biostudies-literatureSalas-Lopez MConsejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT) Mexico85https://www.ebi.ac.uk/biostudies/studies/S-EPMC11767358biostudies-literatureUnknown13(1)Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5-V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens <i>Methanoculleus</i> and <i>MethaMicroorganismsHuman Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria.PMC11767358CONACYT-163235, INFR-2011-01.CONACYT FORDECYT-PRONACES/6669/2020_Programa Presupuestario F003-Ciencia de Frontera 2019.Velez-Ixta JMRojas-Guerrero DLRangel-Calvillo MNHernandez-Hernandez JMGarcia-Mena JSalas-Lopez MPina-Escobedo AJuarez-Castelan CJCorona-Cervantes KPerez-Cruz CfalseHuman Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria.Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5-V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens <i>Methanoculleus</i> and <i>Metha2025-01-01T00:00:00Z2025 Jan2026-04-08T19:55:48.021Z2025-04-04T23:12:55.004ZS-EPMC117673583985885310.3390/microorganisms13010085