Docetaxel for Nonmetastatic Prostate Cancer: Long-Term Survival Outcomes in the STAMPEDE Randomized Controlled Trial.

BACKGROUND: STAMPEDE previously reported adding upfront docetaxel improved overall survival for prostate cancer patients starting long-term androgen deprivation therapy. We report long-term results for non-metastatic patients using, as primary outcome, metastatic progression-free survival (mPFS), an externally demonstrated surrogate for overall survival. METHODS: Standard of care (SOC) was androgen deprivation therapy with or without radical prostate radiotherapy. A total of 460 SOC and 230 SOC plus docetaxel were randomly assigned 2:1. Standard survival methods and intention to treat were used. Treatment effect estimates were summarized from adjusted Cox regression models, switching to restricted mean survival time if non-proportional hazards. mPFS (new metastases, skeletal-related events, or prostate cancer death) had 70% power (α = 0.05) for a hazard ratio (HR) of 0.70. Secondary outcome measures included overall survival, failure-free survival (FFS), and progression-free survival (PFS: mPFS, locoregional progression). RESULTS: Median follow-up was 6.5 years with 142 mPFS events on SOC (3 year and 54% increases over previous report). There was no good evidence of an advantage to SOC plus docetaxel on mPFS (HR = 0.89, 95% confidence interval [CI] = 0.66 to 1.19; P = .43); with 5-year mPFS 82% (95% CI = 78% to 87%) SOC plus docetaxel vs 77% (95% CI = 73% to 81%) SOC. Secondary outcomes showed evidence SOC plus docetaxel improved FFS (HR = 0.70, 95% CI = 0.55 to 0.88; P = .002) and PFS (nonproportional P = .03, restricted mean survival time difference = 5.8 months, 95% CI = 0.5 to 11.2; P = .03) but no good evidence of overall survival benefit (125 SOC deaths; HR = 0.88, 95% CI = 0.64 to 1.21; P = .44). There was no evidence SOC plus docetaxel increased late toxicity: post 1 year, 29% SOC and 30% SOC plus docetaxel grade 3-5 toxicity. CONCLUSIONS: There is robust evidence that SOC plus docetaxel improved FFS and PFS (previously shown to increase quality-adjusted life-years), without excess late toxicity, which did not translate into benefit for longer-term outcomes. This may influence patient management in individual cases.

Layers, broiler chickens and their F1 cross develop distinctly different caecal microbial communities when hatched and reared together.

AIM: To compare the caecal microbiota of layer, broiler, and intermediate F1 layer × broiler cross birds with the hypothesis that significant differences in caecal microbial composition would persist between the three groups when host and environmental interactions were minimized. METHODS AND RESULTS: Caecal contents were characterized using 16S rRNA for males of broiler (n = 12), layer (n = 12) and F1 layer × broiler cross (n = 9) birds that were hatched and reared under the same conditions. The microbial community structure differed significantly between the three groups of birds at phylum, genus and OTU levels, with clear separation of the groups observed. Firmicutes was the phylum most represented across samples; however, the high abundance of Proteobacteria in the layer birds at d28 post-hatch was unexpected, and driven by a higher abundance of E. coli. CONCLUSIONS: The microbiota phylotype between broilers, layers and their F1 cross significantly differed in community structure, diversity and relative abundance in the absence of environmental confounding, which is generally difficult to avoid in microbial studies. SIGNIFICANCE AND IMPACT OF STUDY: The results provide a unique comparison and evidence that there is a strong genetic component driving microbial composition within poultry strains, despite the embryonic development occurring in ovo.

Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences in Japanese quail.

Gastrointestinal colonisation by commensal microbiota is essential for the health and well-being of the host. We aimed to evaluate the influence of a reduced bacterial load environment on microbiota development and maturation, and the possibility of targeted colonisation via at-hatch administration of a selected bacterial strain. Japanese quail (Coturnix japonica) were inoculated within 1 h of hatch with a freshly grown culture of a Lactobacillus agilis isolate derived from a healthy adult quail. Hatchlings were kept in a mouse isolator for one week and then housed between one and four weeks of age, with a flock of normally grown adult quail to expose the bacteria-restricted birds to normal commensal quail bacteria. The bacterial isolate used to inoculate the birds was found to completely dominate the microbiota of the intestine of L.agilis at-hatch inoculated birds. Despite 3 weeks of co-housing of the test birds with an adult flock harbouring normal rich gut microbiota, neither the Lactobacillus inoculated nor PBS inoculated birds reached the level of bacterial diversity seen in birds raised under normal conditions. Neither PBS nor Lactobacillus inoculated birds were able to adopt normal quail microbiota after one week of restricted exposure to bacteria, indicating that contact with diverse microbiota during the early days of gut development in birds is critical for the establishment of healthy intestinal community. Very early intervention in the form of a suitable bacterial probiotic inoculant immediately post-hatch protected birds grown in extreme hygiene conditions from developing anomalous gut microbiota and intestinal damage. Our data shows that it is possible to induce dominance of desired strain using simple timed manipulation.

Ultrastructure of the gastro intestinal tract of healthy Japanese quail (Coturnix japonica) using light and scanning electron microscopy.

The Japanese quail (Coturnix japonica) are popular both as an alternative protein source and as a model of choice for scientific research in several disciplines. There is limited published information on the histological features of the intestinal tract of Japanese quail. The only comprehensive reference is a book published in 1969. This study aims to fill that niche by providing a reference of general histological features of the Japanese quail, covering all the main sections of the intestinal tract. Both light and scanning electron microscope (SEM) images are presented. Results showed that the Japanese quail intestinal tract is very similar to that of the chicken with the exception of the luminal koilin membrane of the gizzard. Scanning electron microscopic photomicrographs show that in the Japanese quail koilin vertical rods are tightly packed together in a uniform manner making a carpet-like appearance. This differs in chicken where the conformations of vertical rods are arranged in clusters.

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry.

Immune function is influenced by the diversity and stability of the intestinal microbiota. A likely trade-off of immune function for growth has been demonstrated in heavier breeds of poultry that have been genetically selected for growth and feed efficiency traits. We investigated the expression of selected innate immune genes and genes encoding products involved in intestinal barrier function to determine whether function changes could be consistently linked to the phenotypic expression of feed conversion ratio (FCR), a common measure of performance within poultry broiler flocks. In addition, we compared individual cecal microbial composition with innate immune gene expression. Samples were utilised from two replicate trials termed P1E1 and P1E2. High (n = 12) and low (n = 12) performing birds were selected based on their individual FCR data from each replicate and combined for microbiota phylogenetic composition and immune gene expression analysis. Toll-like receptor 1 (TLR1La) and zonula occludens 1 (ZO1) were differentially expressed between high- and low-performing broilers. Several taxa were correlated with FCR; of these, unclassified YS2 and ZO1 were also positively correlated with each other. Interactions between taxa and differentially expressed innate immune genes between P1E1 and P1E2 were much greater compared to relationships between high- and low-performing birds. At the level of phylum, reciprocal correlations between tight junction proteins and Toll-like receptors with Bacteroidetes and Firmicutes were evident, as were correlations at the genus level.

Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential.

BACKGROUND: Divergent selection for meat and egg production in poultry has resulted in strains of birds differing widely in traits related to these products. Modern strains of meat birds can reach live weights of 2 kg in 35 d, while layer strains are now capable of producing more than 300 eggs per annum but grow slowly. In this study, RNA-Seq was used to investigate hepatic gene expression between three groups of birds with large differences in growth potential; meat bird, layer strain as well as an F1 layer x meat bird. The objective was to identify differentially expressed (DE) genes between all three strains to elucidate biological factors underpinning variations in growth performance. RESULTS: RNA-Seq analysis was carried out on total RNA extracted from the liver of meat bird (n = 6), F1 layer x meat bird cross (n = 6) and layer strain (n = 6), males. Differential expression of genes were considered significant at P < 0.05, and a false discovery rate of < 0.05, with any fold change considered. In total, 6278 genes were found to be DE with 5832 DE between meat birds and layers (19%), 2935 DE between meat birds and the cross (9.6%) and 493 DE between the cross and layers (1.6%). Comparisons between the three groups identified 155 significant DE genes. Gene ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the 155 DE genes showed the FoxO signalling pathway was most enriched (P = 0.001), including genes related to cell cycle regulation and insulin signalling. Significant GO terms included 'positive regulation of glucose import' and 'cellular response to oxidative stress', which is also consistent with FoxOs regulation of glucose metabolism. There were high correlations between FoxO pathway genes and bodyweight, as well as genes related to glycolysis and bodyweight. CONCLUSIONS: This study revealed large transcriptome differences between meat and layer birds. There was significant evidence implicating the FoxO signalling pathway (via cell cycle regulation and altered metabolism) as an active driver of growth variations in chicken. Functional analysis of the FoxO genes is required to understand how they regulate growth and egg production.

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota.

Recent advances in culture-free microbiological techniques bring new understanding of the role of intestinal microbiota in heath and performance. Intestinal microbial communities in chickens assume a near-stable state within the week which leaves a very small window for permanent microbiota remodelling. It is the first colonisers that determine the fate of microbial community in humans and birds alike, and after the microbiota has matured there are very small odds for permanent modification as stable community resists change. In this study we inoculated broiler chicks immediately post hatch, with 3 species of Lactobacillus, identified by sequencing of 16S rRNA and pheS genes as L. ingluviei, L. agilis and L. reuteri. The strains were isolated from the gut of healthy chickens as reproducibly persistent Lactobacillus strains among multiple flocks. Birds inoculated with the probiotic mix reached significantly higher weight by 28 days of age. Although each strain was able to colonise when administered alone, administering the probiotic mix at-hatch resulted in colonisation by only L. ingluviei. High initial abundance of L. ingluviei was slowly reducing, however, the effects of at-hatch administration of the Lactobacillus mix on modifying microbiota development and structure remained persistent. There was a tendency of promotion of beneficial and reduction in pathogenic taxa in the probiotic administered group.

Effect of restricted feed intake in broiler breeder hens on their stress levels and the growth and immunology of their offspring.

The prenatal environment has been shown to have significant effects on the lifelong health of offspring in humans and other species. Such effects have not been studied extensively in avian species but could prove important, especially in the case of severe feed restriction imposed on broiler breeder hens to prevent obesity and reduce rate of lay. Feed restriction can potentially affect not only nutrient supply to the embryo but stress hormone levels within the hen. This study investigated the impact of nutrient restriction of the breeder hen on growth rate and immune responses in the progeny with the objective to measure the impact of feed restriction of broiler breeder hens on growth and immune response of the progeny. Broiler breeder hens were feed restricted from 24 wk of age and maintained at three bodyweights; 3.4, 3.6, and 4.0 kg until 43 wk of age and behavioral and physiological measures of stress recorded. Chicks were hatched from each hen treatment and at day 7 vaccinated for infectious bronchitis virus (IBV) and at 16, 18, and 20 d old given an immune challenge of lipopolysaccharide. Growth and immune responses of these birds were then recorded. Sex ratio was affected by hen bodyweight, with a significantly increased proportion of males hatched from heavy hens. Growth rate from 35 to 42 d of age was reduced in male progeny from low bodyweight hens. Female progeny from heavy hens responded to an immune challenge by reduced live weight and increased heterophil: lymphocyte ratio, suggesting a more robust immune response in these birds than in the progeny from lower bodyweight hens. Overall, progeny from heavy hens had increased antibodies at day 35 to the vaccination of IBV compared with progeny of low bodyweight hens, also suggesting an improved immune response in these birds. Breeder hens restricted to the lowest feed level showed behaviors indicative of increased stress (object pecking) and an increased heterophil: lymphocyte ratio. Feed restriction of broiler breeder hens increased indices of stress in hens and resulted in offspring that have reduced growth rate and immune response in a sex-dependent way.

Selenium nanoparticles in poultry feed modify gut microbiota and increase abundance of Faecalibacterium prausnitzii.

The poultry industry aims to improve productivity while maintaining the health and welfare of flocks. Pathogen control has been achieved through biosecurity, vaccinations and the use of antibiotics. However, the emergence of antibiotic resistance, in animal and human pathogens, has prompted researchers and chicken growers alike to seek alternative approaches. The use of new and emerging approaches to combat pathogen activity including nanotechnology, in particular, silver nanoparticles (NPs), has been found to not only eradicate pathogenic bacteria but also include issues of toxicity and bioaccumulation effects. Other novel metal nanoparticles could provide this pathogen reducing property with a more tailored and biocompatible nanomaterial for the model used, something our study represents. This study investigated the benefits of nanomaterial delivery mechanisms coupled with important health constituents using selenium as a biocompatible metal to minimise toxicity properties. Selenium NPs were compared to two common forms of bulk selenium macronutrients already used in the poultry industry. An intermediate concentration of selenium nanoparticles (0.9 mg/kg) demonstrated the best performance, improving the gut health by increasing the abundance of beneficial bacteria, such as Lactobacillus and Faecalibacterium, and short-chain fatty acids (SCFAs), in particular butyric acid. SCFAs are metabolites produced by the intestinal tract and are used as an energy source for colonic cells and other important bodily functions. Selenium nanoparticles had no significant effect on live weight gain or abundance of potentially pathogenic bacteria.

Evaluation of fatty acid metabolism and innate immunity interactions between commercial broiler, F1 layer × broiler cross and commercial layer strains selected for different growth potentials.

BACKGROUND: The broiler industry has undergone intense genetic selection over the past 50 yr. resulting in improvements for growth and feed efficiency, however, significant variation remains for performance and growth traits. Production improvements have been coupled with unfavourable metabolic consequences, including immunological trade-offs for growth, and excess fat deposition. To determine whether interactions between fatty acid (FA) metabolism and innate immunity may be associated with performance variations commonly seen within commercial broiler flocks, total carcass lipid %, carcass and blood FA composition, as well as genes involved with FA metabolism, immunity and cellular stress were investigated in male birds of a broiler strain, layer strain and F1 layer × broiler cross at d 14 post hatch. Heterophil: lymphocyte ratios, relative organ weights and bodyweight data were also compared. RESULTS: Broiler bodyweight (n = 12) was four times that of layers (n = 12) by d 14 and had significantly higher carcass fat percentage compared to the cross (n = 6; P = 0.002) and layers (P = 0.017) which were not significantly different from each other (P = 0.523). The carcass and whole blood FA analysis revealed differences in the FA composition between the three groups indicating altered FA metabolism, despite all being raised on the same diet. Genes associated with FA synthesis and ß-oxidation were upregulated in the broilers compared to the layers indicating a net overall increase in FA metabolism, which may be driven by the larger relative liver size as a percentage of bodyweight in the broilers. Genes involved in innate immunity such as TLR2 and TLR4, as well as organelle stress indicators ERN1 and XBP1 were found to be non-significant, with the exception of high expression levels of XBP1 in layers compared to the cross and broilers. Additionally there was no difference in heterophil: lymphocytes between any of the birds. CONCLUSIONS: The results provide evidence that genetic selection may be associated with altered metabolic processes between broilers, layers and their F1 cross. Whilst there is no evidence of interactions between FA metabolism, innate immunity or cellular stress, further investigations at later time points as growth and fat deposition increase would provide useful information as to the effects of divergent selection on key metabolic and immunological processes.

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs.

BACKGROUND: The microbial populations that inhabit the gastrointestinal tract (GIT) are known to influence the health and growth performance of the host. Clean hatcheries and machine-based incubation practices in the commercial poultry industry can lead to the acquisition of aberrant microbiota in the GIT of chickens and a very high level of bird-to-bird variation. The lack of microbial profile flock uniformity presents challenges for harnessing and manipulating intestinal bacteria to better serve the host. METHODS: Cecal contents from high or low performing chickens were used to inoculate the surface of eggs prior to hatching and then the initial gut colonisation was monitored and subsequent changes in gut microbiota composition were followed over time. Two different cecal treatment groups were compared to an untreated control group (n = 32). Bacterial communities were characterised using high-throughput 16S rRNA gene sequencing techniques. RESULTS: Cecal microbiota transfer via egg surface application did not transfer the performance profile of the donors to the recipient birds. One of the cecal inoculations provided a more uniform gut microbiota, but this was not reproduced in the second group with a different inoculum. Development of the intestinal community was reproducible in all three groups with some genera like Lactobacillus showing no change, others like Faecalibacterium increased in abundance slowly and steadily over time and others like Enterobacter were abundant only in the first days of life. DISCUSSION: The cecal treatment reduced bird-to-bird variation in microbiota composition. Although the high FCR performance of donor birds was not transferred with the cecal microbiota, all three groups, including the control, performed better than standard for the breed. The pattern of microbiota development was similar in all three flocks, indicating that the normal processes of microbiota acquisition largely swamped any effect of the cecal material applied to eggs.

Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens.

Unravelling the mechanisms of how antibiotics influence growth performance through changes in gut microbiota can lead to the identification of highly productive microbiota in animal production. Here we investigated the effect of zinc bacitracin and avilamycin on growth performance and caecal microbiota in chickens and analysed associations between individual bacteria and growth performance. Two trials were undertaken; each used 96 individually caged 15-day-old Cobb broilers. Trial 1 had a control group (n = 48) and a zinc bacitracin (50 ppm) treatment group (n = 48). Trial 2 had a control group (n = 48) and an avilamycin (15 ppm) treatment group (n = 48). Chicken growth performance was evaluated over a 10-day period, and caecal microbiota was characterised by sequencing of bacterial 16S rRNA gene amplicons. Avilamycin produced no effect on growth performance and exhibited little significant disturbance of the microbiota structure. However, zinc bacitracin reduced the feed conversion ratio (FCR) in treated birds, changed the composition and increased the diversity of their caecal microbiota by reducing dominant species. Avilamycin only produced minor reductions in the abundance of two microbial taxa, whereas zinc bacitracin produced relatively large shifts in a number of taxa, primarily Lactobacillus species. Also, a number of phylotypes closely related to lactobacilli species were positively or negatively correlated with FCR values, suggesting contrasting effects of Lactobacillus spp. on chicken growth performance. By harnessing such bacteria, it may be possible to develop high-productivity strategies in poultry that rely on the use of probiotics and less on in-feed antibiotics.

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens.

This study compared the effects of wheat- and sorghum-based diets on broiler chickens. The growth performance and caecal microbial community of chickens were measured and correlations between productivity and specific gut microbes were observed. Cobb broilers 15 days of age were individually caged and two dietary treatments were used, one with a wheat-based diet (n = 48) and another one with a sorghum-based diet (n = 48). Growth performance measurements were taken over a 10 day period and samples for microbiota analysis were taken at the end of that period. Caecal microbiota was characterised by sequencing of 16S bacterial rRNA gene amplicons. Overall, the results indicated that a sorghum-based diet produced higher apparent metabolisable energy (AME) and body-weight gain (BWG) values in chickens, compared to a wheat-based diet. Nevertheless, sorghum-fed birds had higher feed conversion ratio (FCR) values than wheat-fed birds, possibly because of some anti-nutritional factors in sorghum. Further analyses showed that caecal microbial community was significantly associated with AME values, but microbiota composition differed between dietary treatments. A number of bacteria were individually correlated with growth performance measurements. Numerous OTUs assigned to strains of Lactobacillus crispatus and Lachnospiraceae, which were prevalent in sorghum-fed chickens, were correlated with high AME and BWG values, respectively. Additionally, a number of OTUs assigned to Clostridiales that were prevalent in wheat-fed chickens were correlated with low FCR values. Overall, these results suggest that between-diet variations in growth performance were partly associated with changes in the caecal microbiota.

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.

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica.

Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2-3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the diversity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT; however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections.

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

BACKGROUND: The 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. RESULTS: Cecal 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. CONCLUSIONS: Fecal 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.

Mucin gene mRNA levels in broilers challenged with eimeria and/or Clostridium perfringens.

The effects of Eimeria (EM) and Clostridium perfringens (CP) challenges on the mRNA levels of genes involved in mucin (Muc) synthesis (Muc2, Muc5ac, Muc13, and trefoil family factor-2 [TFF2]), inflammation (tumor necrosis factor alpha [TNF-alpha] and interleukin-18 [IL-18]), and metabolic processes (cluster of differentiation [CD]36) in the jejunum of broilers were investigated. Two parallel experiments involving 1) EM challenge and 2) EM and CP challenges were conducted. The first experiment was a 2 X 2 study with 12 birds per treatment (N = 48) involving fishmeal substitution (25%) in the diet (FM) and EM challenge. The treatments were: Control (FM-, EM-), Fishmeal (FM+, EM-), EM challenge (FM-, EM+), and fishmeal substitution and EM challenge (FM+, EM+). The second experiment was a 2 X 2 X 2 experiment with six birds per treatment (N = 48) involving fishmeal (FM-, FM+), Eimeria (EM-, EM+), and C perfringens (CP-, CP+). In both arms of the study, male broilers were given a starter diet for the whole period of 16 days, except those assigned to FM+, where 25% of the starter ration was replaced with fishmeal from days 8 to 14. EM inoculation was performed on day 9 and CP inoculation on days 14 and 15. The EM challenge birds were euthanatized for sampling on day 13; postmortem examination and sampling for the Eimeria plus C perfringens challenge arm of the study were on day 16. In the Eimeria challenge arm of the study, fishmeal supplementation significantly suppressed the mRNA levels of TNF-alpha, TFF2, and IL-18 pre-CP inoculation but simultaneously increased the levels of Muc13 and CD36 mRNAs. Birds challenged with Eimeria exhibited increased mRNA levels of Muc13, Muc5ac, TNF-alpha, and IL-18. In the Eimeria and C. perfringens challenge arm, birds exposed to EM challenge exhibited significantly lower mRNA levels of Muc2 and CD36. The mRNA levels of CD36 were also significantly suppressed by CP challenge. Our results showed that the transcription of mucin synthesis genes in the jejunum of broilers is modulated by fishmeal inclusion in the diet. Furthermore, we show for the first time suppression of CD36 mRNA levels in the intestine of broilers challenged with Eimeria or C. perfringens.

Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease.

Recent advances in the technology available for culture-independent methods for identification and enumeration of environmental bacteria have invigorated interest in the study of the role of chicken intestinal microbiota in health and productivity. Chickens harbour unique and diverse bacterial communities that include human and animal pathogens. Increasing public concern about the use of antibiotics in the poultry industry has influenced the ways in which poultry producers are working towards improving birds' intestinal health. Effective means of antibiotic-independent pathogen control through competitive exclusion and promotion of good protective microbiota are being actively investigated. With the realisation that just about any change in environment influences the highly responsive microbial communities and with the abandonment of the notion that we can isolate and investigate a single species of interest outside of the community, came a flood of studies that have attempted to profile the intestinal microbiota of chickens under numerous conditions. This review aims to address the main issues in investigating chicken microbiota and to summarise the data acquired to date.

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 host's 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 host's 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.

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.