1
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Prevalence of Actinobacteria in the production of 2-methylisoborneol and geosmin, over Cyanobacteria in a temperate eutrophic reservoir. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2021.100226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2
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Balaji A, Sapoval N, Seto C, Leo Elworth R, Fu Y, Nute MG, Savidge T, Segarra S, Treangen TJ. KOMB: K-core based de novo characterization of copy number variation in microbiomes. Comput Struct Biotechnol J 2022; 20:3208-3222. [PMID: 35832621 PMCID: PMC9249589 DOI: 10.1016/j.csbj.2022.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response to perturbations. We describe KOMB, a novel method for tracking genome level dynamics within microbiomes. KOMB utilizes K-core decomposition to identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV) within microbiomes. K-core decomposition partitions the graph into shells containing nodes of induced degree at least K, yielding reduced computational complexity compared to prior approaches. Through validation on a synthetic community, we show that KOMB recovers and profiles repetitive genomic regions in the sample. KOMB is shown to identify functionally-important regions in Human Microbiome Project datasets, and was used to analyze longitudinal data and identify keystone taxa in Fecal Microbiota Transplantation (FMT) samples. In summary, KOMB represents a novel graph-based, taxonomy-oblivious, and reference-free approach for tracking CNV within microbiomes. KOMB is open source and available for download at https://gitlab.com/treangenlab/komb.
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Affiliation(s)
- Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Charlie Seto
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - R.A. Leo Elworth
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Michael G. Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Santiago Segarra
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Corresponding author.
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Corresponding author.
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3
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Renn D, Shepard L, Vancea A, Karan R, Arold ST, Rueping M. Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. Front Microbiol 2021; 12:732856. [PMID: 34777282 PMCID: PMC8578733 DOI: 10.3389/fmicb.2021.732856] [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: 06/29/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.
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Affiliation(s)
- Dominik Renn
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Organic Chemistry, RWTH Aachen, Aachen, Germany
| | - Lera Shepard
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ram Karan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Aachen, Germany
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4
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Davies-Bolorunduro OF, Ajayi A, Adeleye IA, Kristanti AN, Aminah NS. Bioprospecting for antituberculosis natural products – A review. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
There has been an increase in the reported cases of tuberculosis, a disease caused by Mycobacterium tuberculosis, which is still currently affecting most of the world’s population, especially in resource-limited countries. The search for novel antitubercular chemotherapeutics from underexplored natural sources is therefore of paramount importance. The renewed interest in studies related to natural products, driven partly by the growing incidence of MDR-TB, has increased the prospects of discovering new antitubercular drug leads. This is because most of the currently available chemotherapeutics such as rifampicin and capreomycin used in the treatment of TB were derived from natural products, which are proven to be an abundant source of novel drugs used to treat many diseases. To meet the global need for novel antibiotics from natural sources, various strategies for high-throughput screening have been designed and implemented. This review highlights the current antitubercular drug discovery strategies from natural sources.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Centre for Tuberculosis Research, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Microbiology, University of Lagos , Akoka , Lagos , Nigeria
| | | | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
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5
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High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Davies-Bolorunduro O, Osuolale O, Saibu S, Adeleye I, Aminah N. Bioprospecting marine actinomycetes for antileishmanial drugs: current perspectives and future prospects. Heliyon 2021; 7:e07710. [PMID: 34409179 PMCID: PMC8361068 DOI: 10.1016/j.heliyon.2021.e07710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
Revived analysis interests in natural products in the hope of discovering new and novel antileishmanial drug leads have been driven partially by the increasing incidence of drug resistance. However, the search for novel chemotherapeutics to combat drug resistance had previously concentrated on the terrestrial environment. As a result, the marine environment was often overlooked. For example, actinomycetes are an immensely important group of bacteria for antibiotic production, producing two-thirds of the known antibiotics. However, these bacteria have been isolated primarily from terrestrial sources. Consequently, there have been revived efforts to discover new compounds from uncharted or uncommon environments like the marine ecosystem. Isolation, purification and structure elucidation of target compounds from complex metabolic extract are major challenges in natural products chemistry. As a result, marine-derived natural products from actinomycetes that have antileishmanial bioactivity potentials have been understudied. This review highlights metagenomic and bioassay approaches which could help streamline the drug discovery process thereby greatly reducing time and cost of dereplication to identify suitable antileishmanial drug candidates.
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Affiliation(s)
- O.F. Davies-Bolorunduro
- Microbiology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
- Postdoc Fellow Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - O. Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research Group (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - S. Saibu
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - I.A. Adeleye
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - N.S. Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, 60115, Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga, Indonesia
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7
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Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:958-972. [PMID: 33631428 PMCID: PMC9402790 DOI: 10.1016/j.gpb.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/23/2019] [Accepted: 06/06/2019] [Indexed: 12/01/2022]
Abstract
Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.
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8
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Liguori L, Monticelli M, Allocca M, Cubellis MV, Hay Mele B. Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach. BMC Bioinformatics 2020; 21:348. [PMID: 32838733 PMCID: PMC7447578 DOI: 10.1186/s12859-020-03560-z] [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] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. RESULTS We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. CONCLUSION Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.
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Affiliation(s)
- Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy.
- Biology and Evolution of Marine Organisms Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Bruno Hay Mele
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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9
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Tian N, Guo X, Wang M, Chen C, Cui H, Zhang L, Tang H. Bacterial community diversity of shilixiang baijiu Daqu based on metagenomics. J Food Biochem 2020; 44:e13410. [PMID: 32729122 DOI: 10.1111/jfbc.13410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/29/2022]
Abstract
Daqu is a fermentative saccharifying agent that is used to initiate fermentation in the production of Chinese baijiu. In this study, we performed metagenomic analysis of microorganisms present in shilixiang baijiu Daqu in order to analyze the bacterial community diversity of shilixiang baijiu Daqu from four different fermentation batches and determine the effect of fermentation process on microorganisms. An understanding of the composition and structure of bacterial communities of the shilixiang baijiu Daqu can provide a theoretical basis for the stability and quality evaluation of shilixiang baijiu Daqu-making technology. The results showed that the microbial community structure was different among Daqu samples from different fermentation batches, and at different fermentation days within the same fermentation batch. In general, the abundance and diversity of microorganisms found in Daqu samples from the four batches increased after 30 days of fermentation. The analysis of community structure showed that after 30 days of fermentation, Firmicutes was the predominant phylum in the four batches of the shilixiang baijiu Daqu samples. After 30 days of fermentation, the proportion of Lactobacillus, Pediococcus, and Staphylococcus increased, while the proportion of Pseudomonas decreased; Lactobacillus was the dominant microorganism in the shilixiang baijiu Daqu samples. We also determined that Lactobacillus, Pseudomonas, Leuconostoc, Lactococcus, Saccharopolyspora, and Enterococcus were present in Jannanchun, Maotai, and shilixiang baijiu Daqu samples. In addition, every batch had its own unique genus. We discovered genera that had not been found before in shilixiang baijiu Daqu samples. Through the prediction of functional gene composition, we confirmed that the bacterial population in shilixiang baijiu Daqu mainly had metabolic, genetic information processing, and environmental information processing functions. This study contributes to expanding our understanding of the functional characteristics of Daqu bacterial communities and provides new ideas for future in-depth studies of the diversity and functionality of Daqu bacteria. PRACTICAL APPLICATIONS: This study contributes to expanding our understanding of the functional characteristics of Daqu bacterial communities and provides new ideas for future in-depth studies of the diversity and functionality of Daqu bacteria. Based on these results, we can further select functional strains related to the performance of koji. The results of this study point out the direction for future studies on the formation mechanism of trace aroma substances in baijiu and the improvement of koji quality.
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Affiliation(s)
- Ning Tian
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Xuan Guo
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Mengzhen Wang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Chen Chen
- Shilixiang Co., Ltd, Cangzhou, China
- Hebei Beijing Brewing Technology Innovation Center, Cangzhou, China
| | - Haihao Cui
- Shilixiang Co., Ltd, Cangzhou, China
- Hebei Beijing Brewing Technology Innovation Center, Cangzhou, China
| | - Liping Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Hui Tang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
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10
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Fernandes GL, Shenoy BD, Damare SR. Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing. Front Microbiol 2020; 10:3153. [PMID: 32038585 PMCID: PMC6985565 DOI: 10.3389/fmicb.2019.03153] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/30/2019] [Indexed: 11/13/2022] Open
Abstract
The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.
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Affiliation(s)
- Genevieve L Fernandes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India.,Department of Microbiology, Goa University, Taleigao, India
| | | | - Samir R Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India
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11
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Quan DH, Nagalingam G, Luck I, Proschogo N, Pillalamarri V, Addlagatta A, Martinez E, Sintchenko V, Rutledge PJ, Triccas JA. Bengamides display potent activity against drug-resistant Mycobacterium tuberculosis. Sci Rep 2019; 9:14396. [PMID: 31591407 PMCID: PMC6779907 DOI: 10.1038/s41598-019-50748-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
Mycobacterium tuberculosis infects over 10 million people annually and kills more people each year than any other human pathogen. The current tuberculosis (TB) vaccine is only partially effective in preventing infection, while current TB treatment is problematic in terms of length, complexity and patient compliance. There is an urgent need for new drugs to combat the burden of TB disease and the natural environment has re-emerged as a rich source of bioactive molecules for development of lead compounds. In this study, one species of marine sponge from the Tedania genus was found to yield samples with exceptionally potent activity against M. tuberculosis. Bioassay-guided fractionation identified bengamide B as the active component, which displayed activity in the nanomolar range against both drug-sensitive and drug-resistant M. tuberculosis. The active compound inhibited in vitro activity of M. tuberculosis MetAP1c protein, suggesting the potent inhibitory action may be due to interference with methionine aminopeptidase activity. Tedania-derived bengamide B was non-toxic against human cell lines, synergised with rifampicin for in vitro inhibition of bacterial growth and reduced intracellular replication of M. tuberculosis. Thus, bengamides isolated from Tedania sp. show significant potential as a new class of compounds for the treatment of drug-resistant M. tuberculosis.
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Affiliation(s)
- Diana H Quan
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
| | - Gayathri Nagalingam
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, Sydney, NSW, Australia
| | - Ian Luck
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Nicholas Proschogo
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | | | - Anthony Addlagatta
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Secunderabad, India
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology, The Westmead Institute, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
| | - Peter J Rutledge
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - James A Triccas
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia. .,Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia. .,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia.
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12
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Al-Wahaibi ASM, Lapinska E, Rajarajan N, Dobretsov S, Upstill-Goddard R, Burgess JG. Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach. Front Microbiol 2019; 10:969. [PMID: 31134017 PMCID: PMC6514286 DOI: 10.3389/fmicb.2019.00969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/16/2019] [Indexed: 01/23/2023] Open
Abstract
The vast majority of bacteria present in the natural environment are present in the form of aggregates and/or biofilms. Microbial aggregates are ubiquitous in the marine environment and are inhabited by diverse microbial communities which often express intense extracellular enzymatic activities. However, the secretion of an important group of enzymes, DNases, by bacteria from marine aggregates has not been studied, despite the importance of these aggregates in biogeochemical cycling of nutrients in the oceans. In this work, we therefore, employed both culture-based and bioinformatics approaches to understand the diversity of bacterial DNases in marine bacterioplankton. We found that 34% of 345 strains of attached and non-attached marine bacteria showed extracellular DNase activity. Most of these isolates belong to Proteobacteria (53%) and Firmicutes (34%). Secretion of DNases by bacteria isolated from marine gel particles (MGP) is reported here for the first time. Then, to further understand the wider diversity of the potential to produce DNases, sequences were compared using 2316 whole genome and 42 metagenome datasets. Thirty-nine different taxonomic groups corresponding to 10 bacterial phyla were found to encode genes responsible for DNase secretion. This study highlights the unexpected and widespread presence of DNase secretion in bacteria in general and in MGP more specifically. This has important implications for understanding the dynamics and fate of marine microbial aggregates in the oceans.
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Affiliation(s)
- Aisha S. M. Al-Wahaibi
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, Al Khoud, Oman
| | - Emilia Lapinska
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nithyalakshmy Rajarajan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sergey Dobretsov
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, Al Khoud, Oman
- Department of Marine Science and Fisheries, Sultan Qaboos University, Al Khoud, Oman
| | - Robert Upstill-Goddard
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J. Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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13
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Li J, Gu X, Pan A. Multifunctional α-amylase Amy19 possesses agarase, carrageenase, and cellulase activities. Int J Biol Macromol 2019; 126:585-594. [DOI: 10.1016/j.ijbiomac.2018.12.217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/29/2018] [Accepted: 12/22/2018] [Indexed: 11/28/2022]
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14
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Secondary Metabolites from Marine Endophytic Fungi: Emphasis on Recent Advances in Natural Product Research. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-03589-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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15
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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Rajalaxmi M, Beema Shafreen R, Chithiraiselvi K, Karutha Pandian S. An in vitro and in silico identification of antibiofilm small molecules from seawater metaclone SWMC166 against Vibrio cholerae O1. Mol Cell Probes 2018; 39:14-24. [PMID: 29574083 DOI: 10.1016/j.mcp.2018.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 01/27/2023]
Abstract
This study aimed to determine the antibiofilm activity of seawater microbes against Vibrio cholerae (VCO1) through functional metagenomics approach. A metagenomic library was constructed from Palk Bay seawater and the library was screened to identify the biofilm inhibitory metaclone. Metaclone SWMC166 (harbouring ∼30 kb metagenomic insert) was found to exhibit antibiofilm activity against VCO1. The biofilm inhibitory potential of partially purified ethyl acetate extract of SWMC166 (EA166) was further evaluated through microscopic studies and biochemical assays. Further, EA166 treated VCO1 divulged up-regulation of genes involved in high cell density-mediated quorum sensing (QS) pathway which was analysed by real-time PCR. In order to identify the genes of interest (within ∼30 kb insert), subcloning was performed through shotgun approach. Small molecules from positive subclones SC5 and SC8 were identified through HRLC-MS analysis. Resulted small molecules were docked against QS receptors of V. cholerae to identify the bioactive metabolites. Docking studies revealed that totally seven metabolites were able to interact with QS receptors that can possibly trigger the QS cascade and sequentially inhibit the biofilm formation and virulence factors of VCO1.
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Affiliation(s)
- Murugan Rajalaxmi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, 630 003, India
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The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea. Extremophiles 2018; 22:499-510. [PMID: 29442249 DOI: 10.1007/s00792-018-1012-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/05/2018] [Indexed: 01/25/2023]
Abstract
In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.
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Reyes-Duarte D, Coscolín C, Martínez-Martínez M, Ferrer M, García-Arellano H. Functional-Based Screening Methods for Detecting Esterase and Lipase Activity Against Multiple Substrates. Methods Mol Biol 2018; 1835:109-117. [PMID: 30109647 DOI: 10.1007/978-1-4939-8672-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Functional screens have been extensively used for searching native enzymes or mutant variants in clone libraries. Esterases and lipases are the most retrieved enzymes, because they are within the more demanded industrial enzymes and because a number of simple and generic screening methods can be applied for their screen. Here, we describe the use of a generic pH indicator assay protocol which unambiguously allows detecting in high-throughput manner esterase and lipase activity and quantifying specific activities using an ester concentration above 0.5 mM. The described method is simple and generic to allow the selection of esterases and lipases targeting desired esters.
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Affiliation(s)
- Dolores Reyes-Duarte
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa (UAM-C), CDMX, México.
| | - Cristina Coscolín
- Departamento de Biocatálisis Aplicada, Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Mónica Martínez-Martínez
- Departamento de Biocatálisis Aplicada, Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Manuel Ferrer
- Departamento de Biocatálisis Aplicada, Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Humberto García-Arellano
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana, Unidad Lerma (UAM-L), Lerma de Villada, Edo. de México, México
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations. Mar Drugs 2017; 15:md15060165. [PMID: 28587290 PMCID: PMC5484115 DOI: 10.3390/md15060165] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled de novo, we simulate Illumina and PacBio sequencing of the Salinispora tropica genome focusing on assembly of the salinilactam (slm) BGC.
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Takemura AF, Corzett CH, Hussain F, Arevalo P, Datta M, Yu X, Le Roux F, Polz MF. Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome. Environ Microbiol 2017; 19:2422-2433. [PMID: 28419782 DOI: 10.1111/1462-2920.13765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade-off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.
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Affiliation(s)
- Alison F Takemura
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Fatima Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Philip Arevalo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Manoshi Datta
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Xiaoqian Yu
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frederique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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Indole Derivatives Produced by the Metagenome Genes of the Escherichia coli-Harboring Marine Sponge Discodermia calyx. Molecules 2017; 22:molecules22050681. [PMID: 28441364 PMCID: PMC6154727 DOI: 10.3390/molecules22050681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/23/2022] Open
Abstract
Three indole derivatives, a novel benzoxazine-indole hybrid (1) and two known indole trimers (2, 3), were isolated from the metagenomic library of the marine sponge Discodermia calyx based on functional screening. Their structures were elucidated by extensive spectroscopic analysis and comparison of their NMR data to that of known compounds. The antibacterial assay indicated that only compound 2 displayed significant antibacterial activity against Bacillus cereus, with approximately 20 mm diameter growth inhibition at 10 µg/paper. HPLC analyses revealed that compound 2 is a newly induced metabolite, and the concentration of 3 was obviously enhanced in contrast to negative control, while 1 was not detected, allowing us to predict that the formation of 2 might be induced by exogenous genes derived from the sponge metagenome, whereas compound 1 could be formed through a non-enzymatic process during the isolation procedure.
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Nikolaivits E, Dimarogona M, Fokialakis N, Topakas E. Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation. Front Microbiol 2017; 8:265. [PMID: 28265269 PMCID: PMC5316534 DOI: 10.3389/fmicb.2017.00265] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/07/2017] [Indexed: 12/31/2022] Open
Abstract
The aim of the present review is to highlight the potential use of marine biocatalysts (whole cells or enzymes) as an alternative bioprocess for the degradation of aromatic pollutants. Firstly, information about the characteristics of the still underexplored marine environment and the available scientific tools used to access novel marine-derived biocatalysts is provided. Marine-derived enzymes, such as dioxygenases and dehalogenases, and the involved catalytic mechanisms for the degradation of aromatic and halogenated compounds, are presented, with the purpose of underpinning their potential use in bioremediation. Emphasis is given on persistent organic pollutants (POPs) that are organic compounds with significant impact on health and environment due to their resistance in degradation. POPs bioaccumulate mainly in the fatty tissue of living organisms, therefore current efforts are mostly focused on the restriction of their use and production, since their removal is still unclear. A brief description of the guidelines and criteria that render a pollutant POP is given, as well as their potential biodegradation by marine microorganisms by surveying recent developments in this rather unexplored field.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Maria Dimarogona
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Nikolas Fokialakis
- Division of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Athens Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
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Yaniv K, Golberg K, Kramarsky-Winter E, Marks R, Pushkarev A, Béjà O, Kushmaro A. Functional marine metagenomic screening for anti-quorum sensing and anti-biofilm activity. BIOFOULING 2017; 33:1-13. [PMID: 27882771 DOI: 10.1080/08927014.2016.1253684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
Quorum sensing (QS), a cell-to-cell communication process, entails the production of signaling molecules that enable synchronized gene expression in microbial communities to regulate myriad microbial functions, including biofilm formation. QS disruption may constitute an innovative approach to the design of novel antifouling and anti-biofilm agents. To identify novel quorum sensing inhibitors (QSI), 2,500 environmental bacterial artificial chromosomes (BAC) from uncultured marine planktonic bacteria were screened for QSI activity using soft agar overlaid with wild type Chromobacterium violaceum as an indicator. Of the BAC library clones, 7% showed high QSI activity (>40%) against the indicator bacterium, suggesting that QSI is common in the marine environment. The most active compound, eluted from BAC clone 14-A5, disrupted QS signaling pathways and reduced biofilm formation in both Pseudomonas aeruginosa and Acinetobacter baumannii. The mass spectra of the active BAC clone (14-A5) that had been visualized by thin layer chromatography was dominated by a m/z peak of 362.1.
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Affiliation(s)
- Karin Yaniv
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Karina Golberg
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Esti Kramarsky-Winter
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Robert Marks
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
- b The Ilse Katz Center for Meso and Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer-Sheva , Israel
| | - Alina Pushkarev
- c Faculty of Biology , Technion-Israel Institute of Technology , Haifa , Israel
| | - Oded Béjà
- c Faculty of Biology , Technion-Israel Institute of Technology , Haifa , Israel
| | - Ariel Kushmaro
- a Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Faculty of Engineering Sciences , Ben-Gurion University of the Negev , Beer-Sheva , Israel
- b The Ilse Katz Center for Meso and Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer-Sheva , Israel
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25
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Bekiesch P, Basitta P, Apel AK. Challenges in the Heterologous Production of Antibiotics inStreptomyces. Arch Pharm (Weinheim) 2016; 349:594-601. [DOI: 10.1002/ardp.201600058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/27/2016] [Accepted: 05/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Paulina Bekiesch
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Patrick Basitta
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
| | - Alexander K. Apel
- Pharmaceutical Biology; Pharmaceutical Institute; Eberhard-Karls-Universität Tübingen; Tübingen Germany
- German Centre for Infection Research (DZIF); Partner Site Tübingen; Tübingen Germany
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Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. Mar Drugs 2016; 14:md14040080. [PMID: 27092515 PMCID: PMC4849084 DOI: 10.3390/md14040080] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.
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Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products. Mar Drugs 2016; 14:md14040078. [PMID: 27089350 PMCID: PMC4849082 DOI: 10.3390/md14040078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 12/17/2022] Open
Abstract
Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects.
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Biosurfactants Produced by Marine Microorganisms with Therapeutic Applications. Mar Drugs 2016; 14:md14020038. [PMID: 26901207 PMCID: PMC4771991 DOI: 10.3390/md14020038] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/20/2022] Open
Abstract
Marine microorganisms possess unique metabolic and physiological features and are an important source of new biomolecules, such as biosurfactants. Some of these surface-active compounds synthesized by marine microorganisms exhibit antimicrobial, anti-adhesive and anti-biofilm activity against a broad spectrum of human pathogens (including multi-drug resistant pathogens), and could be used instead of existing drugs to treat infections caused by them. In other cases, these biosurfactants show anti-cancer activity, which could be envisaged as an alternative to conventional therapies. However, marine biosurfactants have not been widely explored, mainly due to the difficulties associated with the isolation and growth of their producing microorganisms. Culture-independent techniques (metagenomics) constitute a promising approach to study the genetic resources of otherwise inaccessible marine microorganisms without the requirement of culturing them, and can contribute to the discovery of novel biosurfactants with significant biological activities. This paper reviews the most relevant biosurfactants produced by marine microorganisms with potential therapeutic applications and discusses future perspectives and opportunities to discover novel molecules from marine environments.
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Cuadrat RRC, Ferrera I, Grossart HP, Dávila AMR. Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:76-87. [PMID: 26871866 PMCID: PMC4770915 DOI: 10.1089/omi.2015.0142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.
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Affiliation(s)
- Rafael R C Cuadrat
- 1 Computational and Systems Biology Laboratory, Oswaldo Cruz Institute , Fiocruz, Brazil .,2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,5 Berlin Center for Genomics in Biodiversity Research , Berlin, Germany
| | - Isabel Ferrera
- 2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,4 Institut de Ciències del Mar , CSIC, Barcelona, Spain
| | - Hans-Peter Grossart
- 2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,3 Potsdam University, Institute for Biochemistry and Biology , Potsdam, Germany
| | - Alberto M R Dávila
- 1 Computational and Systems Biology Laboratory, Oswaldo Cruz Institute , Fiocruz, Brazil
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Martínez-Córdova LR, Martínez-Porchas M, Emerenciano MGC, Miranda-Baeza A, Gollas-Galván T. From microbes to fish the next revolution in food production. Crit Rev Biotechnol 2016; 37:287-295. [PMID: 26863376 DOI: 10.3109/07388551.2016.1144043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Increasing global population and the consequent increase in demand for food are not a new story. Agroindustrial activities such as livestock help meet this demand. Aquaculture arose decades ago and revolutionized the agroindustrial activity as a significant food generator. However, like livestock, aquaculture is based on finite resources and has been accused of being unsustainable. Abandoning aquaculture is not an option considering the food, foreign exchange, and employment it generates, and therefore must be reinvented. Among the many alternatives suggested to make aquaculture more sustainable, microorganisms have been highlighted as a direct food source for cultured fish and crustaceans, a strategy that promises to revolutionize aquaculture by eliminating waste. Considering waste, as part of a cycle, it can increase stock densities and reduce emissions of contaminants and operational costs.
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Affiliation(s)
- Luis Rafael Martínez-Córdova
- a Universidad De Sonora, Departamento De Investigaciones Científicas Y Tecnológicas De La Universidad De Sonora (DICTUS) , Hermosillo , Sonora , México
| | - Marcel Martínez-Porchas
- b Centro De Investigación En Alimentación Y Desarrollo a.C. (CIAD) , Hermosillo , Sonora , México
| | - Maurício Gustavo Coelho Emerenciano
- c Universidade Estadual De Santa Catarina (UDESC), Laboratório De Aquicultura (LAQ), Laguna, Santa Catarina, Brazil and Programa De Pós-Graduação Em Zootecnia , Chapecó, Santa Catarina , Brazil , and
| | - Anselmo Miranda-Baeza
- d Universidad Estatal De Sonora (UES). Carretera a Huatabampo Y Periférico Sur , Navojoa , Sonora , México
| | - Teresa Gollas-Galván
- b Centro De Investigación En Alimentación Y Desarrollo a.C. (CIAD) , Hermosillo , Sonora , México
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Mori T, Iwamoto K, Wakaoji S, Araie H, Kohara Y, Okamura Y, Shiraiwa Y, Takeyama H. Characterization of a novel gene involved in cadmium accumulation screened from sponge-associated bacterial metagenome. Gene 2016; 576:618-25. [DOI: 10.1016/j.gene.2015.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Diepens NJ, Dimitrov MR, Koelmans AA, Smidt H. Molecular Assessment of Bacterial Community Dynamics and Functional End Points during Sediment Bioaccumulation Tests. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:13586-13595. [PMID: 26466173 DOI: 10.1021/acs.est.5b02992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in artificial sediment during a 28 day bioaccumulation test with polychlorinated biphenyls, chlorpyrifos, and four marine benthic invertebrates. DGGE and 454-pyrosequencing of PCR-amplified 16S rRNA genes were used to characterize bacterial community composition. Abundance of total bacteria and selected genes encoding enzymes involved in important microbially mediated ecosystem functions were measured by qPCR. Community composition and diversity responded most to the time course of the experiment, whereas organic matter (OM) content showed a low but significant effect on community composition, biodiversity and two functional genes tested. Moreover, OM content had a higher influence on bacterial community composition than invertebrate species. Medium OM content led to the highest gene abundance and is preferred for standard testing. Our results also indicated that a pre-equilibration period is essential for growth and stabilization of the bacterial community. The observed changes in microbial community composition and functional gene abundance may imply actual changes in such functions during tests, with consequences for exposure and toxicity assessment.
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Affiliation(s)
- Noël J Diepens
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
| | - Mauricio R Dimitrov
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Albert A Koelmans
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- IMARES, Institute for Marine Resources & Ecosystem Studies, Wageningen UR , P.O. Box 68, 1970 AB IJmuiden, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:310-20. [PMID: 26549842 PMCID: PMC4678792 DOI: 10.1016/j.gpb.2015.07.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/08/2015] [Accepted: 07/22/2015] [Indexed: 11/20/2022]
Abstract
Covering a quarter of the world's tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%-85%), while Basidiomycota was less abundant (14%-24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.
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Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:480386. [PMID: 26509157 PMCID: PMC4609784 DOI: 10.1155/2015/480386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/17/2015] [Indexed: 11/17/2022]
Abstract
Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems.
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Trindade M, van Zyl LJ, Navarro-Fernández J, Abd Elrazak A. Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front Microbiol 2015; 6:890. [PMID: 26379658 PMCID: PMC4552006 DOI: 10.3389/fmicb.2015.00890] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products exhibit immense structural diversity and complexity and have captured the attention of researchers for several decades. They have been explored for a wide spectrum of applications, most noteworthy being their prominent role in medicine, and their versatility expands to application as drugs for many diseases. Accessing unexplored environments harboring unique microorganisms is expected to yield novel bioactive metabolites with distinguishing functionalities, which can be supplied to the starved pharmaceutical market. For this purpose the oceans have turned out to be an attractive and productive field. Owing to the enormous biodiversity of marine microorganisms, as well as the growing evidence that many metabolites previously isolated from marine invertebrates and algae are actually produced by their associated bacteria, the interest in marine microorganisms has intensified. Since the majority of the microorganisms are uncultured, metagenomic tools are required to exploit the untapped biochemistry. However, after years of employing metagenomics for marine drug discovery, new drugs are vastly under-represented. While a plethora of natural product biosynthetic genes and clusters are reported, only a minor number of potential therapeutic compounds have resulted through functional metagenomic screening. This review explores specific obstacles that have led to the low success rate. In addition to the typical problems encountered with traditional functional metagenomic-based screens for novel biocatalysts, there are enormous limitations which are particular to drug-like metabolites. We also present how targeted and function-guided strategies, employing modern, and multi-disciplinary approaches have yielded some of the most exciting discoveries attributed to uncultured marine bacteria. These discoveries set the stage for progressing the production of drug candidates from uncultured bacteria for pre-clinical and clinical development.
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Affiliation(s)
- Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
| | - José Navarro-Fernández
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
- Centro Regional de Hemodonación, Servicio de Hematología y Oncología Médica, Universidad de Murcia, IMIB-Arrixaca, MurciaSpain
| | - Ahmed Abd Elrazak
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
- Botany Department, Faculty of Science, Mansoura University, MansouraEgypt
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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Reen FJ, Gutiérrez-Barranquero JA, Dobson ADW, Adams C, O’Gara F. Emerging concepts promising new horizons for marine biodiscovery and synthetic biology. Mar Drugs 2015; 13:2924-54. [PMID: 25984990 PMCID: PMC4446613 DOI: 10.3390/md13052924] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/22/2015] [Accepted: 04/28/2015] [Indexed: 12/23/2022] Open
Abstract
The vast oceans of the world, which comprise a huge variety of unique ecosystems, are emerging as a rich and relatively untapped source of novel bioactive compounds with invaluable biotechnological and pharmaceutical potential. Evidence accumulated over the last decade has revealed that the diversity of marine microorganisms is enormous with many thousands of bacterial species detected that were previously unknown. Associated with this diversity is the production of diverse repertoires of bioactive compounds ranging from peptides and enzymes to more complex secondary metabolites that have significant bioactivity and thus the potential to be exploited for innovative biotechnology. Here we review the discovery and functional potential of marine bioactive peptides such as lantibiotics, nanoantibiotics and peptidomimetics, which have received particular attention in recent years in light of their broad spectrum of bioactivity. The significance of marine peptides in cell-to-cell communication and how this may be exploited in the discovery of novel bioactivity is also explored. Finally, with the recent advances in bioinformatics and synthetic biology, it is becoming clear that the integration of these disciplines with genetic and biochemical characterization of the novel marine peptides, offers the most potential in the development of the next generation of societal solutions.
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Affiliation(s)
- F. Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork—National University of Ireland, Cork, Ireland; E-Mails: (F.J.R.); (J.A.G.-B.); (C.A.)
| | - José A. Gutiérrez-Barranquero
- BIOMERIT Research Centre, School of Microbiology, University College Cork—National University of Ireland, Cork, Ireland; E-Mails: (F.J.R.); (J.A.G.-B.); (C.A.)
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork—National University of Ireland, Cork, Ireland; E-Mail:
| | - Claire Adams
- BIOMERIT Research Centre, School of Microbiology, University College Cork—National University of Ireland, Cork, Ireland; E-Mails: (F.J.R.); (J.A.G.-B.); (C.A.)
| | - Fergal O’Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork—National University of Ireland, Cork, Ireland; E-Mails: (F.J.R.); (J.A.G.-B.); (C.A.)
- School of Biomedical Sciences, Curtin University, Perth WA 6845, Australia
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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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Jackson SA, Borchert E, O'Gara F, Dobson ADW. Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems. Curr Opin Biotechnol 2015; 33:176-82. [PMID: 25812477 DOI: 10.1016/j.copbio.2015.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/28/2015] [Accepted: 03/06/2015] [Indexed: 12/26/2022]
Abstract
Research focused on the search for new biosurfactants aims to replace chemical surfactants, which while being cost-effective are ecologically undesirable. Metagenomics can lead to discovery of novel biosurfactants, tackling issues of low production yields. Recent successes include the heterologous production of biosurfactants. The dearth of biosurfactants discovered to date through metagenomics is puzzling given that good screening systems and heterologous host systems are available.
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Affiliation(s)
- Stephen A Jackson
- Marine Biotechnology Centre, Environmental Research Institute, National University of Ireland, Cork, Ireland
| | - Erik Borchert
- Marine Biotechnology Centre, Environmental Research Institute, National University of Ireland, Cork, Ireland
| | - Fergal O'Gara
- Marine Biotechnology Centre, Environmental Research Institute, National University of Ireland, Cork, Ireland; School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland; BIOMERIT Research Centre, University College Cork, National University of Ireland, Cork, Ireland
| | - Alan D W Dobson
- Marine Biotechnology Centre, Environmental Research Institute, National University of Ireland, Cork, Ireland; School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
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Wang X, Wang Q, Guo X, Liu L, Guo J, Yao J, Zhu H. Functional genomic analysis of Hawaii marine metagenomes. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-014-0658-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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41
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Barbosa TM, Phelan RW, Leong D, Morrissey JP, Adams C, Dobson ADW, O’Gara F. A novel erythromycin resistance plasmid from Bacillus sp. strain HS24, isolated from the marine sponge Haliclona simulans. PLoS One 2014; 9:e115583. [PMID: 25548909 PMCID: PMC4280177 DOI: 10.1371/journal.pone.0115583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
Abstract
A better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus.
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Affiliation(s)
| | - Robert W. Phelan
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Dara Leong
- Department of Microbiology, University College Cork, Cork, Ireland
| | - John P. Morrissey
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Claire Adams
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Fergal O’Gara
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Curtin University, School of Biomedical Sciences, Perth WA 6845, Australia
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Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics 2014; 15:918. [PMID: 25336203 PMCID: PMC4218995 DOI: 10.1186/1471-2164-15-918] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/06/2014] [Indexed: 12/04/2022] Open
Abstract
Background Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis. Results Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results. Conclusion CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, George Washington University, Washington DC 20037, USA.
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Marine biotechnologies and synthetic biology, new issues for a fair and equitable profit-sharing commercial use. Mar Genomics 2014; 17:79-83. [DOI: 10.1016/j.margen.2014.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 11/19/2022]
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Production of avaroferrin and putrebactin by heterologous expression of a deep-sea metagenomic DNA. Mar Drugs 2014; 12:4799-809. [PMID: 25222668 PMCID: PMC4178481 DOI: 10.3390/md12094799] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/12/2014] [Accepted: 09/01/2014] [Indexed: 11/25/2022] Open
Abstract
The siderophore avaroferrin (1), an inhibitor of Vibrio swarming that was recently identified in Shewanella algae B516, was produced by heterologous expression of the biosynthetic gene cluster cloned from a deep-sea sediment metagenomic DNA, together with two analogues, bisucaberin (2) and putrebactin (3). Avaroferrin (1) is a macrocyclic heterodimer of N-hydroxy-N-succinyl cadaverine (4) and N-hydroxy-N-succinyl-putrescine (5), whereas analogues 2 and 3 are homodimers of 4 and 5, respectively. Heterologous expression of two other related genes from culturable marine bacteria resulted in production of compounds 1–3, but in quite different proportions compared with production through expression of the metagenomic DNA.
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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Borziak K, Posner MG, Upadhyay A, Danson MJ, Bagby S, Dorus S. Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea. PLoS One 2014; 9:e87063. [PMID: 24489835 PMCID: PMC3904984 DOI: 10.1371/journal.pone.0087063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/18/2013] [Indexed: 02/04/2023] Open
Abstract
Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.
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Affiliation(s)
- Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Mareike G. Posner
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
| | - Abhishek Upadhyay
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
| | - Michael J. Danson
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
- Centre for Extremophile Research, University of Bath, Claverton Down, United Kingdom
| | - Stefan Bagby
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
- * E-mail: (SB); (SD)
| | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
- * E-mail: (SB); (SD)
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Jackson SA, Flemer B, McCann A, Kennedy J, Morrissey JP, O’Gara F, Dobson ADW. Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges. PLoS One 2013; 8:e84438. [PMID: 24386380 PMCID: PMC3875569 DOI: 10.1371/journal.pone.0084438] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 11/14/2013] [Indexed: 11/18/2022] Open
Abstract
Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ~60% and ~72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (~11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ~88% and ~89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (~0.2% and ~0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.
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Affiliation(s)
- Stephen A. Jackson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Burkhardt Flemer
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Angela McCann
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jonathan Kennedy
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - John P. Morrissey
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O’Gara
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis. PLoS One 2013; 8:e81910. [PMID: 24282619 PMCID: PMC3839897 DOI: 10.1371/journal.pone.0081910] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/28/2013] [Indexed: 11/22/2022] Open
Abstract
The functional dynamics of microbial communities are largely responsible for the clean-up of hydrocarbons in the environment. However, knowledge of the distinguishing functional genes, known as the metabolic footprint, present in hydrocarbon-impacted sites is still scarcely understood. Here, we conducted several multivariate analyses to characterise the metabolic footprints present in a variety of hydrocarbon-impacted and non-impacted sediments. Non-metric multi-dimensional scaling (NMDS) and canonical analysis of principal coordinates (CAP) showed a clear distinction between the two groups. A high relative abundance of genes associated with cofactors, virulence, phages and fatty acids were present in the non-impacted sediments, accounting for 45.7 % of the overall dissimilarity. In the hydrocarbon-impacted sites, a high relative abundance of genes associated with iron acquisition and metabolism, dormancy and sporulation, motility, metabolism of aromatic compounds and cell signalling were observed, accounting for 22.3 % of the overall dissimilarity. These results suggest a major shift in functionality has occurred with pathways essential to the degradation of hydrocarbons becoming overrepresented at the expense of other, less essential metabolisms.
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Analysis of hydrocarbon-contaminated groundwater metagenomes as revealed by high-throughput sequencing. Mol Biotechnol 2013; 54:900-12. [PMID: 23307295 DOI: 10.1007/s12033-012-9639-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The tendency for chlorinated aliphatics and aromatic hydrocarbons to accumulate in environments such as groundwater and sediments poses a serious environmental threat. In this study, the metabolic capacity of hydrocarbon (aromatics and chlorinated aliphatics)-contaminated groundwater in the KwaZulu-Natal province of South Africa has been elucidated for the first time by analysis of pyrosequencing data. The taxonomic data revealed that the metagenomes were dominated by the phylum Proteobacteria (mainly Betaproteobacteria). In addition, Flavobacteriales, Sphingobacteria, Burkholderiales, and Rhodocyclales were the predominant orders present in the individual metagenomes. These orders included microorganisms (Flavobacteria, Dechloromonas aromatica RCB, and Azoarcus) involved in the degradation of aromatic compounds and various other hydrocarbons that were present in the groundwater. Although the metabolic reconstruction of the metagenome represented composite cell networks, the information obtained was sufficient to address questions regarding the metabolic potential of the microbial communities and to correlate the data to the contamination profile of the groundwater. Genes involved in the degradation of benzene and benzoate, heavy metal-resistance mechanisms appeared to provide a survival strategy used by the microbial communities. Analysis of the pyrosequencing-derived data revealed that the metagenomes represent complex microbial communities that have adapted to the geochemical conditions of the groundwater as evidenced by the presence of key enzymes/genes conferring resistance to specific contaminants. Thus, pyrosequencing analysis of the metagenomes provided insights into the microbial activities in hydrocarbon-contaminated habitats.
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Yang XL, Wakimoto T, Takeshige Y, He R, Egami Y, Awakawa T, Abe I. Indole–porphyrin hybrids produced by metagenomics. Bioorg Med Chem Lett 2013; 23:3810-3. [DOI: 10.1016/j.bmcl.2013.04.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/29/2013] [Indexed: 12/01/2022]
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