{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T01:17:15Z","timestamp":1773883035530,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T00:00:00Z","timestamp":1655337600000},"content-version":"vor","delay-in-days":166,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004360","name":"Sveriges Lantbruksuniversitet","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004360","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood\u2013Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility\/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences.<\/jats:p>\n               <jats:p>Database URL: https:\/\/acetobase.molbio.slu.se<\/jats:p>","DOI":"10.1093\/database\/baac041","type":"journal-article","created":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T14:20:57Z","timestamp":1655389257000},"source":"Crossref","is-referenced-by-count":6,"title":["AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters"],"prefix":"10.1093","volume":"2022","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0807-6080","authenticated-orcid":false,"given":"Abhijeet","family":"Singh","sequence":"first","affiliation":[{"name":"Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas All\u00e9 5, Uppsala SE-750 07, Sweden"}]},{"given":"Anna","family":"Schn\u00fcrer","sequence":"additional","affiliation":[{"name":"Department of Molecular Sciences, BioCenter, Anaerobic Microbiology and Biotechnology Group, Swedish University of Agricultural Sciences , Almas All\u00e9 5, Uppsala SE-750 07, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2022,6,16]]},"reference":[{"key":"2022061614204784800_R1","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1007\/978-1-4615-1777-1_8","volume-title":"Acetogenesis","author":"Lovell","year":"1994"},{"key":"2022061614204784800_R2","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/S0076-6879(05)97028-6","article-title":"Community-level analysis: key genes of CO2-reductive acetogenesis","volume":"397","author":"Lovell","year":"2004","journal-title":"Meth. Enzymol."},{"key":"2022061614204784800_R3","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baz142","article-title":"AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences","volume":"2019","author":"Singh","year":"2019","journal-title":"Database"},{"key":"2022061614204784800_R4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2020.02066","article-title":"High-throughput sequencing and unsupervised analysis of formyltetrahydrofolate synthetase (FTHFS) gene amplicons to estimate acetogenic community structure","volume":"11","author":"Singh","year":"2020","journal-title":"Front Microbiol."},{"key":"2022061614204784800_R5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4615-1777-1","volume-title":"Acetogenesis. Chapman & Hall Microbiology Series","author":"Drake"},{"key":"2022061614204784800_R6","doi-asserted-by":"crossref","first-page":"2602","DOI":"10.1128\/aem.57.9.2602-2609.1991","article-title":"Design and testing of a functional group-specific DNA probe for the study of natural populations of acetogenic bacteria","volume":"57","author":"Lovell","year":"1991","journal-title":"Appl. Environ. Microbiol."},{"key":"2022061614204784800_R7","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1128\/AEM.67.3.1392-1395.2001","article-title":"Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria","volume":"67","author":"Leaphart","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"2022061614204784800_R8","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1128\/AEM.69.1.693-696.2003","article-title":"Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups","volume":"69","author":"Leaphart","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"2022061614204784800_R9","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1196\/annals.1419.016","article-title":"Old Acetogens, new light","volume":"1125","author":"Drake","year":"2008","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"2022061614204784800_R10","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-3-642-30141-4_61","volume-title":"The Prokaryotes","author":"Drake","year":"2013"},{"key":"2022061614204784800_R11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-92658-2","article-title":"Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP","volume":"11","author":"Singh","year":"2021","journal-title":"Sci. Rep."},{"key":"2022061614204784800_R12","article-title":"Microbiological Surveillance of Biogas Plants: Focusing on the Acetogenic Community [Internet]","author":"Singh","year":"2021"},{"key":"2022061614204784800_R13","doi-asserted-by":"publisher","DOI":"10.1101\/074161","article-title":"SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences","author":"Edgar","journal-title":"bioRxiv"},{"key":"2022061614204784800_R14","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1002\/bit.22508","article-title":"Microbial community structure in a biofilm anode fed with a fermentable substrate: the significance of hydrogen scavengers","volume":"105","author":"Parameswaran","year":"2010","journal-title":"Biotechnol. Bioeng."},{"key":"2022061614204784800_R15","article-title":"DupRemover: A Simple Program to Remove Duplicate Sequences from Multi-Fasta File","volume-title":"ResearchGate\/GitHub","author":"Singh"},{"key":"2022061614204784800_R16","article-title":"FilterByLength: Filter Fasta Sequences by Length and Count the Sequences in a Multifasta File","volume-title":"ResearchGate\/GitHub","author":"Singh"},{"key":"2022061614204784800_R17","article-title":"Clean_AMINOACID_fasta: Program to Clean AMINO ACID Fasta Sequences and Removes and Illegal Characters in Sequence or Any Non-Natural Amino Acid Residue","volume-title":"ResearchGate\/GitHub","author":"Singh"},{"key":"2022061614204784800_R18","article-title":"Clean_DNA_fasta: Program to Clean DNA Fasta Sequences and Removes and Illegal Characters in Sequence or Any Non-Natural Residue","volume-title":"ResearchGate\/GitHub","author":"Singh"},{"key":"2022061614204784800_R19","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"2022061614204784800_R20","doi-asserted-by":"publisher","DOI":"10.1038\/srep33964","article-title":"FAMSA: fast and accurate multiple sequence alignment of huge protein families","volume":"6","author":"Deorowicz","year":"2016","journal-title":"Sci. Rep."},{"key":"2022061614204784800_R21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2022061614204784800_R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"2022061614204784800_R23","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1590\/S1516-35982009001300034","article-title":"Recent developments in nucleic acid based techniques for use in rumen manipulation","volume":"38","author":"McSweeney","year":"2009","journal-title":"Rev. Bras. Zootec."},{"key":"2022061614204784800_R24","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.700256","article-title":"Microbiological surveillance of biogas plants: targeting acetogenic community","author":"Singh","year":"2021","journal-title":"Front Microbiol."},{"key":"2022061614204784800_R25","doi-asserted-by":"publisher","DOI":"10.1186\/s13068-020-01679-y","article-title":"New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters","volume":"13","author":"Campanaro","year":"2020","journal-title":"Biotechnol. Biofuels"},{"key":"2022061614204784800_R26","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1038\/ismej.2017.39","article-title":"Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments","volume":"11","author":"Hernsdorf","year":"2017","journal-title":"ISME J."},{"key":"2022061614204784800_R27","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00197","article-title":"The transcriptional response of microbial communities in thawing Alaskan permafrost soils","volume":"6","author":"Coolen","year":"2015","journal-title":"Front Microbiol."},{"key":"2022061614204784800_R28","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02242-17","article-title":"Effect of start-up strategies and electrode materials on carbon dioxide reduction on biocathodes","volume":"84","author":"Saheb-Alam","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"2022061614204784800_R29","doi-asserted-by":"publisher","DOI":"10.1186\/s13068-016-0454-9","article-title":"Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria","volume":"9","author":"M\u00fcller","journal-title":"Biotechnol. Biofuels"},{"key":"2022061614204784800_R30","doi-asserted-by":"publisher","DOI":"10.3389\/fnut.2017.00029","article-title":"Abundance and diversity of hydrogenotrophic microorganisms in the infant gut before the weaning period assessed by denaturing gradient gel electrophoresis and quantitative PCR","volume":"4","author":"Sagheddu","year":"2017","journal-title":"Front. Nutr."},{"key":"2022061614204784800_R31","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1111\/j.1574-6968.1990.tb04929.x","article-title":"Microbial H2\/CO2 acetogenesis in animal guts: nature and nutritional significance","volume":"87","author":"Breznak","year":"1990","journal-title":"FEMS Microbiol. Lett."},{"key":"2022061614204784800_R32","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.1128\/aem.60.4.1370-1373.1994","article-title":"Acetate synthesis in soil from a Bavarian beech forest","volume":"60","author":"K\u00fcsel","year":"1994","journal-title":"Appl. Environ. Microbiol."},{"key":"2022061614204784800_R33","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/978-1-61779-089-8_8","article-title":"Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities","author":"Zhang","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"2022061614204784800_R34","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.syapm.2018.12.003","article-title":"Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov","volume":"42","author":"Martinez","year":"2019","journal-title":"Syst. Appl. Microbiol."},{"key":"2022061614204784800_R35","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1007\/978-1-4615-1777-1_13","article-title":"Acetogenesis from CO2 in the human colonic ecosystem","author":"Wolin","year":"1994","journal-title":"Acetogenesis"},{"key":"2022061614204784800_R36","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1007\/0-387-22731-8_14","article-title":"Electron-transport system in acetogens","author":"Das","year":"2003","journal-title":"Biochemistry and physiology of anaerobic bacteria"},{"key":"2022061614204784800_R37","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1146\/annurev-marine-120709-142712","article-title":"Beyond the Calvin cycle: autotrophic carbon fixation in the ocean","volume":"3","author":"H\u00fcgler","year":"2011","journal-title":"Ann. Rev. Mar. Sci."},{"key":"2022061614204784800_R38","doi-asserted-by":"publisher","DOI":"10.3390\/fermentation4020040","article-title":"Acetogen communities in the gut of herbivores and their potential role in syngas fermentation","volume":"4","author":"Yang","journal-title":"Fermentation"},{"key":"2022061614204784800_R39","doi-asserted-by":"crossref","first-page":"22082","DOI":"10.1074\/jbc.M110.117713","article-title":"Dissecting the in vivo metabolic potential of two human gut acetogens","volume":"285","author":"Rey","year":"2010","journal-title":"J. Biol. Chem."},{"key":"2022061614204784800_R40","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.14389","article-title":"Glycine betaine metabolism in the acetogenic bacterium Acetobacterium woodii","author":"Lechtenfeld","journal-title":"Environ. Microbiol."},{"key":"2022061614204784800_R41","doi-asserted-by":"crossref","first-page":"11971","DOI":"10.1074\/jbc.RA120.012934","article-title":"MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase","volume":"295","author":"Kountz","year":"2020","journal-title":"J. Biol. Chem."},{"key":"2022061614204784800_R42","doi-asserted-by":"crossref","first-page":"13697","DOI":"10.1074\/jbc.RA119.009886","article-title":"MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation","volume":"294","author":"Picking","year":"2019","journal-title":"J. Biol. Chem."},{"key":"2022061614204784800_R43","doi-asserted-by":"crossref","first-page":"19039","DOI":"10.1007\/s11356-015-5117-z","article-title":"The roles of methanogens and acetogens in dechlorination of trichloroethene using different electron donors","volume":"22","author":"Wen","year":"2015","journal-title":"Environ. Sci. Pollut. Res."},{"key":"2022061614204784800_R44","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/B978-0-12-397154-8.00029-4","volume-title":"Bioactive Food as Dietary Interventions for Liver and Gastrointestinal Disease","author":"Collado","year":"2013"},{"key":"2022061614204784800_R45","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1017\/S0007114514003274","article-title":"Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet","volume":"113","author":"Panasevich","year":"2015","journal-title":"Br. J. Nutr."},{"key":"2022061614204784800_R46","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1146\/annurev-pharmtox-051920-093829","article-title":"The gut microbiome, metformin, and aging","volume":"62","author":"Induri","year":"2022","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"key":"2022061614204784800_R47","first-page":"175","article-title":"Increased growth of Bifidobacterium and Eubacterium by germinated barley foodstuff, accompanied by enhanced butyrate production in healthy volunteers","volume":"3","author":"Kanauchi","year":"1999","journal-title":"Int. J. Mol. Med."},{"key":"2022061614204784800_R48","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1111\/j.1574-6941.1995.tb00152.x","article-title":"Enumeration of H2-utilizing methanogenic archaea, acetogenic and sulfate-reducing bacteria from human feces","volume":"17","author":"Dore","year":"1995","journal-title":"FEMS Microbiol. Ecol."},{"key":"2022061614204784800_R49","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1016\/B978-0-12-815249-2.00033-6","volume-title":"Microbiome and Metabolome in Diagnosis, Therapy, and Other Strategic Applications","author":"de Oliveira","year":"2019"},{"key":"2022061614204784800_R50","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/B978-0-12-804024-9.00040-9","article-title":"Probiotics and nonalcoholic fatty liver disease","author":"Eslamparast","year":"2013","journal-title":"Middle East J. Dig. Dis."},{"key":"2022061614204784800_R51","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/bs.pbr.2020.01.004","article-title":"The gut microbiome in Parkinson\u2019s disease: a culprit or a bystander?","author":"Keshavarzian","year":"2020","journal-title":"Prog. Brain Res."},{"key":"2022061614204784800_R52","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/B978-0-12-813679-9.00007-5","article-title":"Pathogen identification using novel sequencing methods","author":"Raghavendra","year":"2018","journal-title":"Adv. Cell Mol. Diagn."},{"key":"2022061614204784800_R53","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/B978-0-12-804024-9.00031-8","volume-title":"The Microbiota in Gastrointestinal Pathophysiology","author":"Floch","year":"2017"},{"key":"2022061614204784800_R54","doi-asserted-by":"crossref","first-page":"37","DOI":"10.12938\/bifidus.26.37","article-title":"Analysis of Acetogenic Bacteria in human feces with formyltetrahydrofolate synthetase sequences","volume":"26","author":"Ohashi","year":"2007","journal-title":"Biosci. Microflora"},{"key":"2022061614204784800_R55","doi-asserted-by":"crossref","first-page":"17","DOI":"10.12938\/bifidus.28.17","article-title":"Acetogenic Bacteria mainly contribute to the disposal of hydrogen in the colon of healthy Japanese","volume":"28","author":"Ohashi","year":"2009","journal-title":"Biosci. Microflora"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac041\/44109158\/baac041.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac041\/44109158\/baac041.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T14:21:23Z","timestamp":1655389283000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baac041\/6609150"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":55,"URL":"https:\/\/doi.org\/10.1093\/database\/baac041","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2022,1,1]]},"article-number":"baac041"}}