Microbiota Of Chickens Research Articles

Effects of Caulis Spatholobi Polysaccharide on Immunity, Intestinal Mucosal Barrier Function, and Intestinal Microbiota in Cyclophosphamide-Induced Immunosuppressive Chickens.

The protective effects of Caulis Spatholobi polysaccharide (CSP) on immune function, intestinal mucosal barrier, and intestinal microflora in cyclophosphamide (CY)-induced immunosuppressed chickens have been rarely reported. This study was designed to investigate the cecal microbiota in chickens and to elucidate the immune mechanism involved in the CSP effect on CY induced-immunosuppressed chickens. A total of 288 cocks were equally divided into six groups and used to evaluate the immune effect of CSP. Results showed that the CSP increased the body weight and immune organ index of immunosuppressed chickens, significantly increased the secretion of cytokines (IL-4, IL-10) and immunoglobulins (IgG, IgM) in sera of chickens, and restored the body immune function. The CSP reduced intestinal injury of the jejunum and ileum, increased the ratio of the intestinal villus height to crypt depth (V/C), improved the expression of tight junction protein, and protected intestinal health. The CSP activated the toll-like receptor (TLR)/MyD88/NF-κB pathway and enhanced the expression of TLR4, MyD88, NF-κB, Claudin1, and Zo-1, protecting the intestinal tract. High-throughput sequencing of the 16S rRNA gene showed that CSP increased species richness, restored CY-induced intestinal microbiome imbalance, and enhanced the abundance of Lactobacillus in the intestinal tract. In conclusion, our study provided a scientific basis for CSP as an immune enhancer to regulate intestinal microflora and protect intestinal mucosal damage in chickens.

Evolution and predicted functions of the microbiota of the medium‐slow growing chicken during the first 4 weeks of chick development

AbstractChicken gut microbiota–host interactions play essential roles in the productivity and health of chickens. Deciphering the microbial composition and its functions are crucial for understanding the roles of gut microbiota within chickens. Although there are some research studies focusing on different chicken microbiota, none of them have considered medium‐slow growing chicken as a model host. Here, the microbial composition of the faeces of medium‐slow growing chicken, grown in an organic farming system, has been elucidated through 16S rRNA gene amplicon‐based metagenomics. We found a diverse microbiota that does not present major shifts during the first 4 weeks of the animal's life, although the abundance of only 2 OTUs (LactobacillusandBacteroides) increase during this time.Lactobacillusappear to govern the bacterial composition, followed distantly byClostridiales(mainlyFaecalibacterium,Ruminococcusand unidentified genera from the familiesPeptostreptococaceaeandRuminococcaceae) andBacteroidales(BacteroidesandParabacteroides). The roles of Redbro faeces microbiota have been revealed through in silico functional predictions. We found thatLactobacillusmembers may play relevant roles within its host and seem to highly influence the metabolism of fructose and mannose among other relevant functions.

The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail

The microbiota in broiler chicken intestines affects the animals’ health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers’ drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota’s structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.

Моделирование процессов взаимодействия микроорганизмов в кишечнике кур

The study of an integral microbial-organismal biosystem in chickens, which is in a state of dynamic equilibrium with a relatively constant taxonomic composition of the microbiome, which varies depending on feed and a number of other factors, can be determined by the ratio of individual groups of microorganisms. The work is devoted to the development of a unified fractal model that allows assessing the state of the intestinal microbiota of chickens under the influence of factors correcting microbiocenoses (probiotics, prebiotics, phytobiotics, etc.). Based on the results of metagenomic studies, fractal portraits of microbial profiles under the influence of probiotic, prebiotic and phytobiotic were built. The parameters of the Fr3 fractal model, the indices of bioconsolidation of microbial communities in the intestines of birds were calculated according to the experimental variants.

Gut Microbiota Dysbiosis Aggravates Mycoplasma gallisepticum Colonization in the Chicken Lung

Mycoplasma gallisepticum (MG) is the pathogen that causes chronic respiratory diseases in chickens. Gut microbiota plays an important role in maintaining body health and resisting respiratory infection, but the correlation between gut microbiota and MG infection is poorly defined. Therefore, in this study, the correlation between gut microbiota and MG infection was explored by disturbing gut microbiota in chickens with antibiotic cocktail. The results showed that the gut microbiota dysbiosis impairs pulmonary immune response against MG infection. It has been noted that MG colonization in the lung was significantly increased following gut microbiota dysbiosis, and this could be reversed by intranasally administrated toll-like receptor 2 (TLR2) ligand, recombinant chicken IL-17 protein or recombinant chicken granulocyte-macrophage colony-stimulating factor (GM-CSF) protein. In addition, the levels of short-chain fatty acids (SCFAs) and vitamin A were significantly reduced in gut microbiota dysbiosis group, however, butyric acid or vitamin A as feed additives promoted MG clearance in the lung of gut microbiota dysbiosis group via increasing TLR2/IL17/GM-CSF and host defense peptides genes expression. The present study revealed an important role of gut microbiota in the defense against MG colonization in the lung of chicken.

Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life

The cecal microbiota plays numerous roles in chicken health and nutrition. Where such microbiota differs between lines exhibiting distinct phenotypes, microbiota transplantation offers scope to dissect the role of gut microbial communities in those traits. However, the composition and stability of transplants over time is relatively ill-defined and varying levels of success have been reported. In this study, we transplanted cecal contents from adult Roslin broilers into chicks from a different broiler line. Within <12 h posthatch, Ross 308 chicks received an oral gavage of cecal contents (n = 26) or a PBS control (n = 24). Cecal contents samples were collected postmortem from birds on d 1, 2, 3, 4, and 7 posthatch. DNA was extracted from these samples and the transplant inoculum and the V4 region of the 16S rRNA gene was amplified and sequenced. The cecal microbiota of chickens receiving the microbiota transplant was significantly different in composition and significantly richer and more diverse, in comparison to control birds. At the final timepoint (d 7), of the 150 Operational Taxonomic Units (OTUs) that were >0.1% abundant (average) in the donor sample, 137 were detected in the treated group (75 were >0.1% abundant (average)) while only 88 were detected in the control group (29 were >0.1% abundant (average)). Our data therefore suggests that stable transplantation of the cecal microbiota between lines is achievable using the methods described in this paper.

Environmental hexavalent chromium exposure induces gut microbial dysbiosis in chickens

Hexavalent chromium [Cr (VI)] is a hazardous heavy metal that pollutes soil, water and crops. Moreover, its prolonged exposure can harm the gastrointestinal system, liver and respiratory tract in different species, but knowledge regarding Cr (VI) influence on gut microbiota in chickens remains scarce. Therefore, this study was performed to investigate the impact of Cr (VI) on gut microbiota in chickens. Results revealed that the gut microbiota in Cr (VI)-induced chickens exhibited a distinct reduction in alpha diversity, accompanied by significant shifts in microbial composition. Specifically, Firmicutes and Bacteroidetes were the most dominant phyla in the control chickens, whereas Firmicutes and Actinobacteria were observed to be predominant in the Cr (VI)-induced populations. Moreover, the types and relative abundances of predominant bacterial genus in control and Cr (VI)-induced chickens were also different. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla and 7 genera obviously increased, whereas 8 phyla and 30 genera dramatically decreased during Cr (VI) induction. Among them, 1 phylum (Deferribacteres) and 5 genera (Butyricicoccus, Butyricimonas, Intestinimonas, Lachnospiraceae_FCS020_group and Ruminococcaceae_V9D2013_group) even could not be found in the gut microbial community of Cr (VI)-induced chickens. Taken together, our study indicated that the long-term exposure to Cr (VI) dramatically alter the gut microbial diversity and composition in chickens. Notably, it represents a breakthrough in understanding the impact of Cr (VI) on the intestinal microbiota of chickens.

Bacillus pumilus and Bacillus subtilis Promote Early Maturation of Cecal Microbiota in Broiler Chickens.

Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious period before reaching mature configuration. Whether probiotics can play a role in the early maturation of intestinal microbiota is unknown. To address this, day-old chicks were assigned into six groups: NC (basal diet), PC (virginiamycin), low (BPL) and high-dose (BPH) of Bacillus pumilus, and low (BSL) and high-dose (BSH) of Bacillus subtilis. Cecal contents at days 7, 14, 28 and 42 were used to analyze the treatment and time effects on the diversity and composition of microbiota. Overall, the alpha diversity was significantly decreased in the NC group between days 7 and 14, while this decline was prevented in the Bacillus subtilis probiotic (BSL and BSH) and even reversed in the BPH group. The beta-diversity showed significant responses of microbial communities to probiotics in first two weeks of life. Analyses of the abundance of microbiota reflected that members of the family Ruminococcaceae (Ruminnococcus, Oscillospira, Faecalibacterium, Butyricicoccus, and Subdoligranulum), which were dominant in mature microbiota, were significantly higher in abundance at day 14 in the probiotic groups. Conversely, the abundance of genera within the family Lachnospiraceae (Ruminococcus, Blautia, and Coprococcus) was dominant in early dynamic microbiota but was significantly lower in the probiotic groups at day 14. The Lactobacillus and Bifidobacterium abundance was higher, while the Enterobacteriaceae abundance was lower in the probiotic groups. In summary, the probiotics efficiently helped the cecal microbiota reach mature configuration earlier in life. These results could be used for the future manipulation of microbiota from the perspective of improving poultry performance.

The Spatial and Temporal Characterization of Gut Microbiota in Broilers.

The gut microbiota of chickens plays an important role in host physiology. However, the colonization and prevalence of gut microbiota have not been well-characterized. Here, we performed 16S rRNA gene sequencing on the duodenal, cecal and fecal microbiota of broilers at 1, 7, 21, and 35 days of age and characterized the dynamic succession of microbiota across the intestinal tract. Our results showed that Firmicutes was the most abundant phylum detected in each gut site at various ages, while the microbial diversity and composition varied among the duodenum, cecum, and feces at different ages. The microbial diversity and complexity of the cecal microbiota increased with age, gradually achieving stability at 21 days of age. As a specific genus in the cecum, Clostridium_sensu_stricto_1 accounted for 83.50% of the total abundance at 1 day of age, but its relative abundance diminished with age. Regarding the feces, the highest alpha diversity was observed at 1 day of age, significantly separated from the alpha diversity of other ages. In addition, no significant differences were observed in the alpha diversity of duodenal samples among 7, 21, and 35 days of age. The predominant bacterium, Lactobacillus, was relatively low (0.68–6.04%) in the intestinal tract of 1-day-old chicks, whereas its abundance increased substantially at 7 days of age and was higher in the duodenum and feces. Escherichia-Shigella, another predominant bacterium in the chicken intestinal tract, was also found to be highly abundant in fecal samples, and the age-associated dynamic trend coincided with that of Lactobacillus. In addition, several genera, including Blautia, Ruminiclostridium_5, Ruminococcaceae_UCG-014, and [Ruminococcus]_torques_group, which are related to the production of short-chain fatty acids, were identified as biomarker bacteria of the cecum after 21 days of age. These findings shed direct light on the temporal and spatial dynamics of intestinal microbiota and provide new opportunities for the improvement of poultry health and production.

Comparison of Chicken Cecal Microbiota after Metaphylactic Treatment or Following Administration of Feed Additives in a Broiler Farm with Enterococcal Spondylitis History.

Minimizing the clinical signs of Enterococcus cecorum infections causing enterococcal spondylitis in broiler herds is successful when initiated as metaphylaxis in the first week of life. Mechanistically, either the Enterococcus species present at that time are reduced by antibiotic treatment or antibiotic treatment might induce changes in intestinal microbiota composition with an indirect and subsequent influence. The aim of the present study was to examine the cecal microbiota of chickens after administering lincospectin or different additives to evaluate whether these additives have lincospectin-like effects on microbiota. Therefore, 157,400 broiler chickens were reared in four chicken houses (~40,000 birds each) on a broiler farm with history of enterococcal spondylitis. Each flock was treated either with lincospectin or water soluble esterified butyrins, Bacillus (B.) licheniformis or palm oil was added via drinking water during the first days of life. Ten birds per house were dissected at days 11, 20 and 33 of life and cecal microbiota were analyzed (16S rRNA gene sequencing). Lincospectin treatment elicited significant changes in the cecal microbiota composition until slaughter age. Among the tested additives, effects of B. licheniformis on cecal microbiota composition were most similar to those seen after the treatment with lincospectin at day 11.

Identification of an Intestinal Microbiota Signature Associated With the Severity of Necrotic Enteritis.

Necrotic enteritis (NE), an economically devastating disease of poultry caused by pathogenic Clostridium perfringens, is known to induce small intestinal lesions and dysbiosis. However, the intestinal microbes that are associated with NE severity are yet to be characterized. Here, we investigated the link between the ileal microbiota and disease severity in a chicken model of clinical NE using 16S rRNA gene sequencing. Our results indicated that richness and Shannon Index of the ileal microbiota were drastically reduced (p<0.01) as NE was exacerbated. While the relative abundance of C. perfringens increased from 0.02% in healthy chickens to 58–70% in chickens with severe infection, a majority of the ileal microbes were markedly diminished, albeit varying in their sensitivity to NE. Compositionally, a large group of ileal microbes showed a significant correlation with NE severity. Firmicutes, such as group A and B Lactobacillus, Lactobacillus reuteri, Subdoligranulum variabile, Mediterraneibacter, and Staphylococcus as well as two genera of Actinobacteria (Corynebacterium and Kocuria) and two highly related Cyanobacteria were progressively declined as NE was aggravated. Other Firmicutes, such as Weissella, Romboutsia, Kurthia, Cuneatibacter, Blautia, and Aerococcus, appeared much more sensitive and were rapidly abolished in chickens even with mild NE. On the other hand, Enterococcus cecorum and two Escherichia/Shigella species were only enriched in the ileal microbiota of chickens with extremely severe NE, while several other species such as Streptococcus gallolyticus and Bacteroides fragilis remained unaltered by NE. Functionally, secondary bile acid biosynthesis was predicted to be suppressed by NE, while biosynthesis of aromatic and branched-amino acids and metabolism of a majority of amino acids were predicted to be enhanced in the ileum of NE-afflicted chickens. These intestinal microbes showing a strong correlation with NE severity may provide important leads for the development of novel diagnostic or therapeutic approaches to NE and possibly other enteric diseases.

Dietary Supplementation of Shredded, Steam-Exploded Pine Particles Decreases Pathogenic Microbes in the Cecum of Acute Heat-Stressed Broilers

Simple SummaryThe importance of the gut in poultry can be explained by the microbiome action. Prebiotics has gained attention as potential substances for improving gut health. The presence of insoluble dietary fiber from a cheap source such as wood specially prepared by the steam explosion that facilitates the depolymerization of hemicellulose could be an added advantage for microbial existence. Heat stress (HS) has been known to have drastic effects on chickens. In this study, we investigated the effect of dietary steam-exploded pine particle (SPP) supplementation and subsequent acute HS on productive performance and cecum microbiome in broilers. The HS tends to decrease the percent difference in body weight and rectal temperature. Metagenome analysis revealed similar richness and diversity in microbial communities. Firmicutes and Bacteroidetes were the most abundant phylum and were inversely correlated with each other. Furthermore, Firmicutes was also inversely correlated with unfavorable bacterial phyla. Supplementation of SPP in diets helped by enhancing favorable and reducing unfavorable bacterial genus in the cecum of the HS chickens. Although a clear advantage of using SPP on production parameters in broilers was not revealed, this study provided useful information to understand the modulation of microbiota during HS in dietary SPP supplemented chickens.The gut microbiome stimulates nutrient metabolism and could effectively generate heat tolerance in chickens. This study investigates the effects of dietary steam-exploded pine particle (SPP) supplementation and subsequent acute heat stress on productive performance and cecum microbiome in broilers. Eight-day Ross 308 broilers were distributed in three groups with 0%, 1%, and 2% SPP in diets. On the 41st day, forty birds were allocated to four groups with ten birds each. The treatments were control diet at thermoneutral temperature (0% NT) and acute heat-stressed (HS) birds fed control (0% HS), 1% (1% HS), and 2% (2% HS) SPP. Parameters recorded were body weight (BW), feed intake (FI), rectal temperature (RT), relative organ weight, and metagenome analysis from cecum samples. Percent difference in BW, FI, and RT was decreased in HS birds. Metagenome analysis revealed similar richness and diversity in microbial communities. The relative abundance of the bacterial genus such as Limosilactobacillus, Drancourtella, and Ihubacter was increased while that of Alistipes, Alkalibacter, Lachnotalea, and Turicibacter was decreased in SPP supplemented HS birds. Concludingly, the production performance of broilers is negatively influenced during HS, and 2% dietary SPP supplementation may reduce the adverse effects of HS by modifying the microbiota in chickens.

Antibiotic-Induced Dysbiosis of Microbiota Promotes Chicken Lipogenesis by Altering Metabolomics in the Cecum.

Elucidation of the mechanism of lipogenesis and fat deposition is essential for controlling excessive fat deposition in chicken. Studies have shown that gut microbiota plays an important role in regulating host lipogenesis and lipid metabolism. However, the function of gut microbiota in the lipogenesis of chicken and their relevant mechanisms are poorly understood. In the present study, the gut microbiota of chicken was depleted by oral antibiotics. Changes in cecal microbiota and metabolomics were detected by 16S rRNA sequencing and ultra-high performance liquid chromatography coupled with MS/MS (UHPLC–MS/MS) analysis. The correlation between antibiotic-induced dysbiosis of gut microbiota and metabolites and lipogenesis were analysed. We found that oral antibiotics significantly promoted the lipogenesis of chicken. 16S rRNA sequencing indicated that oral antibiotics significantly reduced the diversity and richness and caused dysbiosis of gut microbiota. Specifically, the abundance of Proteobacteria was increased considerably while the abundances of Bacteroidetes and Firmicutes were significantly decreased. At the genus level, the abundances of genera Escherichia-Shigella and Klebsiella were significantly increased while the abundances of 12 genera were significantly decreased, including Bacteroides. UHPLC-MS/MS analysis showed that antibiotic-induced dysbiosis of gut microbiota significantly altered cecal metabolomics and caused declines in abundance of 799 metabolites and increases in abundance of 945 metabolites. Microbiota-metabolite network revealed significant correlations between 4 differential phyla and 244 differential metabolites as well as 15 differential genera and 304 differential metabolites. Three metabolites of l-glutamic acid, pantothenate acid and N-acetyl-l-aspartic acid were identified as potential metabolites that link gut microbiota and lipogenesis in chicken. In conclusion, our results showed that antibiotic-induced dysbiosis of gut microbiota promotes lipogenesis of chicken by altering relevant metabolomics. The efforts in this study laid a basis for further study of the mechanisms that gut microbiota regulates lipogenesis and fat deposition of chicken.

Effects of Bacillus subtilis and Bacillus licheniformis on growth performance, immunity, short chain fatty acid production, antioxidant capacity, and cecal microflora in broilers

This study investigated the effects of dietary supplementation with Bacillus subtilis (B. subtilis) or Bacillus licheniformis (B. licheniformis) on growth performance, immunity, antioxidant capacity, short chain fatty acid (SCFA) production, and the cecal microflora in broiler chickens. In total, 360 male, 1-day-old Cobb 500 birds were randomly divided into 3 groups: the control group was fed a basal diet; the B. subtilis group was fed a basal diet supplemented with 1.5 × 109 CFU/kg B. subtilis; the B. licheniformis group was fed a basal diet supplemented with 1.5 × 109 CFU/kg B. licheniformis. Results showed that chickens supplemented with either B. subtilis or B. licheniformis had comparatively higher (P < 0.05) body weight and average daily gain, whereas no difference (P > 0.05) was observed in feed efficiency. Concentrations of serum IgA, IgY, and IgM, as well as anti-inflammatory IL-10 were significantly increased (P < 0.05), and proinflammatory IL-1β and IL-6 were significantly decreased (P < 0.05) by B. subtilis or B. licheniformis supplementation. Moreover, chickens fed with diets supplemented by either B. subtilis or B. licheniformis had greater antioxidant capacity, indicated by the notable increases (P < 0.05) in glutathione peroxidase, superoxide dismutase, and catalase, along with decrease (P < 0.05) in malondialdehyde. Compared to the control group, levels of SCFA, excluding acetic and propionic acid, in cecal content had improved (P < 0.05) by adding B. licheniformis, and significant increase (P < 0.05) in acetic and butyric acid was observed with B. subtilis supplementation. Microbial analysis showed that both B. subtilis or B. licheniformis supplementation could increase butyrate-producing bacteria such as Alistipes and Butyricicoccus, and decrease pathogenic bacteria such as the Synergistetes and Gammaproteobacteria. In summary, dietary supplemented with B. subtilis or B. licheniformis improved growth performance, immune status, and antioxidant capacity, increased SCFA production, and modulated cecal microbiota in chickens. Moreover, B. licheniformis was more effective than B. subtilis with the same supplemental amount.

Peptides Affecting the Outer Membrane Lipid Asymmetry System (MlaA-OmpC/F) Reduce Avian Pathogenic Escherichia coli (APEC) Colonization in Chickens.

Avian pathogenic Escherichia coli (APEC), an extraintestinal pathogenic E. coli (ExPEC), causes colibacillosis in chickens and is reportedly associated with urinary tract infections and meningitis in humans. Development of resistance is a major limitation of current ExPEC antibiotic therapy. New antibacterials that can circumvent resistance problem such as antimicrobial peptides (AMPs) are critically needed. Here, we evaluated the efficacy of Lactobacillus rhamnosus GG (LGG)-derived peptides against APEC and uncovered their potential antibacterial targets. Three peptides (NPSRQERR [P1], PDENK [P2], and VHTAPK [P3]) displayed inhibitory activity against APEC. These peptides were effective against APEC in biofilm and chicken macrophage HD11 cells. Treatment with these peptides reduced the cecum colonization (0.5 to 1.3 log) of APEC in chickens. Microbiota analysis revealed two peptides (P1 and P2) decreased Enterobacteriaceae abundance with minimal impact on overall cecal microbiota of chickens. Bacterial cytological profiling showed peptides disrupt APEC membranes either by causing membrane shedding, rupturing, or flaccidity. Furthermore, gene expression analysis revealed that peptides downregulated the expression of ompC (>13.0-fold), ompF (>11.3-fold), and mlaA (>4.9-fold), genes responsible for the maintenance of outer membrane (OM) lipid asymmetry. Consistently, immunoblot analysis also showed decreased levels of OmpC and MlaA proteins in APEC treated with peptides. Alanine scanning studies revealed residues crucial (P1, N, E, R and P; P2, D and E; P3, T, P, and K) for their activity. Overall, our study identified peptides with a new antibacterial target that can be developed to control APEC infections in chickens, thereby curtailing poultry-originated human ExPEC infections. IMPORTANCE Avian pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E. coli (ExPEC) and considered a foodborne zoonotic pathogen transmitted through consumption of contaminated poultry products. APEC shares genetic similarities with human ExPECs, including uropathogenic E. coli (UPEC) and neonatal meningitis E. coli (NMEC). Our study identified Lactobacillus rhamnosus GG (LGG)-derived peptides (P1 [NPSRQERR], P2 [PDENK], and P3 [VHTAPK]) effective in reducing APEC infection in chickens. Antimicrobial peptides (AMPs) are regarded as ideal candidates for antibacterial development because of their low propensity for resistance development and ability to kill resistant bacteria. Mechanistic studies showed peptides disrupt the APEC membrane by affecting the MlaA-OmpC/F system responsible for the maintenance of outer membrane (OM) lipid asymmetry, a promising new druggable target to overcome resistance problems in Gram-negative bacteria. Altogether, these peptides can provide a valuable approach for development of novel anti-ExPEC therapies, including APEC, human ExPECs, and other related Gram-negative pathogens. Furthermore, effective control of APEC infections in chickens can curb poultry-originated ExPEC infections in humans.

MiRNA Profiling in the Chicken Liver under the Influence of Early Microbiota Stimulation with Probiotic, Prebiotic, and Synbiotic.

Epigenetic regulation of gene expression is a form of interaction of the external environment on reading and transcription of genetic information encoded in nucleic acids. We provided evidence that early stimulation of the chicken microbiota with in ovo delivered synbiotics influenced gene expression and DNA methylation in the liver. Therefore, we hypothesize that the stimulation of microbiota by administering bioactive substances in ovo also affects the activity of miRNA in liver. For the analysis of miRNA activity, RNA was isolated from liver of adult broiler chicken and native chicken breed. The animals received a prebiotic, probiotic and synbiotic in ovo on day 12 of egg incubation. The analysis of miRNA expression was performed using the LNA method on a miRNA panel selected on the basis of previous microarray experiments. We have found increased miRNA expression activity after probiotic and synbiotic administration, especially in native chicken breed. Our results suggest that prebiotics reduce or do not affect miRNA activity. We have also shown that miRNA activity is regulated by the substance and genotype of the chicken. We can conclude that miRNAs constitute an important component of the molecular mechanism of host–probiotic interaction in liver.

Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies.

Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.

Detection of ESBL/AmpC-Producing and Fosfomycin-Resistant Escherichia coli From Different Sources in Poultry Production in Southern Brazil.

This study discussed the use of antimicrobials in the commercial chicken production system and the possible factors influencing the presence of Extended-spectrum β-lactamase (ESBL)/AmpC producers strains in the broiler production chain. The aim of this study was to perform longitudinal monitoring of ESBL-producing and fosfomycin-resistant Escherichia coli from poultry farms in southern Brazil (Paraná and Rio Grande do Sul states) and determine the possible critical points that may be reservoirs for these strains. Samples of poultry litter, cloacal swabs, poultry feed, water, and beetles (Alphitobius sp.) were collected during three distinct samplings. Phenotypic and genotypic tests were performed for characterization of antimicrobial resistant strains. A total of 117 strains were isolated and 78 (66%) were positive for ESBL production. The poultry litter presented ESBL positive strains in all three sampled periods, whereas the cloacal swab presented positive strains only from the second period. The poultry litter represents a significant risk factor mainly at the beginning poultry production (odds ratio 6.43, 95% confidence interval 1–41.21, p < 0.05). All beetles presented ESBL positive strains. The predominant gene was blaCTX–M group 2, which occurred in approximately 55% of the ESBL-producing E. coli. The cit gene was found in approximately 13% of the ESBL-producing E. coli as AmpC type determinants. A total of 19 out of 26 fosfomycin-resistant strains showed the fosA3 gene, all of which produced ESBL. The correlation between fosA3 and blaCTX–M group 1 (blaCTX–M55) genes was significant among ESBL-producing E. coli isolated from Paraná (OR 3.66, 95% CI 1.9–9.68) and these genetic determinants can be transmitted by conjugation to broiler chicken microbiota strains. Our data revealed that poultry litter and beetles were critical points during poultry production and the presence of fosfomycin-resistant strains indicate the possibility of risks associated with the use of this antimicrobial during production. Furthermore, the genetic determinants encoding CTX-M and fosA3 enzymes can be transferred to E. coli strains from broiler chicken microbiota, thereby creating a risk to public health.

Transition of microbiota in chicken cecal droppings from commercial broiler farms

BackgroundChickens are major sources of human nutrition worldwide, but the chicken intestinal microbiota can be a source of bacterial infection. The microbiota has potential to regulate the colonization of pathogens by competitive exclusion, production of antimicrobial compounds, and stimulation of the mucosal immune system. But information on the microbiota in commercial broiler chickens is limited because of the difficulty of conducting studies at commercial farms. To obtain fundamental information that can be used to control pathogens in chickens, we determined the 6-week dynamics of microbiota in chicken cecal droppings from commercial broiler farms.ResultsCecal droppings from four chickens were collected once a week from 1 to 6 weeks of age at three commercial broiler farms. A total of 168 samples were collected from 7 flocks and subjected to 16S rRNA amplicon sequencing. Despite the farms have distinctly different climate conditions, the microbiota in the same growth stages were similar among farms. Moreover, as the chickens grew and the feed types were switched, the richness and diversity of the microbiota gradually increased and convergence of the composition of the microbiota was apparent. Notably, minor bacterial taxa (i.e. OTUs with relative abundance < 0.05%) within the microbiota were changed by the chicken age, switching of feed types, and presence of Campylobacter. In particular, the effects of switching of feed types on the microbiota were larger than the effects of age and Campylobacter.ConclusionsIrrespective of the locations of the farms, the microbiota of chicken cecum, especially minor bacteria, was successively changed more affected by feed types than by ages. Switching of feed types inducing the alteration of the microbiota may be associated with the colonization of pathogens in the chicken gut. These results will also help with extrapolation of studies in experimental animals to those in the commercial farms.

Changes in the ceca microbiota of broilers vaccinated for coccidiosis or supplemented with salinomycin

The objective of this study was to characterize differences in the cecal microbiota of chickens vaccinated for coccidiosis or receiving salinomycin in the diet. In this study, 140 male 1-day-old broiler chickens were divided in 2 groups: vaccine group (live vaccine) vaccinated at the first day and salinomycin group (60 ppm/kg since the first day until 35 d of age). Each treatment was composed for 7 replicates of 10 birds per pen. At 28 d, the cecal content of one bird per replicate was collected for microbiota analysis. The genetic sequencing was conducted by the Miseq Illumina platform. Vaccine group showed lower body weight, weight gain, and poorer feed conversion in the total period (P < 0.05). Bacterial 16S rRNA genes were classified as 3 major phyla (Bacteroidetes, Firmicutes, and Proteobacteria), accounting for more than 98% of the total bacterial community. The microbiota complexity in the cecal was estimated based on the α-diversity indices. The vaccine did not reduce species richness and diversity (P > 0.05). The richness distribution in the salinomycin group was larger and more uniform than the vaccinated birds. Salinomycin group was related to the enrichment of Bacteroidetes, whereas Firmicutes and Proteobacteria phyla were in greater proportions in the vaccine group. The last phylum includes a wide variety of pathogenic bacteria. The vaccine did not decrease the species richness but decreased the percentage of Bacteroidetes, a phylum composed by genera that produce short-chain fatty acids improving intestinal health. Vaccine group also had higher Proteobacteria phylum, which may help explain its poorer performance.