Robert J. Hughes

Highly variable microbiota development in the chicken gastrointestinal tract

Studies investigating the role that complex microbiotas associated with animals and humans play in health and wellbeing have been greatly facilitated by advances in DNA sequencing technology. Due to the still relatively high sequencing costs and the expense of establishing and running animal trials and collecting clinical samples, most of the studies reported in the literature are limited to a single trial and relatively small numbers of samples. Results from different laboratories, investigating similar trials and samples, have often produced quite different pictures of microbiota composition. This study investigated batch to batch variations in chicken cecal microbiota across three similar trials, represented by individually analysed samples from 207 birds. Very different microbiota profiles were found across the three flocks. The flocks also differed in the efficiency of nutrient use as indicated by feed conversion ratios. In addition, large variations in the microbiota of birds within a single trial were noted. It is postulated that the large variability in microbiota composition is due, at least in part, to the lack of colonisation of the chicks by maternally derived bacteria. The high hygiene levels maintained in modern commercial hatcheries, although effective in reducing the burden of specific diseases, may have the undesirable effect of causing highly variable bacterial colonization of the gut. Studies in humans and other animals have previously demonstrated large variations in microbiota composition when comparing individuals from different populations and from different environments but this study shows that even under carefully controlled conditions large variations in microbiota composition still occur.

Prebiotics Modulate Immune Responses in the Gut-Associated Lymphoid Tissue of Chickens

The recent European Union ban on the prophylactic use of in-feed antibiotics has escalated the search for alternatives for use within the poultry industry. When evaluating the efficacy of potential antibiotic alternatives on bird health and productivity, it is important to analyze the competence of the immune cells in the gut-associated lymphoid tissue (GALT), because it is routinely involved in the surveillance of colonizing microbes as well as in interacting with the ingested feed antigens. Therefore, we studied the effect of the prebiotics mannan-oligosaccharide (MOS) and fructo-oligosaccharide (FOS) on the phenotypic and functional competence of immune cells in cecal tonsil (CT), which is a major GALT. Day-old Cobb 500 male broilers were randomized to 4 groups. Control chickens were fed the basal diet only. Chickens in experimental groups received 0.05 g/kg zinc bacitracin or 5 g/kg of either FOS or MOS in addition to basal diet. At the end of 25 d, our comparison of the experimental groups with controls revealed that the addition of prebiotics to diet resulted in a significant reduction in the proportion of B cells and in mitogen responsiveness of lymphocytes in CT. Furthermore, FOS treatment significantly enhanced the IgM and IgG antibody titers in plasma. These findings emphasize the need for the analyses of the gut immune function following treatment with novel feed additives. The knowledge obtained from such analyses may aid in understanding the mechanisms underlying the immune competence of the birds, which needs consideration when selecting and optimizing new feed additives instead of antibiotics for poultry production.

Influence of different litter materials on cecal microbiota colonization in broiler chickens.

A chicken growth study was conducted to determine if litter type influenced gut microbiota and performance in broilers. Seven bedding materials were investigated and included soft and hardwood sawdust, softwood shavings, shredded paper, chopped straw, rice hulls, and reused softwood shavings. Microbial profiling was done to investigate changes in cecal bacterial communities associated with litter material and age. Cecal microbiota were investigated at 14 and 28 d of age (n = 12 birds/litter material). At both ages, the cecal microbiota of chickens raised on reused litter was significantly (P < 0.05) different from that of chickens raised on any of the other litter materials, except softwood shavings at d 28. Cecal microbiota was also significantly different between birds raised on shredded paper and rice hulls at both ages. Age had a significant influence on cecal microbiota composition regardless of litter material. Similarity in cecal microbial communities among birds raised on the same litter treatment was greater at 28 d of age (29 to 40%) than at 14 d of age (25 to 32%). Bird performance on the different litter materials was measured by feed conversion ratio, live weight, and feed intake. Significant (P < 0.05) differences were detected in live weight at 14 d of age and feed intake at 14 and 28 d of age among birds (n = 160/treatment) raised on some of the different litter materials. However, no significant (P > 0.05) differences were observed in feed conversion ratio among birds raised on any of the 7 different litter materials at either 14 or 28 d of age. The type of litter material can influence colonization and development of cecal microbiota in chickens. Litter-induced changes in the gut microbiota may be partially responsible for some of the significant differences observed in early rates of growth; therefore, litter choice may have an important role in poultry gut health particularly in the absence of in-feed antibiotics.

Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed.

The microbiota of the gastrointestinal tract is a complex community of many different species of microorganisms, dominated by bacteria. This diverse population provides the host with an extensive array of enzymes and substrates which, together with the hosts metabolic capabilities, provides an extensive metabolome available for nutrient and energy collection. We investigated broiler chickens to determine whether the abundance of certain members of the microbiota was correlated with the relative ability to extract energy from a typical wheat soybean diet. A number of mostly uncultured phylotypes were identified that significantly differed in abundance between birds with high apparent metabolizable energy (AME), measured as the difference between energy consumed and energy excreted, and those with low AME. Among the phylotypes that were more prevalent in birds with high energy efficiency, most were closely associated with isolates of bacterial groups that are commonly recognized as producing enzymes that degrade cellulose and/or resistant starch. Phylotypes that were negatively correlated with performance were all unknown and uncultured, a significant number belonging to an unknown class of Firmicutes. The identification of bacterial phylotypes correlated with the efficiency of energy use opens up the possibility of harnessing these bacteria for the manipulation of the hosts ability to utilize energy. Increasing the ability to convert food to body weight is of interest to the agricultural industries, while the opposite is applicable in weight management and obesity control in humans.

Effect of food enzymes on utilisation of lupin carbohydrates by broilers

1. The effects of 3 commercial enzyme products on the nutritive value of 2 lupin species were investigated with the emphasis on changes in composition of non-starch polysaccharides (NSPs) along the digestive tract. Enzyme A contained primarily cellulase, β -glucanase and xylanase activities, enzyme B primarily hemicellulase, pentosanase and xylanase activities, and enzyme C primarily hemicellulase, pectinase and β -glucanase activities. 2. The enzymes were added to semi-purified diets based on sorghum and casein containing 35% whole seed lupins (Lupinus angustifolius cv Gungurru or Lupinus albus cv Kiev mutant). Control diets contained no lupins. 3. Food conversion ratio (FCR), excreta moisture content and apparent metabolisable energy (AME) were affected by lupin species but not by enzyme supplementation. 4. In diets with L. angustifolius, enzyme C significantly increased digesta viscosity and increased the concentration of soluble NSPs in all sections of the intestine. 5. Digestibility of protein and NSPs in the ileum and microbial fermentation in the ileum and caeca were not affected by adding enzymes to diets containing L. angustifolius. 6. Enzyme addition to diets with L. albus did not affect digesta viscosity nor concentration of soluble NSPs but caused a significantly (P <0.05) reduced concentration of insoluble NSP in the ileum. 7. Enzyme addition to L. albus significantly (P <0.05) increased NSP digestibility in the ileum but had no effects on protein digestibility and fermentation in the ileum and caeca.

Bacteria within the Gastrointestinal Tract Microbiota Correlated with Improved Growth and Feed Conversion: Challenges Presented for the Identification of Performance Enhancing Probiotic Bacteria

Identification of bacteria associated with desirable productivity outcomes in animals may offer a direct approach to the identification of probiotic bacteria for use in animal production. We performed three controlled chicken trials (n = 96) to investigate caecal microbiota differences between the best and poorest performing birds using four performance measures; feed conversion ratio (FCR), utilization of energy from the feed measured as apparent metabolisable energy, gain rate (GR), and amount of feed eaten (FE). The shifts in microbiota composition associated with the performance measures were very different between the three trials. Analysis of the caecal microbiota revealed that the high and low FCR birds had significant differences in the abundance of some bacteria as demonstrated by shifts in microbiota alpha and beta diversity. Trials 1 and 2 showed significant overall community shifts, however, the microbial changes driving the difference between good and poor performers were very different. Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae families and genera Ruminococcus, Faecalibacterium and multiple lineages of genus Clostridium (from families Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae) were highly abundant in good FCR birds in Trial 1. Different microbiota was associated with FCR in Trial 2; Catabacteriaceae and unknown Clostridiales family members were increased in good FCR and genera Clostridium (from family Clostridiaceae) and Lactobacillus were associated with poor FCR. Trial 3 had only mild microbiota differences associated with all four performance measures. Overall, the genus Lactobacillus was correlated with feed intake which resulted in poor FCR performance. The genus Faecalibacterium correlated with improved FCR, increased GR and reduced FE. There was overlap in phylotypes correlated with improved FCR and GR, while different microbial cohorts appeared to be correlated with FE. Even under controlled conditions different cohorts of birds developed distinctly different microbiotas. Within the different trial groups the abundance of certain bacterial groups correlated with productivity outcomes. However, with different underlying microbiotas there were different bacteria correlated with performance. The challenge will be to identify probiotic bacteria that can reliably deliver favorable outcomes from diverse microbiotas.

Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences

BackgroundThe majority of chicken microbiota studies have used the ceca as a sampling site due to the specific role of ceca in chicken productivity, health and wellbeing. However, sampling from ceca and other gastrointestinal tract sections requires the bird to be sacrificed. In contrast, fecal sampling does not require sacrifice and thus allows the same bird to be sampled repeatedly over time. This is a more meaningful and preferred way of sampling as the same animals can be monitored and tracked for temporal studies. The commonly used practice of selecting a subset of birds at each time-point for sacrifice and sampling introduces added variability due to the known animal to animal variation in microbiota.ResultsCecal samples and fecal samples via cloacal swab were collected from 163 birds across 3 replicate trials. DNA was extracted and 16S rRNA gene sequences amplified and pyrosequenced to determine and compare the phylogenetic profile of the microbiota within each sample. The fecal and cecal samples were investigated to determine to what extent the microbiota found in fecal samples represented the microbiota of the ceca.It was found that 88.55% of all operational taxonomic units (OTUs), containing 99.25% of all sequences, were shared between the two sample types, with OTUs unique for each sample type found to be very rare. There was a positive correlation between cecal and fecal abundance in the shared sequences, however the two communities differed significantly in community structure, represented as either alpha or beta diversity. The microbial populations present within the paired ceca of individual birds were also compared and shown to be similar.ConclusionsFecal sample analysis captures a large percentage of the microbial diversity present in the ceca. However, the qualitative similarities in OTU presence are not a good representation of the proportions of OTUs within the microbiota from each sampling site. The fecal microbiota is qualitatively similar to cecal microbiota but quantitatively different. Fecal samples can be effectively used to detect some shifts and responses of cecal microbiota.

Dietary alpha-linolenic acid enhances omega-3 long chain polyunsaturated fatty acid levels in chicken tissues

The effects of enriching broiler chicken diets with a vegetable source of n-3 fat in the form of alpha-linolenic acid (ALA, 18:3n-3) on the accumulation of n-3 long chain polyunsaturated fatty acids (LCPUFA) in chicken meat were investigated. Sixty unsexed one-day-old broiler chickens (Cobb 500) were randomly allocated to one of six diets (n=10 birds/diet) for 4 weeks. The ALA levels varied from 1 to 8% energy (%en) while the level of the n-6 fatty acid linoleic acid (LA, 18:2n-6) was held to less than 5%en in all diets. At harvest (day 28) the levels of n-3 LCPUFA including eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA) in breast and thigh meat increased in a curvilinear manner as dietary ALA increased, reaching 4- to 9-fold above the levels seen in control birds. In contrast, arachidonic acid (AA) was reduced in response to increasing dietary ALA.

Quantitative analyses of genes associated with mucin synthesis of broiler chickens with induced necrotic enteritis

Clostridial infection of the intestine can result in necrotic enteritis (NE), compromising production and health of poultry. Mucins play a major role in protecting the intestinal epithelium from infection. The relative roles of different mucins in gut pathology following bacterial challenge are unclear. This study was designed to quantify the expression of mucin and mucin-related genes, using intestinal samples from an NE challenge trial where birds were fed diets with or without in-feed antimicrobials. A method for quantifying mucin gene expression was established using a suite of reference genes to normalize expression data. This method was then used to quantify the expression of 11 candidate genes involved in mucin, inflammatory cytokine, or growth factor biosynthesis (IL-18, KGF, TLR4, TFF2, TNF-α, MUC2, MUC4, MUC5ac, MUC5b, MUC13, and MUC16). The only genes that were differentially expressed in the intestine among treatment groups were MUC2, MUC13, and MUC5ac. Expression of MUC2 and MUC13 was depressed by co-challenge with Eimeria spp. and Clostridium perfringens. Antimicrobial treatment prevented an NE-induced decrease in MUC2 expression but did not affect MUC13. The expression of MUC5ac was elevated in birds challenged with Eimeria spp./C. perfringens compared with unchallenged controls and antimicrobial treatment. Changes to MUC gene expression in challenged birds is most likely a consequence of severe necrosis of the jejunal mucosa.

Effect of food enzymes on AME and composition of digesta from broiler chickens fed on diets containing non-starch polysaccharides isolated from lupin kernel

1. The effects of lupin non-starch polysaccharides (NSPs) on apparent metabolisable energy (AME) and composition of digesta from broiler chickens were examined in a dose-response experiment in conjunction with a single combination of 2 commercial enzyme products known from previous studies to partially depolymerise NSPs in diets containing sorghum, casein and lupin kernel. The 7-d experiment was conducted on broiler chickens (24 to 31 d of age) in metabolism cages. 2. The basal diet used in this study contained (in g/kg) sorghum (low tannin) 800, casein 134, celite 20 and vitamins and minerals 46. The inclusion rate for each enzyme product was 0.2 g/kg. Lupin kernel isolate (containing 560 g/kg total NSPs) replaced some of the sorghum and casein. The dose rates of lupin kernel isolate (50, 100 and 150 g/kg) were equivalent to dietary inclusion rates of 80, 160 and 240 g/kg, approximately, of untreated lupin kernel from Lupinus angustifolius cultivar Gungurru. 3. Inclusion of lupin kernel isolate in the diet depressed AME and bird performance, and raised ileal viscosity and excreta moisture, in a dose-dependent manner. 4. A combination of 2 proprietary enzyme products improved dietary AME by 0.3 MJ/kg dry matter. Enzymes reduced excreta moisture when inclusion of lupin kernel isolate was 50 g/kg (equivalent to lupin kernel at 80 g/kg, approximately) but not at higher inclusions. 5. Food enzymes partially depolymerised some insoluble NSPs in lupin kernel isolate, which increased ileal viscosity and soluble NSP content of digesta. 6. It was concluded that development of appropriate exogenous enzyme products could lead to lupin NSPs being used as an energy source for poultry.