The new version of the dataset includes the raw data and R scripts necessary to reproduce the analyses and figures explained in the manuscript "Indirect maternal effects via nest microbiome composition drives gut colonization in altricial chicks". The manuscript linked to this data has undergone a first round of peer-reviewed, which explains the differences between the first and second (current) version of the dataset. Notice that the manuscript has a new title and consequently the dataset title has been updated. This dataset includes: - ASV.xlxs: Complete ASV table of the field experiment. We collected cloacal swabs from parents and chicks in ten nests of Great tits (Parus major) and ten nests of Blue tis (Cyanistes caeruleus) together with nest and water microbiome. The Genbank accession numbers of the samples are given in each column (Bioproject: PRJNA800248). This file has been placed out of the folder "project data & code" for easy access. - README.docx: Complete explanation of the different raw data used for the statistical analyses, together with the link to the R script where data is analyzed. We recommend to read this document before diving into the data and scripts. - Project data & code: Two separate folders for raw data and code.