Effects of the rearing mode on gastro-intestinal (GIT) microbiota and development, immunocompetence, sanitary status and growth performance of newborn lambs

International audienceArtificial rearing system is commonly used in prolific meat breeds of sheep or in dairy breeds of goats. However, it represents a welfare issue due to increased mortality rates and morbidity. In this study we compared 14 lambs kept with their dams until weaning (mothered=MOT) to their twin counterparts separated 12h after birth from their mothers and reared artificially (ART), to better understand how the rearing mode, and thus the maternal presence, affect GIT microbiome, immunocompetence, health status and performance of lambs until two weeks postweaning.Rumen and fecal microbiota establishment was monitored with qPCR quantification of targeted populations and 16S and 18S amplicon sequencing. Rumen fermentative parameters and serum IgG and sanitary status were measured. Growth was recorded until 2 weeks postweaning. Then, 5 lambs per group were slaughtered, the GIT segments were weighted, and rumen papillae measurements were performed. In rumen and colon tissues, expression of targeted genes encoding for immune function, metabolic activity, and epithelium integrity was measured by RT-qPCR.Early separation with the dam clearly affected digestive microbiota establishment, with a strong delay in colonization by key members of rumen microbiome in ART vs MOT lambs. Fecal concentrations of lactic acid producing bacteria were higher in ART than in MOT in the first weeks of life suggesting differences in fermentation capacities in the hindgut, maybe associated to dysbiosis. A limited immune passive transfer was observed in ART compared to MOT lambs. ART lambs had lower ADG in early phase but finally caught up postweaning. Little or no changes in GIT anatomy, rumen papillae development, or epithelium gene expression were measured at slaughter. The presence of the mother and rearing mode influence GIT microbiota and health associated parameters in offspring in early life and the first month of life is a crucial period in artificial rearing system

Revealing microbial species diversity using sequence capture by hybridization

International audienceTargeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought

Revealing large microbial species diversity hidden behind 16S rRNA OTUs obtained from metabarcoding

International audienceTargeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind OTUs of interest, and particularly those belonging to the rare biosphere, we developed an innovative strategy using gene capture by hybridization that allowed us to recover the corresponding full-length sequences. From three rare OTU sequences of the human gut microbiota which increased upon polyphenol supplementation, we designed specific probes to capture the adjacent sequences of these OTUs from metagenomic DNA libraries. The resulting OTU-enriched libraries were then sequenced and analysed. Using our approach, we revealed 59 nearly full-length 16S rRNA genes sharing ≥ 97% identity with the targeted OTUs and representing 35% of all the retrieved 16S rDNA genes. We highlighted high bacterial diversity hidden behind each OTU and revealed novel taxa. In total, we identified 1 new family belonging to the Clostridiales order, 39 new genera and 52 new species. From each OTU, the revealed 16S rDNA full-length sequences could be highly distant from each other with similarities down to 85%, underlying the poor link between OTU, species and their putative functions. Using a genome mining strategy, we found bacteria related to the novel 16S sequences that are potentially involved in polyphenol degradation. Overall, our results suggest that the human gut microbiota could be much more diverse than previously thought

Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

Abstract Background Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs’ growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice. Results Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning. Conclusions The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants

Changes in Digestive Microbiota, Rumen Fermentations and Oxidative Stress around Parturition Are Alleviated by Live Yeast Feed Supplementation to Gestating Ewes

International audienceBackground: In ruminants, physiological and nutritional changes occur peripartum. We investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected around parturition and what could be the impact of a daily supplementation of a live yeast additive in late gestating ewes. Methods: Rumen, feces and blood samples were collected from 2 groups of 14 ewes one month and a few days before parturition, and 2 weeks postpartum. Results: In the control ewes close to parturition, slight changes in the ruminal microbiota were observed, with a decrease in the concentration F. succinogenes and in the relative abundance of the Fibrobacteres phylum. Moreover, a decrease in the alpha-diversity of the bacterial community and a reduced relative abundance of the Fibrobacteres phylum were observed in their feces. Control ewes were prone to oxidative stress, as shown by an increase in malondialdehyde (MDA) concentration, a lower total antioxidant status, and higher glutathione peroxidase (GPx) activity in the blood. In the yeast supplemented ewes, most of the microbial changes observed in the control group were alleviated. An increase in GPx activity, and a significant decrease in MDA concentration were measured. Conclusions: The live yeast used in this study could stabilize gastro-intestinal microbiota and reduce oxidative stress close to parturitio

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Additional file 1 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

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Additional file 3 of Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

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