Sylvie Combes

StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profiles

Molecular fingerprint methods are widely used to compare microbial communities in various habitats. The free program StatFingerprints can import, process, and display fingerprint profiles and perform numerous statistical analyses on them, and also estimate diversity indexes. StatFingerprints works with the free program R, providing an environment for statistical computing and graphics. No programming knowledge is required to use StatFingerprints, thanks to its friendly graphical user interface. StatFingerprints is useful for analysing the effect of a controlled factor on the microbial community and for establishing the relationships between the microbial community and the parameters of its environment. Multivariate analyses include ordination, clustering methods and hypothesis‐driven tests like 50–50 multivariate analysis of variance, analysis of similarity or similarity percentage procedure and the program offers the possibility of plotting ordinations as a three‐dimensional display.

Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential

Establishment of ruminal bacterial community in dairy calves.

Feed restriction strategy in the growing rabbit. 2. Impact on digestive health, growth and carcass characteristics

A field enquiry mentioned the potential positive impact of a feed restriction on the health of young rabbits, but no objective information relates the intake to digestive health. The effects of a post-weaning feed restriction strategy were thus studied on digestive health and growth and carcass parameters of the growing rabbit, using a monofactorial design that produces a quantitative linear reduction of the intake, from ad libitum (AL group) to 80%, 70% and 60% of AL. The study was performed simultaneously in six experimental sites, on 1984 growing rabbits (496 per treatment) collectively caged from weaning (34 to 38 days of age, depending on the site) to slaughter (68 to 72 days). The feeding programme was applied as followed: restriction during 21 days after weaning, and then ad libitum till slaughter. During the feed restriction period the growth rate was linearly reduced with the restriction level, by 0.5 g/day for each percent of intake reduction. When returning to ad libitum intake (after 54 days old) a compensatory growth and a higher feed efficiency occurred. Therefore, the impact of the feeding programme on the slaughter weight (SW) was significant (-4.5 g/% of restriction), but relatively moderate: the weight loss of the more-restricted rabbits (60%) reached 7.7% (-200 g) compared to the AL group. Over the whole fattening period, the feed restriction reduced linearly and significantly the feed conversion (FC) (-0.0077 unit/% of restriction). Carcass traits were little affected by the feeding programme, except for a slightly lower decrease of the dressing percentage (mean: 1.2 units between AL and the three restricted groups). On the six experimental sites, mortality and morbidity were always caused by acute digestive disorders, namely diarrhoea and/or caecal impaction. Independent of the treatment, the mortality rate strongly varied according to the site (between 7% and 18% from weaning to 54 days and for the AL group). During feed restriction, the mortality was significantly lower from a restriction threshold of 80% (meanly: -9% compared to AL). The morbidity was also significantly reduced (-6%) for the two most restricted groups (70% and 60%). The favourable effect of a lower intake on health did not persist after returning to ad libitum intake (54 days to slaughter), since mortality and morbidity were not significantly different among the treatments. Such a feeding strategy thus represents a double benefit in terms of feed costs and lower losses of young rabbits.

Potential core species and satellite species in the bacterial community within the rabbit caecum

A bacteria library was constructed from the caecum of a rabbit maintained under standard conditions. The complete gene 16S rRNA gene was sequenced. The 228 clones obtained were distributed in 70 operational taxonomic units (OTUs). The large majority of the OTUs were composed of one or two clones and seven OTUs contained half of the sequences. Fourteen sequences had high similarity to the sequence already registered in databases (threshold of 97%). Only one of these sequences has been identified as Variovorax sp. (99% identity). Units were distributed mainly (94%) in the Firmicutes phylum. Three sequences were related to Bacteroidetes. Nine clusters were defined in the phylogenic tree. A great diversity of caecal bacteria of the rabbit was shown. Half of the sequences generated in this library were distributed in the phylogenetic tree near the sequences characterized previously in rabbit caecum (potential core species), and the other half of the sequences were well separated (satellite species).

Molecular analysis of the bacterial community in digestive tract of rabbit.

This work aimed to study the stability over time of the bacterial community in caecum and faeces of the rabbit (diversity index and structure) without experimental disturbance and to evaluate its relationships with environmental parameters. Soft and hard faeces of 14 rabbits were sampled for 5 weeks while caecal content was sampled on the 3rd week (by surgery) and the 5th week (at slaughter). Bacterial communities were assessed by studying CE-SSCP profiles of 16S rRNA genes fragments. Redox potential, pH, NH3-N concentration and volatile fatty acid concentrations were measured in the caecum. Data showed that bacterial communities of soft and hard faeces barely differed from that of the caecum (ANOSIM-R<0.25; p<0.05). Without disturbance, the bacterial communities of faeces were stable over time (ANOSIM-R<0.25; p<0.001). However, the bacterial communities of caecum and faeces were affected by the surgery (ANOSIM-R=0.22-0.33; p<0.001). The caecal content was an acidic (pH=6.03+/-0.33) and an anaerobic environment (redox potential=-160+/-43 mV). Only the redox potential was correlated with the diversity index of the bacterial community of the caecum (R(2)=0.35; p<0.05) and no environmental parameters were correlated to its structure.

Postnatal development of the rabbit caecal microbiota composition and activity

This study describes the development of the rabbit caecum microbiota and its metabolic activities from the neonatal (day 2) until the subadult period (day 70). The caecal microbiota was analysed using 16S rRNA gene approaches coupled with capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) and qPCR. At day 2, rabbits harboured population levels up to 8.4, 7.2 and 7.4 log(10) copy number g(-1) full caecum of the total bacteria, Bacteroides-Prevotella and Firmicutes groups, respectively. These populations reached their maximum levels from day 14 for Firmicutes groups (10.8 log(10) copy number g(-1) caecal content) and day 21 (11.4 and 10.7 log(10) copy number g(-1) caecal content of the total bacteria and the Bacteroides-Prevotella group, respectively). The archaeal population could be detected only from day 7 onwards (5.5 log(10) copy number g(-1) full caecum) and reached its maximum level at day 35 (7.4 log(10) copy number g(-1) caecal content). Similarity analysis, diversity calculation and quantitative evaluation of the stability of bacterial community CE-SSCP profiles provided some evidence that the caecal microbiota develops progressively from a simple and unstable community after birth into a complex and climax community in subadult rabbits. Meanwhile, the microbial activity evolved with the progressive decrease of the propionate/butyrate ratio towards a rabbit-specific value <1.

Divergent selection on 63-day body weight in the rabbit: response on growth, carcass and muscle traits

The effects of selection for growth rate on weights and qualitative carcass and muscle traits were assessed by comparing two lines selected for live body weight at 63 days of age and a cryopreserved control population raised contemporaneously with generation 5 selected rabbits. The animals were divergently selected for five generations for either a high (H line) or a low (L line) body weight, based on their BLUP breeding value. Heritability (h2) was 0.22 for 63-d body weight (N = 4754). Growth performance and quantitative carcass traits in the C group were intermediate between the H and L lines (N = 390). Perirenal fat proportion (h2 = 0.64) and dressing out percentage (h2 = 0.55) ranked in the order L < H = C (from high to low). The weight and cross-sectional area of the Semitendinosus muscle, and the mean diameter of the constitutive myofibres were reduced in the L line only (N = 140). In the Longissimus muscle (N = 180), the ultimate pH (h2 = 0.16) and the maximum shear force reached in the Warner-Braztler test (h2 = 0.57) were slightly modified by selection.

Feed intake limitation strategies for the growing rabbit: effect on feeding behaviour, welfare, performance, digestive physiology and health: a review

This review aims to present the different effects produced by a post-weaning intake limitation strategy on the growing rabbit, now largely used by French professional rabbit breeders. Although a quantitative feed restriction leads to slower growth, feed conversion (FC) is improved, particularly when the rabbits are again fed freely, as compensatory growth occurs. This better FC or the healthy rabbit is because of better digestion resulting from slower passage through the intestine, whereas the digestive physiology is slightly modified (morphometry of the intestinal mucosa, fermentation pattern, microbiota). Meat quality and carcass characteristics are not greatly affected by feed restriction, except for a lower dressing-out percentage. One of the main advantages of limiting post-weaning intake of the rabbit is to reduce the mortality and morbidity rate due to digestive disorders (particularly epizootic rabbit enteropathy syndrome). The consequences for animal welfare are debatable, as feed restriction probably leads to hunger, but it reduces the incidence of digestive troubles after weaning. However, the growing rabbit adapts very well to an intake limitation strategy, without any aggressive behaviour for congener. In conclusion, restriction strategies could improve profitability of rabbit breeding, but they should be adapted to any specific breeding situation, according to the national market, feed prices, etc.

Spatial and temporal variations of the bacterial community in the bovine digestive tract.

Aims:  Improved knowledge of the bacterial community of the digestive tract is required to enhance the efficiency of digestion in herbivores. This work aimed to study spatial and temporal variations of the bacterial communities in the bovine digestive tract and their correlation with gut environmental parameters.

Starch and oil in the donor cow diet and starch in substrate differently affect the in vitro ruminal biohydrogenation of linoleic and linolenic acids

Trans isomers of fatty acids exhibit different health properties. Among them, trans-10,cis-12 conjugated linoleic acid has negative effects on milk fat production and can affect human health. A shift from the trans-11 to the trans-10 pathway of biohydrogenation (BH) can occur in the rumen of dairy cows receiving high-concentrate diets, especially when the diet is supplemented with highly unsaturated fat sources. The differences of BH patterns between linoleic acid (LeA) and linolenic acid (LnA) in such ruminal conditions remain unknown; thus, the aim of this work was to investigate in vitro the effects of starch and sunflower oil in the diet of the donor cows and starch level in the incubates on the BH patterns and efficiencies of LeA and LnA. The design was a 4 × 4 Latin square design with 4 cows, 4 periods, and 4 diets with combinations of 21 or 34% starch and 0 or 5% sunflower oil. The rumen content of each cow during each period was incubated with 4 substrates, combining 2 starch levels and either LeA or LnA addition. Capillary electrophoresis single-strand conformation polymorphism of incubates showed that dietary starch decreased the diversity of the bacterial community and the high-starch plus oil diet modified its structure. High-starch diets poorly affected isomerization and first reduction of LeA and LnA, but decreased the efficiencies of trans-11,cis-15-C18:2 and trans C18:1 reduction. Dietary sunflower oil increased the efficiency of LeA isomerization but decreased the efficiency of trans C18:1 reduction. An interaction between dietary starch and dietary oil resulted in the highest trans-10 isomers production in incubates when the donor cow received the high-starch plus oil diet. The partition between trans-10 and trans-11 isomers was also affected by an interaction between starch level and the fatty acid added to the incubates, showing that the trans-10 shift only occurred with LeA, whereas LnA was mainly hydrogenated via the more usual trans-11 pathway, whatever the starch level in the substrate, although the bacterial communities were not different between LeA and LnA incubates. In LeA incubates, trans-10 isomer production was significantly related to the structure of the bacterial community.