Gene expression in the chicken caecum is dependent on microbiota composition

Effects of Salmonella Enteritidis infection on TLRs gene expression and microbial diversity in cecum of laying hens

Salmonella Enteritidis (SE) is an important foodborne pathogen primarily causing human disease through contaminated food and water. In the current study, to assess the effect of Salmonella Enteritidis infection on the immune system and the microbial diversity of cecum and oviduct in chickens, twelve 24-week-old SE-negative White Leghorn layers were randomly selected and divided into 2 groups. Chickens in the challenge group were orally inoculated with SE, and chickens in the control group received an equal amount of sterilized Phosphate Buffered Saline solution. Serum and tissue samples (cecum, oviduct, ovary, liver, spleen, and pancreas) were collected at 7 days and 14 days post-infection (dpi). Quantitative PCR was used to detect the expression of Toll-like receptors (TLRs) in the cecum, oviduct and ovary. To understand the influence of SE infection on the microbial profile of the cecum and oviduct, microbial community composition of the cecal contents and oviducal contents were analyzed through 16S rRNA sequencing. Results showed that SE infection caused damage to the digestive organs, reproductive organs, and immune organs in laying hens. The expression of TLR1a, TLR1b, TLR2, TLR4, TLR5, TLR7 and TLR15 in the cecum were induced, and the content of IFN-γ, TNF-α, IL-2 and IL-18 in serum increased after SE infection. The composition of the microbial community significantly changed in cecal content, the dominant phylum of Firmicutes increased, and Bacteroidetes decreased significantly. In the oviduct, the microbial diversity became complicated, the dominant bacteria Faecalibacterium was significantly increased, and Bacteroides was significantly decreased. This study investigated the effects of SE infection in laying hens, including host innate immunity, the expression of TLRs, and changes in the composition of microbes in the cecum and reproductive tract. Our results may provide a scientific basis for the Salmonella Enteritidis control in chicken, the maintenance of oviduct function, and the guarantee of clean egg production.

Moringa oleifera Leaf Powder as New Source of Protein-Based Feedstuff Improves Growth Performance and Cecal Microbial Diversity of Broiler Chicken

Currently, the lack of protein source feed has become a pressing issue. Moringa oleifera leaf powder (MOLP) has good potential for the development of protein-derived feeds due to its good protein quality and abundance, but little is known about its effects on broiler growth performance and cecal microbiota. In this study, the chickens were fed different rates of MOLP (1%, 3%, 5%, 7%, and 9%) instead of the rape seed cake, and the effects of different levels of MOLP on growth performance, carcass characteristics, and cecal microbiota of the broilers were evaluated at two different growth stages (day 28 and day 56). In terms of growth performance, the best results were obtained at the 3% MOLP level in the early stages (p < 0.05). In terms of carcass characteristics, in the early stage, the level of 5% MOLP had the best effect; in the later stage, 5% MOLP also had the best effect. In terms of cecal microbial changes, the alpha diversity analysis revealed that 5% MOLP enhanced the richness and diversity of broiler intestinal flora. At the phylum level, the addition of 5% MOLP adjusted the relative abundance of Firmicutes and Bacteroidetes to a level close to that of the A1 group on day 28, while 5% MOLP significantly reduced the relative abundance of Bacteroidetes (p < 0.05) compared to the A2 group on day 56, and the relative abundance of Firmicutes was still higher in the D2 group than in the A2 group (p < 0.05). At the genus level, MOLP addition consistently and significantly increased the relative abundance of Bacteroides (p < 0.05), except for 3% on day 28 and 1% on day 56. For Oscillospira, increasing MOLP levels in the pre- and post-period resulted in a significant decrease in the relative abundance of Oscillospira (p < 0.05). In conclusion, MOLP helps to enhance growth performance and carcass characteristics and improve the cecal microbial structure of broilers. The recommended rate of MOLP addition for broilers is 5% in both the early and late stages.

Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics

Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.

Role of Physiology, Immunity, Microbiota, and Infectious Diseases in the Gut Health of Poultry

“Gut health” refers to the physical state and physiological function of the gastrointestinal tract and in the livestock system; this topic is often focused on the complex interacting components of the intestinal system that influence animal growth performance and host-microbial homeostasis. Regardless, there is an increasing need to better understand the complexity of the intestinal system and the various factors that influence gut health, since the intestine is the largest immune and neuroendocrine organ that interacts with the most complex microbiome population. As we face the post-antibiotic growth promoters (AGP) era in many countries of the world, livestock need more options to deal with food security, food safety, and antibiotic resilience to maintain agricultural sustainability to feed the increasing human population. Furthermore, developing novel antibiotic alternative strategies needs a comprehensive understanding of how this complex system maintains homeostasis as we face unpredictable changes in external factors like antibiotic-resistant microbes, farming practices, climate changes, and consumers’ preferences for food. In this review, we attempt to assemble and summarize all the relevant information on chicken gut health to provide deeper insights into various aspects of gut health. Due to the broad and complex nature of the concept of “gut health”, we have highlighted the most pertinent factors related to the field performance of broiler chickens.

Detoxification, Hydrogen Sulphide Metabolism and Wound Healing Are the Main Functions That Differentiate Caecum Protein Expression from Ileum of Week-Old Chicken

Simple Summary

Although the ileum and caecum represent adjacent parts of the gastrointestinal tract, both compartments differ by function as well as inner environment parameters such as oxygen availability or density of colonising microbiota. As the function of a particular tissue is generally reflected by protein expression, mass spectrometry proteomics was used to characterise expressed proteins of both segments of the gastrointestinal tract. Differentially expressed proteins were identified and grouped according to biological processes specific to both gut compartments.

Abstract

Sections of chicken gut differ in many aspects, e.g., the passage of digesta (continuous vs. discontinuous), the concentration of oxygen, and the density of colonising microbiota. Using an unbiased LC-MS/MS protocol, we compared protein expression in 18 ileal and 57 caecal tissue samples that originated from 7-day old ISA brown chickens. We found that proteins specific to the ileum were either structural (e.g., 3 actin isoforms, villin, or myosin 1A), or those required for nutrient digestion (e.g., sucrose isomaltase, maltase–glucoamylase, peptidase D) and absorption (e.g., fatty acid-binding protein 2 and 6 or bile acid–CoA:amino acid N-acyltransferase). On the other hand, proteins characteristic of the caecum were involved in sensing and limiting the consequences of oxidative stress (e.g., thioredoxin, peroxiredoxin 6), cell adhesion, and motility associated with wound healing (e.g., fibronectin 1, desmoyokin). These mechanisms are coupled with the activation of mechanisms suppressing the inflammatory response (galectin 1). Rather prominent were also expressions of proteins linked to hydrogen sulphide metabolism in caecum represented by cystathionin beta synthase, selenium-binding protein 1, mercaptopyruvate sulphurtransferase, and thiosulphate sulphurtransferase. Higher mRNA expression of nuclear factor, erythroid 2-like 2, the main oxidative stress transcriptional factor in caecum, further supported our observations.

Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria

The gut microbiome is crucial for both maturation of the immune system and colonization resistance against enteric pathogens. Although chicken are important domesticated animals, the impact of their gut microbiome on the immune system is understudied. Therefore, we investigated the effect of microbiome-based interventions on host mucosal immune responses. Increased levels of IgA and IgY were observed in chickens exposed to maternal feces after hatching compared with strict hygienic conditions. This was accompanied by increased gut bacterial diversity as assessed by 16S rRNA gene amplicon sequencing. Cultivation work allowed the establishment of a collection of 43 bacterial species spanning 4 phyla and 19 families, including the first cultured members of 3 novel genera and 4 novel species that were taxonomically described. This resource is available at www.dsmz.de/chibac. A synthetic community consisting of nine phylogenetically diverse and dominant species from this collection was designed and found to be moderately efficient in boosting immunoglobulin levels when provided to chickens early in life.

IMPORTANCE The immune system plays a crucial role in sustaining animal health. Its development is markedly influenced by early microbial colonization of the gastrointestinal tract. As chicken are fully dependent on environmental microbes after hatching, extensive hygienic measures in production facilities are detrimental to the microbiota, resulting in low colonization resistance against pathogens. To combat enteric infections, antibiotics are frequently used, which aggravates the issue by altering gut microbiota colonization. Intervention strategies based on cultured gut bacteria are proposed to influence immune responses in chicken.

The effect of delayed feeding post-hatch on caeca development in broiler chickens

1. Broiler chicks are frequently deprived of food up to 72 h due to uneven hatching rates, management procedures and transportation to farms. Little is known about the effect of delayed feeding due to extended hatching times on the early neonatal development of the caeca. Therefore, the objective of this study was to investigate the developmental changes and effects of a 48-h delay in feed access immediately post-hatch (PH) on the caeca.2. After hatch, birds (Ross 708) were randomly divided into two treatment groups (n = 6 battery pen/treatment). One group (early fed; EF) received feed and water immediately after hatch, while the second group (late fed; LF) had access to water but had delayed access to feed for 48 h. Contents averaging across all regions of the caeca were collected for mRNA expression as well as for histological analysis at -48, 0, 4 h PH and then at 1, 2, 3, 4, 6, 8, 10, 12 and 14 days PH.3. Expression of MCT-1 (a nutrient transporter), Cox7A2 (related to mitochondrial function) IgA, pIgR, and ChIL-8 (immune function) genes was affected by delayed access to feed that was dependent by the time PH. Expression of immune and gut barrier function-related genes (LEAP2 and MUC2, respectively) was increased in LF group. There was no effect of feed delay on expression of genes related to mitochondrial functions in the caeca, although developmental changes were observed (ATP5F1B, Cox4|1). Caecal mucus and muscle thickness were affected by delayed access to feed during caeca development.4. The data suggested a limited effect of delayed feed access PH on the developmental changes in caecal functions. However, the caeca seemed to be relatively resistant to delayed access to feed early PH, with only a few genes affected.

Identification of hub genes involved in apparent metabolizable energy of chickens

Feed efficiency is one of the most economically significant traits in a breeding program. Apparent metabolizable energy is the most used method to evaluate energy utilization for feed efficiency. The purpose of this study was to identify candidate genes of chickens with divergent apparent metabolizable energy by bioinformatics analysis. The gene expression profile of duodenal of the highest and lowest apparent metabolizable energy-ranked birds were analyzed. Differentially expressed genes were picked out using GEO2R tool. Gene ontology and pathway analysis were performed using bioinformatics tools. Cytoscape software was used to visualize protein-protein network. There were 201 DEGs, including 99 up-regulated genes enriched in metabolic pathways, Cellular senescence and Focal adhesion, and 102 down-regulated genes enriched in metabolic pathways, Regulation of actin cytoskeleton, Neuroactive ligand-receptor interaction, Calcium signaling pathway and Focal adhesion. Two important modules were detected and pathway enrichment analysis showed that they were mainly associated with Focal adhesion, Regulation of actin cytoskeleton and RNA transport. Fifteen hub genes were selected and among them, ITGA8, CDC42 and GSK3B might be the core genes related to apparent metabolizable energy of chickens. These hub genes can be used as biomarkers for apparent metabolizable energy and feed efficiency in breeding program of chickens.

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes

The microbiome is an assemblage of microorganisms living in association with a multicellular host. Numerous studies have identified a role for the microbiome in host physiology, development, immunity, and behaviour. The generation of axenic (germ-free) and gnotobiotic model systems has been vital to dissecting the role of the microbiome in host biology. We have previously reported the generation of axenic Aedes aegypti mosquitoes, the primary vector of several human pathogenic viruses, including dengue virus and Zika virus. In order to better understand the influence of the microbiome on mosquitoes, we examined the transcriptomes of axenic and conventionally reared Ae. aegypti before and after a blood meal. Our results suggest that the microbiome has a much lower effect on the mosquito's gene expression than previously thought with only 170 genes influenced by the axenic state, while in contrast, blood meal status influenced 809 genes. The pattern of expression influenced by the microbiome is consistent with transient changes similar to infection rather than sweeping physiological changes. While the microbiome does seem to affect some pathways such as immune function and metabolism, our data suggest the microbiome is primarily serving a nutritional role in development with only minor effects in the adult.

Impact of galactooligosaccharides delivered in ovo on mitigating negative effects of heat stress on performance and welfare of broilers

Galactooligosaccharides (GOS) delivered in ovo improve intestinal health of broiler chickens. This study aimed to demonstrate the impact of in ovo stimulation with GOS prebiotic on day 12 of egg incubation on performance and welfare traits in broiler chickens. The incubating eggs were divided into 3 groups, based on the substance injected in ovo: 3.5 mg of GOS dissolved in 0.2 mL physiological saline (GOS), 0.2 mL physiological saline (S), or uninjected controls (C). Constant heat stress (HS) was induced on days 32 to 42 post-hatch by increasing environmental temperature to 30°C. Thermoneutral (TN) animals were kept at 25°C. The performance (body weight [BW], daily feed intake [DFI], daily weight gain [DWG], and feed conversion rate [FCR]) were measured and mortality was scored for starter (days 0 to 13), grower (days 14 to 27), and finisher (days 28 to 42) feeding phases. Rectal temperature was scored on days 32 to 42. Food-pad dermatitis (FPD) was scored post-mortem (day 42). GOS increased (P < 0.01) BW on day 42 (2.892 kg in GOS vs. 2.758 kg in C). Heat stress significantly reduced (P < 0.01) final BW (2.516 kg in TN vs. 3.110 kg in HS). During finisher phase, DFI was significantly higher in GOS vs. C (173.2 g vs. 165.7 g; P < 0.05). FCR calculated for the entire rearing period (days 0 to 42) ranged from 1.701 in C to 1.653 in GOS (P < 0.05). GOS improved FCR in HS animals during finisher phase (P < 0.05). Rectal temperature of GOS chickens under HS reached 42.5°C 1 day earlier than C and S (P < 0.05), which suggests that those birds recovered earlier from the high environmental temperature. Heat stress increased (P < 0.05) mortality about 5 times compared to TN during finisher phase (from 1.59% in TN to 7.69% in HS). GOS decreased FPD in TN conditions by 20% (no lesions in 81% in GOS vs. 60% in C). GOS delivered in ovo mitigated negative effects of HS on performance and welfare in broiler chickens.

Exploring Differential Transcriptome between Jejunal and Cecal Tissue of Broiler Chickens

The study proposed an exploratory functional analysis on differential gene expression of the jejunum and of cecum in chickens. For this study, 150 Ross 308 male chickens were randomly allotted in six pens (25 birds/pen) and fed the same commercial diet. From 19 birds of 42 days of age, jejunum and cecum mucosae were collected for RNA extraction for transcriptome microarray analysis. Differentially expressed genes (DEGs) submitted to DAVID (Database for Annotation, Visualization, and Integrated Discovery) and Gene Set Enrichment Analysis (GSEA) software evidenced enriched gene clusters for biological functions differentiated in the tissues. DAVID analysis in the jejunum showed enriched annotations for cell membrane integral components, PPAR (peroxisome proliferator-activated receptor) signaling pathway, and peroxisome and lipid metabolism, and showed DEGs for gluconeogenesis, not previously reported in chicken jejunum. The cecum showed enriched annotations for disulfide bond category, cysteine and methionine metabolism, glycoprotein category, cell cycle, and extracellular matrix (ECM). GSEA analysis in the jejunum showed peroxisome and PPAR signaling pathway-related gene sets, as found with DAVID, and gene sets for immune regulation, tryptophan and histidine metabolism, and renin-angiotensin system, like in mammals. The cecum showed cell cycle and regulation processes, as well as ECM receptor interaction and focal adhesion-related gene sets. Typical intestinal functions specific for the gut site and interesting functional genes groups emerged, revealing tissue-related key aspects which future studies might take advantage of.

Modulation of microbial communities and mucosal gene expression in chicken intestines after galactooligosaccharides delivery In Ovo

Intestinal mucosa is the interface between the microbial content of the gut and the host's milieu. The goal of this study was to modulate chicken intestinal microflora by in ovo stimulation with galactooligosaccharides (GOS) prebiotic and to demonstrate the molecular responses of the host. The animal trial was performed on meat-type chickens (Ross 308). GOS was delivered by in ovo injection performed into the air cell on day 12 of egg incubation. Analysis of microbial communities and mucosal gene expression was performed at slaughter (day 42 post-hatching). Chyme (for DNA isolation) and intestinal mucosa (for RNA isolation) from four distinct intestinal segments (duodenum, jejunum, ileum, and caecum) was sampled. The relative abundance of Bifidobacterium spp. and Lactobacillus spp. in DNA isolated from chyme samples was determined using qPCR. On the host side, the mRNA expression of 13 genes grouped into two panels was analysed with RT-qPCR. Panel (1) included genes related to intestinal innate immune responses (IL-1β, IL-10 and IL-12p40, AvBD1 and CATHL2). Panel (2) contained genes involved in intestinal barrier function (MUC6, CLDN1 and TJAP1) and nutrients sensing (FFAR2 and FFAR4, GLUT1, GLUT2 and GLUT5). GOS increased the relative abundance of Bifidobacterium in caecum (from 1.3% to 3.9%). Distinct effects of GOS on gene expression were manifested in jejunum and caecum. Cytokine genes (IL-1β, IL-10 and IL-12p40) were up-regulated in the jejunum and caecum of the GOS-treated group. Host defence peptides (AvBD1 and CATHL2) were up-regulated in the caecum of the GOS-treated group. Free fatty acid receptors (FFAR2 and FFAR4) were up-regulated in all three compartments of the intestine (except the duodenum). Glucose transporters were down-regulated in duodenum (GLUT2 and GLUT5) but up-regulated in the hindgut (GLUT1 and GLUT2). In conclusion, GOS delivered in ovo had a bifidogenic effect in adult chickens. It also modulated gene expression related to intestinal immune responses, gut barrier function, and nutrient sensing.

Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses

Commensal gut microbiota plays an important role in health and disease. The current study was designed to assess the role of gut microbiota of chickens in the initiation of antiviral responses against avian influenza virus. Day-old layer chickens received a cocktail of antibiotics for 12 (ABX-D12) or 16 (ABX-D16) days to deplete their gut microbiota, followed by treatment of chickens from ABX-12 with five Lactobacillus species combination (PROB), fecal microbial transplant suspension (FMT) or sham treatment daily for four days. At day 17 of age, chickens were challenged with H9N2 virus. Cloacal virus shedding, and interferon (IFN)-α, IFN-β and interleukin (IL)-22 expression in the trachea, lung, ileum and cecal tonsils was assessed. Higher virus shedding, and compromised type I IFNs and IL-22 expression was observed in ABX-D16 chickens compared to control, while PROB and FMT showed reduced virus shedding and restored IL-22 expression to levels comparable with undepleted chickens. In conclusion, commensal gut microbiota of chickens can modulate innate responses to influenza virus subtype H9N2 infection in chickens, and modulating the composition of the microbiome using probiotics- and/or FMT-based interventions might serve to promote a healthy community that confers protection against influenza virus infection in chickens.