Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken

The Joint Contribution of Host Genetics and Probiotics to Pig Growth Performance

Intestinal probiotics significantly regulate the growth performance of their host, with their composition being influenced by various factors. While many studies have explored how gut microbiota composition affects growth traits such as body weight and BMI, the research on probiotics influenced by host genetic factors, and their subsequent impact on host growth performance, remains limited. To address this research gap, we collected fecal and tissue samples, as well as phenotypic data, from 193 Yunong black pigs at 280 days of age. We then sequenced and genotyped all 193 subjects using the 50K SNP BeadChip, yielding a comprehensive dataset for genetic and microbiome analyses. We then employed microbiome-wide association studies (MWAS), a meta-analysis, and microbiome-wide genetic association studies (MGWASs) to examine the relationship between host genetics, gut microbiota, and growth performance. Four key microbial taxa, namely Coprococcus, Blautia, Ruminococcaceae, and RF16, were identified as being significantly associated with body weight and BMI. The MGWAS analysis revealed that both Coprococcus and Ruminococcaceae were significantly associated with host genomic variations. A total of four important single nucleotide polymorphisms (SNPs) were mapped to two chromosomal regions, corresponding to three candidate genes. Among them, the candidate genes INPP4B, SCOC, and PABPC4L were identified as being related to the abundance of key microbes. This study provides new insights into the joint contributions of host genetics and probiotics to host growth traits, offering theoretical guidance and data support for the development of efficient and targeted breeding strategies.

Estimates of microbiome heritability across hosts

Microbiomes contribute to variation in many plant and animal traits, suggesting that microbiome-mediated traits could evolve through selection on the host. However, for such evolution to occur, microbiomes must exhibit sufficient heritability to contribute to host adaptation. Previous work has attempted to estimate the heritability of a variety of microbiome attributes. Here we show that most published estimates are limited to vertebrate and plant hosts, but significant heritability of microbiome attributes has been frequently reported. This indicates that microbiomes could evolve in response to host-level selection, but studies across a wider range of hosts are necessary before general conclusions can be made. We suggest future studies focus on standardizing heritability measurements for the purpose of meta-analyses and investigate the role of the environment in contributing to heritable microbiome variation. This could have important implications for the use of microbiomes in conservation, agriculture and medicine.

Implication of digestive functions and microbiota in the establishment of muscle glycogen differences between divergent lines for ultimate pH

Both the quality of chicken meat and the quality of chicks are influenced by the level of breast muscle glycogen reserves. In order to study the role of digestive metabolism in establishing this muscular phenotype, we compared two divergent chicken lines for the ultimate pH (pHu) of the breast meat, a proxy for glycogen reserves. Males aged 4 weeks had twice the breast muscle glycogen content in the pHu- line (low pHu) than in the pHu +  line (high pHu). The increase in glycogen reserves (pHu-) was associated with a higher relative weight of the proventriculus and gizzard, as well as better apparent ileal digestibility of nitrogen and calcium. The diversity of the cecal microbiota was comparable, but three bacterial genera (Lachnospira, Lachnospiraceae UCG-010, Caproiciproducens) varied between the lines. The differences observed could lead to down-regulation of carbon fixation in prokaryotes and of the citrate cycle in the pHu + line. RNA-seq analysis of the jejunum, the major site of nutrient absorption, revealed 149 genes differentially expressed (DE) between the lines, including several genes linked to immunity, hormonal response and circadian rhythms that are less expressed in pHu + animals. Others involved in cell migration and proliferation, and more generally tissue morphogenesis, also differed between the lines. Among the DE genes, several co-localized with Quantitative Trait Loci (QTL) controlling pHu and selection signatures identified in the divergent lines, such as the gene coding for ghrelin, a hormone regulating appetite.

Gut microbiota intervention alleviates pulmonary inflammation in broilers exposed to fine particulate matter from broiler house

The gut microbiota of poultry is influenced by a variety of factors, including feed, drinking water, airborne dust, and footpads, among others. Gut microbiota can affect the immune reaction and inflammation in the lungs. To investigate the effect of gut microbiota variation on lung inflammation induced by PM2.5 (fine particulate matter) in broilers, 36 Arbor Acres (AA) broilers were randomly assigned to three groups: control group (CON), PM2.5 exposure group (PM), and PM2.5 exposure plus oral antibiotics group (PMA). We used non-absorbable antibiotics (ABX: neomycin and amikacin) to modify the microbiota composition in the PMA group. The intervention was conducted from the 18th to the 28th day of age. Broilers in the PM and PMA groups were exposed to PM by a systemic exposure method from 21 to 28 days old, and the concentration of PM2.5 was controlled at 2 mg/m3. At 28 days old, the lung injury score, relative mRNA expression of inflammatory factors, T-cell differentiation, and dendritic cell function were significantly increased in the PM group compared to the CON group, and those of the PMA group were significantly decreased compared to the PM group. There were significant differences in both α and β diversity of cecal microbiota among these three groups. Numerous bacterial genera showed significant differences in relative abundance among the three groups. In conclusion, gut microbiota could affect PM2.5-induced lung inflammation in broilers by adjusting the capacity of antigen-presenting cells to activate T-cell differentiation.

IMPORTANCE

Gut microbes can influence the development of lung inflammation, and fine particulate matter collected from broiler houses can lead to lung inflammation in broilers. In this study, we explored the effect of gut microbes modified by intestinal non-absorbable antibiotics on particulate matter-induced lung inflammation. The results showed that modification in the composition of gut microbiota could alleviate lung inflammation by attenuating the ability of dendritic cells to stimulate T-cell differentiation, which provides a new way to protect lung health in poultry farms.

Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment

Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn [LEG] and Rhode Island Red [RIR]). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.

OMICs approaches and technologies for understanding low-high feed efficiency traits in chicken: implication to breeding

In poultry production, there has been a trend of continuous increase in cost of feed ingredients which represents the major proportion of the production costs. Feed costs can be reduced by improving feed efficiency traits which increase the possibility of using various indigestible feed sources and decrease the environmental impact of the enhanced poultry production. Therefore, feed efficiency has been used as one of the most important economic traits of selection in the breeding program of chickens. Recently, many OMICs experimental studies have been designed to characterize biological differences between the high and low feed efficiency chicken phenotypes. Biological complexity cannot be fully captured by main individual OMICs such as genomics, transcriptomics, proteomics and metabolomics. Therefore, researchers have combined multiple assays from the same set of samples to create multi-OMICs datasets. OMICs findings are crucial in improving existing approaches to poultry breeding. The current review aimed to highlight the components of feed efficiency and general OMICs approaches and technologies. Besides, individual and multi-OMICs based understanding of chicken feed efficiency traits and the application of the acquired knowledge in the chicken breeding program were addressed.

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.

Microbial Community and Abundance of Selected Antimicrobial Resistance Genes in Poultry Litter from Conventional and Antibiotic-Free Farms

In this study, a culture-independent approach was applied to compare the microbiome composition and the abundance of the antimicrobial resistance genes (ARGs) aadA2 for aminoglycosides, tet(A), tet(B), tet(K), and tet(M) for tetracyclines, and mcr-1 for colistin in broiler litter samples collected from conventional and antibiotic-free flocks located in Central Italy. A total of 13 flocks and 26 litter samples, collected at the beginning and at the end of each rearing cycle, were submitted to 16s rRNA sequence analysis and quantitative PCR for targeted ARGs. Firmicutes resulted in the dominant phylum in both groups of flocks, and within it, the Clostridia and Bacilli classes showed a similar distribution. Conversely, in antibiotic-free flocks, a higher frequency of Actinobacteria class and Clostridiaceae, Lactobacillaceae, Corynebacteriaceae families were reported, while in the conventional group, routinely treated with antibiotics for therapeutic purposes, the Bacteroidia class and the Enterobacteriaceae and Bacillaceae families were predominant. All investigated samples were found to be positive for at least one ARG, with the mean values of aadA2 and tet(A) the highest in conventional flocks by a significant margin. The results suggest that antibiotic use can influence the frequency of resistance determinants and the microbial community in poultry flocks, even though other environmental factors should also be investigated more deeply in order to identify additional drivers of antimicrobial resistance.

Association between diet and the gut microbiome of young captive red-crowned cranes (Grus japonensis)

BACKGROUND

Exploring the association of diet and indoor and outdoor environments on the gut microbiome of red-crowned cranes. We investigated the microbiome profile of the 24 fecal samples collected from nine cranes from day 1 to 35. Differences in the gut microbiome composition were compared across diet and environments.

RESULTS

A total of 2,883 operational taxonomic units (OTUs) were detected, with 438 species-specific OTUs and 106 OTUs common to the gut microbiomes of four groups. The abundance of Dietzia and Clostridium XI increased significantly when the red-crowned cranes were initially fed live mealworms. Skermanella and Deinococcus increased after the red-crowned cranes were fed fruits and vegetables and placed outdoors. Thirty-three level II pathway categories were predicted. Our study revealed the mechanism by which the gut microbiota of red-crowned cranes responds to dietary and environmental changes, laying a foundation for future breeding, nutritional and physiological studies of this species.

CONCLUSIONS

The gut microbiome of red-crowned cranes could adapt to changes in diet and environment, but the proportion of live mealworms in captive red-crowned cranes can be appropriately reduced at the initial feeding stage, reducing the negative impact of high-protein and high-fat foods on the gut microbiome and growth and development.

Host genotype affects endotoxin release in excreta of broilers at slaughter age

Host genotype, early post-hatch feeding, and pre- and probiotics are factors known to modulate the gut microbiome. However, there is a knowledge gap on the effect of both chicken genotype and these dietary strategies and their interplay on fecal microbiome composition and diversity, which, in turn, can affect the release of endotoxins in the excreta of broilers. Endotoxins are a major concern as they can be harmful to both animal and human health. The main goal of the current study was to investigate whether it was possible to modulate the fecal microbiome, thereby reducing endotoxin concentrations in the excreta of broiler chickens. An experiment was carried out with a 2 × 2 × 2 factorial arrangement including the following three factors: 1) genetic strain (fast-growing Ross 308 vs. slower growing Hubbard JA757); 2) no vs. combined use of probiotics and prebiotics in the diet and drinking water; and 3) early feeding at the hatchery vs. non-early feeding. A total of 624 Ross 308 and 624 Hubbard JA757 day-old male broiler chickens were included until d 37 and d 51 of age, respectively. Broilers (N = 26 chicks/pen) were housed in a total of 48 pens, and there were six replicate pens/treatment groups. Pooled cloacal swabs (N = 10 chickens/pen) for microbiome and endotoxin analyses were collected at a target body weight (BW) of 200 g, 1 kg, and 2.5 kg. Endotoxin concentration significantly increased with age (p = 0.01). At a target BW of 2.5 kg, Ross 308 chickens produced a considerably higher amount of endotoxins (Δ = 552.5 EU/mL) than the Hubbard JA757 chickens (p < 0.01). A significant difference in the Shannon index was observed for the interaction between the use of prebiotics and probiotics, and host genotype (p = 0.02), where Ross 308 chickens with pre-/probiotics had lower diversity than Hubbard JA757 chickens with pre-/probiotics. Early feeding did not affect both the fecal microbiome and endotoxin release. Overall, the results suggest that the chicken genetic strain may be an important factor to take into account regarding fecal endotoxin release, although this needs to be further investigated under commercial conditions.

Association of residual feed intake with intestinal microbiome and metabolome in laying period of ducks

Introduction

Residual feed intake (RFI) is a indicator to evaluate animal feed. This experiment was explored to study the relationship between intestinal microbiome and metabolome of ducks with different residual feed intake during laying period.

Methods

A total of 300 Shaoxing ducks aged 42 weeks were randomly selected and fed a diet of 60 d. At the end of the trial, 20 samples were selected according to the phenotype of RFI and divided into two groups (HRFI and LRFI). The cecal microbiota composition was explored by 16S ribosomal RNA gene sequencing and rectal metabolomics uses liquid chromatography-mass spectrometry (LC-MS) to identify the composition of metabolites in a non-targeted manner.

Results

Results show feed intake and feed conversion ratio in the group HRFI were significantly higher than those in the group LRFI (p < 0.05). Chao1 indices were higher in the group LRFI than in the HRFI (p < 0.05), Shannon and Simpson indices were higher in the group LRFI than in the HRFI (p < 0.01). After linear discriminant analysis effect size (p < 0.05, LDA score > 3), Rikenellaceae, Rikenellaceae_RC9_gut_group, Lactobacillales and Ruminococcus_2, etc. were significantly enriched in the group LRFI at the genus level, while Prevotellaceae_NK3B31_group and Bacteria were significantly enriched in the group HRFI. After LC-MS analysis we found 338 metabolic difference products and 10 metabolic pathways, including the ABC transporter system, cysteine and methionine metabolism, arginine and proline metabolism, and vitamin B6 metabolism, were identified to be associated with the significantly differentially expressed between the groups LRFI and HRFI (p < 0.05). We hypothesize that the difference between ducks with different RFIs is mainly due to the fact that ducks with LRFI have more SCFAs-producing bacteria in their gut microorganisms, which regulate the RFI of animals. This process we found that Phascolarctobaterium and Anaerobiospirillum may provide energy for ABC transporter system by producing SCFAs, and regulate RFI to improve feed utilization efficiency.

Discussion

These results revealed the relationship between microbiome and metabonomics in laying ducks with different RFI, and provided theoretical basis for further study on the relationship between them.

The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers

The gut is home to more than millions of bacterial species. The gut bacteria coexist with the host in a symbiotic relationship that can influence the host's metabolism, nutrition, and physiology and even module various immune functions. The commensal gut microbiota plays a crucial role in shaping the immune response and provides a continuous stimulus to maintain an activated immune system. The recent advancements in high throughput omics technologies have improved our understanding of the role of commensal bacteria in developing the immune system in chickens. Chicken meat continues to be one of the most consumed sources of protein worldwide, with the demand expected to increase significantly by the year 2050. Yet, chickens are a significant reservoir for human foodborne pathogens such as Campylobacter jejuni. Understanding the interaction between the commensal bacteria and C. jejuni is essential in developing novel technologies to decrease C. jejuni load in broilers. This review aims to provide current knowledge of gut microbiota development and its interaction with the immune system in broilers. Additionally, the effect of C. jejuni infection on the gut microbiota is addressed.

Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers

Despite the negative impacts of Salmonella intestinal colonization on human health, Salmonella is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of Salmonella across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between Salmonella enterica serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (n = 156/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators/room, 11 chicks/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators/breed, 108 total) were challenged with Salmonella Typhimurium (ST) (1 × 108 CFU/ml) via oral gavage while the remaining chicks (n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq. Salmonella Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7 days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (p < 0.05). Salmonella Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as Mollicutes RF39, Shuttleworthia, Flavonifractor, and Oscillibacter compared to broilers that were unchallenged with Salmonella Typhimurium (p < 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to Salmonella Typhimurium challenge. Thus, both broiler breed and Salmonella Typhimurium can impact the intestinal microbiota.

Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken

Research in mammals has evidenced that proper colonization of the gut by a complex commensal microbial community, the gut microbiota (GM), is critical for animal health and wellbeing. It greatly contributes to the control of infectious processes through competition in the microbial environment while supporting proper immune system development and modulating defence mechanisms at distant organ sites such as the lung: a concept named ‘gut-lung axis’. While recent studies point to a role of the GM in boosting immunity and pathogen resilience also in poultry, the mechanisms underlying this role are largely unknown. In spite of this knowledge gap, GM modulation approaches are today considered as one of the most promising strategies to improve animal health and welfare in commercial poultry production, while coping with the societal demand for responsible, sustainable and profitable farming systems. The majority of pathogens causing economically important infectious diseases in poultry are targeting the respiratory and/or gastrointestinal tract. Therefore, a better understanding of the role of the GM in the development and function of the mucosal immune system is crucial for implementing measures to promote animal robustness in commercial poultry production. The importance of early gut colonization in the chicken has been overlooked or neglected in industrial poultry production systems, where chicks are hampered from acquiring a complex GM from the hen. Here we discuss the concept of strengthening mucosal immunity in the chicken through GM modulation approaches favouring immune system development and functioning along the gut-lung axis, which could be put into practice through improved farming systems, early-life GM transfer, feeding strategies and pre-/probiotics. We also provide original data from experiments with germ-free and conventional chickens demonstrating that the gut-lung axis appears to be functional in chickens. These key principles of mucosal immunity are likely to be relevant for a variety of avian diseases and are thus of far-reaching importance for the poultry sector worldwide.

Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination

Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCR_ϒδ expression on TCR_ϒδ⁺ T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCR_ϒδ⁺ T cells (judged by TCR_ϒδ expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

BACKGROUND

Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

RESULTS

Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host's quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host's quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.

CONCLUSIONS

Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host's quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle

Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

BACKGROUND

Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.

RESULTS

Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.

CONCLUSIONS

Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication

Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.

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.

Association of female reproductive tract microbiota with egg production in layer chickens

BACKGROUND

The microbiota of the female reproductive tract is increasingly recognized as playing fundamental roles in animal reproduction. To explore the relative contribution of reproductive tract microbiomes to egg production in chickens, we investigated the microbiota in multiple reproductive and digestive tract sites from 128 female layer (egg-producing) chickens in comparable environments.

RESULTS

We identified substantial differences between the diversity, composition, and predicted function of site-associated microbiota. Differences in reproductive tract microbiota were more strongly associated with egg production than those in the digestive tract. We identified 4 reproductive tract microbial species, Bacteroides fragilis, Bacteroides salanitronis, Bacteroides barnesiae, and Clostridium leptum, that were related to immune function and potentially contribute to enhanced egg production.

CONCLUSIONS

These findings provide insights into the diverse microbiota characteristics of reproductive and digestive tracts and may help in designing strategies for controlling and manipulating chicken reproductive tract microbiota to improve egg production.

Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency

The composition of the gut microbiome plays important roles in digestion, nutrient absorption, and health. Here, we analyzed the microbial composition in the duodenum and ileum of yellow broilers. Chickens were grouped based on feed efficiency (high feed efficiency [HFE] and low feed efficiency [LFE] groups; n = 22 each). Microbial samples from the duodenum and ileum were collected, and 16S rRNA sequencing of the V3–V4 region was performed. The dominant bacteria in the duodenum were from the phyla Firmicutes and Cyanobacteria and the genera Lactobacillus, Faecalibacterium, and Ruminococcus. In the ileum, the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, SMB53 and Enterococcus were predominant. Alpha diversity analysis showed that the microbiota diversity was significantly higher in the duodenum than in the ileum. The structure of the ileal microbiota was similar between groups, and the species richness of the microbiota in the HFE group was significantly higher than that in the LFE group. In the HFE and LFE groups, Firmicutes and Cyanobacteria were negatively correlated, and Lactobacillus had medium to high negative correlations with most other genera. Functional prediction analysis showed that the gluconeogenesis I pathway was the most abundant differential metabolic pathway and was significantly altered in the LFE group. Moreover, although the microbial community structures were similar in the duodenum and ileum, the diversity of the microbial community was significantly higher in the duodenum than in the ileum. Pearson correlation analysis revealed that the phylum Chloroflexi and genera Acinetobacter, Pseudomonas, Bacillus and Neisseria were with coefficients <−0.3 or >0.3. In the ileum, Ruminococcus may be associated with HFE whereas Faecalibacterium may be associated with LFE. These findings may provide valuable foundations for future research on composition and diversity of intestinal microbes and provide insights into the roles of intestinal microbes in improving feed efficiency and the industrial economic benefits of yellow broilers.

Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found

Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters

Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host's genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.

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.

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.

The microbiota structure in the cecum of laying hens contributes to dissimilar H2S production

BACKGROUND

Host genotype plays a crucial role in microbial composition of laying hens, which may lead to dissimilar odor gas production. The objective of this study was to investigate the relationship among layer breed, microbial structure and odor production.

RESULTS

Thirty Hy-Line Gray and thirty Lohmann Pink laying hens were used in this study to determine the impact of cecal microbial structure on odor production of laying hens. The hens were managed under the same husbandry and dietary regimes. Results of in vivo experiments showed a lower hydrogen sulfide (H₂S) production from Hy-Line hens and a lower concentration of soluble sulfide (S^2-) but a higher concentration of butyrate in the cecal content of the Hy-Line hens compared to Lohmann Pink hens (P < 0.05), which was consistent with the in vitro experiments (P < 0.05). However, ammonia (NH₃) production was not different between genotypes (P > 0.05). Significant microbial structural differences existed between the two breed groups. The relative abundance of some butyrate producers (including Butyricicoccus, Butyricimonas and Roseburia) and sulfate-reducing bacteria (including Mailhella and Lawsonia) were found to be significantly correlated with odor production and were shown to be different in the 16S rRNA and PCR data between two breed groups. Furthermore, some bacterial metabolism pathways associated with energy extraction and carbohydrate utilization (oxidative phosphorylation, pyruvate metabolism, energy metabolism, two component system and secretion system) were overrepresented in the Hy-Line hens, while several amino acid metabolism-associated pathways (amino acid related enzymes, arginine and proline metabolism, and alanine-aspartate and glutamate metabolism) were more prevalent in the Lohmann hens.

CONCLUSION

The results of this study suggest that genotype of laying hens influence cecal microbiota, which in turn modulates their odor production. Our study provides references for breeding and enteric manipulation for defined microbiota to reduce odor gas emission.

Host transcriptome and microbiome interaction modulates physiology of full-sibs broilers with divergent feed conversion ratio

Efficient livestock production relies on effective conversion of feed into body weight gain (BWG). High levels of feed conversion are especially important in production of broiler chickens, birds reared for meat, where economic margins are tight. Traits associated with improved broiler growth and feed efficiency have been subjected to intense genetic selection, but measures such as feed conversion ratio (FCR) remain variable, even between full siblings (sibs). Non-genetic factors such as the composition and function of microbial populations within different enteric compartments have been recognized to influence FCR, although the extent of interplay between hosts and their microbiomes is unclear. To examine host–microbiome interactions we investigated variation in the composition and functions of host intestinal-hepatic transcriptomes and the intestinal microbiota of full-sib broilers with divergent FCR. Progeny from 300 broiler families were assessed for divergent FCR set against shared genetic backgrounds and exposure to the same environmental factors. The seven most divergent full-sib pairs were chosen for analysis, exhibiting marked variation in transcription of genes as well as gut microbial diversity. Examination of enteric microbiota in low FCR sibs revealed variation in microbial community structure and function with no difference in feed intake compared to high FCR sibs. Gene transcription in low and high FCR sibs was significantly associated with the abundance of specific microbial taxa. Highly intertwined interactions between host transcriptomes and enteric microbiota are likely to modulate complex traits like FCR and may be amenable to selective modification with relevance to improving intestinal homeostasis and health.

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review

There is increasing evidence of a pivotal role of the gut microbiota (GUT-M) in key physiological functions in vertebrates. Many studies discuss functional implications of the GUT-M not only on immunity, growth, metabolism, but also on brain development and behavior. However, while the influence of the microbiota-gut-brain axis (MGBA) on behavior is documented in rodents and humans, data on farm animals are scarce. This review will first report the well-known influence of the MGBA on behavior in rodent and human and then describe its influence on emotion, memory, social and feeding behaviors in farm animals. This corpus of experiments suggests that a better understanding of the effects of the MGBA on behavior could have large implications in various fields of animal production. Specifically, animal welfare and health could be improved by selection, nutrition and management processes that take into account the role of the GUT-M in behavior.

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.

Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review

Unlike classical microbiology which focuses on bacteria capable of growing in vitro, metagenomics is a study of genetic information originating from microflora which aims to characterise the microbiome, namely the common genome of bacteria, archaea, fungi, protozoa and viruses living in the host. Metagenomics relies on next-generation sequencing (NGS), a large-scale sequencing technique which allows millions of sequential reactions to be carried out in parallel to decode entire communities of microorganisms. Metagenomic analyses support taxonomic analyses (involving gene fragments encoding ribosomal RNAs 5S and 16S in bacteria) or functional analyses for identifying genes encoding proteins that participate in the regulation of metabolic pathways in the body. New metagenomics technologies expand our knowledge of the phylogenetic structure of microflora in the gastrointestinal tract of poultry, and they support the identification of previously unknown groups of microbiota, mainly those occurring in small numbers. Next-generation sequencing also provides indirect information about the quantitative structure of the genes of gut microorganisms, but microbial activity and changes in the proportions of microbial metabolites that affect the host’s intestinal integrity and metabolism remain insufficiently investigated. Therefore, research studies are undertaken to investigate the proportions of the key microbial metabolites in the intestinal contents of poultry relative to changes in the population size of the most important bacterial groups, including those determined by cheaper techniques.

Intestinal microbiota of broilers submitted to feeding restriction and its relationship to hepatic metabolism and fat mass: Fast-growing strain

The present study was conducted to verify how feed restriction affects gut microbiota and gene hepatic expression in broiler chickens and how these variables are related to body weight gain. For the experiment, 21-d-old Cobb500^TM birds were distributed in a completely randomized experimental design with three treatments: T1. Control (ad libitum-3.176 Mcal/kg ME-metabolizable energy-and 19% CP-crude protein); T2. Energetic restriction (2.224 Mcal/kg ME and 19% CP) from 22 to 42 days with consumption equivalent to control; T3. Quantitative restriction (70% restriction, i.e., restricted broilers ingested only 30% of the quantity consumed by the control group-3.176 Mcal/kg ME and 19% CP) for 7 days, followed by refeeding ad libitum from 28 to 42 days. Ileum and caecum microbiota collections were made at 21, 28 and 42 days of age. Hepatic tissue was collected at 28 and 42 days old for relative gene expression analyses. At 43-d-old, body composition was quantified by DXA (Dual-energy X-ray Absorptiometry). Both feed restriction programmes decreased Lactobacillus and increased Enterococcus and Enterobacteriaceae counts. No differences were found in the refeeding period. Energetic restriction induced the expression of CPT1-A (Carnitine palmitoyltransferase 1A) gene, and decreased body fat mass. Quantitative feed restriction increased lipogenic and decreased lipolytic gene expression. In the refeeding period, CPT1-A gene expression was induced, without changing the broilers body composition. Positive associations were found between BWG (Body Weight Gain) and Lactobacillus and Clostridium cluster IV groups, and negatively associations with Enterobacteriaceae and Enterococcus bacterial groups. In conclusion, differences found in microbiota were similar between the two feed restriction programmes, however, hepatic gene expression differences were only found in quantitative restriction. Higher counts of Lactobacillus and Clostridium cluster IV groups in ileum are likely to be related to better broiler performance and low expression of lipogenic genes.

Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway

Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.

Effects of a gut microbiota transfer on emotional reactivity in Japanese quails (Coturnix japonica)

The interaction between the gut microbiota (GM) and the brain has led to the concept of the microbiota-gut-brain axis but data in birds remain scarce. We tested the hypothesis that colonization of germ-free chicks from a quail line selected for a high emotional reactivity (E+) with GM from a line with low emotional reactivity (E-) would reduce their emotional behaviour in comparison with germ-free chicks from E+ line colonized with GM from the same E+ line. The GM composition analysis of both groups revealed a shift in term of microbial diversity and richness between Day 21 and Day 35 and the GM of the two groups of quails were closer to each other at Day 35 than at Day 21 at a phylum level. Quails that received GM from the E- line expressed a lower emotional reactivity than the quails colonized by GM from the E+line in the tonic immobility and the novel environment tests proceeded during the second week of age. This result was reversed in a second tonic immobility test and an open-field run two weeks later. These behavioural and GM modifications over time could be the consequence of the resilience of the GM to recover its equilibrium present in the E+ host, which is in part driven by the host genotype. This study shows for the first time that a gut microbiota transfer can influence emotional reactivity in Japanese quails strengthening the existence of a microbiota-gut-brain axis in this species of bird.

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs’ microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.

Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens: A review

The poultry industry is continuously facing substantial and different challenges such as the increasing cost of feed ingredients, the European Union's ban of antibiotic as growth promoters, the antimicrobial resistance and the high incidence of muscle myopathies and breast meat abnormalities. In the last decade, there has been an extraordinary development of many genomic techniques able to describe global variation of genes, proteins and metabolites expression level. Proper application of these cutting-edge omics technologies (mainly transcriptomics, proteomics and metabolomics) paves the possibility to understand much useful information about the biological processes and pathways behind different complex traits of chickens. The current review aimed to highlight some important knowledge achieved through the application of omics technologies and proteo-genomics data in the field of feed efficiency, nutrition, meat quality and disease resistance in broiler chickens.

Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks

Background:

Livestock production should respond to societal, environmental and economic changes. Since 2006 and the ban on antibiotics as growth factors in European Union, the use of probiotics has become widespread and has demonstrated the effect of intestinal microbiota on the performance of farm animals.

Objective:

The aim of this study was to investigate the effect of supplementation with Lactobacillus salivarius (as a probiotics strain or combined with other strains) on zootechnical performance, metabolic and immune gene expression and intestinal microbiota diversity in mule ducks using high-throughput sequencing and real-time PCR.

Method:

The mule ducks were reared for 79 days and overfed for 12 days with or without probiotics. Samples were collected at 14 (starting period) and 91 days (end of overfeeding period), 3 hours post feeding.

Results:

Irrespective of digestive content, age, level of feed intake or supplementation with probiotics, Firmicutes, Proteobacteria and Bacteroidetes were the dominant phyla in the bacterial community in mule ducks. At 14 days, both the ileal and cecal samples were dominated by Firmicutes (in particular the Clostridiales order). Overfeeding induced a shift between Clostridiales and Lactobacillales in the ileal samples whereas in the cecal samples, the relative abundance of Firmicutes decreased. Overfeeding also induced hepatic over-expression of Fatty Acid Synthase (FAS) and of the lipid transporter gene Fatty Acid Binding Protein 4 (FABP4). This increase in lipid metabolism genes is associated with a decrease in inflammatory response.

Conclusion:

Finally, probiotic supplementation had only a slight impact on gene expression and microbiota diversity, both at 14 days and after overfeeding.

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.

Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low-abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.

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.

Assessing serum metabolite profiles as predictors for feed efficiency in broiler chickens reared at geographically distant locations

1. The objective of this study was to investigate differences in growth performance, serum intermediary metabolites, acute-phase proteins and white blood cells in low, medium and high-residual feed intake (RFI) chickens. It was also assessed if the environment affects the feed efficiency (FE) and FE-related performance and serum profiles of chickens. 2. Individual body weight (BW) and feed intake (FI) were recorded from d 7 of life. At 5 weeks of age, female and male broiler chickens (Cobb 500) were selected according to their RFI (L1: Austria; L2: UK; n = 9/RFI group, sex and locatity -45on) and blood samples were collected. 3. Chickens at L1 had similar FI but a 15% higher BW gain compared to chickens at L2. The RFI values of female chickens were -231, 8 and 215 g and those of male chickens -197, 0 and 267 g for low, medium and high RFI, respectively. 4. Location affected serum glucose, urea, cholesterol, non-esterified fatty acids (NEFA) and ovotransferrin in females, and serum glucose and triglycerides in male chickens. Serum uric acid and NEFA linearly increased from low to high RFI in females, whereas in males, cholesterol showed the same linear response from low to high RFI. Serum alpha-1-acid glycoprotein and blood heterophil-to-lymphocyte ratio linearly increased by 35% and 68%, respectively, from low to high RFI but only in male chickens at L1. 5. Regression analysis showed significant positive relationships between RFI and serum uric acid (R² = 0.49) and cholesterol (R² = 0.13). 6. It was concluded that RFI-related variation in serum metabolites of chickens was largely similar for the two environments and that serum metabolite patterns could be used to predict RFI in chickens.

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.

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

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

Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history

Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories. The avian egg has multiple characteristics that have evolved to enable effective defense against pathogenic attack. Microbial risk of pathogenic infection is hypothesized to vary with life stage, with early life risk being maximal at either hatching or fledging. For adult birds, microbial infection risk is also proposed to vary with habitat and life stage, with molt inducing a period of increased vulnerability. Bacteria not only play an important role in shaping the immune system as well as trade-offs with other physiological systems, but also for determining digestive efficiency and nutrient uptake. The relevance of avian microbiomes for avian ecology, physiology and behavior is highly topical and will likely impact on our understanding of avian welfare, conservation, captive breeding as well as for our understanding of the nature of host-microbe coevolution.

Direct and correlated responses to selection in two lines of rabbits selected for feed efficiency under ad libitum and restricted feeding: I. Production traits and gut microbiota characteristics

To get insights into selection criteria for feed efficiency, 2 rabbit lines have been created: the ConsoResidual line was selected for residual feed intake (RFI) with ad libitum feeding and the ADGrestrict line was selected for ADG under restricted feeding (-20% of voluntary intake). The first objective of this study was to evaluate, after 9 generations of selection, the direct and correlated responses to selection on production traits in the 2 lines for traits recorded during growth. Second, applying the 2 feeding conditions used for selection to both selected lines plus the control unselected line (generation 0, G0) in a 2 × 3 factorial trial, the line performances were compared and the gut microbiota of the lines was characterized. The correlated responses in feed conversion ratio (FCR) were remarkably equivalent in both selected lines (-2.74 genetic σ) but correlated responses in other traits were notably different. In the ConsoResidual line, selection for decreased RFI resulted in a small negative correlated response in BW at 63 d old (BW63) and in a null response in ADG. In the ADGrestrict line, on the contrary, the correlated response in BW63 was substantial (+1.59 σ). The 2 selected lines had a FCR reduced by 0.2 point compared with the G0 line, and the same difference was found in both feeding regimens ( < 0.001). Indeed, selection on ADG would lead to heavier animals with no significant reduction of feed costs, whereas selection on RFI leads to lower feed costs and no increase of animal BW under ad libitum feeding. Altogether, our results do not suggest any genotype × environment interaction in the response to feeding regimens. The intestinal microbial communities from efficient rabbits differed from their unselected counterparts in terms of fermentation end products and microbial phylotypes, suggesting a central role of these microbes in the better feed efficiency of the rabbits.

Genetic Determinism of Fearfulness, General Activity and Feeding Behavior in Chickens and Its Relationship with Digestive Efficiency

The genetic relationships between behavior and digestive efficiency were studied in 860 chickens from a cross between two lines divergently selected on digestive efficiency. At 2 weeks of age each chick was video-recorded in the home pen to characterize general activity and feeding behavior. Tonic immobility and open-field tests were also carried out individually to evaluate emotional reactivity (i.e. the propensity to express fear responses). Digestive efficiency was measured at 3 weeks. Genetic parameters of behavior traits were estimated. Birds were genotyped on 3379 SNP markers to detect QTLs. Heritabilities of behavioral traits were low, apart from tonic immobility (0.17-0.18) and maximum meal length (0.14). The genetic correlations indicated that the most efficient birds fed more frequently and were less fearful. We detected 14 QTL (9 for feeding behavior, 3 for tonic immobility, 2 for frequency of lying). Nine of them co-localized with QTL for efficiency, anatomy of the digestive tract, feed intake or microbiota composition. Four genes involved in fear reactions were identified in the QTL for tonic immobility on GGA1.