Significant role of the nitrogen recycling system through the ceca occurs in protein-depleted chickens

Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens

BACKGROUND

We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds.

RESULTS

Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet.

CONCLUSIONS

Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome

The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.

An in vitro model for caecal proteolytic fermentation potential of ingredients in broilers

Fermentation of protein in the caeca of chickens may lead to the production of potentially detrimental metabolites, which can reduce gut health. A poor precaecal digestion is expected to increase protein fermentation (PF), as more proteins are likely to enter the caeca. It is unknown if the undigested protein that enters the caeca differs in fermentability depending on their ingredient source. In order to predict which feed ingredients increase the risk of PF, an in vitro procedure was developed, which simulates the gastric and enteric digestion, subsequent caecal fermentation. After digestion, amino acids and peptides smaller than 3.5 kD in the soluble fraction were removed by means of dialysis. These amino acids and peptides are assumed to be hydrolysed and absorbed in the small intestine of poultry and therefore not used in the fermentation assay. The remaining soluble and fine digesta fractions were inoculated with caecal microbes. In chicken, the soluble and fine fractions enter the caeca, to be fermented, while insoluble and coarse fractions bypass them. The inoculum was made N-free to ensure bacteria would require the N from the digesta fractions for their growth and activity. The gas production (GP) from the inoculum, therefore, reflected the ability of bacteria to use N from substrates and was an indirect measure for PF. The Maximum GP rate of ingredients averaged 21.3 ± 0.9 ml/h (mean ± SEM) and was in some cases more rapid than the positive control (urea, maximum GP rate = 16.5 ml/h). Only small differences in GP kinetics were found between protein ingredients. Branched-chain fatty acids and ammonia concentrations in the fermentation fluid after 24 hours showed no differences between ingredients. Results indicate that solubilised undigested proteins larger than 3.5 kD are rapidly fermented independent of its source when an equal amount of N is present.

Large intestinal dynamics differ between fowl and swine: Anatomical modifications, microbial collaboration, and digestive advantages from fibrolytic enzymes

The large intestinal systems of fowl and swine recover nutrients from ileal indigesta by a strategically different manner. Indigesta with fowl enter a short colon where retro-peristalsis using urine from the urodeum carries small particulates and solutes into both ceca while coarse materials collect in the cloaca. Fowl repetitively add fine and soluble materials into both ceca to continue fermentation until complexity of the remainder exceeds microbial action, then contents apart from faeces are entirely evacuated. Indigesta with swine initially enter a short cecum followed by a lengthy progression through to the rectal ampulla. Wall out-pocketings of circular muscle or haustrae occur throughout the length of the pig's cecum and helicoidal colon. Each pocket carries contents acquired earlier in the cecum. Motility collects fines and solutes into haustrae during their progression through the colon whereas coarse particulates assemble in the core. Haustrae contents continually ferment during movement to the distal colon with resulting volatile fatty acids (VFA) and electrolytes being absorbed. Mucin loosely covers the lumen surface in caeca as well as helicoidal colon that may capture microbes from active intestinal contents as well as release others to sustain fermentation. The microbial community continually modifies to accommodate fibre complexity as encountered. Resistant starches (RS) and simple oligosaccharides rapidly ferment to yield VFA while encouraging butyric acid in the cecum and anterior colon, whereas non-starch polysaccharides (NSP) complexity requires extended durations through the remaining colon that enhance acetic acid. Residual fibre eventually results in undue complexity for fermentation and consolidates at termination of the colon. These compact pellets are placed on core contents to form faeces having a nodular surface. Acetic, propionic, and butyric acids represent the bulk of VFA and are derived from non-digestible carbohydrates. Fibrolytic enzymes, when supplemented to feed, may increase the proportion of oligosaccharides and simpler NSP to further the rate as well as extent of fermentation. Active absorption of VFA by mucosal enterocytes employs its ionized form together with Na⁺, whereas direct membrane passage occurs when non-dissociated. Most absorbed VFA favour use by the host with a portion of butyric acid together with by-products from protein digestion being retained to reform mucin and sustain mucosal integrity.

Dynamic Changes in the Gut Microbial Community and Function during Broiler Growth

During the entire growth process, gut microbiota continues to change and has a certain impact on the performance of broilers. Here, we used 16S rRNA gene sequencing to explore the dynamic changes in the fecal bacterial communities and functions in 120 broilers from 4 to 16 weeks of age. We found that the main phyla (Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides) accounted for more than 93.5% of the total bacteria in the feces. The alpha diversity of the fecal microbiota showed a downward trend with time, and the beta diversity showed significant differences at various time points. Then, the study on the differences of microbiota between high-weight (HW) and low-weight (LW) broilers showed that there were differences in the diversity and composition of microbiota between high- and low-weight broilers. Furthermore, we identified 22 genera that may be related to the weight change of broilers. The analysis of flora function reveals their changes in metabolism, genetic information processing, and environmental information processing. Finally, combined with microbial function and cecal transcriptome results, we speculated that microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect body weight (BW). Our results will help to expand our understanding of intestinal microbiota and provide guidance for the production of high-quality broilers.

IMPORTANCE The intestinal microbiota has a certain impact on the performance of broilers. However, the change of intestinal microbiota after 4 weeks of age is not clear, and the mechanism of the effect of microorganisms on the weight change of broilers needs more exploration. After 4 weeks of age, the alpha diversity of microorganisms in broiler feces decreased, and the dominant bacteria were Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides. There were differences in microbiota diversity and composition between high- and low-weight broilers. Intestinal microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect the body weight. The results are helpful to increase the understanding of intestinal microbiota and provide reference for the production of high-quality broilers.

Diet, habitat and flight characteristics correlate with intestine length in birds

A link between diet and avian intestinal anatomy is generally assumed. We collated the length of intestinal sections and body mass of 390 bird species and tested relationships with diet, climate and locomotion. There was a strong phylogenetic signal in all datasets. The total and small intestine scaled more-than-geometrically (95%CI of the scaling exponent > 0.33). The traditional dietary classification (faunivore, omnivore and herbivore) had no significant effect on total intestine (TI) length. Significant dietary proxies included %folivory, %frugi-nectarivory and categories (frugi-nectarivory, granivory, folivory, omnivory, insectivory and vertivory). Individual intestinal sections were affected by different dietary proxies. The best model indicates that higher consumption of fruit and nectar, drier habitats, and a high degree of flightedness are linked to shorter TI length. Notably, the length of the avian intestine depends on other biological factors as much as on diet. Given the weak dietary signal in our datasets, the diet intestinal length relationships lend themselves to narratives of flexibility (morphology is not destiny) rather than of distinct adaptations that facilitate using one character (intestine length) as proxy for another (diet). Birds have TIs of about 85% that of similar-sized mammals, corroborating systematic differences in intestinal macroanatomy between vertebrate clades.

Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome

Antimicrobial growth promoters (AGP) have played a decisive role in animal agriculture for over half a century. Despite mounting concerns about antimicrobial resistance and demand for antibiotic alternatives, a thorough understanding of how these compounds drive performance is missing. Here we investigate the functional footprint of microbial communities in the cecum of chickens fed four distinct AGP. We find relatively few taxa, metabolic or antimicrobial resistance genes similarly altered across treatments, with those changes often driven by the abundances of core microbiome members. Constraints-based modeling of 25 core bacterial genera associated increased performance with fewer metabolite demands for microbial growth, pointing to altered nitrogen utilization as a potential mechanism of narasin, the AGP with the largest performance increase in our study. Untargeted metabolomics of narasin treated birds aligned with model predictions, suggesting that the core cecum microbiome might be targeted for enhanced performance via its contribution to host-microbiota metabolic crosstalk.

This study compares the functional profiles of the cecal microbiome among chickens fed four different antimicrobial growth promoters. Chickens receiving narasin exhibited the largest performance increase via apparent nitrogen recycling by the core cecal microbiome.

A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae

Simple Summary

Feeding poultry with insects could reduce production costs, but the impact of this diet on their gut microbiota and growth is little known because the network of relationships between their weights, the composition of their microbiota and their diet is complex and potentially biased by confounding factors (such as the gut compartment, age and sex of the birds). In this study, we were able to unravel these relationships in local breed chickens fed or not fed with black soldier fly larvae thanks to a technique of artificial intelligence (the probabilistic structural equation model). Bacteria were grouped into few entities with distinctive metabolic attributes and were probably linked nutritionally. Birds’ age influenced body weights and bacterial composition. The proposed methodology was thus able to simplify the complex dependencies among bacteria present in the gut and to highlight links potentially important in the response of chicken to insect feed.

Abstract

Feeding chicken with black soldier fly larvae (BSF) may influence their rates of growth via effects on the composition of their gut microbiota. To verify this hypothesis, we aim to evaluate a probabilistic structural equation model because it can unravel the complex web of relationships that exist between the bacteria involved in digestion and evaluate whether these influence bird growth. We followed 90 chickens fed diets supplemented with 0%, 5% or 10% BSF and measured the strength of the relationship between their weight and the relative abundance of bacteria (OTU) present in their cecum or cloaca at 16, 28, 39, 67 or 73 days of age, while adjusting for potential confounding effects of their age and sex. Results showed that OTUs (62 genera) could be combined into ten latent constructs with distinctive metabolic attributes. Links were discovered between these constructs that suggest nutritional relationships. Age directly influenced weights and microbiotal composition, and three constructs indirectly influenced weights via their dependencies on age. The proposed methodology was able to simplify dependencies among OTUs into knowledgeable constructs and to highlight links potentially important to understand the role of insect feed and of microbiota in chicken growth.

In vitro Modeling of Chicken Cecal Microbiota Ecology and Metabolism Using the PolyFermS Platform

Continuous in vitro fermentation models provide a useful tool for a fast, reproducible, and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. In this study, we used the PolyFermS model to mimic the conditions of the chicken cecum and evaluated three nutritive media for in vitro modeling of the chicken cecal microbiota ecology and metabolism. We observed that our model inoculated with immobilized cecal microbiota and fed with a modified Viande Levure medium (mVL-3) reached a high bacterial cell density of up to approximately 10.5 log cells per mL and stable microbiota composition, akin to the host, during 82 days of continuous operation. Relevant bacterial functional groups containing primary fibrolytic (Bacteroides, Bifidobacteriaceae, Ruminococcaceae), glycolytic (Enterococcus), mucolytic (Bacteroides), proteolytic (Bacteroides), and secondary acetate-utilizing butyrate-producing and propionate-producing (Lachnospiraceae) taxa were preserved in vitro. Besides, conserved metabolic and functional Kyoto Encyclopedia of Genes and Genomes pathways were observed between in vitro microbiota and cecal inoculum microbiota as predicted by functional metagenomics analysis. Furthermore, we demonstrated that the continuous inoculation provided by the inoculum reactor generated reproducible metabolic profiles in second-stage reactors comparable to the chicken cecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. In conclusion, we showed that PolyFermS is a suitable model for mimicking chicken cecal microbiota fermentation allowing ethical and ex vivo screening of environmental factors, such as dietary additives, on chicken cecal fermentation. We report here for the first time a fermentation medium (mVL-3) that closely mimics the substrate conditions in the chicken cecum and supports the growth and metabolic activity of the cecal bacterial akin to the host. Our PolyFermS chicken cecum model is a useful tool to study microbiota functionality and structure ex vivo.

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.

Feng et al. include genome recovery and data analysis of large number of chicken gut metagenomic datasets which significantly expands the reference genomes available from the chicken gut microbial communities, and catalog the genes prevalent in the gut systems. They further depict the countryspecific chicken gut antibiotic resistomes and the effects of geography and host species on the gut resistome.

Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period

Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.

Effects of supplemented nonessential amino acids and nonprotein nitrogen on growth and nitrogen excretion characteristics of broiler chickens fed diets with very low crude protein concentrations

Reducing dietary CP for broiler chickens below a certain threshold results in decreased growth, even when the supply of essential amino acids and glycine equivalent (Gly_equi) is adequate, probably because other nonessential amino acids (neAA) are growth-limiting. Nonprotein nitrogen (NPN) might be used for the synthesis of neAA. Therefore, the effects of specific neAA and ammonium chloride (NH₄Cl) supplementation on the growth and N-excretion characteristics of broiler chickens were investigated. Nine male Ross 308 broiler chickens were kept in each of 81 metabolism units from day 7 to 21 and received 1 of 9 diets in 9 replicates in a one-factorial arrangement of treatments. Two diets with different neAA concentrations, except for Gly_equi, were mixed resulting in CP levels of 180 (CP180) and 160 (CP160) g/kg. In six other diets, CP160 was supplemented with either l-Ala, l-Pro, l-Asp, a mix of l-Asp and l-Asn·H₂O, l-Glu, or a mix of l-Glu and l-Gln to achieve concentrations of the respective neAA as formulated in CP180. In a further diet, NH₄Cl was added to CP160 to achieve the CP concentration of CP180. The ADG and gain:feed ratio (G:F) from day 7 to 21 were highest at CP180. Reduced neAA concentrations in CP160 decreased ADG and G:F. Supplementation of Asp+Asn, Glu, and Glu+Gln to CP160 increased ADG and G:F, but not to the level found for CP180. Compared with CP160, addition of Asp increased G:F but not ADG. Supplementation of Asp+Asn caused higher ADG and G:F than supplementation of Asp alone. The N-utilization efficiency was highest at CP160 and at CP160 supplemented with Ala, Pro, and Glu. Lower N-utilization efficiency was found at CP180 than at CP160, without and with supplemented neAA. The treatment containing NH₄Cl presented the lowest ADG, G:F, and N-utilization efficiency. These results showed that individual supplementation of Asp+Asn, Glu, and Glu+Gln partly compensates for the growth-reducing effects of very low CP diets. Supplementation of NH₄Cl as NPN source is not suitable for broiler chickens.

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Background

Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.

Results

We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.

Conclusions

This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

Characteristics of the fecal microbiota of high- and low-yield hens and effects of fecal microbiota transplantation on egg production performance

The microbiota that resides in the digestive tract plays pivotal role in maintaining intestinal environmental stability by promoting nutrition digestion and intestinal mucosal immunity. However, whether the intestinal microbiota in laying hens affects egg laying- performance is not known. In this study, 16S rDNA gene sequencing and fecal microbiota transplantation were used to determine the structure of the intestinal microbiota and the effect of the intestinal microbiota on egg production. The results revealed that Firmicutes were dominant in both the H (high egg laying rates) and L (low egg laying rates) groups, while Bacteroides, Actinobacteria and Proteobacteria were significantly enriched in the L group compared to the H group. The laying rates were weakly affected in H hens transplanted with the fecal microbiota from L hens, except for temporary fluctuation, while the egg laying rates were significantly increased in L hens transplanted with the fecal microbiota from H hens. Therefore, we concluded that the population structure of the intestinal microbiota varied between the H and L groups, and the intestinal microbiota of high-yield laying hens had significant effects on low-yield laying hens performance.

Effects of encapsulated cinnamaldehyde and citral on the performance and cecal microbiota of broilers vaccinated or not vaccinated against coccidiosis

This study investigated the effects of encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN + CIT) on the growth performance and cecal microbiota of nonvaccinated broilers and broilers vaccinated against coccidiosis. Vaccinated (1,600) and nonvaccinated (1,600) 0-day-old male Cobb500 broilers were randomly allocated to 5 treatments: basal diet (control) and basal diet supplemented with bacitracin (BAC, 55 ppm), CIN (100 ppm), CIT (100 ppm), and CIN (100 ppm) + CIT (100 ppm). In general, body weight (BW) and feed conversion ratio were significantly improved in birds treated with BAC, CIN, CIT, and CIN + CIT (P < 0.05) but were all decreased in vaccinated birds compared with nonvaccinated birds (P < 0.05). Significant interactions (P < 0.05) between vaccination and treatments for average daily gain during the periods of starter (day 0–9) and BW on day 10 were noted. Broilers receiving vaccines (P < 0.01) or feed supplemented with BAC, CIN, CIT, or CIN + CIT (P < 0.01) showed reductions in mortality rate from day 0 to 28. The incidences of minor coccidiosis were higher (P < 0.05) in vaccinated birds than in nonvaccinated birds. Diet supplementation with BAC or tested encapsulated essential oils showed comparable effects on the coccidiosis incidences. Similar to BAC, CIN and its combination with CIT reduced both incidence and severity of necrotic enteritis (P < 0.05). No treatment effects were observed on the cecal microbiota at the phyla level. At the genus level, significant differences between vaccination and treatment groups were observed for 5 (Lactobacillus, Ruminococcus, Faecalibacterium, Enterococcus, and Clostridium) of 40 detected genera (P < 0.05). The genus Lactobacillus was more abundant in broilers fed with CIT, while Clostridium and Enterococcus were less abundant in broilers fed with CIN, CIT, or CIN + CIT in both the vaccinated and nonvaccinated groups. Results from this study suggested that CIN alone or in combination with CIT in feed could improve chicken growth performance to the level comparable with BAC and alter cecal microbiota composition.

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

Background

The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare.

Results

In this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identified significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterised the development of the microbiota at each intestinal site over time.

Conclusions

Our study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

Upregulation of genes encoding digestive enzymes and nutrient transporters in the digestive system of broiler chickens by dietary supplementation of fiber and inclusion of coarse particle size corn

BACKGROUND

Measures to improve bird performance have been sought due to the imminent phase out of in-feed antibiotics in poultry and continued demand for higher poultry feeding efficiency. Increasing grain particle size and dietary fibre may improve gizzard function, digestive efficiency and nutrient absorption. This study was conducted to evaluate the effect increased particle size of corn and inclusion of sugarcane bagasse (SB) on mRNA expression of genes encoding digestive enzymes and nutrient transporters in broilers.

RESULTS

A total of 336 day-old Ross 308 males were assigned in a 2 × 2 factorial arrangement of treatments with corn particle size - coarse 3576 μm or fine 1113 μm geometric mean diameter, and SB - 0 or 2% inclusion. Feed conversion ratio (FCR), weight gain and feed intake were measured from d 0-10 and d 10-24. The relative gizzard weight and mRNA expression of genes encoding digestive enzymes and intestinal nutrient transporters were measured on d 24. During d 10-24, a particle size × SB interaction was observed for FCR (P < 0.01), where birds fed coarsely ground corn (CC) with 2% SB had lower FCR than those fed CC without SB. A particle size × SB interaction was observed for both expression of pepsinogen A and C (P < 0.01) which were negatively correlated with FCR on d 24. Addition of 2% SB upregulated pepsinogen A and C only in CC fed birds. Further, 2% SB also upregulated pancreatic amylase (AMY2A) and intestinal cationic amino acid transporter-1 (CAT1). Inclusion of dietary CC upregulated duodenal amino peptidase N (APN), jejunal alanine, serine, cysteine and threonine transporter-1 (ASCT1), and ileal peptide transporter-2 (PepT2).

CONCLUSION

These results suggest that both SB and coarse particle size modulate expression of genes encoding important digestive enzymes and nutrient transporters and thus are directly related to bird performance. These findings provide insights into the combination effects of dietary fiber and particle size in the future management of broiler feeding.

Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review

Currently, optimization of feed efficiency is one of the main challenges in improvement programs of livestock and poultry genetics. The objective of this review is to present the genetic aspects of feed efficiency related traits in meat-type chicken and possible ways to reduce the environmental impact of poultry meat production with effective breeding. Basic measures of feed efficiency are defined and the genetic background of these traits, including a review of heritabilities is described. Moreover, a number of genomic regions and candidate genes determining feed efficiency traits of broilers that were detected over the past decades are described. Classical and genomic selection strategies for feed efficiency in the context of its relationships with other performance traits are discussed as well. Finally, future strategies to improve feed digestibility are described as it is expected that they will decrease wastes and greenhouse gas emission. Further genetic improvement of feed efficiency, should be examined jointly with appropriate feeding strategies in broilers.

mRNA expression of amino acid transporters, aminopeptidase, and the di- and tri-peptide transporter PepT1 in the intestine and liver of posthatch broiler chicks

Amino acid (AA) transporter proteins are responsible for the movement of amino acids in and out of cells. Aminopeptidase cleaves AAs from the N-terminus of polypeptides making them available for transport, while PepT1 is a di- and tripeptide transporter. In the intestine, these proteins are present on the brush border and basolateral membranes of enterocytes, and are essential for the uptake of AAs into enterocytes and their release into circulation. The purpose of this study was to determine the level of transcription of these genes after hatch in 3 regions of the small intestine, the ceca, and liver. Heritage broiler chicks (n=5) were sampled at day after hatch and days 3, 5, 7, 10, 12, 14, 17, and 21 posthatch, and mRNA expression level was measured using absolute quantitation. The small intestine (duodenum, jejunum, and ileum) expressed the largest quantities of each gene tested. The expression in the ceca and liver was 1 to 3 orders of magnitude less than that of the small intestine. The expression of basolateral transporters in the small intestine was more constant over days posthatch than the expression of brush border transporters. In the ceca the expression of the brush border transporters decreased over the sampling period, while expression of basolateral genes was relatively constant. In the liver the expression of Na+ independent cationic and zwitterionic amino acid transporter (bo,+AT), Na+ independent cationic amino acid transporter 2 (CAT2), excitatory amino acid transporter 3 (EAAT3), and the heavy chain corresponding to the bo,+) system (rBAT) significantly decreased at 12 days posthatch; however, the expression of Na+ independent cationic and Na+ dependent neutral amino acid transporter 1 (y+LAT1), Na+ coupled neutral amino acid transporter 1; (SNAT1), and Na+ coupled neutral amino acid transporter 2 (SNAT2) significantly increased at day 5 posthatch compared to day 1 and these levels remained throughout the rest of the sampling period. The current results suggest that at 1 day posthatch chicks are capable of AA processing and transport in the intestine as well as the liver. Additionally the ability of the ceca in transporting AA from the lumen may decrease with age. The liver should be capable of amino acid transport, but its capabilities may be more specific since the expression of several transporters in this organ is either absent or very low.

Extensive microbial and functional diversity within the chicken cecal microbiome

Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.

Adaptive strategies for post-renal handling of urine in birds

Birds are a diverse vertebrate class in terms of diet and habitat, but they share several common physiological features, including the use of uric acid as the major nitrogenous waste product and the lack of a urinary bladder. Instead, ureteral urine refluxes from the urodeum into the more proximal coprodeum and portions of the hindgut (colon or rectum and ceca). This presents a potential problem in that hyperosmotic ureteral urine in contact with the permeable epithelia of these tissues would counteract renal osmotic work. This review describes and provides examples of different strategies used by avian species to balance renal and post-renal changes in urine composition. The strategies described include: 1. a "reptilian" mode, with moderate renal concentrating ability, but high rates of post-renal salt and water resorption; 2. the "mammalian" strategy, in which the coprodeum effectively functions like a mammalian urinary bladder, preserving the osmotic concentrating work of the kidney; 3. an interaction strategy, in which post-renal transport processes are hormonally regulated in order to optimize renal function under varying conditions of salt or water stress; 4. the salt gland strategy seen in marine or estuarine birds with functional salt glands, in which post-renal transport mechanisms are used to conserve urinary water and to recycle excess NaCl to the nasal salt glands. Finally, we also describe some features of an as-yet unstudied group of birds, the birds of prey. At least some species in this group are relatively good renal concentrators, and would be predicted to have post-renal mechanisms to preserve this work. This new synthesis illustrates the marked diversity of adaptive mechanisms used by avian species to maintain osmotic homeostasis.

Do Nectar- and Fruit-Eating Birds Have Lower Nitrogen Requirements Than Omnivores? an Allometric Test

We used an allometric approach to compare the minimum nitrogen requirements (MNR) and the total endogenous nitrogen loss (TENL) of nectar- and fruit-eating birds with those of omnivorous birds. These two parameters were 4× higher in omnivores than in nectarivores and frugivores. In nectarivorous-frugivorous birds, MNR was 152.8 mg N kg−0.76 day−1; in omnivorous birds, it was 575.4 mg N kg−0.76 day−1. Similarly, TENL was 54.1 mg N kg−0.69 day−1 in nectarivores-frugivores, and 215.3 mg N kg−0.69 day−1 in omnivores. The residuals of the allometric relationships between TENL and MNR and body mass were positively correlated, which suggests that a large proportion of the interspecific variation in MNR is explained by variation in TENL. Although our results show that nectar- and fruit-eating birds have low nitrogen requirements, the mechanisms that these animals use to conserve nitrogen remain unclear.

¿Tienen las Aves Nectrarívoras y Frugívoras Requerimientos de Nitrógeno Menores que las Omnívoras? Una Prueba Alométrica

Impaired immune responses in broiler hatchling hindgut following delayed access to feed

One of the key stimulators of intestinal development in the chick is physical exposure to feed, while feed withholding delays the onset of gut development. A delay of 24-72 h in onset of feeding is quite common in the poultry industry due to variation in hatching time and hatchery treatments. As intestinal development occurs in concert with the development of the gut associated lymphoid tissue (GALT), we investigated the effects of short term feed withholding on development of GALT in broiler hatchlings. GALT activity was determined by antibody production (systemic and locally in the gut), distribution of B and T lymphocytes in the gut, expression of lymphocyte specific genes, and distribution of B and T lymphocytes in the cloacal bursa. Our findings show that while development of GALT in the foregut (duodenum, jejunum, ileum) was only slightly and temporarily impeded by feed withholding, GALT activity in the hindgut and the gut-related cloacal bursa was significantly delayed during the first 2 weeks of life: Systemic and intestinal antibody responses following rectal immunization to antigen were lower, colonization of the hindgut (cecum and colon) by T and B lymphocytes was delayed, as well as the expression of chIL-2 mRNA in hindgut T lymphocytes. We also found that the increase of B and T population size in the cloacal bursa was delayed with time. Full recovery occurred from 2 weeks of age. The 2-week vulnerable period should be seriously considered in circumstances where hatchlings are in transit for extended periods from hatcheries to farms.

Are Hummingbirds Facultatively Ammonotelic? Nitrogen Excretion and Requirements as a Function of Body Size

Most birds are uricotelic. An exception to this rule may be nectar-feeding birds, which excrete significant amounts of ammonia under certain conditions. Although ammonia is toxic, because it is highly water soluble its excretion may be facilitated in animals that ingest and excrete large amounts of water. Bird-pollinated plants secrete carbohydrate- and water-rich floral nectars that contain exceedingly little protein. Thus, nectar-feeding birds are faced with the dual challenge of meeting nitrogen requirements while disposing of large amounts of water. The peculiar diet of nectar-feeding birds suggests two hypotheses: (1) these birds must have low protein requirements, and (2) when they ingest large quantities of water their primary nitrogen excretion product may be ammonia. To test these hypotheses, we measured maintenance nitrogen requirements (MNR) and total endogenous nitrogen losses (TENL) in three hummingbird species (Archilochus alexandri, Eugenes fulgens, and Lampornis clemenciae) fed on diets with varying sugar, protein, and water content. We also quantified the form in which the by-products of nitrogen metabolism were excreted. The MNR and TENL of the hummingbirds examined were exceptionally low. However, no birds excreted more than 50% of nitrogen as ammonia or more nitrogen as ammonia than urates. Furthermore, ammonia excretion was not influenced by either water or protein intake. The smallest species (A. alexandri) excreted a significantly greater proportion (>25%) of their nitrogenous wastes as ammonia than the larger hummingbirds ( approximately 4%). Our results support the hypothesis that nectar-feeding birds have low protein requirements but cast doubt on the notion that they are facultatively ammonotelic. Our data also hint at a possible size-dependent dichotomy in hummingbirds, with higher ammonia excretion in smaller species. Differences in proportionate water loads and/or postrenal modification of urine may explain this dichotomy.

Do mammals, birds, reptiles and fish have similar nitrogen conserving systems?

Comparative physiological studies are a powerful tool for revealing common animal adaptations. Amino acid catabolism produces ammonia which is detoxified through the synthesis of urea (mammals, some fish), uric acid (birds), or urea and uric acid (reptiles). In mammalian herbivores and omnivores, urea nitrogen is salvaged by a series of steps involving urea transfer into the intestine, microbial mediated urea hydrolysis with synthesis of amino acids utilizing the liberated ammonia and transfer of the amino acids back to the host. A similar series of steps occur in omnivorous/granivorous and herbivorous birds, although in this case urine, containing uric acid, is refluxed directly into the intestine where microbes degrade the uric acid and utilize the liberated ammonia for amino acid synthesis. These amino acids are transferred back to the host. In reptiles and ureotelic fish not all of these steps have been experimentally confirmed. Reptiles like birds, reflux urine into the intestine where it is exposed to the microflora. However, the capacity of these microbes to breakdown the uric acid and urea and utilize ammonia for amino acid synthesis has not been documented. Ureotelic fish transfer urea into the intestine where urease (presumably of bacterial origin) hydrolyzes the urea. However, the amino acid synthesizing capacity of the intestinal microflora has not been studied. The series of steps, as outlined, would define the prevailing nitrogen conservation system for herbivores and omnivores at least. However, it would appear that some animals, in particular the fruit-eating bat and perhaps the fruit-eating bird, may have evolved alternative, as yet uncharacterized, adaptations to a very limited nitrogen intake.

Ammonotely in a passerine nectarivore: the influence of renal and post-renal modification on nitrogenous waste product excretion

Most aquatic vertebrates are ammonotelic, whereas terrestrial vertebrates are typically uricotelic or ureotelic. However, the principal form of nitrogenous waste product in the urine of an animal may vary, depending on environmental conditions. Anna's hummingbird (Calypte anna) was found to switch from uricotely at high ambient temperature (Ta)to ammonotely at lower Ta, when energy demands and consequent nectar intake rates were high. In extension of this, we hypothesised that nectarivorous birds would switch from uricotely to ammonotely when water intake rates were high or when protein or salt intake rates were low. We examined the influence of water, electrolyte and protein intake and of Ta on the excretion of ammonia, urea and urate (uric acid and its salts) in nectarivorous Palestine sunbirds(Nectarinia osea). The proportion of ammonia in ureteral urine and excreted fluid was not influenced by total water or salt intake or by Ta. Protein intake did not influence nitrogenous waste product concentrations in ureteral urine. However, when protein intake was reduced, the proportion of ammonia in excreted fluid was higher because of the reduced urate concentration. This reduction in urate concentration leads to`apparent' ammonotely. We suggest that ammonotely may not be a unique feature of nectarivorous birds. It could occur in any species in which breakdown of urate in the hindgut allows the uric acid-nitrogen concentration in the excreta to fall below that of the ammonia-nitrogen concentration.