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This risk can be mitigated through probiotic prophylaxis during admission. This reduction in risk is likely the result of acute modulation of the gut microbiome induced by probiotic species, which has been observed to occur up until discharge. We aimed to determine if this modulation, and the associated probiotic species, persisted beyond discharge. We conducted both a cross-sectional analysis (<jats:italic>n<\/jats:italic>\u2009=\u200918), at\u2009~\u200918\u00a0months of age, and a longitudinal analysis (<jats:italic>n<\/jats:italic>\u2009=\u20096), from admission to 18\u00a0months of the gut microbiome of preterm infants using both shotgun metagenomics and 16S rRNA profiling respectively. The 16S amplicon sequencing revealed that the microbial composition of the probiotic-supplemented infants changed dramatically over time, stabilising at discharge. However, species from the probiotic Infloran<jats:sup>\u00ae<\/jats:sup>, as well as positive modulatory effects previously associated with supplementation, do not appear to persist beyond discharge and once prophylaxis has stopped.<\/jats:p><jats:p>\u00a0 \u00a0<jats:italic>Conclusions<\/jats:italic>: Although differences exist between supplemented and non-supplemented groups, the implications of these differences remain unclear. Additionally, despite a lack of long-term colonisation, the presence of probiotics during early neonatal life may still have modulatory effects on the microbiome assembly and immune system training.<jats:table-wrap><jats:table><jats:tbody><jats:tr><jats:td colspan=\"2\"><jats:bold>What is Known:<\/jats:bold><jats:italic>\u2022\u00a0<\/jats:italic><jats:italic>Evidence suggests modulation of the microbiome occurs during probiotic prophylaxis, which may support key taxa that exert positive immunological benefits.<\/jats:italic>\u2022\u00a0<jats:italic>Some evidence suggests that this modulation can persist post-prophylaxis.<\/jats:italic><\/jats:td><\/jats:tr><jats:tr><jats:td colspan=\"2\"><jats:bold>What is New:<\/jats:bold><jats:italic>\u2022\u00a0<\/jats:italic><jats:italic>We present support for long-term modulation in association with probiotic prophylaxis in a cohort of infants from North Queensland Australia.<\/jats:italic>\u2022\u00a0<jats:italic>We also observed limited persistence of the probiotic species post-discharge.<\/jats:italic><\/jats:td><\/jats:tr><\/jats:tbody><\/jats:table><\/jats:table-wrap><\/jats:p>","DOI":"10.1007\/s00431-022-04548-y","type":"journal-article","created":{"date-parts":[[2022,7,7]],"date-time":"2022-07-07T08:04:47Z","timestamp":1657181087000},"page":"3389-3400","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study"],"prefix":"10.1007","volume":"181","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5171-819X","authenticated-orcid":false,"given":"Jacob A. 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