Coprophagia in early life tunes expression of immune genes after weaning in rabbit ileum

Coprophagia by suckling rabbits, i.e. ingestion of feces from their mother, reduces mortality after weaning. We hypothesized that this beneficial effect of coprophagia is immune-mediated at the intestinal level. Therefore, this study investigated immune development after weaning by analyzing the ileal transcriptome at day 35 and 49 in rabbits with differential access to coprophagia in early life. Rabbit pups had access between day 1 and 15 to (i) no feces (NF) or (ii) feces from unrelated does (Foreign Feces, FF) or (iii) feces from unrelated does treated with antibiotics (FFab). 350 genes were differentially expressed between day 35 and day 49 in suckling rabbits with access to coprophagia. These genes coded for antimicrobial peptides, a mucin, cytokines and chemokines, pattern recognition receptors, proteins involved in immunoglobulin A secretion and in interferon signaling pathway. Strikingly, prevention of coprophagia or access to feces from antibiotic-treated does in early life blunted immune development between day 35 et 49 in the ileum of rabbits. Thus, coprophagia might be crucial for the maturation of intestinal immunity in rabbits and could explain why this behavior improves survival.

Effect of dietary supplementation with algae extracts on growth performance and caecal microbiota of broiler chickens

1. The objective of this study was to test the dose response of dietary supplementation with algae extracts rich in marine-sulphated polysaccharides (MSP1 and MSP2) on the growing performance, body composition at slaughter and caecal microbiota of broiler chickens.2. Male broiler Ross 308 chicks 1-d-old were distributed into eight groups, a control group (unsupplemented), four groups supplemented with increasing doses of algae extract MSP1 (40, 81, 121 and 162 g/ton feed) and three groups supplemented with increasing doses of algae extract MSP2 (40, 81 and 162 g/ton feed). Each group comprised six pens of 56 chickens.3. All chickens were reared under challenging conditions, i.e. high rearing density of 42 kg/m2, fed growing and finishing diets containing, palm oil, rye and high levels of wheat and subjected to short daily fasting periods. The growth performance was recorded during rearing. At 10, 22 and 31 d of age, 12 chickens per group were euthanised to collect the caecal contents and determine microbiota composition and short-chain fatty acid levels. At d 35, the quality of litter and the condition of feathers, footpads and tarsals were scored. At d 36, 7 chickens per pen were slaughtered under commercial conditions to determine carcass composition and breast meat quality (ultimate pH and colour).4. Algal extract MSP1 increased the weight of the caeca and butyrate concentration in the caeca at d 22 (p ≤ 0.05). It increased the ultimate pH of breast fillet measured after slaughter at d 36 (p ≤ 0.05). Moreover, the group receiving 162 g/t MSP1 had a more diverse microbiota at d22. However, algal extract MSP2 had negligible effect on the different measured parameters.

Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbial diversity of dairy calves from birth to weaning

In commercial dairy production systems, feeding calves once a day could be an alternative to reduce labor expenses. Several studies comparing once (OAD) versus twice (TAD) a day milk feeding systems have not evidenced differences in calf growth, rumen development, blood parameters or health scores, but impact on ruminal microbiota remains to be investigated. The objective of this study was to determine the effects of OAD or TAD on the establishment of the ruminal microbiota and its metabolic activity. Sixteen male calves (45.9 ± 5.7 kg at birth) were involved in the trial from birth to weaning (63 d). After the colostrum phase, 2 feeding programs based on a milk replacer were tested and calves were allocated to these programs on d 5. To study the establishment of the bacterial community, ruminal fluid was obtained from each calf one hour after the morning meal at 7 (d 7), 35 (d 35) and 63 (d 63) days of age. The ruminal metabolome was evaluated at a 7 d interval from d 1 to d 63. Ruminal microbiota and metabolite profiles were characterized by 16 S rRNA gene sequencing- and by H-NMR spectroscopy, respectively. Our results showed that feeding milk replacer once or twice a day did not change the ruminal microbiota and metabolites of dairy calves from birth to weaning. Microbial data showed that diversity and richness increased with age, suggesting a shift from an heterogeneous and less diverse community after birth (d 7) to a more diverse but homogeneous community at 35 and 63 d. These findings suggest that feeding milk once a day can be successfully applied to a calf feeding system without compromising microbial establishment and functions.

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 present in more than 20% of individuals 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 had abundances favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had abundances with correlations close to zero with production traits. However, genera abundances 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.

OligoSpecificitySystem: global matching efficiency calculation of oligonucleotide sets taking into account degeneracy and mismatch possibilities

Oligonucleotide sets are widely used in molecular biology to target a group of nucleic acid sequences using Polymerase Chain Reaction (PCR)-based technologies. Currently, the global matching efficiency of an oligonucleotide set is considered to be equal to the lower matching efficiency calculated for each oligonucleotide. However, sequences matching the limiting oligonucleotide did not always match the other oligonucleotide of the set, resulting in a biased evaluation of the matching efficiency. The OligoSpecificitySystem program avoid this bias by calculations of the real global matching efficiency of oligonucleotide sets. It can process all kinds of oligonucleotide sets, including the number of oligonucleotides, base pair degeneracy occurrences or mismatch occurrences.

Lactobacillus sakei modulates mule duck microbiota in ileum and ceca during overfeeding

The supplementation with Lactobacillus sakei as probiotic on the ileal and cecal microbiota of mule ducks during overfeeding was investigated using high-throughput 16S rRNA gene-based pyrosequencing and real-time PCR. The ducks were overfed with or without L. sakei for 12 d with 56% ground corn and 42% whole corn. Samples were collected before the overfeeding period (at 12 wk), at 13 wk (meal 12 of overfeeding), and at 14 wk (meal 24), 3 h postfeeding. Whatever the digestive segment and the level of intake, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla in the bacterial community of mule ducks (at least 90%). Before overfeeding, ileal samples were dominated by Clostridia, Bacteroidia, and Gammaproteobacteria (80% and up), and cecal samples by Bacteroidia and Clostridia (around 85%). The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding increased the relative abundance of Firmicutes and especially the Lactobacillus group in ileal samples. Nonmetric multidimensional scaling profiles separated the bacterial communities with respect to overfeeding only in cecal samples. Richness indicators decreased after L. sakei has been added at mid-overfeeding only in the ileum. In the ceca, the decrease of these indexes only occurred at the end of overfeeding. The addition of L. sakei triggers major changes in the ileum, whereas the ceca are not affected. Lactobacillus sakei decreased the relative abundance of Bacteroides at mid-overfeeding and the relative abundance of Enterobacteria at the end of overfeeding in the ileum.

Coprophagous behavior of rabbit pups affects implantation of cecal microbiota and health status

During the first few weeks after delivery, female rabbits excrete fecal pellets, which are ingested by their pups. We hypothesized that maternal excretion of hard fecal pellets and the coprophagous behavior of their pups were involved in cecal microbiota implantation. Four groups were compared: in 1 group (FM), pups had free access to maternal fecal pellets; in a second group, ingestion of feces was prevented (NF); and in 2 additional groups, pups had access only to fecal pellets excreted by foreign females receiving either no antibiotic (FF) or tiamulin and tetracycline (FFab). A total of 109 litters in 3 batches were used to quantify excretion and ingestion of feces and mortality. Bacterial composition was assessed by 454 pyrosequencing of the V3 to V4 region of 16S RNA genes and fermentative measurements in 128 rabbits of 1 batch at age 14, 35, 49, and 80 d with 8 rabbits per group for each age with 2 rabbits per litter. The number of fecal pellets excreted by does from 2 to 20 d after delivery ranged widely, but was similar among groups (16.1 ± 12.6 fecal pellets/doe). The excretion peaked during the first 6 d after delivery. Foreign fecal ingestion (FF and FFab groups) was 3 times greater (P < 0.001) than ingestion of maternal feces (9.9 ± 7.8). Ingestion of feces in the FF group was greater than in the FFab groups (35.6 ± 9.3 vs. 29.5 ± 9.7; P < 0.05). Compared with the FM group, ingestion of feces in the FF and FFab groups began later (6 to 7 d vs. 2 to 3 d after birth) and peaked at 14 to 17 d (4.0 ± 1.8 hard fecal pellets·litter(-1) · d(-1)) and 13 to 15 d (3.5 ± 1.7 hard fecal pellets litter(-1) d(-1)), respectively. During the 36 to 49 d period, the FF and NF groups exhibited the least (2.8%) and greatest (9.5%) mortality, respectively (P = 0.03). At age 14 d, the cecal bacterial community was dominated by Bacteroidetes phyla (63.3 ± 15.1%), Bacteroidaceae family (36.0 ± 18.8%), and Bacteriodes genus (36.0 ± 2.3%). With increasing age, Firmicutes phyla, Lachnospiraceae, and Ruminococcaceae families became the dominant taxa (92.0 ± 4.7, 44.0 ± 13.7, 37.9 ± 11.6% at age 80 d, respectively). Impairment of fecal ingestion delayed this ecological succession, with greater and lower relative abundance of Bacteroidaceae and Ruminococcaceae, respectively, than in the other 3 groups at age 35 d (P < 0.10). In conclusion, although excretion of hard fecal pellets by does ranged widely, the coprophagous behavior of their pups affected the implantation of cecal bacterial microbiota.

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

AIM

Establishment of ruminal bacterial community in dairy calves.

METHODS AND RESULTS

Rumen bacterial community was analysed on 6 calves bred according to commercial practices from day one to weaning at day 83 of age, using 454 16S rRNA-based pyrosequencing. Samples taken at day 1 did not produce amplicons. Analysis of data revealed a three-stage implantation process with a progressive but important shift of composition. At day 2, the bacterial community was mainly composed of Proteobacteria (70%) and Bacteroidetes (14%), and Pasteurellaceae was the dominant family (58%). The bacterial community abruptly changed between days 2 and 3, and until day 12, dominant genera were Bacteroides (21%), Prevotella (11%), Fusobacterium (5%) and Streptococcus (4%). From 15 to 83 days, when solid food intake rapidly increased, Prevotella became dominant (42%) and many genera strongly decreased or were no longer detected. A limited number of bacteria genera correlated with feed intake, rumen volatile fatty acids and enzymatic activities.

CONCLUSION

The ruminal bacterial community is established before intake of solid food, but solid food arrival in turn shapes this community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides insight into the establishment of calves' rumen bacterial community and suggests a strong effect of diet.

Effects of stocking density on the growth performance and digestive microbiota of broiler chickens

Increased stocking densities are frequently reported to depress chicken growth performance, but the mechanisms behind this are not fully understood. This study was conducted to investigate the effects of stocking density on growth performance and digestive microbiota, known to be sensitive to environmental factors. Chickens were reared at 2 stocking densities, 12 or 17 birds/m(2). Growth performance was recorded between d 1 and 39, and litter was scored for quality on d 25, 31, and 37. Digestive microbiota was analyzed along the digestive tract (crop, ileum, ceca) of 3- and 6-wk-old chickens by using 2 molecular approaches: a qualitative method (fingerprinting by temporal temperature gradient gel electrophoresis) and a quantitative method (real-time PCR). An increase in stocking density was found to negatively affect the feed conversion ratio (+3.1%) and depress the daily BW gain of broilers (-5.5%) during the period from d 32 to 39 (P ≤ 0.05). Litter quality was reduced with the high stocking density as early as d 25. At 3 wk of age, stocking density strongly affected the fingerprint profiles of the bacterial community, with the highest modifications observed in the crop and ceca (R analysis of similarity = 0.77 and 0.69, respectively, P ≤ 0.05). At 6 wk of age, significant differences in the fingerprint profiles between the stocking densities appeared in the crop and ceca (R analysis of similarity = 0.52 and 0.27, respectively, P ≤ 0.05). The abundance of bacterial groups targeted by real-time PCR was affected by stocking density, but only to a limited extent. Because digestive microbiota may have consequences on the physiology of the digestive tract, its modification by an increase in stocking density may be involved in the reduced growth performance of the bird.

Changes over time in the bacterial communities associated with fluid and food particles and the ruminal parameters in the bovine rumen before and after a dietary change

This work aimed to study the changes over time in the bacterial communities associated with the fluid and food particle fractions of the cow rumen following a change in diet. Four cannulated cows were fed a hay-based diet for 21 days and were then switched to a corn-silage-based diet for 33 days. The bacterial communities were regularly characterized by capillary electrophoresis - single-strand conformation polymorphism (CE-SSCP) and qPCR, and the main ruminal parameters were determined. The dietary change led to slight reductions in the diversity index, bacterial concentration, pH, and NH(3)-N concentration, and to an increase in the redox potential and volatile fatty acid concentrations. CE-SSCP profiles were not significantly affected by the dietary change but did change over time, with frequent fluctuations in both fluid and food particle fractions before and after the dietary change. The food particle fraction had a higher diversity index of bacterial community (+1.2 points, P < 0.001) and slightly more total bacteria than the fluid fraction of the rumen.