Epizootic Rabbit Enteropathy (ERE) is a disease of unknown aetiology that mainly affects postweaning animals. Caecotrophs from animals in a farm affected by ERE were analysed to identify changes in the microbiological profile of growing rabbits. Does and kits at weaning (28 d) and the same rabbits ten days later (38 d) were used for a comparison using Roche 454 pyrosequencing of hypervariable V3-V5 regions of the 16S rRNA genes. The caecal bacterial community was dominated by the Firmicutes phylum (about 80%), followed by Bacteroidetes (15%), although relative abundances changed according to animal age (among does and kits at 28 and 38 d) and health status (affected or not by ERE). Two dominant families were classified within the Firmicutes phylum: Ruminococcaceae and Lachnospiraceae (50 and 20% of the sequences, respectively). In kits affected by ERE, relative abundance of Ruminococcus and Bacteroides genera decreased and increased, respectively, compared to healthy kits at the same age (28 and 38 d). The principal coordinate analysis plot revealed that kits at 28 d of age cluster together and apart from the does and the healthy 38-d rabbit groups. When only growing rabbits are considered, kits that showed symptoms of ERE clustered separately. Results suggest a different caecal bacterial community of rabbits affected by ERE. These findings highlight the need to identify different stages of the disease.

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AbstrAct:The effect of neutral detergent fibre (NDF) and neutral detergent soluble fibre (NDSF) on in vivo faecal digestibility and caecal fermentation pattern was studied in growing rabbits, in 4 diets formulated according to 2 levels of NDF, 370 (LI) and 450 (HI) g/kg, and 2 levels of NDSF, 150 (LS) and 180 (HS) g/ kg in substitution of starch, in a 2×2 factorial structure. Twenty four New Zealand White rabbits weaned at 28 d (630±80.2 g weight) were allocated to digestibility cages from 42 to 49 d of age to determine apparent faecal digestibility of each diet (n=6). Urine was collected for determination of purine derivatives (PD). Once the digestibility trial finished, rabbits were fitted with PVC neck collars for 24 h total caecotrophe collection. After 1 d of recovery, animals were slaughtered and caecal contents were used as inocula for 18 h in vitro gas production and caecal degradation (ivDMcD) study, using an HCl-pepsin and pancreatin pre-digested substrate. Diet digestibility was also determined by the in vitro three-step enzymatic procedure. There were no effects of the NDF×NDSF interaction for any digestibility parameter (P>0.10). Both dry matter and organic matter digestibility (DMd and OMd) decreased from 0.518 to 0.442 and from 0.526 to 0.447, respectively, with the increase of NDF (P<0.001), but were unaffected by the NDSF level (P>0.10). In contrast, NDF digestibility (NDFd) and ivDMcD did not respond to NDF (P>0.10) but increased from 0.156 to 0.200 and 0.141 to 0.210 with the proportion of NDSF (P<0.01). Weight of caecal contents increased with both NDF (P<0.001) and NDSF content (P<0.01). However, total production of caecotrophes increased from 20.1 to 25.5 g DM/d with NDF (P<0.05), but was not affected by NDSF. The crude protein (CP) proportion in caecotrophes decreased with NDF (P<0.001) and increased with NDSF level (P<0.01), and total CP recycled as caecotrophes tended (P=0.093) to be higher in HS diets, being unaffected by the dietary level of NDF. Diets rich in NDSF rendered higher gas volumes (P<0.001) than those with LS from 2 to 18 h incubation, whereas inclusion of high proportions of NDF reduced gas volume (P<0.01). Results indicate that NDF reduces faecal digestibility, whereas NDSF promotes better conditions for caecal fermentation.

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A proportion of dietary starch reaches the hindgut, being fermented there. The characteristics of in vitro caecal fermentation and microbial community in pigs given different sources of starch were studied. Twenty-four Duroc × (Landrace × Large White) gilts given diets based on barley (B), broken rice (R), maize (M) or peas (P) (n = 6) for five weeks were slaughtered with 93.6 ± 6.41 kg. No differences (p > 0.10) were recorded in caecal pH, total short chain fatty acid (SCFA) and total bacterial concentration, nor in in vitro gas production from caecal contents, indicating the lack of a quantitative dietary effect on caecal environment. This could be partly due to the length of fasting time before slaughter (around 10 h). Molar SCFA proportions did not differ among diets; however, relative proportion of Lactobacillus sobrius/amylovorus as the species-type in starch digestion in hindgut of pigs, was highest with P diet (p = 0.010), and gas production from potato starch as substrate with P diet was highest at 2 h incubation (p = 0.012), and higher than B and R diets at 4 (p = 0.055) and 6 (p = 0.10) h incubation. Caecal bacterial biodiversity was higher for M and R diets than for P and B diets (Shannon index, p = 0.003). Sources of resistant or slowly digestible starch such as peas promote a microbial community with a different profile and higher capacity to ferment the starch arriving to the organ than other sources which are mostly digested in the small gut.

SummaryMethane is the most important anthropogenic contribution to climate change after carbon dioxide and represents a loss of feed energy for the animal, mainly for herbivorous species. However, our knowledge about the ecology of Archaea, the microbial group responsible for methane synthesis in the gut, is very poor. Moreover, it is well known that hindgut fermentation differs from rumen fermentation. The composition of archaeal communities in fermentation compartments of goats and rabbits were investigated using DGGE to generate fingerprints of archaeal 16S rRNA gene. Ruminal contents and faeces from five Murciano-Granadina goats and caecal contents of five commercial White New Zealand rabbits were compared. Diversity profile of methanogenic archaea was carried out by PCR-DGGE. Quantification of methanogenic archaea and the abundance relative to bacteria was determined by real-time PCR. Methanogenic archaeal species were relatively constant across species. Dendrogram from DGGE of the methanogen community showed one cluster for goat samples with two sub-clusters by type of sample (ruminal and faeces). In a second cluster, samples from rabbit were grouped. No differences were found either in richness or Shannon index as diversity indexes. Although the primer sets used was developed to investigate rumen methanogenic archaeal community, primers specificity did not affect the assessment of rabbit methanogen community structure. Rumen content showed the highest number or methanogenic archaea (log 10 9.36), followed by faeces (log 10 8.52) and showing rabbit caecum the lower values (log 10 5.52). DGGE profile showed that pre-gastric and hindgut fermenters hold a very different methanogen community. Rabbits hold a microbial community of similar complexity than that in ruminants but less abundant, which agrees with the type of fermentation profile.

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