Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits

This study aimed to evaluate how the feeding strategy of rabbit kits at the onset of solid feed intake could affect ecological diversity and co-occurrence patterns of the cecal bacterial community. From birth to 18 days of age kits were exclusively milk-fed, and between 18 and 35 days the young rabbits also had access to solid feed. After weaning at (35 days), young rabbits were exclusively fed solid feed. Three experimental feeds were used: a high concentrate diet [H: 10.16 MJ digestible energy (DE)/kg and 15.3% crude protein (CP)], a low concentrate diet (L: 9.33 MJ DE/kg and 14.7% CP) and a reproductive female diet (R: 10.57 MJ DE/kg and 17.3% CP). The rabbit kits (n = 357) were divided into three groups, differing by the diet received during two periods: from 18 to 28 and from 28 to 49 days of age. In the groups LL and HH, rabbit kits were fed L or H diets, respectively, during both periods. Kits in the group RL received feeds R and L from 18 to 28 and 28 to 49 days of age, respectively. Cecal bacterial communities of 10 rabbits per group were carried out at 18, 28, 35, 43 and 49 days of age by MiSeq Illumina sequencing 16S rRNA encoding genes. Between 18 and 28 days of age, solid feed intake was higher in the group RL compared to the other two groups (+24%; P < 0.01). Overall, 13.4% of the OTUs detected were present in the cecal ecosystem from 18 to 49 days old, whereas 17.4% were acquired with the onset of solid feeding and kept from 28 days on. Exclusive milk consumption constrains the bacterial community toward a similar structure but high phylogenetic beta-diversity. Introduction of solid feed induced a sharp change of microbial community structure and decreased phylogenetic diversity. A strong relationship in bacterial community network occurred only from 43 days on. Our feeding strategy at the onset of solid feed ingestion exhibited only a moderate effect on the microbial community structure (P = 0.072), although the LL group seemed to reach faster maturity compared to the two other groups

Ability of physico-chemical measurements to discriminate rabbit meat from three different productive processes

International audienceBACKGROUND: To fulfil consumers’ requirements for food traceability, it is necessary to have effective tools to differentiate food products according to their origin. The aim of the study was to identify a limited number of physico-chemical measurements that could differentiate rabbit meat from three different rearing systems: standard production system or a high quality norm system or a very low growth breeding system. RESULTS: The stepwise linear discriminant analysis (LDA) provided 14 physico-chemical variables, then combined into two discriminant factors. Most of them (n = 8) were related to bone traits, and especially (n = 5) to mechanical femur assessments. Mechanical characteristics of meat were also relevant in this analysis. Decision tree analysis (DTA) selected two variables only (femur stiffness, and ratio of femur weight to chilled carcass weight) to discriminate the three groups. A total of 96% and 90% of rabbits were correctly assigned to their original group according to LDA and DTA, respectively. CONCLUSION: This work demonstrated that simple physico-chemical traits recorded in carcasses and meat were efficient to discriminate rabbits from three different rearing systems using LDA or DTA procedures. These systems could have further implications for future traceability of breeding origin

Influence de l'ingestion précoce ou du ratio protéine amidon sur les performances de croissance et le microbiote caecal chez le lapin

L’objectif de notre étude était de stimuler l’ingestion solide du lapereau allaité en modulant l’âge d’accès à l’aliment solide granulé (8j vs 18j) ou le ratio protéine/amidon de l’aliment (j18-j42). Dans le lot 1, les lapereaux allaités avaient accès, dès 8j dans le nid, à l’aliment P+A- (protéine digestible 13,5%; amidon 6,8%) ; dans le lot 2, les lapereaux avaient accès au même aliment mais à partir de 18j seulement. Pour le lot 3, les lapereaux étaient nourris à partir de 18 j avec un aliment P-A+ (protéine digestible 9,9%, amidon 8,9%) (17 portées par groupe). Au sevrage (35 j), les lapereaux ont été rationnés à 80% de l’ingestion volontaire. L’état sanitaire a été contrôlé quotidiennement, la production laitière de la lapine a été mesurée 2 fois par semaine, le poids vif et la consommation d'aliment des lapereaux, dans le nid entre 8 et 18j, puis dans la mangeoire (18-35j) ont été mesurés. Le poids relatif des organes, les paramètres fermentaires et la composition du microbiote caecal ainsi que les concentrations d’IgA fécale et d’IgG plasmatique ont été déterminés à 18 et 42 j (n=10 par groupe). Le taux de mortalité n’était pas différent entre les lots (2,8% entre 8 et 35 j ; et 0,4 % entre 35 et 70 j). L’ingestion précoce de granulé (0,75 granulé/lapin/jour 8 et 18j) n’a pas eu d’incidence sur la croissance jusqu’au sevrage des lapereaux. Sur la période 35 – 70 j, le lot 3 présente la croissance la plus élevée (39,5±0,4 g/j), la plus faible est observée pour le lot 2 (37,6 ± 0,4 g/j) tandis que le lot 1 présente une valeur intermédiaire (38,8±0,5 g/j). L’alimentation précoce affecte l’abondance relative de 10 et 20 espèces bactériennes (dont 16 appartiennent à la famille des Ruminococcaceae) à 18 et 42 j respectivement. A 42 j le ratio protéine/amidon de l’aliment modifie l’abondance relative de 45 espèces bactériennes (dont 20 appartiennent à la famille des Lachnospiraceae). L’ingestion précoce ou la qualité de l’aliment impacte modérément le microbiote caecal. Les répercussions sur la maturation du système immunitaire sont en cours d’analyse.The objective of our study was to stimulate the solid intake of suckling rabbit by modulating the age of access to pelleted solid food (8 vs 18d) or protein / starch ratio of the feed from 18d. In group 1, suckling rabbits had access to feed P+A- (8.5% digestible protein, starch 6.8%) as early as 8 d. in the nest. In group 2, the rabbits had access to the same food but only from 18 d. For group 3, rabbits were fed from 18 d with a P-A+ feed (digestible protein: 9.9%, starch 8.9%) (17 litters per group). At weaning (35 d), the rabbits were fed at 80% of the voluntary intake. Health status was monitored daily, milk production was measured twice a week, young rabbits live weight and feed consumption in the nest between 8 and 18 d, and then in the feeder (18 - 35d) were measured. The relative organ weight, fermentation parameters and composition of the caecal microbiota, concentrations of fecal IgA and plasma IgG were determined at 18 and 42 d (n = 10 per group). The mortality rate was not different between the groups (2.8% between 8 and 35 days, and 0.4% between 35 and 70 d). In the nest between 8 and 18 days pellet consumption was 0.75 pellet / rabbit / day. This early pellet consumption did not affect the rabbit growth until weaning. During the period 35-70 days, group 3 had the highest growth (39.5 ± 0.4 g/d), the lowest was observed for lot 2 (37.6 ± 0.4 g/d) While group 1 has an intermediate value (38.8 ± 0.5 g/d). Early feeding affects the relative abundance of 10 and 20 bacterial species (16 belonging to the Ruminococcaceae family) at 18 and 42 d respectively. At 42 d the feed protein / starch ratio alters the relative abundance of 45 bacterial species (20 of which belong to the Lachnospiraceae family). Early ingestion or feed quality moderately influence the composition of the microbiota. The implications on immune system maturation are currently being analyzed

Genetic determinism of dairy sheep ruminal microbiota

The microbiota of herbivorous animals plays a central role in the nutrition of its host, directly affecting his health and his ability to produce. Very few publications reported results concerning the impact of host genetics on the composition of ruminal microbiota. Thus, we proposed to study the genetic determinism of bacterial relative abundances of sheep rumen microbiota. 369 dairy Lacaune ewes raised indoor at the INRA Experimental Farm of La Fage, had a sampling of their rumen fluid done. These ewes were adult animals, fed with a 93% hay-silage based diet and belonged to 4 different lines (lines divergently selected on somatic cells count or on milk persistency). Ruminal metagenome were sequenced using 16s rRNA gene with Illumina Miseq technology. Bioinformatics analysis of the microbiota sequences were implemented with FROGS pipeline to obtain relative abundances of bacteria and R Phyloseq package to estimate biodiversity indices. Heritability estimates of the square root of relative abundances were computed in single trait using the VCE 6.0 software. FROGS pipeline allowed clustering the 4,944,307 informative sequences into 2,135 OTUs, which represented 247 bacteria taxas (140 genera, 50 families, 31 orders, 17 classes and 9 phyla). Significant differences between lines were observed: 4 bacteria generas have abundancies differences according to CCS lines (Olsenella, Prevotella 1, Prevotellaceaea Ga6a1, Syntrophococcus with always higher values for CCS+) and 4 others according to PERS lines (Coprococcus 1, Olsenella, Succonivibrionaceae U2, Syntrophococcus). At the genera scale, heritabilities estimates ranged from 0.00 to 0.49 with a standard error of 0.11 on average: 22% of genera had heritabilities higher than 0.1, which is lower than Estellé et al. on Large White (50% genera with h2>0.1). The most heritable genera (h2>0.25) were Ruminococcaceae UCG002, Lachnospira, Atopobium and Oscillospira which also were taxa with low abundances

Genetic links between feeding behavior and microbiota of Romane lambs

The aim of this study was to explore the ruminal microbiota of lambs genetically extreme for their feeding speed when eating concentrates. From a database of 1001 lambs phenotyped for their feeding behavior, we estimated breeding values for their feeding speed at the visit level, and selected amongst 77 lambs phenotyped, 20 extreme lambs : 10 “high feeding speed” lambs with an average value of 57.8 g/min and 10 “low feeding speed” lambs with an average value of 26.8 g/min. The ruminal microbiota of these animals was profiled – after a first period of concentrates diets then a second period of forage – based diets - using 16S rRNA gene sequencing were analysed with FROGS software leading to 228 OTUs with taxonomic affiliation and characterized by their relative abundances. Microbiota differences was mainly due to the type of feed ingested-with higher bacteroidetes abundances when lambs ingested concentrates-since 211 of the 228 OTUs have abundance differences with respect of diet. Only 6 OTUs were significantly different according to feeding speed of animal and concerned only minor bacterial taxa such as bacteroidales S24_7 group family and the genus Syntrophococcus, Lachnosporacaeae NC2004 group, Ruminiclostridium and Eubacterium cellulosolvens group