00063-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/18/2023] [Indexed: 08/18/2023]
Abstract
Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.
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Affiliation(s)
- Chang Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, People's Republic of China
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China
| | - Jeffrey S Owen
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, 17035, Republic of Korea
| | - Eun-Young Seo
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China
| | - Dawoon Jung
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China.
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315832, People's Republic of China.
- Ningbo Institute of Marine Medicine, Peking University, Ningbo, 315832, People's Republic of China.
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Jung D, Machida K, Nakao Y, Kindaichi T, Ohashi A, Aoi Y. Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms. Front Microbiol 2021; 12:537194. [PMID: 34017313 PMCID: PMC8129545 DOI: 10.3389/fmicb.2021.537194] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/14/2021] [Indexed: 01/21/2023] Open
Abstract
Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, cultivating microbes in a membrane-bound device incubated in nature (in situ cultivation) can be an effective approach to overcome this limitation. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this method's efficiencies with those of the conventional method. Then, we attempted to investigate the key and previously unidentified mechanism of growing uncultivated microorganisms by in situ cultivation focusing on growth triggering via growth initiation factor. Significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). We hypothesized that some of environmental microorganisms which resist cultivation are in a non-growing state and require growth initiation factors for the recovery and that these can be provided from the environment (in this study from marine sponge). According to the hypothesis, the effect of the sponge extract on recovery on agar medium was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or saturated cell densities of all tested strains were not positively affected. These results indicate that, (1) the sponge extract contains chemical compounds that facilitate recovery of non-growing microbes, (2) these substances worked on the in situ strains, and (3) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from non-growing state).
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Affiliation(s)
- Dawoon Jung
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
| | - Koshi Machida
- Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Yoichi Nakao
- Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Department of Chemistry and Biochemistry, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Higashihiroshima, Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Higashihiroshima, Japan
| | - Yoshiteru Aoi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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Tian L, Wang E, Lin X, Ji L, Chang J, Chen H, Wang J, Chen D, Tran LSP, Tian C. Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding. BMC Genomics 2021; 22:278. [PMID: 33865333 PMCID: PMC8052703 DOI: 10.1186/s12864-021-07587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. RESULTS In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. CONCLUSIONS This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Enze Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Xiaolong Lin
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongping Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Dazhou Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
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Wooster MK, Voigt O, Erpenbeck D, Wörheide G, Berumen ML. Sponges of the Red Sea. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Orani AM, Barats A, Zitte W, Morrow C, Thomas OP. Comparative study on the bioaccumulation and biotransformation of arsenic by some northeastern Atlantic and northwestern Mediterranean sponges. CHEMOSPHERE 2018; 201:826-839. [PMID: 29554629 DOI: 10.1016/j.chemosphere.2018.03.078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 02/18/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
The bioaccumulation and biotransformation of arsenic (As) were studied in six representative marine sponges from the French Mediterranean and Irish Atlantic coasts. Methodologies were carefully optimized in one of the species on Haliclona fulva sponges for two critical steps: the sample mineralization for total As analysis by ICP-MS and the extraction of As species for HPLC-ICP-MS analysis. During the optimization, extractions performed with 0.6 mol L-1 H3PO4 were shown to be the most efficient. Extraction recovery of 81% was obtained which represents the best results obtained until now in sponge samples. Total As analyses and As speciation were performed on certified reference materials and allow confirming the measurement quality both during the sample preparation and analysis. Additionally, this study represents an environmental survey demonstrating a high variability of total As concentrations among the different species, probably related to different physiological or microbial features. As speciation results showed the predominance of arsenobetaine (AsB) regardless of the sponge species, as well as the occurrence of low amounts of dimethylarsinic acid (DMA), arsenate (As(+V)), and unknown As species in some samples. The process responsible for As transformation in sponges is most likely related to sponges metabolism itself or the action of symbiont organisms. AsB is supposed to be implied in the protection against osmolytic stress. This study demonstrates the ability of sponges to accumulate and bio-transform As, proving that sponges are relevant bio-monitors for As contamination in the marine environment, and potential tools in environmental bio-remediation.
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Affiliation(s)
- Anna Maria Orani
- Université Nice Sophia Antipolis, CNRS, IRD, Observatoire de la Côte d'Azur, Géoazur, UMR 7329, 250 rue Albert Einstein, Sophia Antipolis 06560 Valbonne, France; International Atomic Energy Agency, Environment Laboratories, 4 Quai Antoine 1er, MC 9800, Monaco.
| | - Aurélie Barats
- Université Nice Sophia Antipolis, CNRS, IRD, Observatoire de la Côte d'Azur, Géoazur, UMR 7329, 250 rue Albert Einstein, Sophia Antipolis 06560 Valbonne, France
| | - Wendy Zitte
- Université Nice Sophia Antipolis, CNRS, IRD, Observatoire de la Côte d'Azur, Géoazur, UMR 7329, 250 rue Albert Einstein, Sophia Antipolis 06560 Valbonne, France
| | - Christine Morrow
- National University of Ireland Galway, Marine Biodiscovery, School of Chemistry, University Road, Galway, Ireland
| | - Olivier P Thomas
- National University of Ireland Galway, Marine Biodiscovery, School of Chemistry, University Road, Galway, Ireland
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Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio. Appl Environ Microbiol 2018; 84:AEM.02516-17. [PMID: 29453252 DOI: 10.1128/aem.02516-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.
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Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M. A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. Environ Microbiol 2018; 20:800-814. [PMID: 29194919 PMCID: PMC5812793 DOI: 10.1111/1462-2920.14013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 01/09/2023]
Abstract
Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.
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Affiliation(s)
- Adi Lavy
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Ray Keren
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Ke Yu
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Brian C. Thomas
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California, Berkeley, USA
| | - Jillian F. Banfield
- Earth and Planetary Science, 369 McCone Hall, University of California, Berkeley, USA
| | - Micha Ilan
- School of Zoology, Faculty of Life Sciences, Tel-Aviv University, Israel
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Keren R, Mayzel B, Lavy A, Polishchuk I, Levy D, Fakra SC, Pokroy B, Ilan M. Sponge-associated bacteria mineralize arsenic and barium on intracellular vesicles. Nat Commun 2017; 8:14393. [PMID: 28233852 PMCID: PMC5333131 DOI: 10.1038/ncomms14393] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023] Open
Abstract
Arsenic and barium are ubiquitous environmental toxins that accumulate in higher trophic-level organisms. Whereas metazoans have detoxifying organs to cope with toxic metals, sponges lack organs but harbour a symbiotic microbiome performing various functions. Here we examine the potential roles of microorganisms in arsenic and barium cycles in the sponge Theonella swinhoei, known to accumulate high levels of these metals. We show that a single sponge symbiotic bacterium, Entotheonella sp., constitutes the arsenic- and barium-accumulating entity within the host. These bacteria mineralize both arsenic and barium on intracellular vesicles. Our results indicate that Entotheonella sp. may act as a detoxifying organ for its host. The marine sponge Theonella swinhoei accumulates toxic arsenic and barium. Here the authors show that these toxic elements are actually accumulated and mineralized within vesicles inside bacteria that live within the sponge tissues.
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Affiliation(s)
- Ray Keren
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Boaz Mayzel
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adi Lavy
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Iryna Polishchuk
- Faculty of Materials Engineering and the Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Davide Levy
- Faculty of Materials Engineering and the Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Boaz Pokroy
- Faculty of Materials Engineering and the Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. Proc Natl Acad Sci U S A 2017; 114:E347-E356. [PMID: 28049838 DOI: 10.1073/pnas.1616234114] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The as-yet uncultured filamentous bacteria "Candidatus Entotheonella factor" and "Candidatus Entotheonella gemina" live associated with the marine sponge Theonella swinhoei Y, the source of numerous unusual bioactive natural products. Belonging to the proposed candidate phylum "Tectomicrobia," Candidatus Entotheonella members are only distantly related to any cultivated organism. The Ca E. factor has been identified as the source of almost all polyketide and modified peptides families reported from the sponge host, and both Ca Entotheonella phylotypes contain numerous additional genes for as-yet unknown metabolites. Here, we provide insights into the biology of these remarkable bacteria using genomic, (meta)proteomic, and chemical methods. The data suggest a metabolic model of Ca Entotheonella as facultative anaerobic, organotrophic organisms with the ability to use methanol as an energy source. The symbionts appear to be auxotrophic for some vitamins, but have the potential to produce most amino acids as well as rare cofactors like coenzyme F420 The latter likely accounts for the strong autofluorescence of Ca Entotheonella filaments. A large expansion of protein families involved in regulation and conversion of organic molecules indicates roles in host-bacterial interaction. In addition, a massive overrepresentation of members of the luciferase-like monooxygenase superfamily points toward an important role of these proteins in Ca Entotheonella. Furthermore, we performed mass spectrometric imaging combined with fluorescence in situ hybridization to localize Ca Entotheonella and some of the bioactive natural products in the sponge tissue. These metabolic insights into a new candidate phylum offer hints on the targeted cultivation of the chemically most prolific microorganisms known from microbial dark matter.
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Newman DJ. Predominately Uncultured Microbes as Sources of Bioactive Agents. Front Microbiol 2016; 7:1832. [PMID: 27917159 PMCID: PMC5114300 DOI: 10.3389/fmicb.2016.01832] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving “state of the art” genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules.
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