دورية أكاديمية

Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries.

التفاصيل البيبلوغرافية
العنوان: Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries.
المؤلفون: de Oliveira Lino FS; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Garg S; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Li SS; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.; School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, 4072, Australia., Misiakou MA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Kang K; Leibniz Institute for Natural Product Research and Infection Biology, Jena, 07745, Germany., Vale da Costa BL; Escola de Engenharia de Alimentos da Universidade de Campinas, 13083-862, Campinas, SP, Brazil., Beyer-Pedersen TS; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark., Giacon TG; Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil., Basso TO; Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil., Panagiotou G; Leibniz Institute for Natural Product Research and Infection Biology, Jena, 07745, Germany., Sommer MOA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark. msom@bio.dtu.dk.
المصدر: Nature communications [Nat Commun] 2024 Jun 22; Vol. 15 (1), pp. 5323. Date of Electronic Publication: 2024 Jun 22.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Ethanol*/metabolism , Fermentation* , Bacteria*/metabolism , Bacteria*/genetics , Bacteria*/classification, Microbiota/physiology ; Biofuels ; Metagenomics ; Industrial Microbiology/methods ; Temperature
مستخلص: Bioethanol is a sustainable energy alternative and can contribute to global greenhouse-gas emission reductions by over 60%. Its industrial production faces various bottlenecks, including sub-optimal efficiency resulting from bacteria. Broad-spectrum removal of these contaminants results in negligible gains, suggesting that the process is shaped by ecological interactions within the microbial community. Here, we survey the microbiome across all process steps at two biorefineries, over three timepoints in a production season. Leveraging shotgun metagenomics and cultivation-based approaches, we identify beneficial bacteria and find improved outcome when yeast-to-bacteria ratios increase during fermentation. We provide a microbial gene catalogue which reveals bacteria-specific pathways associated with performance. We also show that Limosilactobacillus fermentum overgrowth lowers production, with one strain reducing yield by ~5% in laboratory fermentations, potentially due to its metabolite profile. Temperature is found to be a major driver for strain-level dynamics. Improved microbial management strategies could unlock environmental and economic gains in this US $ 60 billion industry enabling its wider adoption.
(© 2024. The Author(s).)
References: Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. (PMID: 28053165)
BMC Bioinformatics. 2016 Apr 19;17:172. (PMID: 27094401)
J Mol Biol. 2000 Sep 8;302(1):205-17. (PMID: 10964570)
Bioinformatics. 2012 Jul 15;28(14):1823-9. (PMID: 22556368)
Nat Methods. 2021 Apr;18(4):366-368. (PMID: 33828273)
ISME J. 2020 May;14(5):1247-1259. (PMID: 32047279)
Adv Appl Microbiol. 2018;105:87-129. (PMID: 30342724)
J Ind Microbiol Biotechnol. 2004 Oct;31(9):401-8. (PMID: 15338420)
Bioinformatics. 2012 Dec 1;28(23):3150-2. (PMID: 23060610)
Microbiome. 2019 Jun 3;7(1):84. (PMID: 31159881)
Bioinformatics. 2006 Jul 1;22(13):1658-9. (PMID: 16731699)
Int J Syst Evol Microbiol. 2017 May;67(5):1613-1617. (PMID: 28005526)
Appl Environ Microbiol. 1997 Nov;63(11):4158-63. (PMID: 9361399)
Braz J Microbiol. 2016 Dec;47 Suppl 1:64-76. (PMID: 27818090)
J Ind Microbiol Biotechnol. 2007 Nov;34(11):739-44. (PMID: 17726620)
Microbiology (Reading). 2001 Oct;147(Pt 10):2635-2642. (PMID: 11577142)
J Ind Microbiol Biotechnol. 2015 Jan;42(1):73-84. (PMID: 25404204)
Cell Rep. 2018 Jul 31;24(5):1190-1202.e5. (PMID: 30067975)
Nucleic Acids Res. 2020 Jan 8;48(D1):D621-D625. (PMID: 31647096)
Genome Biol. 2021 Apr 12;22(1):101. (PMID: 33845884)
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829. (PMID: 34597405)
Bioinformatics. 2015 May 15;31(10):1674-6. (PMID: 25609793)
J Ind Microbiol Biotechnol. 2001 Mar;26(3):171-7. (PMID: 11420658)
Appl Microbiol Biotechnol. 2011 Sep;91(5):1267-75. (PMID: 21735264)
Metab Eng. 2010 Jul;12(4):307-31. (PMID: 20346409)
Nucleic Acids Res. 2021 Jan 8;49(D1):D723-D733. (PMID: 33152092)
World J Microbiol Biotechnol. 2018 May 25;34(6):80. (PMID: 29802468)
BMC Microbiol. 2010 Nov 23;10:298. (PMID: 21092306)
Genome Biol. 2014 Mar 03;15(3):R46. (PMID: 24580807)
J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500. (PMID: 32780112)
Antonie Van Leeuwenhoek. 2017 Jul;110(7):971-983. (PMID: 28470565)
Front Bioeng Biotechnol. 2015 Jun 16;3:84. (PMID: 26137456)
Nat Biotechnol. 2024 Feb;42(2):265-274. (PMID: 37142704)
Nucleic Acids Res. 2010 Jul;38(12):e132. (PMID: 20403810)
Bioinformatics. 2012 Jun 1;28(11):1420-8. (PMID: 22495754)
Cladistics. 2011 Apr;27(2):171-180. (PMID: 34875773)
Nat Commun. 2021 Mar 8;12(1):1498. (PMID: 33686084)
J Comput Biol. 2012 May;19(5):455-77. (PMID: 22506599)
Antonie Van Leeuwenhoek. 2014 Jan;105(1):169-77. (PMID: 24198118)
FEMS Yeast Res. 2008 Nov;8(7):1155-63. (PMID: 18752628)
Biotechnol Bioeng. 2009 May 1;103(1):117-22. (PMID: 19148876)
J Ind Microbiol Biotechnol. 2008 Feb;35(2):75-81. (PMID: 17940817)
BMC Bioinformatics. 2010 Mar 08;11:119. (PMID: 20211023)
Nucleic Acids Res. 2000 Jan 1;28(1):27-30. (PMID: 10592173)
Mol Biol Evol. 2020 Apr 1;37(4):1237-1239. (PMID: 31904846)
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. (PMID: 26553804)
Bioinformatics. 2016 Apr 1;32(7):1088-90. (PMID: 26614127)
Genome Biol. 2019 Nov 28;20(1):257. (PMID: 31779668)
Biotechnol Biofuels. 2018 Aug 11;11:221. (PMID: 30127851)
Bioinformatics. 2014 Jul 15;30(14):2068-9. (PMID: 24642063)
BMC Bioinformatics. 2009 Dec 15;10:421. (PMID: 20003500)
Bioresour Technol. 2015 Nov;196:347-54. (PMID: 26255598)
Nucleic Acids Res. 2021 Jul 2;49(W1):W29-W35. (PMID: 33978755)
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. (PMID: 28460117)
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. (PMID: 30418610)
Bioresour Technol. 2018 Jan;247:357-362. (PMID: 28954248)
معلومات مُعتمدة: NNF10CC1016517 Novo Nordisk Fonden (Novo Nordisk Foundation); ALTF 137-2018 European Molecular Biology Organization (EMBO); APP1166180 Department of Health | National Health and Medical Research Council (NHMRC); 406564/2022-1 Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)
المشرفين على المادة: 3K9958V90M (Ethanol)
0 (Biofuels)
تواريخ الأحداث: Date Created: 20240622 Date Completed: 20240622 Latest Revision: 20240625
رمز التحديث: 20240625
مُعرف محوري في PubMed: PMC11193817
DOI: 10.1038/s41467-024-49683-2
PMID: 38909053
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-49683-2