Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing

Nutritional and physiological responses to dietary phosphorus levels and phytase in pullets and laying hens

The objective of this study was to determine the effects of dietary available phosphorus (P) levels and dietary phytase added into the very low-P diet on the performance, mineral balance, odor emission, and stress responses in growing pullets and laying hens during 13 to 32 wk of age. One hundred sixty-eight pullets (Hy-Line Brown) were randomly assigned into 1 of 4 dietary treatments with 7 replicates of 6 birds each. Experimental diets were formulated to contain 3 graded P levels at 0.25, 0.35, and 0.45% during 13 to 15 wk (phase 1), 0.25, 0.35, and 0.45% during 16 to 18 wk (phase 2), and 0.20, 0.30, and 0.40% during 19 to 32 wk (phase 3). In addition, dietary phytase (500 FTU/kg matrix values) was added into the very low-P diets (0.20% during 13-15 wk, 0.25% during 16-18 wk, and 0.20% during 19-32 wk) to meet the nutritional adequacy with standard P diets. In all phases, decreasing dietary P levels did not affect (P > 0.05) growth, laying performance, and egg qualities. Decreasing dietary P levels linearly increased the relative duodenal and oviduct weights (P < 0.05), and quadratically increased the relative ovary weight in pullets (P = 0.016). Dietary phytase lowered (P = 0.021) the relative duodenal weight compared with the very low-P diet. Tibia breaking strength and tibia Mg contents in pullets were linearly lowered (P < 0.05) as dietary P levels decreased. Dietary phytase tended to increase (P = 0.091) tibia breaking strength and significantly increased (P = 0.025) tibia Mg content compared with the very low-P diet. Dietary P levels and dietary phytase affected (P < 0.05) ileal crypt depth and ileal villus height: crypt depth ratio in pullets. Decreasing dietary P levels linearly decreased (P < 0.01) crude fat digestibility and P excretion in both pullets and laying hens. Dietary phytase reversed (P < 0.05) the very low-P diet-mediated decrease of crude fat digestibility in pullets and laying hens. Dietary P levels and dietary phytase affected (P < 0.05) odor emission including ammonia in pullets and total volatile fatty acids in laying hens. Finally, lowering dietary P levels increased (P < 0.01) yolk corticosterone concentrations and the increased corticosterone concentration by the very low-P diet was reversed by dietary phytase. Collectively, our study shows that decreasing dietary P levels induced nutritional and physiological responses in pullets and laying hens and these P-mediated negative effects were mitigated by dietary phytase.

Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept

BACKGROUND

Different production systems of livestock animals influence various factors, including the gut microbiota.

METHODS

We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment.

RESULTS

Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken.

CONCLUSION

Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.

Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens

AIMS

Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism, and innate immunity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic.

METHODS AND RESULTS

In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the terminal-restriction fragment length polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum, and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic.

CONCLUSIONS

We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.

Microbiota of Chickens and Their Environment in Commercial Production

Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species

The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host's own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.

A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms

The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.

Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens

Simple Summary

The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, metabolism, and health status of the host animal. Previous studies exploring the relationship between chicken growth performance and gut microbiota focused mostly on gut content and excreta samples, neglecting the mucosa that promotes colonisation by distinct groups of microorganisms. These observations emphasised the importance of studying the variations between the bacterial communities of the lumen and mucosa throughout the different sections of the GIT. The novelty of this study is that we have evaluated the microbial communities of the jejunum chymus, jejunum mucosa, and caecum chymus of broiler chickens with different growth rates. Besides the bacteriota composition, the interactions between the bacteria were also evaluated. We have confirmed that the microbiota composition is influenced mostly by the sampling place. However, some body weight (BW)-related changes and interactions have also been found. In these cases, the mucosa seems to play a crucial role.

Abstract

The study reported here aimed to determine whether correlations can be found between the intestinal segment-related microbiota composition and the different growing intensities of broiler chickens. The bacterial community structures of three intestinal segments (jejunum chymus—JC, jejunum mucosa—JM, caecum chymus—CC) from broiler chickens with low body weight (LBW) and high body weight (HBW) were investigated. Similar to the previous results in most cases, significant differences were found in the bacteriota diversity and composition between the different sampling places. However, fewer body weight (BW)-related differences were detected. In the JM of the HBW birds, the Bacteroidetes/Firmicutes ratio (B/F) was also higher. At the genus level significant differences were observed between the BW groups in the relative abundance of Enterococcus, mainly in the JC; Bacteroides and Ruminococcaceae UCG-010, mainly in the JM; and Ruminococcaceae UCG-013, Negativibacillus, and Alistipes in the CC. These genera and others (e.g., Parabacteroides and Fournierella in the JM; Butyricoccus, Ruminiclostridium-9, and Bilophila in the CC) showed a close correlation with BW. The co-occurrence interaction results in the JC revealed a correlation between the genera of Actinobacteria (mainly with Corynebacterium) and Firmicutes Bacilli classes with different patterns in the two BW groups. In the JM of LBW birds, two co-occurring communities were found that were not identifiable in HBW chickens and their members belonged to the families of Ruminococcaceae and Lachnospiraceae. In the frame of the co-occurrence evaluation between the jejunal content and mucosa, the two genera (Trichococcus and Oligella) in the JC were found to have a significant positive correlation with other genera of the JM only in LBW chickens.

Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection

Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.

Relative phytase efficacy values as affected by response traits, including ileal microbiota composition

The objective of this study was to compare the effects of graded inclusions of 2 phytase products and a mineral P source in broiler chickens using different response traits, including ileum microbiota composition. Eleven experimental diets were used. These were a low-P basal diet and diets supplemented with increasing levels of dicalcium phosphate (DCP), Natuphos E 5000 G (NE), or Natuphos 5000 G (N). The performance traits, prececal P digestibility, and tibia and foot ash results were subjected to regression analysis and slope ratios were used to compare the supplements based on the measured evaluation traits. In the microbiota analysis, total nucleic acids were extracted and the 16S rRNA gene was targeted for use in the amplicon sequencing process. Phylogenetic analysis was performed using Mothur, followed by a multivariate statistical analysis. The various response traits caused different estimates of relative efficacy. The mean results of all the response traits showed that a 1.75-fold increase in the activity of N was needed to achieve the same response as NE and the variability among the detected traits ranged from 1.59 (prececally digestible P intake) to 1.91 (amount of tibia ash). The mean slope ratio between DCP and NE was 311 and varied between 208 (ADG) and 349 (foot ash concentration). The mean slope ratio for phytase N with DCP was 552 and varied from 357 (ADG) to 640 (tibia ash concentration). The ileum microbiota composition was not different among the diets. A similar composition was driven in the abundance of Lactobacillus crispatus, Lactobacillus salivarius, and Lactobacillus gallinarum. The results suggest that different response traits cause markedly different estimates of relative phytase efficacy.

Garcia J, Fernández Miyakawa M, Farber MD. Geography as non-genetic modulation factor of chicken cecal microbiota

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term “local microbiota” as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.

Effects of soybean oligosaccharide, stachyose, and raffinose on growth performance and cecal microbiota in broiler chickens

This study was conducted to examine the effects of soybean oligosaccharide, stachyose, and raffinose on growth performance and cecal microbiota in broiler chickens. Three-hundred 1-day-old Arbor Acres broiler chickens were randomly assigned to five dietary treatments: a basal diet (control diet); diets supplemented with soybean oligosaccharide, stachyose, or raffinose at levels of 0.6% total sugar content; and diet with soybean meals (positive control). Results showed that feed-to-gain ratio (F/G) was improved (p < 0.05) in broiler chickens that received stachyose, but not raffinose, while addition of soybean oligosaccharide to the diet significantly (p < 0.05) resulted in decreases in the average daily feed intake (ADFI) and average daily gain (ADG). Supplementation with soybean oligosaccharide, stachyose, or raffinose had a positive effect (p < 0.05) on the nutrient digestibility, but not on the blood immune parameters (p > 0.05). The results of the gene sequencing indicated that, at the family level, Ruminococcaceae, Lachnospiraceae, and Lactobacillaceae were comparatively present in all the treatments but the cecal microbial composition was changed after dietary addition of different oligosaccharides. Our study had led to a greater understanding of prebiotic effects of these oligosaccharides on growth and intestinal health.

Effects of grazing mixed-grass pastures on growth performance, immune responses, and intestinal microbiota in free-range Beijing-you chickens

There is an increasing interest in free-range poultry with the increasing focus on food safety and animal welfare. This study was conducted to evaluate the effects of grazing mixed-grass pastures on growth performance, immune responses, and intestinal microbiota in free-range laying chickens. Ten-week-old female Beijing-you chickens were blocked by the BW and randomly assigned to 3 free-range systems in poplar plantations for 120 d: forage-removed paddocks with a high stocking density of 5 m²/hen (control [CK]); mixed-grass pastures with a low stocking density of 6 m²/hen ;or mixed-grass pastures with a high stocking density of 5 m²/hen. Intestinal microbial community analysis was performed by 16S rRNA gene sequencing using Illumina MiSeq. The results revealed that no differences (P > 0.05) were found between the 3 raising systems for the BW and ADG. Chickens grazing mixed-grass pastures exhibited decreased (P > 0.05) mortality and improved immune responses as evidenced by increased T-lymphocyte proliferation (P > 0.05) and immunoglobulin A (P > 0.05) and immunoglobulin M concentrations (P < 0.05) compared with those raised in forage-removed paddocks. Metagenomic analysis indicated that grazing mixed-grass pastures regulated the intestinal microbiota by increasing the prevalence of beneficial bacteria, such as Lactobacillus, Bacteroides, and Faecalibacterium, and reducing potentially pathogenic bacteria population, such as the Rikenellaceae_RC9_gut_group compared with the CK. Therefore, this study indicated that grazing mixed-grass pastures could positively influence intestinal microbiota that may contribute to the overall growth and immunity of free-range chickens and that a low stocking density of 6 m²/hen was optimal to Beijing-you chickens grazing mixed-grass pastures.

Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae

Pigeons, as the only altricial birds in poultry, are the primary Trichomonas gallinae (T. gallinae) host. To study the effects of T. gallinae infection on gut microbiota, we compared the microbiota diversity and composition in gastrointestinal (GI) tracts of pigeons at the age of 14 and 21 day with different degrees of T. gallinae infection. Thirty-six nestling pigeons were divided into three groups: the healthy group, low-grade and high-grade trichomonosis group. Then, the crop, small intestine and rectum contents were obtained for sequencing of the 16S rRNA gene V3–V4 hypervariable region. The results showed that the microbiota diversity was higher in crop than in small intestine and rectum, and the abundance of Lactobacillus genus was dominant in small intestine and rectum of healthy pigeons at 21 days. T. gallinae infection decreased the microbiota richness in crop at 14 days. The abundance of the Firmicutes phylum and Lactobacillus genus in small intestine of birds at 21 days were decreased by infection, however the abundances of Proteobacteria phylum and Enterococcus, Atopobium, Roseburia, Aeriscardovia and Peptostreptococcus genus increased. The above results indicated that crop had the highest microbiota diversity among GI tract of pigeons, and the gut microbiota diversity and composition of pigeon squabs were altered by T. gallinae infection.

Phytate degradation, myo-inositol release, and utilization of phosphorus and calcium by two strains of laying hens in five production periods

The objective of this study was to compare 2 laying hen strains in 5 production periods regarding phytase activity, phytate (InsP₆) degradation, and myo-inositol (MI) release in the digestive tract and phosphorus (P) and calcium (Ca) utilization. One offspring of 10 nonrelated roosters per strain (Lohmann Brown-classic (LB) or Lohmann LSL-classic (LSL)) was placed in one of 20 metabolic units in a completely randomized block design in week 8, 14, 22, 28, and 58 of life. All hens were fed the same corn and soybean meal–based diet at one time, but the diet composition was adjusted to the requirements in the respective period. For 4 consecutive days, excreta were collected quantitatively at 24-hour intervals. In week 10, 16, 24, 30, and 60, the blood plasma, digesta of crop, gizzard, jejunum, ileum, and ceca, and mucosa of the jejunum was collected. The concentration of inorganic P in the blood plasma was higher in LB than in LSL hens (P = 0.026). Plasma Ca concentrations increased with each period (P < 0.001) in both strains. In jejunum digesta, the MI concentration did not differ between strains, but InsP₆ concentration was higher in LB than in LSL hens (P = 0.002) and the highest in week 30 and 60. Total phosphatase and phytase activities were higher in LB than in LSL hens (P ≤ 0.009). Period effects were also significant for these enzymes. Concentrations of some constituents of the cecal content were different between the strains. The MI concentration in the egg albumen and yolk was higher in LB than in LSL hens. Differences in InsP₆- and MI-related metabolism of the 2 hen strains existed. These differences were partly dependent of the period. Especially, week 24 was a period of remarkable change of metabolism. Great differences also existed among individuals, making it worth to have a closer look at the metabolism of individuals in addition to evaluating treatment means. Further studies on metabolic, genetic, and microbiome level may help explain these differences.

The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models

It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.

Effects on the Ileal Microbiota of Phosphorus and Calcium Utilization, Bird Performance, and Gender in Japanese Quail

In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%-15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems

Improving the digestive efficiency of broiler chickens (Gallus gallus) could reduce organic waste, increase the use of alternative feed not used for human consumption and reduce the impact of feed in production costs. By selecting chicken lines divergently for their digestive efficiency, we showed previously that digestive efficiency is under genetic control and that the two resulting divergent lines, D+ (high digestive efficiency or “digestibility +”) and D- (low digestive efficiency or “digestibility -”), also differ for the abundance of specific bacteria in their caeca. Here we perform a more extensive census of the bacteria present in the digestive microbiota of 60 chickens selected for their low apparent metabolizable energy corrected for nitrogen balance (AMEn-) or high (AMEn+) digestive efficiency in a [D+ x D-] F8 progeny of 200 individuals. We sequenced the 16S rRNA genes of the ileal, jejunal and caecal microbiotas, and compared the compositions and predicted functions of microbiotas from the different intestinal segments for 20 AMEn+ and 19 AMEn- birds. The intestinal segment of origin was the main factor structuring the samples. The caecal microbiota was the most impacted by the differences in digestive efficiency, with 41 bacterial species with abundances differing between highly and poorly efficient birds. Furthermore, we predicted that the caecal microbiota of efficient birds might be enriched in genes contributing to the degradation of short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of the genetic selection led on digestibility on the caecal microbiota taxonomic composition. They open the way toward the identification of specific, causal genes of the host controlling variations in the abundances of bacterial taxons.

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions

Phosphorus is an essential mineral for all living organisms and a limited resource worldwide. Variation and heritability of phosphorus utilization (PU) traits were observed, indicating the general possibility of improvement. Molecular mechanisms of PU, including host and microbial effects, are still poorly understood. The most promising molecules that interact between the microbiome and host are microRNAs. Japanese quail representing extremes for PU were selected from an F2 population for miRNA profiling of the ileal tissue and subsequent association with mRNA and microbial data of the same animals. Sixty-nine differentially expressed miRNAs were found, including 21 novel and 48 known miRNAs. Combining miRNAs and mRNAs based on correlated expression and target prediction revealed enrichment of transcripts in functional pathways involved in phosphate or bone metabolism such as RAN, estrogen receptor and Wnt signaling, and immune pathways. Out of 55 genera of microbiota, seven were found to be differentially abundant between PU groups. The study reveals molecular interactions occurring in the gut of quail which represent extremes for PU including miRNA-16-5p, miR-142b-5p, miR-148a-3p, CTDSP1, SMAD3, IGSF10, Bacteroides, and Alistipes as key indicators due to their trait-dependent differential expression and occurrence as hub-members of the network of molecular drivers of PU.

Short-chain fatty acids and ceca microbiota profiles in broilers and turkeys in response to diets supplemented with phytase at varying concentrations, with or without xylanase

Two independent studies were performed, each with a 3 × 2 factorial arrangement to compare the response in broilers and turkeys to phytase and xylanase supplementation on cecal fermentation and microbial populations. For both studies, 960 Ross 308 and 960 BUT 10 (1-day-old) were allocated to 1 of 6 experimental treatments: (1) control diet, containing the standard dose (100 g/ton) of phytase (STD-Xyl); (2) the control diet with 100 g/ton of xylanase (STD + Xyl); (3) the control diet supplemented on top with 2 fold the standard dose of phytase (200 g/ton), also referred as superdosing (SD-Xyl); (4) the superdosed diet with 100 g/ton of xylanase (SD + Xyl); (5) the control diet supplemented with 5-fold the standard dose of phytase (500 g/ton), also referred as megadosing (MD-Xyl); and (6) the megadosed diet with 100 g/ton of xylanase (MD + Xyl). Each treatment had 8 replicates of 20 animals. Broiler and turkey diets, based on wheat, soybean meal, rapeseed, and barley, and water were available ad libitum. On day 28, the cecal contents from 5 birds per pen were collected. The profile of short-chain fatty acids (SCFA) and microbiome structure (by % guanidine and cytosine [G + C] method) were analyzed. Selected % G + C fractions were used for 16S rDNA sequencing for the identification of bacteria. No treatment effects were noted on SCFA concentrations in either broilers or turkeys. Broilers fed MD diets had greater proportions of unclassified Clostridiales, Mollicutes (RF9) and Faecalibacterium. Xylanase supplementation in broilers resulted in lower proportions of Lactobacillus but increased Mollicutes (RF9), unclassified Ruminococcus, unclassified Clostridiales, and Bifidobacterium. The microbiome in turkeys was unaffected by phytase supplementation, but xylanase supplementation increased the proportions of Lachnospiraceae (Incertae sedis), Lactobacillus, and Bifidobacterium. Supplementation of turkey diets with increasing doses of phytase did not affect the cecal microbiota in contrast to what was observed in broilers. In contrast, xylanase supplementation in both species led to significant changes in the microbial populations, suggesting a positive influence through the provision of oligosaccharides.

Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review

Understanding how dietary nutrients modulate the gut microbiome is of great interest for the development of food products and eating patterns for combatting the global burden of non-communicable diseases. In this narrative review we assess scientific studies published from 2005 to 2019 that evaluated the effect of micro- and macro-nutrients on the composition of the gut microbiome using in vitro and in vivo models, and human clinical trials. The clinical evidence for micronutrients is less clear and generally lacking. However, preclinical evidence suggests that red wine- and tea-derived polyphenols and vitamin D can modulate potentially beneficial bacteria. Current research shows consistent clinical evidence that dietary fibers, including arabinoxylans, galacto-oligosaccharides, inulin, and oligofructose, promote a range of beneficial bacteria and suppress potentially detrimental species. The preclinical evidence suggests that both the quantity and type of fat modulate both beneficial and potentially detrimental microbes, as well as the Firmicutes/Bacteroides ratio in the gut. Clinical and preclinical studies suggest that the type and amount of proteins in the diet has substantial and differential effects on the gut microbiota. Further clinical investigation of the effect of micronutrients and macronutrients on the microbiome and metabolome is warranted, along with understanding how this influences host health.

Development of the Ileal Microbiota in Three Broiler Breeds

The development and succession of the microbiota in ileal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, n = 36; Hubbard JA87, n = 38; and Ross 308, n = 36) was observed between 3 and 42 days post hatch (d.p.h). Chicks were housed in the same room of a climate-controlled, biosecure chicken housing unit. Between 0 and 14 d.p.h, chicks were kept in three circular brooder pens ensuring a mixture of breeds in each brooder. From 22 d.p.h, chicks were removed from the brooders and kept in the same room. DNA was extracted from a pooled sample of ileal mucus and luminal contents taken from five birds of each breed at 3, 7, 14, 21, 28, and 42 d.p.h. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. The initial microbiota in the ileum varied between breeds. The common features were a low diversity and general dominance by one or two taxa such as Enterococcus or Escherichia with relatively low numbers of Lactobacillus. Escherichia became the most abundant genus in samples where Enterococcus was previously the dominant taxa. The next phase of development was marked by an increase in the abundance of Candidatus Arthromitus in the mucus and Lactobacillus in the lumen. The high abundance of Candidatus Arthromitus persisted between 7 and 14 d.p.h after which Lactobacillus became the most abundant genus in both the mucus and lumen. Dominance of the ileal microbiota by Lactobacillus was a transient feature. By 42 d.p.h, the relative abundance of Lactobacillus had fallen while a range of other taxa including Escherichia, Turicibacter, and members of Clostridiales increased. This general pattern was followed by all breeds, however, the rate at which succession occurred differed as Ross matured quicker than Cobb with Hubbard as an intermediate.

Phytate degradation in gnotobiotic broiler chickens and effects of dietary supplements of phosphorus, calcium, and phytase

Gnotobiotic broiler chickens were used to study interactive effects of supplemented phosphorus, calcium (PCa), and phytase (Phy) on myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP₆) degradation and release of myo-inositol in the digestive tract. In 2 subsequent runs, the chickens were subjected to 1 of 4 dietary treatments with and without PCa and Phy supplementation. Sanitized eggs were hatched in 8 germfree isolators, and a minimum of 9 male Ross 308 chickens were placed in each pen (total 16 pens). Treatments implemented on day 10 included gamma-irradiated diets without (PCa−; 4.1 g P and 6.2 g Ca/kg DM) or with (PCa+; 6.9 g P and 10.4 g Ca/kg DM) monosodium phosphate and limestone supplementation and without (Phy−) or with (Phy+) 1,500 FTU Phy/kg feed in a factorial arrangement. On day 15, digesta was collected from different sections of the intestinal tract and analyzed for InsP isomers and myo-inositol. The isolators did not remain germfree, but analysis of contaminants and results of InsP degradation indicated no or minor effects of the identified contaminants. Prececal InsP₆ disappearance was 42% with the PCa−Phy− treatment and 17% with PCa+Phy−. No InsP_3–4 isomers were found in the digesta of the terminal ileum in PCa−Phy−. The concentration of myo-inositol in the ileal digesta from PCa−Phy− (6.1 μmol/g DM) was significantly higher than that from PCa+Phy− (1.7 μmol/g DM), suggesting rapid degradation of the lower InsP isomers by mucosal phosphatases and their inhibition by PCa. Phytase supplementation increased InsP₆ disappearance and prevented inhibitory effects of PCa supplements (72% in PCa−Phy+ and 67% in PCa+Phy+). However, PCa supplementation reduced the degradation of lower InsP isomers mainly in the posterior intestinal sections in the presence of Phy, resulting in significantly lower myo-inositol concentrations. It is concluded that mucosa-derived phosphatases might significantly contribute to InsP₆ degradation in broiler chickens. The potential of mucosa-derived phosphatases to degrade InsP₆ and lower InsP is markedly reduced by dietary PCa supplementation.

Dietary fiber and chicken microbiome interaction: Where will it lead to?

The last few decades have been marked by a rapid genetic improvement in chicken growth rates. The modern-day chicken is more efficient in converting feed into muscle mass than their predecessors. This enhanced efficiency emanates from better nutrient digestion, absorption, and metabolism. The gut has therefore become a research focus especially after the ban on the use of antibiotics as growth promoters (AGP) in poultry. In pursuance of better gut health in the post-AGP era, many different strategies are being continuously sought and tested. The gut is inhabited by more than 900 bacterial species along with fungi and archaea, and they play an important role to maintain a conducive milieu for the host. A beneficial shift in the microbial ecosystem of the chicken can be promoted by many dietary and non-dietary interventions, however, diet is ranked as one of the most important and potent regulators of gut microbiota composition. Therefore, the constituents of the diet warrant special attention in the modulation of the gut ecosystem. Among dietary constituents, fiber possesses a significant ability to modulate the microbiota. In this review, we will highlight the importance of fiber in poultry nutrition and will also discuss the effects of fiber on gut microbiota and its resultant ramifications on the liver and brain.

Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens

Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.

Examination of the Expression of Immunity Genes and Bacterial Profiles in the Caecum of Growing Chickens Infected with Salmonella Enteritidis and Fed a Phytobiotic

Simple Summary

Salmonellosis is among the most common infectious poultry diseases that also represent a high risk to human health. The pathological process caused by Salmonella enterica serovar Enteritidis (SE) triggers in the caecum the expression of certain genes, e.g., avian β-defensins (gallinacins), cytokines (interleukins), etc. On the other hand, gut microbiota influences the infection potential of pathogens. The present study aimed at revealing the differential expression of genes associated with the immune system and changes in the bacterial communities in the intestine of growing chickens in response to SE infection. We also tested a feed additive, essential oils-based phytobiotic Intebio, as a potential alternative to antibiotics and showed effects of its administration on the caecal microbiome composition and the expression of some genes related to immunity. The phytobiotic showed its efficiency for application in poultry rearing and production.

Abstract

This study was performed to investigate the differential expression of eight immunity genes and the bacterial profiles in the caecum of growing chickens challenged with Salmonella enterica serovar Enteritidis (SE) at 1 and 23 days post inoculation (dpi) in response to SE infection at 19 days of age and administration of the phytobiotic Intebio. Following infection, the genes CASP6 and IRF7 were upregulated by greater than twofold. Chicks fed Intebio showed at 1 dpi upregulation of AvBD10, IL6, IL8L2, CASP6 and IRF7. At 23 dpi, expression of AvBD11, IL6, IL8L2, CASP6 and IRF7 lowered in the experiment subgroups as compared with the control. Examination of the caecal contents at 1 dpi demonstrated a significant decrease in the microbial biodiversity in the infected subgroup fed normal diet. Bacterial content of Lactobacillus and Bacillus declined, while that of Enterobacteriaceae rose. In the infected subgroup fed Intebio, a pronounced change in composition of the microflora was not observed. In the early infection stages, the phytobiotic seemed to promote response to infection. Subsequently, an earlier suppression of the inflammatory reaction took place in chickens fed Intebio. Thus, use of Intebio as a drug with phytobiotic activity in chickens, including those infected with Salmonella, proved to be promising.

Effects of protease and phytase supplements on small intestinal microbiota and amino acid digestibility in broiler chickens

The objective of this study was to determine the effects of protease origin and dosage on the prececal (pc) amino acid (AA) digestibility and the influence on composition of the microbial community in the small intestine. In addition, the effects of phytase supplementation were investigated. A total of 8 dietary treatments were included. The basal diet contained mainly corn and soybean meal. Three protease products were added to the basal diet, each at the level recommended by the supplier and at an 8-fold level. Phytase was supplemented in another dietary treatment. Each dietary treatment was allocated to 8 replicates of 15 birds each. The experimental diets were offered from day 15 to 21 for ad libitum consumption. The effect of protease supplementation on the pc AA digestibility depended on the protease product type and the amount supplemented. The pc AA digestibility was significantly increased by 1 protease product when supplemented at high level and when phytase was supplemented. In all the other treatments, protease supplementation had no significant influence or it decreased pc AA digestibility, when compared with the treatment with no enzymes added. In general, Firmicutes was the most abundant phylum among the ileal microbiota across all the treatments. Significant effects on microbiota composition were observed at the genus level for some but not all protease treatments and phytase supplementation. The genera Streptococcus, Lactobacillus, and uncultured Clostridiaceae were responsible for these differences. Furthermore, microbial networks established for each diet showed either high or low number of intergeneric interactions, but without a consistent enzyme effect. We conclude that enzyme supplementation effects were evident in the terminal small intestine microbiota composition, and to a lesser extent, in pc AA digestibility. However, the changes in microbiota composition and pc AA digestibility could not be correlated, indicating absence of a causal relationship.

Impact of coccidiostat and phytase supplementation on gut microbiota composition and phytate degradation in broiler chickens

Background

There is good evidence for a substantial endogenous phytase activity originating from the epithelial tissue or the microbiota resident in the digestive tract of broiler chickens. However, ionophore coccidiostats, which are frequently used as feed additives in broiler diets to prevent coccidiosis, might affect the bacterial composition and the abundance of phytase producers in the gastrointestinal tract. The aim of the present study was to investigate whether supplementation of a frequently used mixture of the coccidiostats Narasin and Nicarbazin alone or together with a phytase affects microbiota composition of the digestive tract of broiler chickens, characteristics of phytate breakdown in crop and terminal ileum, and precaecal phosphorus and crude protein digestibility.

Results

Large differences in the microbial composition and diversity were detected between the treatments with and without coccidiostat supplementation. Disappearance of myo-inositol 1,2,3,4,5,6-hexakis(dihydrogen phosphate) (InsP₆) in the digestive tract, precaecal P digestibility, inorganic P in blood serum, and the concentration of inositol phosphate isomers in the crop and ileum digesta were significantly affected by phytase supplementation, but not by coccidiostat supplementation. Crude protein digestibility was increased by coccidiostat supplementation when more phosphate was available. Neither microbial abundance and diversity nor any other trait measured at the end of the experiment was affected by coccidiostat when it was only supplemented from day 1 to 10 of age.

Conclusions

The coccidiostats used herein had large effects on overall microbiota composition of the digestive tract. The coccidiostats did not seem to affect endogenous or exogenous phytase activity up to the terminal ileum of broiler chickens. The effects of phytase on growth, phosphorus digestibility, and myo-inositol release were not altered by the presence of the coccidiostats. The effects of phytase and coccidiostats on nutrient digestibility can be of significant relevance for phosphorus and protein-reduced feeding concepts if confirmed in further experiments.

Electronic supplementary material

The online version of this article (10.1186/s42523-019-0006-2) contains supplementary material, which is available to authorized users.

Relationship between Gut Microbiota and Phosphorus Metabolism in Hemodialysis Patients: A Preliminary Exploration

Background

Hyperphosphatemia is a risk factor associated with mortality in patients on maintenance hemodialysis. Gut absorption of phosphate is the major source. Recent studies indicated that the intestinal flora of uremic patients changed a lot compared with the healthy population, and phosphorus is an essential element of bacterial survival and reproduction. The purpose of this study was to explore the role of intestinal microbiota in phosphorus metabolism.

Methods

A prospective self-control study was performed from October 2015 to January 2016. Microbial DNA was isolated from the stools of 20 healthy controls and 21 maintenance hemodialysis patients. Fourteen out of the 21 patients were treated with lanthanum carbonate for 12 weeks. Thus, stools were also collected before and after the treatment. The bacterial composition was analyzed based on 16S ribosomal RNA pyrosequencing. Bioinformatics tools, including sequence alignment, abundance profiling, and taxonomic diversity, were used in microbiome data analyses. Correlations between genera and the serum phosphorus were detected with Pearson's correlation. For visualization of the internal interactions and further measurement of the microbial community, SparCC was used to calculate the Spearman correlation coefficient with the corresponding P value between each two genera.

Results

Thirteen genera closely correlated with serum phosphorus and the correlation coefficient was above 0.4 (P < 0.05). We also found that 58 bacterial operational taxonomic units (OTUs) were significantly different and more decreased OTUs were identified and seven genera (P < 0.05) were obviously reduced after using the phosphate binder. Meanwhile, the microbial richness and diversity presented downward trend in hemodialysis patients compared with healthy controls and more downward trend after phosphorus reduction. The co-occurrence network of genera revealed that the network complexity of hemodialysis patients was significantly higher than that of controls, whereas treatment with lanthanum carbonate reduced the network complexity.

Conclusions

Gut flora related to phosphorus metabolism in hemodialysis patients, and improving intestinal microbiota may regulate the absorption of phosphate in the intestine. The use of phosphate binder lanthanum carbonate leads to a tendency of decreasing microbial diversity and lower network complexity.

Insight Into Dynamics of Gut Microbial Community of Broilers Fed With Fructooligosaccharides Supplemented Low Calcium and Phosphorus Diets

We investigated how the microbiota in the ileum and cecum of broiler chickens fed a diet of low calcium (Ca) and available phosphorus (aP) and prebiotic fructooligosaccharides (FOS) supplements changed over a 3 weeks period. Three dietary treatments were randomly assigned to four replicate cages of five birds each, including: positive control (PC), a wheat-corn-soybean meal-based diet; negative control (NC), as PC with 0.2% reduced Ca and aP; and NC + FOS, as NC supplemented with 0.5% of FOS. Ileal and cecal digesta were sampled from each replicate (n = 4) on d21 and processed for 16S rRNA gene amplicon (V4 region) sequencing using Illumina platform. Statistical differences were observed in the microbiome by GI location as determined by 2-way ANOVA and Permutational MANOVA. On average, 24,216 sequence reads per sample were generated resulting in 800 and 1,280 operational taxonomic units in the ileal and cecal digesta, respectively. Difference (P < 0.0001) on alpha diversity and abundances of several phyla was observed between ileal and cecal digesta. ß-diversity was different (P < 0.05) between each treatment groups in the ileum but not in the cecum. In the cecum, species richness, phylogenetic diversity, and the number of observed species were higher in PC compared to NC + FOS (P < 0.05). Several phyla, including Cyanobacteria, Firmicutes, and Proteobacteria, had significantly different abundance in the ileal and cecal digesta (P < 0.05). In the ileal digesta, positive correlation were observed between Salinibacterium and Lysobacter and PC diet. Blautia, Faecalibacterium and Pseudomonas and the NC diet and Lactobacillus and Escherichia and the NC + FOS diet. In the cecal digesta, Butyrivibrio, and Allobaculum were positively correlated to PC. Although, Clostridium and Anaerotruncus were positively correlated to NC + FOS, they showed negative correlation to PC and NC. The study concludes that dietary Ca and aP level and FOS supplementation alters ileal microbiota of the broiler chickens.

Phytate degradation and phosphorus digestibility in broilers and turkeys fed different corn sources with or without added phytase

The aim of the present study was to test whether different dietary corn sources and phytase supplementation affect the prececal phosphorus digestibility (pcdP) and appearance of inositol phosphates in the lower ileum of growing broiler chickens and turkeys. Two experiments were conducted, one with broiler chickens and one with turkeys. Four corn diets were provided; these were formulated to contain low P and calcium (Ca) contents and incorporated 43% of one of the four different corn sources. Diets were either unsupplemented or supplemented with 500 FTU of an Escherichia coli-derived phytase/kg feed. Experimental diets were fed ad libitum from day 20 post-hatch. At 28 d of age, digesta were sampled from the lower ileum of animals to determine pcdP and pc myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP6) degradation and to analyze the concentrations of lower inositol phosphate isomers. The pcdP of non-supplemented diets ranged from 51 to 60% and from 22 to 28% in broilers and turkeys, respectively. A negative correlation was observed between the InsP6 content of the corn source and the pcdP of diets in broilers only. Without phytase supplementation, pc InsP6 degradation ranged from 64 to 76% in broilers and from 6 to 15% in turkeys. Phytase increased the pcdP by around 15% in broilers (P < 0.001) and 9 to 17% in turkeys (P < 0.001). In turkeys, phytase efficacy was greatest when the diets contained corn with higher contents of ether extract and InsP6. An effect of corn source on the appearance of lower InsPs in the ileal digesta was found in broilers only. These results suggest that broilers possess a greater capacity for InsP6 degradation and hydrolysis of lower InsPs compared with turkeys. Furthermore, the results are influenced by the corn source used. Further research is needed to identify the factors responsible for the low level of phytate degradation in turkeys in order to improve the availability of InsP6-P and the efficacy of phytase.

Intestinal Morphologic and Microbiota Responses to Dietary Bacillus spp. in a Broiler Chicken Model

Dietary inclusion of probiotic Bacillus spp. beneficially affect the broiler chickens by balancing the properties of the indigenous microbiota causing better growth performance. The effects of three Bacillus spp. on the growth performance, intestinal morphology and the compositions of jejunal microflora were investigated in broiler chickens. A total of 480 1-day-old male Arbor Acres broilers were randomly divided into four groups. All groups had six replicates and 20 birds were included in each replicate. The control birds were fed with a corn-soybean basal diet, while three treatment diets were supplemented with Bacillus coagulans TBC169, B. subtilis PB6, and B. subtilis DSM32315 with a dosage of 1 × 109 cfu/kg, respectively. The experiment lasted for 42 days. The compositions and diversity of jejunal microflora were analyzed by MiSeq high-throughput sequencing. The B. coagulans TBC169 group showed marked improvements of growth performance, nutrient digestibility and intestinal morphology compared with the other B. subtilis treatments. B. coagulans TBC169 supplementation improved the average body weight (BW), average daily weight gain (ADG), total tract apparent digestibility of crude protein and gross energy (GE), and reduced feed conversion rate (FCR) compared with the control group (P < 0.05). The villus height to crypt depth ratio (VH/CD) of jejunum and duodenum was increased in the birds fed with B. coagulans TBC169 compared with the control group (P < 0.05). However, two B. subtilis treatments presented more positive variation of the jejunum microflora of chickens than that in the B. coagulans TBC169 group. B. subtilis PB6 and B. subtilis DSM32315 treatments improved the diversity of jejunal microbiota on day 21 compared with the control (P < 0.05), while which were decreased on day 42 (P < 0.05). The supplementation with B. coagulans TBC169 significantly improved the proportion of Firmicutes, otherwise two B. subtilis significantly improved the proportion of Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria at the phylum level during starter phase and decreased the proportion of Bacteroidetes during growing phase compared with the control. The supplementation with B.subtilis DSM32315 significantly improved the proportion of Clostridiales during starter phase, whereas two B. subtilis significantly improved the proportion of Pseudomonas, Burkholderia, Prevotella, DA101 during growing phase at the genus level compared with the control. In conclusion, the dietary supplementation with probiotic Bacillus spp. strains improved body weight and intestinal morphology in broiler chickens, which might be associated with the gut microbiota.

Strategies to modulate the intestinal microbiota and their effects on nutrient utilization, performance, and health of poultry

Poultry is widely produced and consumed meat globally. Its demand is expected to continue increasing to meet the animal protein requirement for ever-increasing human population. Thus, the challenge that poultry scientists and industry face are to produce sufficient amount of poultry meat in the most efficient way. In the past, using antibiotics to promote the growth of poultry and manage gut microbiota was a norm. However, due to concerns over potential fatalistic impacts on food animals and indirectly to humans, their use as feed additives are banned or regulated in several jurisdictions. In this changed context, several alternative strategies have been proposed with some success that mimics the functions of antibiotics as growth promoters and modulate gut microbiota for their beneficial roles. These include the use of probiotics, prebiotics, organic acids, and exogenous enzyme, among others. Gut microbiota and their metabolic products improve nutrient digestion, absorption, metabolism, and overall health and growth performance of poultry. This paper reviews the available information on the effect of feed additives used to modulate intestinal microbiota of poultry and their effects on overall health and growth performance. Understanding these functions and interactions will help to develop new dietary and managerial strategies that will ultimately lead to enhanced feed utilization and improved growth performance of poultry. This review will help future researchers and industry to identify alternative feed ingredients having properties like prebiotics, probiotics, organic acids, and exogenous enzymes.

Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.

Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age

The study was conducted to distinguish the effect of dietary non-phytate phosphorus (NPP) levels on the community diversity and structure of the cecal microbiota in meat duck based on 16S rDNA high-throughput sequencing. In total, 525 1-d-old ducklings were fed diets (105 ducklings, 7 pens of 15 ducklings, on each diet) containing five levels of NPP (0.22, 0.34, 0.40, 0.46, and 0.58%) for 21 days. The results showed that dietary NPP levels linearly and quadratically increased (P < 0.05) 21 d body weight, 1 to 21 d feed intake and NPP intake, and contrarily, linearly decreased (P < 0.05) β-diversity of cecal microbial population in ducks. ß-diversity analyses showed that microbiota clustering based on dietary NPP levels occured, with 0.22% NPP groups distinctly different from the 0.46% and 0.58% NPP group samples. Moreover, dietary NPP levels could change the relative abundance of the phylum Proteobacteria (linear, P < 0.05), genera Eubacterium coprostanoligenes (quadratic, P < 0.05), Ruminococcaceae UCG-014 (quadratic, P < 0.05) and Subdoligrannulum (linear, P < 0.05), and Lachnospiraceae family (quadratic, P < 0.05) in cecal microbiota of ducks. Increasing the dietary NPP level influenced the cecal microbiota and positively affected the growth of meat ducks.

Effect of supplemental phytase and xylanase in wheat-based diets on prececal phosphorus digestibility and phytate degradation in young turkeys

This study aimed to investigate the effect of phytase and a combination of phytase and xylanase on the prececal phosphorus digestibility (pcdP) of wheat-based diets in turkeys. A low-P basal diet (BD) based on cornstarch and soybean meal, and 2 diets containing 43% of different wheat genotypes (genotype diets GD₆ or GD₇) were fed to turkeys from 20 to 27 d of age. Diets were fed either without enzyme supplementation or supplemented with phytase (500 FTU/kg) or a combination of phytase and xylanase (16,000 BXU/kg). At 27 d of age, digesta were sampled from the lower ileum of animals to determine pcdP and pc myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP₆) disappearance, and to analyze the concentrations of lower inositol phosphate isomers. Similar pcdP was observed in non-supplemented BD and GD (∼36%). Phytase alone increased the pcdP in all diets by 8 to 12%, but a beneficial effect of xylanase was found only for BD. Similar results were found for pc InsP₆ disappearance, although xylanase addition compared to phytase alone decreased pc InsP₆ disappearance in GD₇ compared to phytase alone. Animals fed GD₇ performed better than those fed GD₆; however, these differences could not be linked to the pcdP. The pattern of lower inositol phosphates in digesta also changed with enzyme supplementation, resulting in lower proportions of InsP₅ and higher proportions of InsP₄. Phytase alone decreased Ins(1,2,3,4,6)P₅ but increased D-Ins(1,2,3,4,5)P₅ and D-Ins(1,2,5,6)P₄ concentrations. An additional increase in D-Ins(1,2,3,4,5)P₅ and D-Ins(1,2,5,6)P₄ concentrations was achieved with xylanase, although for the former isomer, this was observed only with GD. These results indicate that enzyme supplementation alters the pc degradation of InsP₆, and that combining both enzymes had a minor additional effect on the pcdP from wheat-based diets when compared to phytase alone.

Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome

The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics. However, the respective analyses are still at the beginning and currently there is a lack of information in regard to the activity and functional characterization of the gut microbial communities. In the future, the use of multi-omics approaches may enhance research related to chicken production, animal and also public health. Furthermore, combinations with other disciplines such as genomics, immunology and physiology may have the potential to elucidate the definition of a "healthy" gut microbiota.

Results of an international phosphorus digestibility ring test with broiler chickens

The objective of this ring test was to investigate the prececal phosphorus (P) digestibility of soybean meal (SBM) in broiler chickens using the trial protocol proposed by the World's Poultry Science Association. It was hypothesized that prececal P digestibility of SBM determined in the collaborating stations is similar. Three diets with different inclusion levels of SBM were mixed in a feed mill specialized in experimental diets and transported to 17 collaborating stations. Broiler chicks were raised on commercial starter diets according to station-specific management routine. Then they were fed the experimental diets for a minimum of 5 d before content of the posterior half of the ileum was collected. A minimum of 6 experimental replicates per diet was used in each station. All diets and digesta samples were analyzed in the same laboratory. Diet, station, and their interaction significantly affected (P < 0.05) the prececal digestibility values of P and calcium of the diets. The prececal P digestibility of SBM was determined by linear regression and varied among stations from 19 to 51%, with significant differences among stations. In a subset of 4 stations, the prececal disappearance of myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate)-P; InsP6-P) also was studied. The prececal InsP6-P disappearance correlated well with the prececal P digestibility. We hypothesized that factors influencing InsP6 hydrolysis were main contributors to the variation in prececal P digestibility among stations. These factors were probably related to the feeding and housing conditions (floor pens or cages) of the birds in the pre-experimental phase. Therefore, we suggest that the World's Poultry Science Association protocol for the determination of digestible P be should extended to the standardization of the pre-experimental period. We also suggest that comparisons of P digestibility measurements among studies are made only with great caution until the protocol is more refined.

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing

Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.

Insights into Broilers' Gut Microbiota Fed with Phosphorus, Calcium, and Phytase Supplemented Diets

Phytase supplementation in broiler diets is a common practice to improve phosphorus (P) availability and to reduce P loss by excretion. An enhanced P availability, and its concomitant supplementation with calcium (Ca), can affect the structure of the microbial community in the digestive tract of broiler chickens. Here, we aim to distinguish the effects of mineral P, Ca, and phytase on the composition of microbial communities present in the content and the mucosa layer of the gastrointestinal tract (GIT) of broiler chickens. Significant differences were observed between digesta and mucosa samples for the GIT sections studied (p = 0.001). The analyses of 56 individual birds showed a high microbial composition variability within the replicates of the same diet. The average similarity within replicates of digesta and mucosa samples across all diets ranged from 29 to 82% in crop, 19-49% in ileum, and 17-39% in caeca. Broilers fed with a diet only supplemented with Ca had the lowest body weight gain and feed conversion values while diets supplemented with P showed the best performance results. An effect of each diet on crop mucosa samples was observed, however, similar results were not obtained from digesta samples. Microbial communities colonizing the ileum mucosa samples were affected by P supplementation. Caeca-derived samples showed the highest microbial diversity when compared to the other GIT sections and the most prominent phylotypes were related to genus Faecalibacterium and Pseudoflavonifractor, known for their influence on gut health and as butyrate producers. Lower microbial diversity in crop digesta was linked to lower growth performance of birds fed with a diet only supplemented with Ca. Each diet affected microbial communities within individual sections, however, no diet showed a comprehensive effect across all GIT sections, which can primarily be attributed to the great variability among replicates. The substantial community differences between digesta and mucosa derived samples indicate that both habitats have to be considered when the influence of diet on the gut microbiota, broiler growth performance, and animal health is investigated.