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      Butanol as a major product during ethanol and acetate chain elongation

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          Abstract

          Chain elongation is a relevant bioprocess in support of a circular economy as it can use a variety of organic feedstocks for production of valuable short and medium chain carboxylates, such as butyrate (C4), caproate (C6), and caprylate (C8). Alcohols, including the biofuel, butanol (C4), can also be generated in chain elongation but the bioreactor conditions that favor butanol production are mainly unknown. In this study we investigated production of butanol (and its precursor butyrate) during ethanol and acetate chain elongation. We used semi-batch bioreactors (0.16 L serum bottles) fed with a range of ethanol concentrations (100–800 mM C), a constant concentration of acetate (50 mM C), and an initial total gas pressure of ∼112 kPa. We showed that the butanol concentration was positively correlated with the ethanol concentration provided (up to 400 mM C ethanol) and to chain elongation activity, which produced H 2 and further increased the total gas pressure. In bioreactors fed with 400 mM C ethanol and 50 mM C acetate, a concentration of 114.96 ± 9.26 mM C butanol (∼2.13 g L −1) was achieved after five semi-batch cycles at a total pressure of ∼170 kPa and H 2 partial pressure of ∼67 kPa. Bioreactors with 400 mM C ethanol and 50 mM C acetate also yielded a butanol to butyrate molar ratio of 1:1. At the beginning of cycle 8, the total gas pressure was intentionally decreased to ∼112 kPa to test the dependency of butanol production on total pressure and H 2 partial pressure. The reduction in total pressure decreased the molar ratio of butanol to butyrate to 1:2 and jolted H 2 production out of an apparent stall. Clostridium kluyveri (previously shown to produce butyrate and butanol) and Alistipes (previously linked with butyrate production) were abundant amplicon sequence variants in the bioreactors during the experimental phases, suggesting the microbiome was resilient against changes in bioreactor conditions. The results from this study clearly demonstrate the potential of ethanol and acetate-based chain elongation to yield butanol as a major product. This study also supports the dependency of butanol production on limiting acetate and on high total gas and H 2 partial pressures.

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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            Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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              BLAST+: architecture and applications

              Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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                Author and article information

                Contributors
                Journal
                Front Bioeng Biotechnol
                Front Bioeng Biotechnol
                Front. Bioeng. Biotechnol.
                Frontiers in Bioengineering and Biotechnology
                Frontiers Media S.A.
                2296-4185
                18 May 2023
                2023
                : 11
                : 1181983
                Affiliations
                [1] 1 Biodesign Swette Center for Environmental Biotechnology , Arizona State University , Tempe, AZ, United States
                [2] 2 School of Sustainable Engineering and the Built Environment , Arizona State University , Tempe, AZ, United States
                [3] 3 Engineering Research Center for Bio-Mediated and Bio-Inspired Geotechnics , Arizona State University , Tempe, AZ, United States
                Author notes

                Edited by: David Strik, Wageningen University and Research, Netherlands

                Reviewed by: Christian Kennes, University of A Coruña, Spain

                Silvia Greses, IMDEA Energy Institute, Spain

                *Correspondence: Aide Robles, arobles9@ 123456asu.edu ; Anca G. Delgado, anca.delgado@ 123456asu.edu
                Article
                1181983
                10.3389/fbioe.2023.1181983
                10233103
                37274171
                dc210777-073e-4f79-ae87-c845aaf3d41e
                Copyright © 2023 Robles, Sundar, Mohana Rangan and Delgado.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 08 March 2023
                : 08 May 2023
                Funding
                This work was funded by US National Science Foundation (NSF) award CBET-2221805 and a Non-Academic Research Internships for Graduate Students (INTERN) supplement to award NSF EEC-1449501. Any opinions, findings and conclusions or recommendations expressed in this article are those of the authors and do not necessarily reflect those of the NSF.
                Categories
                Bioengineering and Biotechnology
                Original Research
                Custom metadata
                Bioprocess Engineering

                butanol,butyrate,hydrogen partial pressure,carboxylate reduction,clostridium kluyveri,microbial chain elongation,total gas pressure

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