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      Microbial biosurfactant research: time to improve the rigour in the reporting of synthesis, functional characterization and process development

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          Abstract

          The demand for microbially produced surface‐active compounds for use in industrial processes and products is increasing. As such there has been a comparable increase in the number of publications relating to the characterisation of novel surface‐active compounds; novel producers of already characterised surface‐active compounds and production processes for the generation of these compounds. We devised this review as a guide to both researchers and the peer review process to improve the stringency of future studies and publications within this field of science.

          Summary

          The demand for microbially produced surface‐active compounds for use in industrial processes and products is increasing. As such, there has been a comparable increase in the number of publications relating to the characterization of novel surface‐active compounds: novel producers of already characterized surface‐active compounds and production processes for the generation of these compounds. Leading researchers in the field have identified that many of these studies utilize techniques are not precise and accurate enough, so some published conclusions might not be justified. Such studies lacking robust experimental evidence generated by validated techniques and standard operating procedures are detrimental to the field of microbially produced surface‐active compound research. In this publication, we have critically reviewed a wide range of techniques utilized in the characterization of surface‐active compounds from microbial sources: identification of surface‐active compound producing microorganisms and functional testing of resultant surface‐active compounds. We have also reviewed the experimental evidence required for process development to take these compounds out of the laboratory and into industrial application. We devised this review as a guide to both researchers and the peer‐reviewed process to improve the stringency of future studies and publications within this field of science.

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          Most cited references184

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

            Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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              Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

              The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
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                Author and article information

                Contributors
                m.twigg@ulster.ac.uk
                Journal
                Microb Biotechnol
                Microb Biotechnol
                10.1111/(ISSN)1751-7915
                MBT2
                Microbial Biotechnology
                John Wiley and Sons Inc. (Hoboken )
                1751-7915
                29 November 2020
                January 2021
                : 14
                : 1 , Thematic Issue: Crystal Ball ( doiID: 10.1111/mbt2.v14.1 )
                : 147-170
                Affiliations
                [ 1 ] School of Biomedical Sciences Ulster University Coleraine, Co. Londonderry BT52 1SA UK
                [ 2 ] Centre National de la Recherche Scientifique Laboratoire de Chimie de la Matière Condensée de Paris Sorbonne Université LCMCP Paris F‐75005 France
                [ 3 ] Centre Armand‐Frappier Santé Biotechnologie Institut National de la Recherche Scientifique (INRS) 531, Boul. Des Prairies Laval QC H7V 1B7 Canada
                [ 4 ] Centre for Industrial Biotechnology and Biocatalysis (InBio.be) Faculty of Bioscience Engineering Ghent University Ghent Belgium
                [ 5 ] Bio Base Europe Pilot Plant Rodenhuizenkaai 1 Ghent 9042 Belgium
                [ 6 ] Centre for Synthetic Biology Department of Biotechnology Ghent University Coupure Links 653 Ghent 9000 Belgium
                Author notes
                [*] [* ] For correspondence. E‐mail m.twigg@ 123456ulster.ac.uk ; Tel. +44(0)2870 123097; Fax +44(0)2870 324906.

                Author information
                https://orcid.org/0000-0002-8601-1960
                https://orcid.org/0000-0003-3142-3228
                https://orcid.org/0000-0001-8964-2840
                https://orcid.org/0000-0002-4609-0115
                https://orcid.org/0000-0001-5213-229X
                https://orcid.org/0000-0002-3596-6951
                https://orcid.org/0000-0001-8144-6466
                Article
                MBT213704
                10.1111/1751-7915.13704
                7888453
                33249753
                fad566b8-adf7-49ad-a07e-0fce81f299b0
                © 2020 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 September 2020
                : 16 October 2020
                : 23 October 2020
                Page count
                Figures: 4, Tables: 2, Pages: 24, Words: 35818
                Funding
                Funded by: European Union’s Horizon 2020 research and innovation programme
                Award ID: 635340
                Funded by: Invest Northern Ireland Proof of Concept
                Award ID: 826
                Categories
                Minireview
                Minireviews
                Custom metadata
                2.0
                January 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.7 mode:remove_FC converted:17.02.2021

                Biotechnology
                Biotechnology

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