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A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g\/l to an average of 12.3 g\/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. Lactiplantibacillus\u00a0pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.<\/jats:p>","DOI":"10.1093\/femsmc\/xtag035","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T11:17:33Z","timestamp":1781695053000},"source":"Crossref","is-referenced-by-count":0,"title":["Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9820-3452","authenticated-orcid":false,"given":"Laura G","family":"Schaerer","sequence":"first","affiliation":[{"name":"Colorado State University Department of Civil and Environmental Engineering, , Fort Collins, CO 80523 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7572-1668","authenticated-orcid":false,"given":"Ryan S","family":"Anderson","sequence":"additional","affiliation":[{"name":"Colorado State University Department of Civil and Environmental Engineering, , Fort Collins, CO 80523 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Biomedical and Chemical Engineering, Colorado State University , Fort Collins, CO 80523 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3160-2392","authenticated-orcid":false,"given":"Susan K","family":"De\u00a0Long","sequence":"additional","affiliation":[{"name":"Colorado State University Department of Civil and Environmental Engineering, , Fort Collins, CO 80523 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"2026062312590352000_bib1","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1007\/978-1-4614-1040-9_2","article-title":"A brief history of anaerobic digestion and \u201cBiogas","volume-title":"Biogas Energy","author":"Abbasi","year":"2012"},{"key":"2026062312590352000_bib2","doi-asserted-by":"publisher","first-page":"3704","DOI":"10.1128\/JB.00321-13","article-title":"Effect of an oxygen-tolerant bifurcating butyryl coenzyme a sehydrogenase\/electron-transferring flavoprotein complex from clostridium difficile on butyrate production in Escherichia coli","volume":"195","author":"Aboulnaga","year":"2013","journal-title":"J Bacteriol"},{"key":"2026062312590352000_bib3","doi-asserted-by":"publisher","first-page":"93","DOI":"10.3390\/mps9030093","article-title":"Design, Preparation and characterization of nationally representative synthetic food waste for reproducible waste valorization research","volume":"9","author":"Anderson","year":"2026","journal-title":"Methods Protoc"},{"key":"2026062312590352000_bib4","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/s00248-024-02357-4","article-title":"Revisiting the multifaceted roles of bacteriocins: the multifaceted roles of bacteriocins","volume":"87","author":"Arbulu","year":"2024","journal-title":"Microb Ecol"},{"key":"2026062312590352000_bib5","doi-asserted-by":"publisher","first-page":"btaf147","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"CoverM: read alignment statistics for metagenomics","volume":"41","author":"Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"2026062312590352000_bib6","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","article-title":"Keystone taxa as drivers of microbiome structure and functioning","volume":"16","author":"Banerjee","year":"2018","journal-title":"Nat Rev Micro"},{"key":"2026062312590352000_bib7","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B Stat Methodol"},{"key":"2026062312590352000_bib8","doi-asserted-by":"publisher","first-page":"100018","DOI":"10.1016\/j.yjsbx.2019.100018","article-title":"Structural basis for differentiation between two classes of thiolase: degradative vs biosynthetic thiolase","volume":"4","author":"Bhaskar","year":"2020","journal-title":"J Struct Biol X"},{"key":"2026062312590352000_bib9","doi-asserted-by":"publisher","first-page":"401","DOI":"10.3389\/fmicb.2018.00401","article-title":"Flavin-based electron bifurcation, ferredoxin, flavodoxin, and anaerobic respiration with protons (Ech) or NAD+ (Rnf) as electron acceptors: a historical review","volume":"9","author":"Buckel","year":"2018","journal-title":"Front Microbiol"},{"key":"2026062312590352000_bib10","article-title":"BBMap: A Fast, Accurate, Splice-Aware Aligner. 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