DOI: 10.5281/zenodo.17233688
title: Early-life microbiota in the LIMIT cohort: unveiling neonatal microbiota types beyond maternal lifestyle

description:  

This dataset originates from the LIMIT prospective birth cohort (ClinicalTrials.gov Identifier: NCT04960670), it contains data and associated metadata from the LIMIT cohort study on meconium microbiota (i.e. Time 0 only). the LIMIT study is designed to investigate the interplay between maternal lifestyle and environmental factors, infant growth, and gut microbiota development. For the present analysis, 200 pregnant women were initially enrolled at Fondazione IRCCS Policlinico San Matteo (Pavia, Italy) between October 2022 and June 2024. Based on inclusion criteria and sample availability, 168 mother–infant pairs were selected. Samples data were collected togheter with maternal information on pre-pregnancy BMI, gestational weight gain, and selected lifestyle/environmental factors.

Dataset content included the raw-derived data from 16S rRNA gene amplicon sequences (V1–V8 regions) generated using the Oxford Nanopore PromethION platform and sample-related metadata, including pre-pregnancy BMI, gestational weight gain, and selected lifestyle factors (diet, physical activity, smoking habits), collected through validated questionnaires and structured interviews.

The data allow for the investigation of microbial community composition, diversity metrics, and clustering patterns in neonatal meconium, as well as their potential associations with maternal anthropometric and lifestyle variables.
description: File: otutable.csv

Description: OTU abundance table with taxonomic annotation and sample metadata. Sample metadata labels are reported following anonymous format. Rows represent OTUs, columns represent samples and taxonomic ranks.

 

File: OTUs_clean.fa

Description: FASTA file containing representative OTU (Operational Taxonomic Unit) sequences obtained from meconium 16S rRNA gene sequencing. In this file the non-standard characters were removed, generating a cleaned FASTA file in which sequences contain only valid DNA symbols.

 

File: metadata.csv

Description: Metadata file containing maternal, neonatal, and lifestyle variables associated with each sample. Each row corresponds to one mother–infant pair included in the study. All samples are reported using anonymous format.

 

File: summary_table.csv

Description: Summary table file provides a detailed overview of sample-level metadata, DNA extraction metrics, sequencing statistics, and diversity estimates for all meconium samples analyzed in the study. For each sample, the table reports the sample identifier and name, the DNA extraction method used, dsDNA concentration measured, library identifiers, and library DNA concentrations prior to sequencing. Sequencing statistics derive from long-read 16S rRNA gene (V1–V8) sequencing performed on the Oxford Nanopore PromethION platform are also reported and include the total number of raw reads, read length distribution (N50), average Phred quality scores before and after filtering, the number of quality-filtered reads, the number of reads mapped to the reference 16S rRNA database, and the ratio of mapped to filtered reads. In addition, the table reports downstream microbiota-related analysis outputs, including, the total number of observed OTUs (richness), alpha-diversity indices (Shannon and Simpson), and ratios describing taxonomic assignment consistency across phylum, class, order, family, genus, and species levels.