Biology subjects

Quesnel, H.

Publications and source records attributed to Quesnel, H..

3 recordsLinked to original sources

bioRxiv2026

Late lactation represents the main window for sow-to-piglet transmission of persistent gut strains

The gut microbiota plays a key role in piglet health, and maternal microbial transmission may represent a promising lever to shape early-life microbiota and prevent post-weaning digestive disorders. This study aimed to better characterize sow-to-piglet microbiota transmission and persistence using a long-read metabarcoding approach targeting the 16S-ITS-23S region. Fecal samples (n = 204) were collected from 17 families, a family being as sow and three of her piglets, at multiple stages: late gestation (G110), early (L6) and late lactation (L28) for sows; early lactation (L6), late lactation (L28), and 5 days post-weaning for piglets. To approximate strain-level resolution, a putative strain (PS) approach was developed by clustering ASVs (n = 6064) affiliated with the same species based on abundance covariance (r > 0.9), resulting in 4857 PS. Piglet microbiota progressively diversified during lactation and converged toward that of sow. In sows, 27 {+/-} 6% of PS were persistent from late gestation to late lactation. In piglets, only 4.2 {+/-} 2.5% of PS persisted from d6 to 5 days post-weaning. Persistent PS in piglets were mainly affiliated with Limosilactobacillus reuteri and Lactobacillus amylovorus followed with Holdemanella porci and H. biformis, Lentihominibacter hominis and Dorea formicigenerans. Shared PS were significantly higher within families than between unrelated pairs (p < 0.05). Maternal transmission peaked at the end of lactation (35 {+/-} 7% at L28). Persistent transmitted PS represented 2.7 {+/-} 1.6% (d6-post-weaning) and 15.4 {+/-} 5.6% (d28-post-weaning). Early-transmitted persistent PS were mainly affiliated with Limosilactobacillus reuteri, Lactobacillus amylovorus, and Paraeggerthella hominis, whereas late-transmitted persistent PS were associated with Prevotella spp., Sphaerochaeta globosa, and Bariatricus comes. These findings highlight the significance of maternal transmission in shaping the post-weaning microbiota and identify late lactation as a critical window for microbiota transfer.

zoology↗

bioRxiv2020

The maturity in fetal pigs using a multi-fluid metabolomic approach

In mammalian species, the first days after birth are an important period for survival and the rates of mortality before weaning are high. In pigs, the perinatal deaths average 20% of the litter, with important economic and societal consequences. Among the factors influencing piglet survival at birth, the maturity is likely to be one of the most important. Maturity can be defined as the outcome of complex mechanisms of intra-uterine development and maturation occurring during the last month of gestation. Here, we provide new insights on maturity by studying the end of gestation at two different stages (three weeks before term and close to term) in two breeds of pigs that strongly differ in terms of neonatal survival. Since metabolomics is a promising approach for phenotype characterization or biomarker discovery, we provide a complete understanding of the metabolome of the fetuses in late gestation in three fluids (plasma, urine, and amniotic fluid). We found that biological processes related to amino acid and carbohy-drate metabolisms are critical for piglet maturity. We also confirmed some previously described metabolites associated with delayed growth (e.g., proline and myo-inositol). Altogether, our study proposes new routes for a better characterization of piglet maturity at birth.

developmental biology↗

bioRxiv2018

ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra

In metabolomics, the detection of new biomarkers from NMR spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses.\n\nWe present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independant datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketting. It also found new relevant metabolites involved in metabolic pathways related to risk factors associated with the conditions.\n\nThis workflow is available through the R package ASICS, available on the Bioconductor platform.

systems biology↗