{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T16:20:11Z","timestamp":1792686011511,"version":"4.5.0"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T00:00:00Z","timestamp":1760918400000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2022\/15256-0"],"award-info":[{"award-number":["2022\/15256-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2022\/03293-8"],"award-info":[{"award-number":["2022\/03293-8"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2018\/17172-2"],"award-info":[{"award-number":["2018\/17172-2"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2022\/03052-0"],"award-info":[{"award-number":["2022\/03052-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["306190\/2022-2"],"award-info":[{"award-number":["306190\/2022-2"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["406564\/2022-1"],"award-info":[{"award-number":["406564\/2022-1"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["310649\/2021-8"],"award-info":[{"award-number":["310649\/2021-8"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["304294\/2022-5"],"award-info":[{"award-number":["304294\/2022-5"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The production of fuel ethanol in sugarcane biorefineries is a nonaseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.<\/jats:p>","DOI":"10.1093\/femsec\/fiaf100","type":"journal-article","created":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T11:46:30Z","timestamp":1760787990000},"source":"Crossref","is-referenced-by-count":5,"title":["Microbial ecology applied to fuel ethanol production from sugarcane"],"prefix":"10.1093","volume":"101","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7765-4297","authenticated-orcid":false,"given":"Thiago O","family":"Basso","sequence":"first","affiliation":[{"name":"Universidade de S\u00e3o Paulo Departamento de Engenharia Qu\u00edmica, , S\u00e3o Paulo, SP 05508-010 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andressa M","family":"Venturini","sequence":"additional","affiliation":[{"name":"Stanford University Department of Biology, , Stanford, CA 94305 ,","place":["USA"]},{"name":"20016 American University Department of Environmental Science, , WA, DC ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0723-1704","authenticated-orcid":false,"given":"Sandra Regina","family":"Ceccato-Antonini","sequence":"additional","affiliation":[{"name":"Universidade Federal de S\u00e3o Carlos, Centro de Ci\u00eancias Agr\u00e1rias , Departamento de Tecnologia Agroindustrial e Socioeconomia Rural, Via Anhanguera km 174, Araras, SP 13600-970 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9557-3773","authenticated-orcid":false,"given":"Andreas K","family":"Gombert","sequence":"additional","affiliation":[{"name":"Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos , Rua Monteiro Lobato 80, Campinas, SP 13083-862 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,10,20]]},"reference":[{"key":"2025102411430657200_bib1","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.ijfoodmicro.2003.10.013","article-title":"Saccharomyces cerevisiae-Oenococcus oeni interactions in wine: current knowledge and perspectives","volume":"93","author":"Alexandre","year":"2004","journal-title":"Int J Food Microbiol"},{"key":"2025102411430657200_bib2","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1007\/s00253-011-3437-6","article-title":"Scientific challenges of bioethanol production in Brazil","volume":"91","author":"Amorim","year":"2011","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib3","doi-asserted-by":"publisher","first-page":"foaf044","DOI":"10.1093\/femsyr\/foaf044","article-title":"Perspectives on current and future yeast technologies for ethanol-based biofuels and bioproducts","volume":"25","author":"Attfield","year":"2025","journal-title":"FEMS Yeast Res"},{"key":"2025102411430657200_bib4","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1007\/s10482-018-1056-2","article-title":"Interaction of Saccharomyces cerevisiae-Lactobacillus fermentum-Dekkera bruxellensis and feedstock on fuel ethanol fermentation","volume":"111","author":"Bassi","year":"2018","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2025102411430657200_bib5","doi-asserted-by":"publisher","DOI":"10.5772\/959","article-title":"Ethanol production in Brazil: the industrial process and its impact on yeast fermentation","volume-title":"Dos Santos Bernardes MA, Biofuel Production-Recent Developments and Prospects [internet]","author":"Basso","year":"2011"},{"key":"2025102411430657200_bib6","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1111\/j.1567-1364.2008.00428.x","article-title":"Yeast selection for fuel ethanol production in Brazil","volume":"8","author":"Basso","year":"2008","journal-title":"FEMS Yeast Res"},{"key":"2025102411430657200_bib8","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/s10482-013-0063-6","article-title":"Homo- and heterofermentative lactobacilli differently affect sugarcane-based fuel ethanol fermentation","volume":"105","author":"Basso","year":"2014","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2025102411430657200_bib9","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1007\/s10295-004-0156-3","article-title":"Inhibition of yeast by lactic acid bacteria in continuous culture: nutrient depletion and\/or acid toxicity?","volume":"31","author":"Bayrock","year":"2004","journal-title":"J Ind Microbiol Biotechnol"},{"key":"2025102411430657200_bib10","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1111\/j.1472-765X.2011.03124.x","article-title":"Microbial contamination of fuel ethanol fermentations","volume":"53","author":"Beckner","year":"2011","journal-title":"Lett Appl Microbiol"},{"key":"2025102411430657200_bib11","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/0922-338X(90)90057-4","article-title":"Automatic detection of assimilable nitrogen deficiencies during alcoholic fermentation in oenological conditions","volume":"70","author":"Bely","year":"1990","journal-title":"J Ferment Bioeng"},{"key":"2025102411430657200_bib12","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1111\/jam.14107","article-title":"Kefir micro-organisms: their role in grain assembly and health properties of fermented milk","volume":"126","author":"Bengoa","year":"2019","journal-title":"J Appl Microbiol"},{"key":"2025102411430657200_bib13","doi-asserted-by":"publisher","first-page":"foab065","DOI":"10.1093\/femsyr\/foab065","article-title":"Ethanol yield calculations in biorefineries","volume":"21","author":"Bermejo","year":"2021","journal-title":"FEMS Yeast Res"},{"key":"2025102411430657200_bib14","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1002\/bit.22244","article-title":"Modeling bacterial contamination of fuel ethanol fermentation","volume":"103","author":"Bischoff","year":"2009","journal-title":"Biotech Bioeng"},{"key":"2025102411430657200_bib15","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnx159","article-title":"Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production","volume":"364","author":"Bonatelli","year":"2017","journal-title":"FEMS Microbiol Lett"},{"key":"2025102411430657200_bib16","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.biotechadv.2017.04.002","article-title":"Lactobacilli and pediococci as versatile cell factories\u2014Evaluation of strain properties and genetic tools","volume":"35","author":"Bosma","year":"2017","journal-title":"Biotechnol Adv"},{"key":"2025102411430657200_bib17","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/s13040-017-0138-4","article-title":"Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles","volume":"10","author":"Braga","year":"2017","journal-title":"BioData Mining"},{"key":"2025102411430657200_bib18","doi-asserted-by":"crossref","first-page":"109799","DOI":"10.1016\/j.bej.2025.109799","article-title":"Fermentative and physiological responses of Saccharomyces cerevisiae LMQA SRC-143 and PE-2 in co-culture with Lactobacillus fermentum: insights with flow cytometry in the Melle-Boinot process","volume":"221","author":"Brex\u00f3","year":"2025","journal-title":"Biochem Eng J"},{"key":"2025102411430657200_bib19","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s12934-015-0196-6","article-title":"Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production","volume":"14","author":"Carvalho-Netto","year":"2015","journal-title":"Microb Cell Fact"},{"key":"2025102411430657200_bib20","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1007\/s11274-018-2463-2","article-title":"Conventional and nonconventional strategies for controlling bacterial contamination in fuel ethanol fermentations","volume":"34","author":"Ceccato-Antonini","year":"2018","journal-title":"World J Microbiol Biotechnol"},{"key":"2025102411430657200_bib21","doi-asserted-by":"crossref","DOI":"10.11606\/T.11.2003.tde-10092003-144216","article-title":"Efeitos da viabilidade da levedura e da contamina\u00e7\u00e3o bacteriana na fermenta\u00e7\u00e3o alco\u00f3lica","author":"Cherubin","year":"2003"},{"key":"2025102411430657200_bib23","doi-asserted-by":"publisher","first-page":"3027","DOI":"10.1007\/s00253-021-11270-6","article-title":"The ecology of wine fermentation: a model for the study of complex microbial ecosystems","volume":"105","author":"Conacher","year":"2021","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib24","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1111\/lam.12819","article-title":"Ethanol addition enhances acid treatment to eliminate Lactobacillus fermentum from the fermentation process for fuel ethanol production","volume":"66","author":"Costa","year":"2018","journal-title":"Lett Appl Microbiol"},{"key":"2025102411430657200_bib25","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/s10295-014-1533-1","article-title":"Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method","volume":"42","author":"Costa","year":"2015","journal-title":"J Ind Microbiol Biotechnol"},{"key":"2025102411430657200_bib26","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1590\/S1413-70542008000200025","article-title":"Production of acetic acid, ethanol and optical isomers of lactic acid by Lactobacillus strains isolated from industrial ethanol fermentations","volume":"32","author":"Costa","year":"2008","journal-title":"Ci\u00eanc Agrotec"},{"key":"2025102411430657200_bib27","doi-asserted-by":"publisher","first-page":"foz054","DOI":"10.1093\/femsyr\/foz054","article-title":"Forever panting and forever growing: physiology of Saccharomyces cerevisiae at extremely low oxygen availability in the absence of ergosterol and unsaturated fatty acids","volume":"19","author":"da\u00a0Costa","year":"2019","journal-title":"FEMS Yeast Res"},{"key":"2025102411430657200_bib28","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1007\/s10482-004-7283-8","article-title":"Yeast population dynamics of industrial fuel-ethanol fermentation process assessed by PCR-fingerprinting","volume":"88","author":"da\u00a0Silva-Filho","year":"2005","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2025102411430657200_bib30","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1126\/science.aap9516","article-title":"A global atlas of the dominant bacteria found in soil","volume":"359","author":"Delgado-Baquerizo","year":"2018","journal-title":"Science"},{"key":"2025102411430657200_bib31","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1007\/s00253-012-4631-x","article-title":"What do we know about the yeast strains from the Brazilian fuel ethanol industry?","volume":"97","author":"Della-Bianca","year":"2013","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib32","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1007\/s10482-018-1050-8","article-title":"Biofilm formation and antimicrobial sensitivity of lactobacilli contaminants from sugarcane-based fuel ethanol fermentation","volume":"111","author":"Dellias\u00a0M\u00a0de","year":"2018","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2025102411430657200_bib33","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1007\/BF00327963","article-title":"Evaluation of bacterial contamination in a fed-batch alcoholic fermentation process","volume":"10","author":"de\u00a0Oliva-Neto","year":"1994","journal-title":"World J Microbiol Biotechnol"},{"key":"2025102411430657200_bib34","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1590\/S1517-83822001000100003","article-title":"Susceptibility of Saccharomyces cerevisiae and lactic acid bacteria from the alcohol industry to several antimicrobial compounds","volume":"32","author":"de\u00a0Oliva-Neto","year":"2001","journal-title":"Braz J Microbiol"},{"key":"2025102411430657200_bib35","doi-asserted-by":"crossref","DOI":"10.47749\/T\/UNICAMP.1990.28215","article-title":"Influ\u00eancia da contamina\u00e7\u00e3o por bact\u00e9rias l\u00e1cticas na fermenta\u00e7\u00e3o alco\u00f3lica pelo processo de batelada alimentada","author":"De\u00a0Oliva-Neto","year":"1990"},{"key":"2025102411430657200_bib36","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s12010-014-1258-7","article-title":"Mineral composition of the sugarcane juice and its influence on the ethanol fermentation","volume":"175","author":"de\u00a0Souza","year":"2015","journal-title":"Appl Biochem Biotechnol"},{"key":"2025102411430657200_bib37","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1111\/j.1365-2672.2006.03082.x","article-title":"Identification of Dekkera bruxellensis as a major contaminant yeast in continuous fuel ethanol fermentation","volume":"102","author":"de\u00a0Souza\u00a0Liberal","year":"2007","journal-title":"J Appl Microbiol"},{"key":"2025102411430657200_bib38","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.fm.2013.06.002","article-title":"Microbial ecology of sourdough fermentations: diverse or uniform?","volume":"37","author":"de\u00a0Vuyst","year":"2014","journal-title":"Food Microbiol"},{"key":"2025102411430657200_bib39","doi-asserted-by":"publisher","first-page":"5002","DOI":"10.1128\/JB.00542-10","article-title":"The human oral microbiome","volume":"192","author":"Dewhirst","year":"2010","journal-title":"J Bacteriol"},{"key":"2025102411430657200_bib40","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/s11130-006-0032-6","article-title":"Antioxidant activity of phenolics compounds from sugar cane (Saccharum officinarum L.) juice","volume":"61","author":"Duarte-Almeida","year":"2006","journal-title":"Plant Foods Hum Nutr"},{"key":"2025102411430657200_bib41","doi-asserted-by":"crossref","first-page":"10567","DOI":"10.1038\/s41598-023-37618-8","article-title":"Physiology of Saccharomyces cerevisiae during growth on industrial sugar cane molasses can be reproduced in a tailor-made defined synthetic medium","volume":"13","author":"Eliod\u00f3rio","year":"2023","journal-title":"Sci Rep"},{"key":"2025102411430657200_bib42","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1016\/j.funbio.2023.06.009","article-title":"Effects of caramelization and Maillard reaction products on the physiology of Saccharomyces cerevisiae","volume":"127","author":"Eliod\u00f3rio","year":"2023","journal-title":"Fungal Biol"},{"key":"2025102411430657200_bib43","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.fm.2014.08.018","article-title":"Metabolism of phenolic compounds by Lactobacillus spp. during fermentation of cherry juice and broccoli puree","volume":"46","author":"Filannino","year":"2015","journal-title":"Food Microbiol"},{"key":"2025102411430657200_bib44","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1007\/s10295-019-02254-7","article-title":"Characterization of microbial communities in ethanol biorefineries","volume":"47","author":"Firmino","year":"2020","journal-title":"J Ind Microbiol Biotechnol"},{"key":"2025102411430657200_bib45","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/s41564-022-01083-2","article-title":"Towards a deeper understanding of the vaginal microbiota","volume":"7","author":"France","year":"2022","journal-title":"Nat Microbiol"},{"key":"2025102411430657200_bib46","article-title":"Determina\u00e7\u00e3o da microbiota bacteriana de mosto e de dornas na fermenta\u00e7\u00e3o alco\u00f3lica","author":"Gallo","year":"1989"},{"key":"2025102411430657200_bib48","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.copbio.2014.12.012","article-title":"Improving conversion yield of fermentable sugars into fuel ethanol in 1st generation yeast-based production processes","volume":"33","author":"Gombert","year":"2015","journal-title":"Curr Opin Biotechnol"},{"key":"2025102411430657200_bib49","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1007\/s00253-006-0573-5","article-title":"Interaction effects of lactic acid and acetic acid at different temperatures on ethanol production by Saccharomyces cerevisiae in corn mash","volume":"73","author":"Graves","year":"2007","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib50","doi-asserted-by":"publisher","first-page":"2597","DOI":"10.1007\/s00253-021-11198-x","article-title":"Effects of Lactobacillus plantarum on the ethanol tolerance of Saccharomyces cerevisiae","volume":"105","author":"He","year":"2021","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib51","doi-asserted-by":"publisher","first-page":"134318","DOI":"10.1016\/j.foodchem.2022.134318","article-title":"Precursors and formation pathways of furfural in sugarcane juice during thermal treatment","volume":"402","author":"Huang","year":"2023","journal-title":"Food Chem"},{"key":"2025102411430657200_bib52","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1042\/EBC20200160","article-title":"Saccharomyces cerevisiae strains used industrially for bioethanol production","volume":"65","author":"Jacobus","year":"2021","journal-title":"Essays Biochem"},{"key":"2025102411430657200_bib53","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/nclimate3410","article-title":"Brazilian sugarcane ethanol as an expandable green alternative to crude oil use","volume":"7","author":"Jaiswal","year":"2017","journal-title":"Nature Clim Change"},{"key":"2025102411430657200_bib54","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1016\/j.cell.2014.07.025","article-title":"Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism","volume":"158","author":"Jarosz","year":"2014","journal-title":"Cell"},{"key":"2025102411430657200_bib55","doi-asserted-by":"publisher","first-page":"4986","DOI":"10.1038\/s41598-023-32062-0","article-title":"Deletion of QDR genes in a bioethanol-producing yeast strain reduces propagation of contaminating lactic acid bacteria","volume":"13","author":"Kapetanakis","year":"2023","journal-title":"Sci Rep"},{"key":"2025102411430657200_bib56","doi-asserted-by":"publisher","DOI":"10.1093\/oso\/9780198789406.001.0001","volume-title":"Processes in Microbial Ecology","author":"Kirchman","year":"2018","edition":"2nd ed."},{"key":"2025102411430657200_bib57","doi-asserted-by":"publisher","first-page":"e61644","DOI":"10.7554\/eLife.61644","article-title":"The diversity and function of sourdough starter microbiomes","volume":"10","author":"Landis","year":"2021","journal-title":"eLife"},{"key":"2025102411430657200_bib58","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1007\/s00248-015-0673-9","article-title":"Bacterial community structure and dynamics during corn-based bioethanol fermentation","volume":"71","author":"Li","year":"2016","journal-title":"Microb Ecol"},{"key":"2025102411430657200_bib59","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.1038\/S41467-021-21844-7","article-title":"Complex yeast\u2013bacteria interactions affect the yield of industrial ethanol fermentation","volume":"12","author":"Lino","year":"2021","journal-title":"Nat Commun"},{"key":"2025102411430657200_bib60","doi-asserted-by":"publisher","first-page":"5323","DOI":"10.1038\/s41467-024-49683-2","article-title":"Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries","volume":"15","author":"Lino","year":"2024","journal-title":"Nat Commun"},{"key":"2025102411430657200_bib61","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/j.micpath.2017.06.044","article-title":"Study on spoilage capability and VBNC state formation and recovery of Lactobacillus plantarum","volume":"110","author":"Liu","year":"2017","journal-title":"Microb Pathog"},{"key":"2025102411430657200_bib62","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/s13068-015-0325-9","article-title":"Bacteriophage application restores ethanol fermentation characteristics disrupted by Lactobacillus fermentum","volume":"8","author":"Liu","year":"2015","journal-title":"Biotechnol Biofuels"},{"key":"2025102411430657200_bib63","doi-asserted-by":"publisher","first-page":"e0162423","DOI":"10.1128\/spectrum.01624-23","article-title":"Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes","volume":"11","author":"Liu","year":"2023","journal-title":"Microbiol Spectr"},{"key":"2025102411430657200_bib64","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1007\/s12602-022-09976-8","article-title":"Antibacterial property and metagenomic analysis of milk kefir","volume":"14","author":"Liu","year":"2022","journal-title":"Probiotics Antimicro Prot"},{"key":"2025102411430657200_bib65","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.bjm.2016.10.003","article-title":"Ethanol production in Brazil: a bridge between science and industry","volume":"47","author":"Lopes","year":"2016","journal-title":"Braz J Microbiol"},{"key":"2025102411430657200_bib66","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1186\/1471-2180-10-298","article-title":"Diversity of lactic acid bacteria of the bioethanol process","volume":"10","author":"Lucena","year":"2010","journal-title":"BMC Microbiol"},{"key":"2025102411430657200_bib67","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1590\/S0101-20612001000100014","article-title":"Quantifica\u00e7\u00e3o da flocula\u00e7\u00e3o de Saccharomyces cerevisiae por bact\u00e9rias contaminantes da fermenta\u00e7\u00e3o alco\u00f3lica","volume":"21","author":"Ludwig","year":"2001","journal-title":"Ci\u00eanc Tecnol Aliment"},{"key":"2025102411430657200_bib68","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1146\/annurev-micro-092611-150157","article-title":"The vaginal microbiome: rethinking health and diseases","volume":"66","author":"Ma","year":"2012","journal-title":"Annu Rev Microbiol"},{"key":"2025102411430657200_bib69","doi-asserted-by":"publisher","first-page":"8237","DOI":"10.1007\/s00253-017-8548-2","article-title":"Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells","volume":"101","author":"Nielsen","year":"2017","journal-title":"Appl Microbiol Biotechnol"},{"key":"2025102411430657200_bib70","doi-asserted-by":"publisher","first-page":"105","DOI":"10.5772\/65204","article-title":"Waste degradation and utilization by lactic acid bacteria: use of lactic acid bacteria in production of food additives, bioenergy and biogas","volume-title":"Food Additives","author":"Novik","year":"2017"},{"key":"2025102411430657200_bib71","first-page":"7","article-title":"Mechanism underlying the effects of lactic acid bacteria (LAB) on phenolic compounds","volume":"1","author":"Ozcan","year":"2016","journal-title":"Int J Food Biosyst Eng"},{"key":"2025102411430657200_bib72","doi-asserted-by":"publisher","first-page":"D785","DOI":"10.1093\/nar\/gkab776","article-title":"GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy","volume":"50","author":"Parks","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025102411430657200_bib73","doi-asserted-by":"publisher","first-page":"4354","DOI":"10.1128\/AEM.00437-07","article-title":"Dekkera bruxellensis and Lactobacillus vini form a stable ethanol-producing consortium in a commercial alcohol production process","volume":"73","author":"Passoth","year":"2007","journal-title":"Appl Environ Microb"},{"key":"2025102411430657200_bib74","doi-asserted-by":"publisher","first-page":"7270","DOI":"10.1021\/jf060808o","article-title":"Comparison of the concentrations of phenolic constituents in cane sugar manufacturing products with their antioxidant activities","volume":"54","author":"Payet","year":"2006","journal-title":"J Agric Food Chem"},{"key":"2025102411430657200_bib75","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1146\/annurev-food-022811-101255","article-title":"Aerobic respiration metabolism in lactic acid bacteria and uses in biotechnology","volume":"3","author":"Pedersen","year":"2012","journal-title":"Annu Rev Food Sci Technol"},{"key":"2025102411430657200_bib76","doi-asserted-by":"publisher","first-page":"16182","DOI":"10.1021\/acs.iecr.8b03943","article-title":"A new methodology to calculate the ethanol fermentation efficiency at bench and industrial scales","volume":"57","author":"Pereira","year":"2018","journal-title":"Ind Eng Chem Res"},{"key":"2025102411430657200_bib77","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/s41586-018-0030-5","article-title":"Genome evolution across 1011 Saccharomyces cerevisiae isolates","volume":"556","author":"Peter","year":"2018","journal-title":"Nature"},{"key":"2025102411430657200_bib78","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1016\/j.cels.2017.09.002","article-title":"Yeast creates a niche for symbiotic lactic acid bacteria through nitrogen overflow","volume":"5","author":"Ponomarova","year":"2017","journal-title":"Cell Syst"},{"key":"2025102411430657200_bib79","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1002\/9781118655252","article-title":"The genus Lactobacillus","author":"Pot","year":"2014","journal-title":"Lactic Acid Bact: Biodiv Taxonomy"},{"key":"2025102411430657200_bib80","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025102411430657200_bib81","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1007\/s42770-019-00147-6","article-title":"Dynamics of microbial contaminants is driven by selection during ethanol production","volume":"51","author":"Queiroz","year":"2020","journal-title":"Braz J Microbiol"},{"key":"2025102411430657200_bib82","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1007\/s10482-017-0868-9","article-title":"A simple scaled down system to mimic the industrial production of first generation fuel ethanol in Brazil","volume":"110","author":"Raghavendran","year":"2017","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2025102411430657200_bib83","first-page":"131","article-title":"The direct method of calculation of bacteria in water: comparison with the Koch method","volume":"1","author":"Razumov","year":"1932","journal-title":"Mikrobiologija"},{"key":"2025102411430657200_bib84","doi-asserted-by":"publisher","first-page":"jkad104","DOI":"10.1093\/g3journal\/jkad104","article-title":"Yeast population dynamics in Brazilian bioethanol production","volume":"13","author":"Rego-Costa","year":"2023","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"2025102411430657200_bib85","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s13568-018-0556-9","article-title":"Effects of feedstock and co-culture of Lactobacillus fermentum and wild Saccharomyces cerevisiae strain during fuel ethanol fermentation by the industrial yeast strain PE-2","volume":"8","author":"Reis","year":"2018","journal-title":"AMB Expr"},{"key":"2025102411430657200_bib86","doi-asserted-by":"publisher","first-page":"100433","DOI":"10.1016\/j.biteb.2020.100433","article-title":"Microbial contamination of commercial corn-based fuel ethanol fermentations","volume":"11","author":"Rich","year":"2020","journal-title":"Bioresour Technol Rep"},{"key":"2025102411430657200_bib87","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.biortech.2017.09.067","article-title":"Resolving bacterial contamination of fuel ethanol fermentations with beneficial bacteria\u2014an alternative to antibiotic treatment","volume":"247","author":"Rich","year":"2018","journal-title":"Bioresour Technol"},{"key":"2025102411430657200_bib88","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/j.biortech.2015.07.071","article-title":"Biofilm formation and ethanol inhibition by bacterial contaminants of biofuel fermentation","volume":"196","author":"Rich","year":"2015","journal-title":"Bioresour Technol"},{"key":"2025102411430657200_bib89","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1016\/j.biortech.2010.08.118","article-title":"Rapid evaluation of the antibiotic susceptibility of fuel ethanol contaminant biofilms","volume":"102","author":"Rich","year":"2011","journal-title":"Bioresour Technol"},{"key":"2025102411430657200_bib90","article-title":"Contaminantes bacterianos da fermenta\u00e7\u00e3o etan\u00f3lica: isolamento em meios diferenciais, identifica\u00e7\u00e3o e avalia\u00e7\u00e3o de desinfetantes","author":"Rosales","year":"1989"},{"key":"2025102411430657200_bib91","article-title":"Biotecnologia Industrial","volume-title":"Engenharia Bioqu\u00edmica","author":"Schmidell","year":"2001"},{"key":"2025102411430657200_bib92","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1016\/j.copbio.2018.11.015","article-title":"Bioprotective mechanisms of lactic acid bacteria against fungal spoilage of food","volume":"56","author":"Siedler","year":"2019","journal-title":"Curr Opin Biotechnol"},{"key":"2025102411430657200_bib93","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.lwt.2017.12.022","article-title":"Mutually stimulating interactions between lactic acid bacteria and Saccharomyces cerevisiae in sourdough fermentation","volume":"90","author":"Sieuwerts","year":"2018","journal-title":"LWT"},{"key":"2025102411430657200_bib94","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/s13068-014-0123-9","article-title":"Bacteriophages as antimicrobial agents against bacterial contaminants in yeast fermentation processes","volume":"7","author":"Silva","year":"2014","journal-title":"Biotechnol Biofuels"},{"key":"2025102411430657200_bib95","doi-asserted-by":"publisher","first-page":"fny228","DOI":"10.1093\/femsle\/fny228","article-title":"Volatile phenols are produced by strains of Dekkera bruxellensis under Brazilian fuel ethanol industry-like conditions","volume":"365","author":"Silva","year":"2018","journal-title":"FEMS Microbiol Lett"},{"key":"2025102411430657200_bib96","doi-asserted-by":"publisher","first-page":"45","DOI":"10.4103\/0973-7847.156340","article-title":"Phytochemical profile of sugarcane and its potential health aspects","volume":"9","author":"Singh","year":"2015","journal-title":"Pharmacogn Rev"},{"key":"2025102411430657200_bib97","doi-asserted-by":"publisher","first-page":"298","DOI":"10.3390\/fermentation10060298","article-title":"The impact of physicochemical conditions on lactic acid bacteria survival in food products","volume":"10","author":"Sionek","year":"2024","journal-title":"Fermentation"},{"key":"2025102411430657200_bib98","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/s10295-004-0159-0","article-title":"Bacterial contaminants of fuel ethanol production","volume":"31","author":"Skinner","year":"2004","journal-title":"J Ind Microbiol Biotechnol"},{"key":"2025102411430657200_bib99","doi-asserted-by":"publisher","first-page":"eadj3502","DOI":"10.1126\/science.adj3502","article-title":"Microbiome diversity protects against pathogens by nutrient blocking","volume":"382","author":"Spragge","year":"2023","journal-title":"Science"},{"key":"2025102411430657200_bib100","first-page":"487","article-title":"Production of fuel alcohol from wheat by VHG technology effect of sugar concentration and fermentation temperature","volume":"39","author":"Thomas","year":"1993","journal-title":"Appl Biochem Biotechnol"},{"key":"2025102411430657200_bib103","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/S0065-2164(04)54008-X","article-title":"Metals in yeast fermentation processes","volume":"54","author":"Walker","year":"2004","journal-title":"Adv Appl Microbiol"},{"key":"2025102411430657200_bib104","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1093\/bbb\/zbad167","article-title":"Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation","volume":"88","author":"Watanabe","year":"2024","journal-title":"Biosci Biotechnol Biochem"},{"key":"2025102411430657200_bib105","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/S0958-6946(01)00153-4","article-title":"Mannitol production by lactic acid bacteria: a review","volume":"12","author":"Wisselink","year":"2002","journal-title":"Int Dairy J"},{"key":"2025102411430657200_bib106","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1002\/bit.25586","article-title":"Reduction of invasive bacteria in ethanol fermentations using bacteriophages","volume":"112","author":"Worley-Morse","year":"2015","journal-title":"Biotech Bioeng"},{"key":"2025102411430657200_bib107","doi-asserted-by":"publisher","first-page":"100178","DOI":"10.1016\/j.engmic.2024.100178","article-title":"Exploring interspecific interaction variability in microbiota: a review","volume":"4","author":"Yu","year":"2024","journal-title":"Eng Microbiol"},{"key":"2025102411430657200_bib108","doi-asserted-by":"publisher","first-page":"2782","DOI":"10.1099\/ijsem.0.004107","article-title":"A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae","volume":"70","author":"Zheng","year":"2020","journal-title":"Int J Syst Evol Microbiol"}],"container-title":["FEMS Microbiology Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/femsec\/advance-article-pdf\/doi\/10.1093\/femsec\/fiaf100\/64819387\/fiaf100.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsec\/advance-article-pdf\/doi\/10.1093\/femsec\/fiaf100\/64819387\/fiaf100.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsec\/advance-article-pdf\/doi\/10.1093\/femsec\/fiaf100\/64819387\/fiaf100.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T15:43:13Z","timestamp":1761320593000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsec\/article\/doi\/10.1093\/femsec\/fiaf100\/8293218"}},"subtitle":[],"editor":[{"given":"Marcus","family":"Horn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,10,13]]},"references-count":102,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,10,13]]}},"URL":"https:\/\/doi.org\/10.1093\/femsec\/fiaf100","relation":{},"ISSN":["1574-6941"],"issn-type":[{"value":"1574-6941","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,11]]},"published":{"date-parts":[[2025,10,13]]},"article-number":"fiaf100"}}