Biology subjects

Zemb, O.

Publications and source records attributed to Zemb, O..

6 recordsLinked to original sources

bioRxiv2026

Study of holobiont resilience following a break in symbiotic transmission in two rabbit lines selected for feed efficiency

This study was carried out on two rabbit lines, each selected for a feed efficiency criterion (growth on restricted feed for the AlimR line or residual consumption on an adlibitum diet for the ConsR line), introduced into a facility by adoption of newborn kits by SPF (specific pathogen free) females. Following this break in symbiotic transmission, fecal samples from females were used to study the microbiota composition of the two lines over seven generations (17 females per line and per generation). The proportion of Firmicutes was significantly higher in the AlimR line than in the ConsR line (82.22% vs 78.21%, p<0.0001). Conversely, the proportion of Bacteroidota was significantly higher in the ConsR line than in the AlimR line (20.38% vs 16.50%, p<0.0001). The effect of generation was also significant for the abundance of Firmicutes and Bacteroidota (p=0.0009 and p<0.0001, respectively). The Shannon diversity index was significantly higher in the AlimR line than in the ConsR line (5.23 vs 5.14, p=0.02). The effect of generation was also significant for the Shannon index (p=0.003). Finally, a discriminant principal component analysis of the microbiota composition allowed us to distinguish both the two lines and the generations, in particular the 11th selected generation (animals adopted by SPF females) and the 18th generation.

microbiology↗

bioRxiv2024

Genetic selection for residual feed intake impacts the functional redundancy of the gut microbiota in pigs during the growing-finishing period

BackgroundImproving feed efficiency is an unvarying goal in livestock production. The role of gut microbial communities in feed efficiency was investigated in two divergent pig lines selected for their residual feed intake (RFI), which is the difference between the observed feed consumption of an animal and that predicted for its maintenance and production requirements. Hence, RFI is a measure of net feed efficiency. ResultsBy sequencing the 16S rRNA genes from fecal samples, we found that the microbiota of low RFI pigs (LRFI; n=12) was significantly depleted in four operational taxonomic units (OTUs) belonging to Prevotella, Feacalibacterium and Lactobacillus genera by comparison to high RFI pigs (HRFI; n=11). Inferring KEGG orthologs from the 16S rRNA gene sequencing data showed that LRFI pigs have 20% more functional redundancy than HRFI pigs. The inferred orthologs held more discriminative power than the OTU approach, which might be inherently flawed if functionally equivalent OTUs compete for the same niche. ConclusionsGut microbiota of LRFI pigs had different microbial operational taxonomic units and a higher functional redundancy, which were more shared suggesting a role of the gut microbiota in the global feed efficiency according to Tax4Fun but this inference based on 16S data has to be verified in future work.

microbiology↗

bioRxiv2021

Genetic relationships between efficiency traits and gut microbiota traits in growing pigs fed a conventional or a high fiber diet

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices), and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera with less than 20% of zeros were retained for genetic analyses. Heritability (h2) of microbiota traits were similar between diets (from null to 0.38 {+/-} 0.12 in the CO diet and to 0.39 {+/-} 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h2 in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h2 significantly different from zero. Based on the genetic correlations between these genera and ADG, FE and DE traits, three groups of genera could be identified. A group of 29 genera was favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had correlations close to zero with production traits. However, genera favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.

genetics↗

bioRxiv2021

Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

microbiology↗

bioRxiv2020

Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets

The objective of this study was to analyze in piglets the impact of weaning on the production of metabolites by gut bacteria and to determine whether early life environment influences the functional maturation of the gut microbiota. Fecal metabolome and microbiome were analyzed in piglets raised in two separate maternity farms and mixed at weaning. In piglets from both maternity farms, the relative abundance of Lactobacillus and of the predicted function "Fucose degradation" decreased after weaning while the relative abundance of Ruminococcus 2 and of the predicted function "Starch degradation" increased. In piglets from the first maternity farm, the relative concentration of biogenic amines and the relative abundance of Escherichi-Shigella decreased after weaning while the relative concentration of short chain fatty acids and the relative abundance of Christensenellaceae R-7 group and Ruminococcaceae UCG-002 increased. These changes were not observed at weaning in piglets from the second maternity farm probably because they already had high relative concentration of short chain fatty acids and higher relative abundance of Christensenellaceae R-7 group and Ruminococcaceae UCG-002 during the suckling period. In conclusion, the functional maturation of the microbiota at weaning is highly dependent on the maternal environment in piglets. ORIGINALITY - SIGNIFICANCE STATEMENTBacterial metabolites are key molecular intermediates between the gut microbiota and host cells. Our study in piglets reveals that the metabolic activity of the gut microbiota shifts at weaning, a key developmental period for intestinal and immune health. We also show that this functional maturation of the gut microbiota is strongly influenced by maternal environment. Thus, targeting early life environmental factors is a promising strategy to program health trough the production of beneficial bacterial metabolites at the suckling-to-weaning transition.

microbiology↗

bioRxiv2019

The fecal microbiota of piglets is influenced by the farming environment and is associated with piglet robustness at weaning

This study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal samples and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera were Prevotella, Faecalibacterium, Roseburia, and Lachnospira. They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding individual characteristics, piglets whose growth was less perturbed by weaning had more Bacteroidetes (P < 0.01) and less Proteobacteria (P < 0.001). In response to weaning, they showed a greater increase in Prevotella (P < 0.01), Coprococcus (P< 0.01) and Lachnospira (P < 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.

microbiology↗