Biology subjects

Le Huerou-Luron, I.

Publications and source records attributed to Le Huerou-Luron, I..

3 recordsLinked to original sources

bioRxiv2025

Human milk bacteria assembled into functionally distinct synthetic communities in infant formula differently affect intestinal physiology and microbiota in neonatal mini-piglets

The contribution of Human milk (HM) microbiota to infant gut health was addressed by evaluating the impact of HM bacteria, combined in two synthetic communities (SynComs) exhibiting anti-inflammatory (AI) or high immunomodulatory (HI) properties in vitro, on gut immune and barrier functions, and microbiota. Neonatal mini-piglets were fed either a formula without supplementation (CTRL) or supplemented with AI or HI SynComs, and were compared to sow milk-fed (SM) piglets over a period of 24 days. Feces were collected on postnatal day (PND) 8, and ileal, colonic and fecal samples were collected on PND24. The multifactorial analysis indicated that the two HM-derived SynComs impacted microbiota and intestinal functions differently. Several genera, mainly belonging to Bacillota, displayed different relative abundances between the formula-fed groups at both PND8 and PND24. At PND8, the fecal sIgA level in HI piglets was slightly lower than in SM piglets but markedly higher than in CTRL and AI piglets. SynComs HI and/or AI slightly increased the expression of genes involved in pro-inflammatory (IL6, TNFaR1), antioxidant (SOD2), anti-inflammatory (SOCS3) and Treg (FOXP3) pathways in ileal and colonic tissues compared with the CTRL group. Systemic immune functions were also modulated with a cytokine secretion capacity of peripheral blood mononuclear cells that tended to be higher with HI supplementation. Interestingly, SynCom bacteria were correlated with several ileal and colonic genera, and both were correlated with physiological variables. Overall, our findings support the influence of HM bacteria, provided in formulas as SynCom at a physiological concentration, on gut microbiota and functions. ImportanceEarly-life environmental factors, such as neonatal diet, influence the gut microbiota, which plays a key role in the functional development of the gut. However, the role of the human milk (HM) microbiota, particularly with regard to the immunomodulatory properties of HM bacteria, is not well understood. This study investigates the differential effects of two synthetic communities with a similar taxonomic composition representative of the taxonomic diversity of the HM microbiota. Thse communities exhibit contrasting immunomodulatory properties that were previously characterized using an in vitro intestinal quadricellular model. Daily supplementation with these two SynComs modulated the composition of the gut microbiota and the gut physiology differently, particularly the intestinal immune signatures. In conclusion, the functional profile of bacteria within the HM microbiota may induce distinct developmental profiles of gut physiology in infants.

physiology↗

bioRxiv2024

New insights into the cultivability of human milk microbiota from ingestion to digestion and implications for its immunomodulatory properties

Human milk (HM) microbiota is increasingly studied for its potential health benefits. However, the physiological state of HM bacteria and consequently their effects on gut homeostasis remain a question. This study investigated the physiological state of the HM microbiota by characterizing its cultivable fraction, as it might be at the point of ingestion and assessing the effects of digestion on the cultivability and immunomodulatory properties of six prevalent HM strains. The microbiota of 28 HM samples was analysed by 16S metabarcoding either directly on raw milk (raw milk microbiota, RM) or on the complete cultivable fraction obtained from seven non-selective media (cultivable milk microbiota, CM). Diversity was lower in CM than in RM, with 32 versus 435 genera and a median of 7 versus 69 genera per sample in CM and RM, respectively. CM also showed under-representation of strictly anaerobic genera. Factors like parity and iron or vitamin supplementation affected RM and/or CM. In vitro gastrointestinal digestion moderately impacted strain cultivability. However, most strains partially or completely lost their immunomodulatory properties on the monocyte THP1 cell line after digestion, except a Staphylococcus epidermidis strain that gained immunomodulatory potential.

microbiology↗

bioRxiv2024

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects.

The composition of the gut microbiota is a known factor in various diseases, and has proven to be a strong basis for automatic classification of disease state. A need for a better understanding of this community on the functional scale has since been voiced, as it would enhance these approaches biological interpretability. In this paper, we have developed a computational pipeline for integrating the functional annotation of the gut microbiota to an automatic classification process, and facilitating downstream interpretation of its results. The process takes as input taxonomic composition data (such as tables of Operational Taxonomic Unit (OTU) or Amplicon Sequence Variant (ASV) abundances), and links each component to its functional annotations through interrogation of the UniProt database. A functional profile of the gut microbiota is built from this basis. Both profiles, microbial and functional, are used to train Random Forest classifiers to discern unhealthy from control samples. An automatic variable selection is then performed on the basis of variable importance, and the method can be iterated until classification performances diminish. This process shows that the translation of the microbiota into functional profiles gives comparable, albeit slightly inferior performances when compared to microbial profiles. Through repetition, it also outputs a robust subset of discriminant variables. These selections were shown to be more reliable than those obtained by a state of the art method, and its contents were validated through a manual bibliographic research. The interconnections between selected OTUs and functional annotations were also analyzed, and revealed that important annotations emerge from the cumulated influence of non-selected OTUs.

bioinformatics↗