Please enable JS and disable any ad blocker Metrics details The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding If this diet transition is recognized as a major step in the young’s development the mechanistic understanding of the changes occurring in the gut and the long-term consequences of pre-weaning experiences remain unknown with a dynamic follow-up appears necessary to capture the process occurring at the suckling-weaning transition rabbits present a specific behaviour pattern allowing mother-offspring separation most of the time Easy control of early-life ingestion (milk and food) can therefore be performed to investigate post-natal food ingestion apart from nursing influence a better understanding of the multidimensional aspects of gut health in rabbits appears essential to improve rabbit breeding practices Experimental design (a) and data collection (b) This study aimed to provide insights into host and gut microbiota responses to changes in the timing of solid food introduction (groups STA-/STA+) when two different diets were provided throughout the life (diets STA and RFF) STA-: access to starch-enriched food in a pellet form from 15 to 70 days-old STA+: access to starch-enriched food from 3 to 18 days-old in a gel form and from 15 to 70 days-old in a pellet form RFF+: access to food rich in rapidly fermentable fibers from 3 to 18 days-old in a gel form and from 15 to 70 days-old in a pellet form with this work intended to provide further methods descriptions and validation to facilitate re-use New data are presented compared to our previous publication technical replicates for 16S rDNA sequencing rabbit nest quality evaluation and ileal gene expression we demonstrated that the ingestion of small quantity of solid food in early life while maintaining milking could effectively accelerate gut microbiota maturation Increasing the ingestion of rapidly fermentable fibers contributed to a specialization of the microbiota towards fibers-degradation activities Effects of those strategies on the gut transcriptome and the host phenotype were limited in a context of good sanitation facilities data analysis was restricted to single-omics approach Time-monitoring of gut bacterial communities with associated host responses can allow researchers to extract a better picture of early-life developmental process This comprehensive and reusable collection of data can be further explored by integrating the different types of datasets provided (multi-omics approaches) This could help revel some interplay mechanisms some data were generated for the first time with this experiment thus providing new information to scientific community (e.g investigation of caecal and appendix microbiomes in the same individuals or evaluation of plasmatic fatty acids and protein contents in rabbits at different stages) Controls for technical and biological reproductibility of the data were generated thus leading to valuable data resources for microbiologists and physiologists We provided herein the description of the methods used together with raw and processed data to ensure easy sharing and re-processing thanks to analysis script provided on the Github platform Detailed procedures or additional information such as complete lab steps for performing NMR measurements and RNA extraction are provided here to ensure that our datasets are understandable and reusable the cages used for the experiment are described in more detail as the housing system was specifically designed for this study Additional data collection on nest quality is also presented 3D model of the experimental housing system used before weaning View from the top of a nursing cage where the doe and its kits are raised together for 35 days Blue arrows represent possible movements of the kits while red arrow represents possible path for the doe the nest was only opened once a day for suckling (dottled arrows) The sampling dates were chosen based on the feed transition process11: 18 days of age (solid food consumption remains minor) 25 days (dietary switch with marked increase of solid food ingestion proportion compared to milk) 30 days (solid-based diet with low amounts of milk consumed) 38 days (beginning of exclusive solid diet related with high susceptibility to digestive diseases) 58 days (settled exclusive solid feeding with more stable sanitary status) pups that exhibited interest for gel food were preferably selected while at days 25 the killing procedure was performed 1 to 2 hours after suckling while after weaning the rabbits were sampled 2 to 3 hours after feed distribution to obtain similar postprandial state After the determination of sex and body weight of the animals chosen they were killed by electronarcosis and exsanguination Blood was collected at exsanguination in EDTA and dry tubes for plasma and serum preparation respectively EDTA tubes were immediately put on ice until centrifugation (800 g for 10 min at 4 °C) dry tubes were let undisturbed at room temperature for 20 minutes The clot was then removed by centrifugation (1 800 g for 10 min in a regular centrifuge) Resulting supernatants were collected and stored at −20 °C After isolation of the caecum and the appendix vermiformis USA) and up to 500 mg of luminal contents were collected in sterile tubes stored at −80 °C until the extraction step protective gloves were replaced and the material was sterilized to prevent crossed contamination 0.5 cm of tissues from proximal caecum and distal ileon were quickly extracted at 3 cm up and down the Sacculus Rototondus they were immediately snap-frozen in liquid nitrogen and stored at −80 °C prior to further processing 1 g of caecal content was collected and diluted in H2SO4 (at 2% w/v) to quantify ammoniac (NH3) concentrations at days 25 38 and 58 (insufficient quantities at day 18) Caecal pH was measured after previous samplings by introducing a glass electrode at the ileocecal junction (VWR Collection SP225 around 2 g of caecal contents were collected to determine dry matter level after heating at 103 °C for 24 h Caecal contents (100 mg) were homogenized in 500 µL phosphate buffer (sodium phosphate 0.2 M and 20% water) in 2 mL FastPrep tubes (Lysing D matrix) by using a FastPrep Instrument (MP biomedicals the supernatant was transferred to a new tube The pellet was resuspended in 500 µL phosphate buffer and the homogenization and centrifugation steps were repeated Supernatants from both extraction steps were pooled and centrifuged twice to remove particles (18 000 g The resulting supernatants (600 µL) were transferred to 5 mm NMR tubes NMR spectra were obtained with an Avance III HD NMR spectrometer operating at 600.13 MHz for 1H resonance frequency using a 5 mm inverse detection CryoProbe (Bruker Biospin Germany) in the MetaboHUB-MetaToul-AXIOM metabolomics platform (Toulouse The 1H NMR spectra were acquired at 300 K using the Carr-Purcell-Meiboom-Gill (CPMG) spin-echo pulse sequence with presaturation A total of 128 scans (16 dummy scans) were collected in 32 K data points using a spectral width of 20 ppm and an acquisition time of 1.36 s To improve the reproducibility of our work we provide below new information on our RT-qPCR protocol Caecal (n = 149) and ileal (n = 149) tissues were homogenized in 800 μL TRI reagent (ZymoResearch) with one sterile stainless steel 5 mm diameter bead (Qiagen Germany) by using a TissueLyzer (Qiagen) with two 3 min cycles at 30 Hz 300 μL of supernatant was used for RNA extraction by using Direct-zol kit (ZymoResearch) following the manufacturer instruction including a DNAse I treatment with DNA digestion buffer RNA concentration and quality (260:280 and 260:230 ratios) were analyzed with NanoDrop 8000 (Thermo Fisher Scientific) 1 μL Oligo(dT) (100 µM) and 1 μL dNTP Mix (10 mM each) (Promega After heating the mixture to 65 °C for 5 min and quick chill on ice the contents of the tube was mixed with 4 μL 5X First-Strand Buffer (Invitrogen 1 μLSuperscript II Reverse Transcriptase (ThermoFisher Scientific) and 1 μL RNasin®Ribonuclease Inhibitor (Promega) the reaction was inactivated by heating at 70 °C for 15 min cDNA synthesis was checked with the house keeping gene GAPDH by using real-time quantitative PCR performed in QuantStudio 6 (Thermo Fisher Scientific USA) with a reaction solution containing 2.5 μl of SybrGreen fluorescent DNA-binding dye (ThermoFisher Scientific) 0.9 μM of sterile water and 1 µL of DNA diluted at 1:10 We performed 40 PCR amplification cycles with an annealing temperature of 60 °C high throughput real-time qPCR was performed for each tissue using the Biomark microfluidics system using a 96.96 Dynamic Array™ IFC for gene expression (Fluidigm 1.3 μL of cDNA (5 ng.μl−1) was added to the array and processed on the fluidics system according to the guidelines of the GENOTOUL platform an initial high temperature activation step of 10 minutes was performed into the PCR reaction with 35 amplification cycles at 60 °C later on The sequences of the primers used are presented in our companion paper good efficiency (>90% and < 110%) and linearity were kept for statistical analysis GAPDH and TOP1 gene were selected as housekeeping genes for caecal and ileal tissue respectively based on their stability over time and between groups in order to calculate gene expression using the 2−ΔΔCt method such as the construction of the calibration curve are given below for better reproducibility In order to extract the immunoglobulins A (IgA) from the caecal content 200–500 mg of digesta was diluted at 50 mg/mL in cold TBS and centrifugation at 3000 g for 10 min at 4 °C the supernatant was collected for measurement Total plasma IgG or caecal content IgA levels were determined in duplicates by sandwich ELISA in 96-well plates coated with specific polyclonal goat anti-rabbit IgG or IgA antibody (Bethyl Laboratories USA) with further plate reading at 450 nm after fixation of the reaction between HRP conjugated antibodies (Bethyl Laboratories) and TMB IgG were quantified using a reference IgG serum (Bethyl Laboratories) 12 samples were pooled to build a reference sample for the standard curve construction seven calibrator points and water blank were added in duplicate to the microwell plates along with the samples While linear standard curves were sufficient to fit the seven calibrators used for IgG quantification in plasma a 4-parametric logistic model (4-PL) was used to improve the fit of caecal IgA calibration curve (average R2 with the 7 calibrators points = 0.98) 26 µL of plasma per sample were collected for the dosage of free fatty acids the dosages were performed with Pentra 400 device (HORIBA Medical France) at the Anexplo Phenotypage GENOTOUL platform (Toulouse One sample (ID: 334) was diluted at 1:30 to fit the absorbance linearity range A summary of all the data collected during this experiment and their repository access are given in Table 1 and Fig. 1b Assessment of microbiota variability due to the DNA extraction step Bray Curtis dissimilarities were computed using 16S rDNA from caecal contents extracted several time with the same procedure and similar follow-up processing (sequencing and bioinformatics analysis) The numbers refer to the individuals sampled (rabbits of different litters aged from 18 to 58 days) and the letters a Rarefaction curves, constructed for each individual sample, generally approached saturation which indicated sufficient read depth (Fig. 4). Furthermore, rarefaction curves showed different asymptotes according to rabbit physiological development, which was expected given the limited amount of plant polysaccharides in the diets of young suckling rabbits. Rarefaction curves for caecal and appendix sites of each individuals (n = 30 individuals per sampling time with two gut sections investigated Biochemical measurements of blood content were performed on two batches with a repeated control of known concentration (human serum) and a repeated pool of samples (two repetitions per batch) The control measurements fell within appropriate confidence limits and the CV values for the pool repetitions were between 2 and 4% thus ensuring comparable results between batches for the three analytes measured Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution Role of the gut microbiota in immunity and inflammatory disease Succession of microbial consortia in the developing infant gut microbiome introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model From pre- to postweaning: Transformation of the young calf’s gastrointestinal tract Regulation of intestinal epithelial permeability by tight junctions Feeding strategy for young rabbit around weaning: a review of digestive capacity and nutritional needs The Locus of Enterocyte Effacement-Encoded Effector Proteins All Promote Enterohemorrhagic Escherichia coli Pathogenicity in Infant Rabbits Yum, L. K. & Agaisse, H. Mechanisms of bacillary dysentery: lessons learnt from infant rabbits. Gut Microbes 1–6 https://doi.org/10.1080/19490976.2019.1667726 (2019) Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits Paës, C. et al. Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions. mSystems https://doi.org/10.1128/msystems.00243-22 (2022) Mesure quantitative de la production laitière chez la lapine Le système d’information Sicpa Experimentations Les systèmes d’Informations de phénotypage des animaux à l’Inra Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics Paës, C. et al. Source code for present data analysis. Github. https://github.com/charlottepaes/early_life_nutrition_rabbit (2020) NCBI Sequence Read. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615661 ID 615661 - BioProject Paës, C. & Combes, S. Impact of feeding strategies on young rabbit and its gut microbiota. Data INRAE. https://doi.org/10.15454/QSTXWF (2021) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Download references The authors would also like to thank the metabolomics platform Metatoul-AXIOM and the GENOTOUL phenotypic platform in Toulouse summarized the data results and drafted the manuscript carried out the in vivo experiments and measured the phenotypes with the data recording system built by F.L contributed to the sequencing of 16S rDNA amplicons helped to perform the Galaxy-supported pipeline FROGS The research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Download citation DOI: https://doi.org/10.1038/s41597-024-03471-1 Anyone you share the following link with will be able to read this content: a shareable link is not currently available for this article Sign up for the Nature Briefing newsletter — what matters in science