{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T03:53:14Z","timestamp":1762660394309,"version":"3.41.2"},"reference-count":63,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T00:00:00Z","timestamp":1687737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment and in the host (in this case,<jats:italic>Solea senegalensis<\/jats:italic>). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2\u2009days before hatching and up to 146\u2009days after hatching (\u22122 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. Using the Bray\u2013Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria (<jats:italic>Bacillus<\/jats:italic>and<jats:italic>Enterococcus<\/jats:italic>) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera<jats:italic>Tenacibaculum<\/jats:italic>and<jats:italic>Vibrio<\/jats:italic>were inherited from the eggs, while<jats:italic>Photobacterium<\/jats:italic>and<jats:italic>Mycobacterium<\/jats:italic>seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between<jats:italic>Tenacibaculum<\/jats:italic>and both<jats:italic>Photobacterium<\/jats:italic>and<jats:italic>Vibrio<\/jats:italic>. On the other hand, significantly negative correlations were detected between<jats:italic>Vibrio<\/jats:italic>and<jats:italic>Streptococcus<\/jats:italic>,<jats:italic>Bacillus<\/jats:italic>,<jats:italic>Limosilactobacillus<\/jats:italic>and<jats:italic>Gardnerella<\/jats:italic>. Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1188876","type":"journal-article","created":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T10:00:26Z","timestamp":1687773626000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Sole microbiome progression in a hatchery life cycle, from egg to juvenile"],"prefix":"10.3389","volume":"14","author":[{"given":"Diana Bastos","family":"Almeida","sequence":"first","affiliation":[]},{"given":"Miguel","family":"Semedo","sequence":"additional","affiliation":[]},{"given":"Catarina","family":"Magalh\u00e3es","sequence":"additional","affiliation":[]},{"given":"Isidro","family":"Blanquet","sequence":"additional","affiliation":[]},{"given":"Ana Paula","family":"Mucha","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2023,6,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"736592","DOI":"10.1016\/j.aquaculture.2021.736592","article-title":"Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis)","volume":"539","author":"Almeida","year":"2021","journal-title":"Aquaculture"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1007\/s12602-018-9439-2","article-title":"Isolation and partial characterization of lactic acid Bacteria from the gut microbiota of marine fishes for potential application as probiotics in aquaculture","volume":"11","author":"Alonso","year":"2019","journal-title":"Probiotics. 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