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Virgens GS, Oliveira J, Cardoso MIO, Teodoro JA, Amaral DT. BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration. J Mol Graph Model 2024; 128:108721. [PMID: 38308972 DOI: 10.1016/j.jmgm.2024.108721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as blind docking or site-specific targeting, which are invaluable in applications ranging from drug repositioning to the exploration of new allosteric binding sites and toxicity assessments. BioProtIS has been designed with modularity at its core. This inherent flexibility empowers users to make custom modifications directly within the source code, tailoring the pipeline to their specific research needs. Moreover, it lays the foundation for seamless integration of diverse docking algorithms in future iterations, promising ongoing advancements in the field of computational biology. This pipeline is available for free distribution and can be download at: https://github.com/BBMDO/BioProtIS.
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Affiliation(s)
- Graziela Sória Virgens
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Júlia Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | | | - João Alfredo Teodoro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil.
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Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide. Appl Biochem Biotechnol 2023; 195:753-771. [PMID: 36166154 DOI: 10.1007/s12010-022-04154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/24/2023]
Abstract
Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.
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Kalendar R, Hunter C, Orbovic V. Editorial: Innovative applications of sequencing technologies in plant science. FRONTIERS IN PLANT SCIENCE 2022; 13:1058347. [PMID: 36388574 PMCID: PMC9644194 DOI: 10.3389/fpls.2022.1058347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 05/28/2023]
Affiliation(s)
- Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Charles Hunter
- Chemistry Research Unit, United States Department of Agriculture (USDA) Agricultural Research Service, Gainesville, FL, United States
| | - Vladimir Orbovic
- Citrus Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences (IFAS), Lake Alfred, FL, United States
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4
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Vasudeva G, Singh H, Paliwal S, Pinnaka AK. Metagenomics: An Approach for Unraveling the Community Structure and Functional Potential of Activated Sludge of a Common Effluent Treatment Plant. Front Microbiol 2022; 13:933373. [PMID: 35958153 PMCID: PMC9358654 DOI: 10.3389/fmicb.2022.933373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/23/2022] Open
Abstract
The common effluent treatment plant (CETP) located at Baddi treats the industrial effluent from various industries, leading to the pooling of a diverse range of substrates and metabolites. The nutrient loading and its availability decide the balance of the microbial community and its diversity. The samples thus collected from the activated sludge (BS14) of CETP and Sirsa river (SR1) from the vicinity of CETP effluent discharge were processed for the whole metagenome analysis to reveal the microbial community and its functional potential. The taxonomic classification of the BS14 sample showed the dominance of the bacterial community with 96% of abundance, whereas the SR1 was populated by eukaryotes representing 50.4% of the community of SR1. The bacterial community of SR1 was constituted of 47.2%. The functional analysis of BS14 and SR1 with GhostKOALA against the KEGG database assigned 43.7% and 27.8% of the open reading frames (ORFs) with functions. It revealed the xenobiotic degradation modules with complete pathways along with resistance against the beta-lactams. The analysis with the comprehensive antibiotic resistance database (CARD) revealed 33 and 32 unique types of antimicrobial resistance in BS14 and SR1, respectively. Both the samples were dominated by the beta-lactam resistance genes. The carbohydrate-active enzyme (CAZy) database assigned a total of 6,611 and 2,941 active enzymes to BS14 and SR1, respectively. In contrast, the glycosyl hydrolases (GH) and glycosyltransferases (GT) class of enzymes were found to be abundant in both the samples as compared with polysaccharide lyases (PL), auxiliary activities (AA), carbohydrate esterases (CE), and carbohydrate-binding module (CBM).
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Pooalai R, Khongfak S, Leungtongkam U, Thummeepak R, Kunthalert D, Sitthisak S. Genomic analysis uncovers laccase-coding genes and biosynthetic gene clusters encoding antimicrobial compounds in laccase-producing Acinetobacter baumannii. Sci Rep 2022; 12:11932. [PMID: 35831359 PMCID: PMC9279374 DOI: 10.1038/s41598-022-16122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/05/2022] [Indexed: 11/15/2022] Open
Abstract
Laccases are multicopper oxidase family enzymes that can oxidize various substrates. In this study, we isolated laccase-producing Acinetobacter spp. from the environment, and one isolate of laccase-producing Acinetobacter baumannii, designated NI-65, was identified. The NI-65 strain exhibited constitutive production of extracellular laccase in a crude extract using 2,6-dimethoxyphenol as a substrate when supplemented with 2 mM CuSO4. Whole-genome sequencing of the NI-65 strain revealed a genome size of 3.6 Mb with 3,471 protein-coding sequences. The phylogenetic analysis showed high similarity to the genome of A. baumannii NCIMB8209. Three laccase proteins, PcoA and CopA, that belong to bacterial CopA superfamilies, and LAC-AB, that belongs to the I-bacterial bilirubin oxidase superfamily, were identified. These proteins were encoded by three laccase-coding genes (pcoA, copA, and lac-AB). The lac-AB gene showed a sequence similar to that of polyphenol oxidase (PPO). Gene clusters encoding the catabolized compounds involved in the utilization of plant substances and secondary metabolite biosynthesis gene clusters encoding antimicrobial compounds were identified. This is the first report of whole-genome sequencing of laccase-producing A. baumannii, and the data from this study help to elucidate the genome of A. baumannii to facilitate its application in synthetic biology for enzyme production.
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Affiliation(s)
- Renuka Pooalai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Supat Khongfak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Udomluk Leungtongkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Rapee Thummeepak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand. .,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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6
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Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species. World J Microbiol Biotechnol 2021; 37:162. [PMID: 34448059 DOI: 10.1007/s11274-021-03128-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/12/2021] [Indexed: 12/23/2022]
Abstract
The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes.
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Songserm P, Srimongkol P, Thitiprasert S, Tanasupawat S, Cheirsilp B, Assabumrungrat S, Karnchanatat A, Thongchul N. Differential Gene Expression Analysis
of Aspergillus terreus Reveals Metabolic
Response and Transcription Suppression under Dissolved Oxygen and
pH Stress. J EVOL BIOCHEM PHYS+ 2020. [DOI: 10.1134/s0022093020060101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Pornputtapong N, Acheampong DA, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Jun SR, Yongkiettrakul S, Chokesajjawatee N, Nookaew I. KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. Front Bioeng Biotechnol 2020; 8:556413. [PMID: 33072720 PMCID: PMC7538862 DOI: 10.3389/fbioe.2020.556413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022] Open
Abstract
Genomic DNA is the best “unique identifier” for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification. Although this approach is not novel, selecting the appropriate k-mer length to obtain the optimal resolution is rather arbitrary. However, it is a very important parameter for achieving the appropriate resolution for genome/sequence distances to infer biologically meaningful phylogenetic relationships. Thus, there is a need for a systematic approach to identify the appropriate k-mer from whole-genome sequences. We present K-mer–length Iterative Selection for UNbiased Ecophylogenomics (KITSUNE), a tool for assessing the empirically optimal k-mer length of any given set of genomes of interest for phylogenomic analysis via a three-step approach based on (1) cumulative relative entropy (CRE), (2) average number of common features (ACF), and (3) observed common features (OCF). Using KITSUNE, we demonstrated the feasibility and reliability of these measurements to obtain empirically optimal k-mer lengths of 11, 17, and ∼34 from large genome datasets of viruses, bacteria, and fungi, respectively. Moreover, we demonstrated a feature of KITSUNE for accurate species identification for the two de novo assembled bacterial genomes derived from error-prone long-reads sequences, and for a published yeast genome. In addition, KITSUNE was used to identify the shortest species-specific k-mer accurately identifying viruses. KITSUNE is freely available at https://github.com/natapol/kitsune.
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Affiliation(s)
- Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, and Research Unit of DNA Barcoding of Thai Medicinal Plants, Chulalongkorn University, Bangkok, Thailand
| | - Daniel A Acheampong
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Preecha Patumcharoenpol
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Suganya Yongkiettrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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9
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Ferrer M, Méndez-García C, Bargiela R, Chow J, Alonso S, García-Moyano A, Bjerga GEK, Steen IH, Schwabe T, Blom C, Vester J, Weckbecker A, Shahgaldian P, de Carvalho CCCR, Meskys R, Zanaroli G, Glöckner FO, Fernández-Guerra A, Thambisetty S, de la Calle F, Golyshina OV, Yakimov MM, Jaeger KE, Yakunin AF, Streit WR, McMeel O, Calewaert JB, Tonné N, Golyshin PN. Decoding the ocean's microbiological secrets for marine enzyme biodiscovery. FEMS Microbiol Lett 2019; 366:5232402. [PMID: 30534987 PMCID: PMC6322442 DOI: 10.1093/femsle/fny285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
A global census of marine microbial life has been underway over the past several decades. During this period, there have been scientific breakthroughs in estimating microbial diversity and understanding microbial functioning and ecology. It is estimated that the ocean, covering 71% of the earth's surface with its estimated volume of about 2 × 1018 m3 and an average depth of 3800 m, hosts the largest population of microbes on Earth. More than 2 million eukaryotic and prokaryotic species are thought to thrive both in the ocean and on its surface. Prokaryotic cell abundances can reach densities of up to 1012 cells per millilitre, exceeding eukaryotic densities of around 106 cells per millilitre of seawater. Besides their large numbers and abundance, marine microbial assemblages and their organic catalysts (enzymes) have a largely underestimated value for their use in the development of industrial products and processes. In this perspective article, we identified critical gaps in knowledge and technology to fast-track this development. We provided a general overview of the presumptive microbial assemblages in oceans, and an estimation of what is known and the enzymes that have been currently retrieved. We also discussed recent advances made in this area by the collaborative European Horizon 2020 project ‘INMARE’.
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Affiliation(s)
- Manuel Ferrer
- Department of Applied Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Marie Curie 2, 28049 Madrid, Spain
| | - Celia Méndez-García
- Department of Applied Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Marie Curie 2, 28049 Madrid, Spain
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom
| | - Jennifer Chow
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Sandra Alonso
- Department of Applied Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Marie Curie 2, 28049 Madrid, Spain
| | - Antonio García-Moyano
- NORCE Environment, NORCE Norwegian Research Centre AS, Thormøhlens gate 55, 5008 Bergen, Norway
| | - Gro E K Bjerga
- NORCE Environment, NORCE Norwegian Research Centre AS, Thormøhlens gate 55, 5008 Bergen, Norway
| | - Ida H Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, Thormøhlensgt 53A/B, 5020 Bergen, Norway
| | - Tatjana Schwabe
- CLIB2021 - Cluster industrielle Biotechnologie, Voelklinger Str. 4, 40219 Düsseldorf, Germany
| | | | - Jan Vester
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Andrea Weckbecker
- evoxx technologies GmbH, Alfred-Nobel-Str. 10, 40789 Monheim am Rhein, Germany
| | - Patrick Shahgaldian
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 35, CH-4132 Muttenz, Switzerland
| | - Carla C C R de Carvalho
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Rolandas Meskys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257 Vilnius, Lithuania
| | - Giulio Zanaroli
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, via Terracini 28, 40131 Bologna, Italy
| | - Frank O Glöckner
- Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany.,Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | | | - Siva Thambisetty
- London School of Economics and Political Science, Houghton Street, WC2A 2AE London, United Kingdom
| | - Fernando de la Calle
- Microbiology R&D Dpt., Pharma Mar, S.A., Avda. Los Reyes, 1, 28770 Colmenar Viejo, Madrid, Spain
| | - Olga V Golyshina
- School of Natural Sciences, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom
| | - Michail M Yakimov
- Institute for Biological Resources and Marine Biotechnology, IRBIM-CNR, Spianata S. Raineri 86, 98122 Messina, Italy.,Institute of Living Systems, Immanuel Kant Baltic Federal University, Nevskogo 14 a, 236016 Kaliningrad, Russia
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf and Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Alexander F Yakunin
- School of Natural Sciences, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Ontario, Canada
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Oonagh McMeel
- Seascape Belgium bvba, Kindermansstraat 14/19, 1000 Brussels, Belgium
| | | | - Nathalie Tonné
- Seascape Belgium bvba, Kindermansstraat 14/19, 1000 Brussels, Belgium
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, LL57 2UW Bangor, United Kingdom
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10
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Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community. Int J Mol Sci 2019; 20:ijms20184415. [PMID: 31500341 PMCID: PMC6770359 DOI: 10.3390/ijms20184415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/23/2022] Open
Abstract
Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO2/H2). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH4 L−1 d−1) was highest in the culture grown with tryptone, yeast extract, and CO2/H2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.
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van den Bogert B, Boekhorst J, Pirovano W, May A. On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications. Front Genet 2019; 10:721. [PMID: 31447883 PMCID: PMC6696986 DOI: 10.3389/fgene.2019.00721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023] Open
Abstract
Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Correspondingly, commercial interest has risen for applications where microbial communities make important contributions. These include food production, probiotics, cosmetics, and enzyme discovery. Other commercial applications include software that takes the user's gut microbiome data as one of its inputs and outputs evidence-based, automated, and personalized diet recommendations for balanced blood sugar levels. These applications pose several bioinformatic and data science challenges that range from requiring strain-level resolution in community profiles to the integration of large datasets for predictive machine learning purposes. In this perspective, we provide our insights on such challenges by touching upon several industrial areas, and briefly discuss advances and future directions of bioinformatics and data science in microbiome research.
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Affiliation(s)
| | | | | | - Ali May
- Research and Development Dept., BaseClear, Leiden, Netherlands
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