Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

[1]  M. Bizukojć,et al.  Effects of the Coculture Initiation Method on the Production of Secondary Metabolites in Bioreactor Cocultures of Penicillium rubens and Streptomyces rimosus , 2023, Molecules.

[2]  Barbara R. Terlouw,et al.  antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation , 2023, Nucleic Acids Res..

[3]  R. Krull,et al.  Morphology engineering for novel antibiotics: Effect of glass microparticles and soy lecithin on rebeccamycin production and cellular morphology of filamentous actinomycete Lentzea aerocolonigenes , 2023, Frontiers in Bioengineering and Biotechnology.

[4]  Luiz M. R. Gadelha,et al.  MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry , 2023, Journal of Cheminformatics.

[5]  I. Castro-Gamboa,et al.  Enhancing chemical and biological diversity by co-cultivation , 2023, Frontiers in Microbiology.

[6]  A. Papachristodoulou,et al.  Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. , 2023, Biotechnology advances.

[7]  Yunsheng Wang,et al.  Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis , 2023, Frontiers in Microbiology.

[8]  Roger G. Linington,et al.  Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting , 2023, Nature Communications.

[9]  Ahmad S. Khalil,et al.  Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability , 2023, Materials today. Bio.

[10]  T. B. Grangeiro,et al.  Antagonism of volatile organic compounds of the Bacillus sp. against Fusarium kalimantanense , 2022, World Journal of Microbiology and Biotechnology.

[11]  J. Hegemann,et al.  Current developments in antibiotic discovery , 2022, EMBO reports.

[12]  T. Hesterkamp,et al.  Fighting antibiotic resistance—strategies and (pre)clinical developments to find new antibacterials , 2022, EMBO reports.

[13]  B. Menghe,et al.  Metabolomic analysis of cooperative adaptation between Co-cultured Lacticaseibacillus casei Zhang and Lactiplantibacillus plantarum P8 , 2022, LWT.

[14]  Dong Wang,et al.  Genomic and metabolic features of Bacillus cereus, inhibiting the growth of Sclerotinia sclerotiorum by synthesizing secondary metabolites , 2022, Archives of Microbiology.

[15]  J. V. D. van der Hooft,et al.  Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools , 2022, Metabolomics.

[16]  P. Hess,et al.  Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus , 2022, Environmental microbiology.

[17]  Guoying Zhang,et al.  Application of Metabolomics in Fungal Research , 2022, Molecules.

[18]  Chris S. Thomas,et al.  Microbiome composition modulates secondary metabolism in a multispecies bacterial community , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. de Saeger,et al.  Deciphering Alternaria metabolic responses in microbial confrontation via an integrated mass spectrometric targeted and non-targeted strategy. , 2022, Food chemistry.

[20]  J. Büchs,et al.  Tunable population dynamics in a synthetic filamentous coculture , 2022, MicrobiologyOpen.

[21]  M. Bizukojć,et al.  Production of secondary metabolites in stirred tank bioreactor co-cultures of Streptomyces noursei and Aspergillus terreus , 2022, Frontiers in Bioengineering and Biotechnology.

[22]  Y. Arakawa,et al.  Comparative Metabolomics Reveals a Bifunctional Antibacterial Conjugate from Combined-Culture of Streptomyces hygroscopicus HOK021 and Tsukamurella pulmonis TP-B0596. , 2022, ACS chemical biology.

[23]  Zeping Liu,et al.  Effects of Cell-Cell Interactions between a. Oryzae and Z. Rouxii on Morphology and Secondary Metabolites , 2022, SSRN Electronic Journal.

[24]  A. Murray,et al.  Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery , 2022, Analytical chemistry.

[25]  Jing Ye,et al.  Mechanism of enhanced production of triterpenoids in algal–fungal consortium , 2022, Bioprocess and Biosystems Engineering.

[26]  T. Boruta,et al.  Co-cultivation of filamentous microorganisms in the presence of aluminum oxide microparticles , 2022, Applied Microbiology and Biotechnology.

[27]  A. Driessen,et al.  Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi , 2022, Frontiers in bioengineering and biotechnology.

[28]  T. Felföldi,et al.  A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria , 2022, PloS one.

[29]  A. Kundaje,et al.  Automated sequence-based annotation and interpretation of the human genome , 2022, Nature Genetics.

[30]  Syun-ichi Urayama,et al.  Antibacterial diphenyl ether production induced by co-culture of Aspergillus nidulans and Aspergillus fumigatus , 2022, Applied Microbiology and Biotechnology.

[31]  Guang-Rong Zhao,et al.  Systems Metabolic Engineering of Escherichia coli Coculture for De Novo Production of Genistein. , 2022, ACS synthetic biology.

[32]  D. Weuster‐Botz,et al.  Artificial microbial consortia for bioproduction processes , 2022, Engineering in life sciences.

[33]  A. Mohanty,et al.  Investigation of interspecies crosstalk between probiotic Bacillus subtilis BR4 and Pseudomonas aeruginosa using metabolomics analysis. , 2022, Microbial pathogenesis.

[34]  W. Gerwick,et al.  Secondary Metabolite Variation and Bioactivities of Two Marine Aspergillus Strains in Static Co-Culture Investigated by Molecular Network Analysis and Multiple Database Mining Based on LC-PDA-MS/MS , 2022, Antibiotics.

[35]  Alejandra Prieto-Davó,et al.  Insights into the Chemical Diversity of Selected Fungi from the Tza Itzá Cenote of the Yucatan Peninsula , 2022, ACS omega.

[36]  A. Demain,et al.  Impact of novel microbial secondary metabolites on the pharma industry , 2022, Applied Microbiology and Biotechnology.

[37]  H. Cao,et al.  Advances in mining and expressing microbial biosynthetic gene clusters , 2022, Critical reviews in microbiology.

[38]  H. Raja,et al.  Fungal–fungal co-culture: a primer for generating chemical diversity , 2022, Natural product reports.

[39]  M. Blümel,et al.  Induction of Isochromanones by Co-Cultivation of the Marine Fungus Cosmospora sp. and the Phytopathogen Magnaporthe oryzae , 2022, International journal of molecular sciences.

[40]  Zhi-Long Xiu,et al.  Co-culture of Aspergillus sydowii and Bacillus subtilis induces the production of antibacterial metabolites. , 2022, Fungal biology.

[41]  Zeping Liu,et al.  Metabolomic profiles of the liquid state fermentation in co-culture of A. oryzae and Z. rouxii. , 2021, Food microbiology.

[42]  L. You,et al.  Engineered microbial consortia: strategies and applications , 2021, Microbial Cell Factories.

[43]  M. Bizukojć,et al.  Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors , 2021, Biomolecules.

[44]  Jeffrey A. Kimbrel,et al.  Prokaryotic Genome Annotation. , 2021, Methods in molecular biology.

[45]  Yan Xu,et al.  Use of elicitors to enhance or activate the antibiotic production in streptomyces , 2021, Critical reviews in biotechnology.

[46]  T. Boruta,et al.  Enhanced Oxytetracycline Production by Streptomyces rimosus in Submerged Co-Cultures with Streptomyces noursei , 2021, Molecules.

[47]  M. Bizukojć,et al.  “Microbial Wars” in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites , 2021, Frontiers in Bioengineering and Biotechnology.

[48]  Neil L Kelleher,et al.  Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. , 2021, Natural product reports.

[49]  Bin Wu,et al.  Comparative Metabolomics Reveals Fungal Conversion of Co-Existing Bacterial Metabolites within a Synthetic Aspergillus-Streptomyces Community , 2021, Marine drugs.

[50]  Kevin V. Solomon,et al.  Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship , 2021, mBio.

[51]  S. Santos,et al.  Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani. , 2021, Microbiological research.

[52]  S. E. Nybo,et al.  Renewed interests in the discovery of bioactive actinomycete metabolites driven by emerging technologies , 2021, Journal of applied microbiology.

[53]  Karthik Raman,et al.  Modelling microbial communities: Harnessing consortia for biotechnological applications , 2021, Computational and structural biotechnology journal.

[54]  S. Schuster,et al.  Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices , 2021, Nature Methods.

[55]  Ophelia S. Venturelli,et al.  Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. , 2021, Current opinion in microbiology.

[56]  R. Bauer,et al.  Natural products in drug discovery: advances and opportunities , 2021, Nature Reviews Drug Discovery.

[57]  M. Diender,et al.  Synthetic co-cultures: novel avenues for bio-based processes. , 2021, Current opinion in biotechnology.

[58]  Zhihui Zheng,et al.  Inducing secondary metabolite production of Aspergillus sydowii through microbial co-culture with Bacillus subtilis , 2020, Microbial Cell Factories.

[59]  M. Vansteelandt,et al.  Dynamics of Chemical Diversity during Co‐Cultures: An Integrative Time‐Scale Metabolomics Study of Fungal Endophytes Cophinforma mamane and Fusarium solani , 2020, Chemistry & biodiversity.

[60]  P. Dorrestein,et al.  Molecular Networking: A Useful Tool for the Identification of New Psychoactive Substances in Seizures by LC–HRMS , 2020, Frontiers in Chemistry.

[61]  R. Krull,et al.  An image analysis method to quantify heterogeneous filamentous biomass based on pixel intensity values – Interrelation of macro- and micro-morphology in Actinomadura namibiensis , 2020 .

[62]  Juan Nogales,et al.  Metabolic modelling approaches for describing and engineering microbial communities , 2020, Computational and structural biotechnology journal.

[63]  N. Kelleher,et al.  An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes , 2020, Proceedings of the National Academy of Sciences.

[64]  S. Sørensen,et al.  The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity , 2020, The ISME journal.

[65]  V. Wendisch,et al.  Synthetic microbial consortia for small molecule production. , 2020, Current opinion in biotechnology.

[66]  S. Foote,et al.  Transcriptomic and exometabolomic profiling reveals antagonistic and defensive modes of Clonostachys rosea action against Fusarium graminearum. , 2020, Molecular plant-microbe interactions : MPMI.

[67]  W. Ko,et al.  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges , 2020, International Journal of Antimicrobial Agents.

[68]  E. Holmes,et al.  Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding , 2020, The Lancet.

[69]  D. Arora,et al.  Expanding the chemical diversity through microorganisms co-culture: Current status and outlook. , 2020, Biotechnology advances.

[70]  David S. Wishart,et al.  Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis , 2019, Current protocols in bioinformatics.

[71]  M. Elliot,et al.  Unlocking the trove of metabolic treasures: activating silent biosynthetic gene clusters in bacteria and fungi. , 2019, Current opinion in microbiology.

[72]  Christine M. Aceves,et al.  Reproducible molecular networking of untargeted mass spectrometry data using GNPS , 2019, Nature Protocols.

[73]  J. Bertrand-Michel,et al.  Study of in vitro interaction between Fusarium verticillioides and Streptomyces sp. using metabolomics , 2019, Folia Microbiologica.

[74]  Ping Zheng,et al.  A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger , 2019, Biotechnology for Biofuels.

[75]  Alan R. Pacheco,et al.  A multidimensional perspective on microbial interactions , 2019, FEMS microbiology letters.

[76]  Steven L Salzberg,et al.  Next-generation genome annotation: we still struggle to get it right , 2019, Genome Biology.

[77]  M. Bizukojć,et al.  Evaluating the outcomes of submerged co-cultivation: production of lovastatin and other secondary metabolites by Aspergillus terreus in fungal co-cultures , 2019, Applied Microbiology and Biotechnology.

[78]  Song Yang,et al.  Unusual and Highly Bioactive Sesterterpenes Synthesized by Pleurotus ostreatus during Coculture with Trametes robiniophila Murr , 2019, Applied and Environmental Microbiology.

[79]  N. Keller.  Fungal secondary metabolism: regulation, function and drug discovery , 2018, Nature Reviews Microbiology.

[80]  D. Oh,et al.  Coculture of Marine Streptomyces sp. With Bacillus sp. Produces a New Piperazic Acid-Bearing Cyclic Peptide , 2018, Front. Chem..

[81]  M. Blümel,et al.  Molecular Networking-Based Metabolome and Bioactivity Analyses of Marine-Adapted Fungi Co-cultivated With Phytopathogens , 2018, Front. Microbiol..

[82]  A. Jemain,et al.  Partial least squares-discriminant analysis (PLS-DA) for classification of high-dimensional (HD) data: a review of contemporary practice strategies and knowledge gaps. , 2018, The Analyst.

[83]  M. Bizukojć,et al.  Morphological evolution of various fungal species in the presence and absence of aluminum oxide microparticles: Comparative and quantitative insights into microparticle‐enhanced cultivation (MPEC) , 2018, MicrobiologyOpen.

[84]  O. Puel,et al.  From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. , 2018, Natural product reports.

[85]  S. Rudaz,et al.  Dynamics of Metabolite Induction in Fungal Co-cultures by Metabolomics at Both Volatile and Non-volatile Levels , 2018, Front. Microbiol..

[86]  H. Fan,et al.  Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum , 2018, Front. Microbiol..

[87]  V. Meyer,et al.  From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology. , 2017, Trends in microbiology.

[88]  L. Buydens,et al.  Combining ANOVA-PCA with POCHEMON to analyse micro-organism development in a polymicrobial environment. , 2017, Analytica chimica acta.

[89]  Kristian Fog Nielsen,et al.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.

[90]  Robert Powers,et al.  PCA as a practical indicator of OPLS-DA model reliability. , 2016, Current Metabolomics.

[91]  Serge Rudaz,et al.  Exploring Omics data from designed experiments using analysis of variance multiblock Orthogonal Partial Least Squares. , 2016, Analytica chimica acta.

[92]  Mattheos A G Koffas,et al.  Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. , 2016, Metabolic engineering.

[93]  Jorge Cadima,et al.  Principal component analysis: a review and recent developments , 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[94]  Jeroen J. Jansen,et al.  Identification of Pseudomonas aeruginosa and Aspergillus fumigatus mono- and co-cultures based on volatile biomarker combinations , 2016, Journal of breath research.

[95]  Doug R. Braun,et al.  Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach , 2015, Marine drugs.

[96]  N. Keller.  Translating biosynthetic gene clusters into fungal armor and weaponry. , 2015, Nature chemical biology.

[97]  Michael A Fischbach,et al.  Computational approaches to natural product discovery. , 2015, Nature chemical biology.

[98]  L. Buydens,et al.  Projected Orthogonalized CHemical Encounter MONitoring (POCHEMON) for microbial interactions in co-culture , 2015, Metabolomics.

[99]  David I. Ellis,et al.  A tutorial review: Metabolomics and partial least squares-discriminant analysis--a marriage of convenience or a shotgun wedding. , 2015, Analytica chimica acta.

[100]  G. V. van Wezel,et al.  Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation , 2015, Scientific Reports.

[101]  Arnald Alonso,et al.  Analytical Methods in Untargeted Metabolomics: State of the Art in 2015 , 2015, Front. Bioeng. Biotechnol..

[102]  K. Gindro,et al.  Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. , 2014, Biotechnology advances.

[103]  J. Schrenzel,et al.  Multi-well fungal co-culture for de novo metabolite-induction in time-series studies based on untargeted metabolomics. , 2014, Molecular bioSystems.

[104]  Age K. Smilde,et al.  Principal Component Analysis , 2003, Encyclopedia of Machine Learning.

[105]  Roger G. Linington,et al.  Molecular networking as a dereplication strategy. , 2013, Journal of natural products.

[106]  P. Dorrestein,et al.  Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome , 2013, mBio.

[107]  Nuno Bandeira,et al.  MS/MS networking guided analysis of molecule and gene cluster families , 2013, Proceedings of the National Academy of Sciences.

[108]  K. Gindro,et al.  Detection of metabolite induction in fungal co-cultures on solid media by high-throughput differential ultra-high pressure liquid chromatography-time-of-flight mass spectrometry fingerprinting. , 2013, Journal of chromatography. A.

[109]  Axel A. Brakhage,et al.  Regulation of fungal secondary metabolism , 2012, Nature Reviews Microbiology.

[110]  Mick Watson,et al.  The automatic annotation of bacterial genomes , 2012, Briefings Bioinform..

[111]  R. Krull,et al.  Morphology engineering - Osmolality and its effect on Aspergillus niger morphology and productivity , 2011, Microbial cell factories.

[112]  David J. Barry,et al.  Morphological quantification of filamentous fungal development using membrane immobilization and automatic image analysis , 2009, Journal of Industrial Microbiology & Biotechnology.

[113]  Trupti Joshi,et al.  Quantitative assessment of relationship between sequence similarity and function similarity , 2007, BMC Genomics.

[114]  Johan Trygg,et al.  Chemometrics in metabonomics. , 2007, Journal of proteome research.

[115]  M. Rantalainen,et al.  OPLS discriminant analysis: combining the strengths of PLS‐DA and SIMCA classification , 2006 .

[116]  Axel Zeeck,et al.  Big Effects from Small Changes: Possible Ways to Explore Nature's Chemical Diversity , 2002, Chembiochem : a European journal of chemical biology.

[117]  Lincoln Stein,et al.  Genome annotation: from sequence to biology , 2001, Nature Reviews Genetics.

[118]  P. Cox,et al.  Image analysis of the morphology of filamentous micro-organisms. , 1998, Microbiology.

[119]  Nanfang Xu,et al.  Co-culture of Trichoderma atroviride SG3403 and Bacillus subtilis 22 improves the production of antifungal secondary metabolites , 2020 .

[120]  Alexander Raskind,et al.  Statistical methods in metabolomics. , 2012, Methods in molecular biology.

[121]  A. Fleming,et al.  Classics in infectious diseases: on the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae by Alexander Fleming, Reprinted from the British Journal of Experimental Pathology 10:226-236, 1929. , 1980, Reviews of infectious diseases.