Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum

Effects of rearing systems (cage versus floor) on the microbial composition and transcriptome of goose ileum

There is a gradual transition from water to dryland rearing of geese. In this study, we performed 16S rRNA sequencing (16S rRNA-seq) and transcriptome sequencing (RNA-seq) to reveal the effects of cage rearing (CR) and floor rearing (FR) systems on the microbial composition and transcriptome of the goose ileum. Through 16S rRNA-seq, Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 2 (hgcI_clade and Faecalibacterium) and 14 (Bacteroides, Proteiniphilum, Proteiniclasticum, etc.) differential microbiota in CR and FR, respectively. The rearing system influenced 4 pathways including biosynthesis of amino acids in ileal microbiota. Moreover, we identified 1,198 differentially expressed genes (DEGs) in the ileum mucosa, with 957 genes up-regulated in CR and 241 genes up-regulated in FR. In CR, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the significant enrichment (p < 0.05) of 28 KEGG pathways, most of which were associated with amino acid metabolism. In FR, up-regulated DEGs were mainly enriched in KEGG pathways associated with cellular processes, including apoptosis, necroptosis, and cellular senescence. Spearman correlation analysis of differential microbiota and amino acid metabolism-related DEGs in CR showed a significant positive correlation. Additionally, differential microbiota of FR, Phascolarctobacterium and Sutterella, were positively correlated with FGF10 (p < 0.05) and PIK3R1 (p < 0.01), respectively. In conclusion, there might be differences in ileal amino acid metabolism levels between CR and FR geese, and the observed increase in harmful bacterial species in FR might impact the activity of ileal cells.

Modulation of chicken gut microbiota for enhanced productivity and health: A review

Microbiota in the digestive tract has become an interesting topic for researchers in recent years. The profile of chicken digestive tract microbiota and its relationship with health and production efficiency have become basic data for modulating the diversity and abundance of the digestive tract microbiota. This article reviews the techniques used to analyze the diversity, role, and function of the gastrointestinal microbiota and the mechanisms by which they are modulated. The gut microbiota plays an important role in animal production, especially during feed digestion and animal health, because it interacts with the host against pathogens. Feed modulation can be a strategy to modulate gut composition and diversity to increase production efficiency by improving growth conditions.

Essential oils mix effect on chicks ileal and caecal microbiota modulation: a metagenomics sequencing approach

Introduction

Microbiota plays a pivotal role in promoting the health and wellbeing of poultry. Essential oils (EOs) serve as an alternative solution for modulating poultry microbiota. This study aimed to investigate, using amplicon sequencing, the effect of a complex and well-defined combination of EOs feed supplement on both ileal and caecal broiler microbiota, within the context of Salmonella and Campylobacter intestinal colonization.

Material and methods

For this experiment, 150-day-old Ross chicks were randomly allocated to two groups: T+ (feed supplementation with EO mix 500 g/t) and T- (non-supplemented). At day 7, 30 birds from each group were orally inoculated with 106 CFU/bird of a Salmonella enteritidis and transferred to the second room, forming the following groups: TS+ (30 challenged birds receiving infeed EO mix at 500g/t) and TS- (30 challenged birds receiving a non-supplemented control feed). At day 14, the remaining birds in the first room were orally inoculated with 103 CFU/bird of two strains of Campylobacter jejuni, resulting in the formation of groups T+C+ and T-C+. Birds were sacrificed at day 7, D10, D14, D17, and D21. Ileal and caecal microbiota samples were analyzed using Illumina MiSeq sequencing. At D7 and D14, ileal alpha diversity was higher for treated birds (p <0.05).

Results and discussion

No significant differences between groups were observed in caecal alpha diversity (p>0.05). The ileal beta diversity exhibited differences between groups at D7 (p < 0.008), D10 (p = 0.029), D14 (p = 0.001) and D17 (p = 0.018), but not at D21 (p = 0.54). For all time points, the analysis indicated that 6 biomarkers were negatively impacted, while 10 biomarkers were positively impacted. Sellimonas and Weissella returned the lowest (negative) and highest (positive) coefficient, respectively. At each time point, treatments influenced caecal microbiota beta diversity (p < 0.001); 31 genera were associated with T+: 10 Ruminoccocaceae genera were alternatively more abundant and less abundant from D7, 7 Lachnospiraceae genera were alternatively more and less abundant from D10, 6 Oscillospiraceae genera were variable depending on the date and 4 Enterobacteriaceae differed from D7. During all the experiment, Campylobacter decreased in treated birds (p < 0.05). This study showed that EO mix modulates ileal and caecal microbiota composition both before and during challenge conditions, increasing alpha diversity, especially in ileum during the early stages of chick life.

Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage-Application of Next-Generation Amplicon and Shotgun Metagenome Sequences

"Pakhoi" is an ethnic drink of the Tons valley, Uttarakhand, India produced by fermenting jaggery and barley with the help of a starter culture called "keem". In the present study, we investigated the microbial diversity and associated functional potential of "keem" using shotgun metagenome sequencing and amplicon sequencing. We also compared the taxonomic data obtained using these two sequencing techniques. The results showed that shotgun sequencing revealed a higher resolution of taxonomic profiling as compared to the amplicon sequencing. Furthermore, it was found that the genera detected by shotgun sequencing were valuable for facilitating the fermentation process. Additionally, to understand the functional profiling of the genera, different databases were used for annotation, resulting in a total of 13 metabolic pathways. The five most abundant KEGG functions were genetic information processing, metabolism, translation, cofactor and vitamin metabolism and xenobiotic degradation. In contrast, the top five COG were in order of highest frequency sequences belonging to transcription, followed by general function prediction, carbohydrate transport metabolism, amino acid transport and metabolism and translation and biogenesis. Gene ontology revealed many pathways, biochemical processes and molecular functions associated with the organisms forming the starter culture. Overall, the present study can help to understand the microbial diversity and its role in fermentation of traditional alcoholic beverages using "Keem".

Emission and Migration of Nanoscale Particles during Osseointegration and Disintegration of Dental Implants in the Clinic and Experiment and the Influence on Cytokine Production

The emission of nanoscale particles from the surfaces of dental implants leads to the cumulative effect of particle complexes in the bone bed and surrounding soft tissues. Aspects of particle migration with the possibility of their involvement in the development of pathological processes of systemic nature remain unexplored. The aim of this work was to study protein production during the interaction of immunocompetent cells with nanoscale metal particles obtained from the surfaces of dental implants in the supernatants. The ability to migrate nanoscale metal particles with possible involvement in the formation of pathological structures, in particular in the formation of gallstones, was also investigated. The following methods were used: microbiological studies, X-ray microtomography, X-ray fluorescence analysis, flow cytometry, electron microscopy, dynamic light scattering, and multiplex immunofluorescence analysis. For the first time, titanium nanoparticles in gallstones were identified by X-ray fluorescence analysis and electron microscopy with elemental mapping. The multiplex analysis method revealed that the physiological response of the immune system cells, in particular neutrophils, to nanosized metal particles significantly reduced TNF-a production both through direct interaction and through double lipopolysaccharide-induced signaling. For the first time, a significant decrease in TNF-a production was demonstrated when supernatants containing nanoscale metal particles were co-cultured with proinflammatory peritoneal exudate obtained from the peritoneum of the C57Bl/6J inbred mice line for one day.

Effects of Phage Cocktail, Probiotics, and Their Combination on Growth Performance and Gut Microbiota of Broiler Chickens

Phages, which are often used therapeutically, have begun to receive interest as alternatives to antibiotic growth promoters (AGPs) for enhancing chicken growth. Another option that has been extensively studied as a growth promoter in chickens is probiotics. To the best of our knowledge, there is currently no study available on the use of phages and probiotics in combination as potential feed additives for broiler chickens. Therefore, this study demonstrated the effects of a phage cocktail, probiotics, and their combination on the growth performance and gut microbiota of broiler chickens. A total of 288 one-day-old male Cobb 500 broilers were randomly allotted to one of six treatments in a completely randomised design. The treatments were (i) C (basal diet (BD) only), (ii) 1ϕ (BD + 0.1% phage cocktail), (iii) 2ϕ (BD + 0.2% phage cocktail), (iv) P (BD + 0.1% probiotic), (v) 1ϕP (BD + 0.1% phage cocktail + 0.1% probiotic), and (vi) 2ϕP (BD + 0.2% phage cocktail + 0.1% probiotic). The 1ϕP treatment had significantly (p < 0.05) better BW (35 days), BWG (22-35 days, 1-35 days), and FCR (1-21 days, 22-35 days, 1-35 days) compared to C. Unique gut microbiota diversity was also found between the ϕP (1ϕP and 2ϕP) and non-ϕP groups (C, 1ϕ, 2ϕ, and P) in ilea, particularly in the 35-day-old chickens. Microorganisms associated with short-chain fatty acid (SCFA) producers were significantly (p < 0.05) more present in the ϕP group than in the non-ϕP group. The predicted genes related to carbohydrate and amino acid metabolism were significantly upregulated in ϕP groups compared to non-ϕP groups. These genes were involved in the digestion and absorption of nutrients, as well as the production of energy. Our findings showed that the 1ϕP treatment could be a potential alternative to AGPs for poultry, as growth performance was enhanced, and gut microbiota was positively modulated.

Determination of the Prevalence and Antimicrobial Resistance of Enterococcus faecalis and Enterococcus faecium Associated with Poultry in Four Districts in Zambia

The presence of antimicrobial-resistant Enterococci in poultry is a growing public health concern worldwide due to its potential for transmission to humans. The aim of this study was to determine the prevalence and patterns of antimicrobial resistance and to detect drug-resistant genes in Enterococcus faecalis and E. faecium in poultry from four districts in Zambia. Identification of Enterococci was conducted using phenotypic methods. Antimicrobial resistance was determined using the disc diffusion method and antimicrobial resistance genes were detected using polymerase chain reaction and gene-specific primers. The overall prevalence of Enterococci was 31.1% (153/492, 95% CI: 27.1–35.4). Enterococcus faecalis had a significantly higher prevalence at 37.9% (58/153, 95% CI: 30.3–46.1) compared with E. faecium, which had a prevalence of 10.5% (16/153, 95% CI: 6.3–16.7). Most of the E. faecalis and E. faecium isolates were resistant to tetracycline (66/74, 89.2%) and ampicillin and erythromycin (51/74, 68.9%). The majority of isolates were susceptible to vancomycin (72/74, 97.3%). The results show that poultry are a potential source of multidrug-resistant E. faecalis and E. faecium strains, which can be transmitted to humans. Resistance genes in the Enterococcus species can also be transmitted to pathogenic bacteria if they colonize the same poultry, thus threatening the safety of poultry production, leading to significant public health concerns.

Passion fruit peel and its zymolyte enhance gut function in Sanhuang broilers by improving antioxidation and short-chain fatty acids and decreasing inflammatory cytokines

The passion fruit peel (PFP) is the by-product of juice processing and is rich in phenolic compounds and dietary fibers. As the high ADF content in PFP (34.20%), we proceeded to treat PFP with cellulase. The ADF decreased to 16.70% after enzymatic processing, and we supposed that enzymolytic passion fruit peel (EPF) should have a greater growth performance than PFP to broilers. Two trials were conducted to evaluate the effects of dietary PFP or EPF supplementation on growth performance, serum biochemical indices, meat quality, and cecal short-chain fatty acids, microbiota, and metabolites in broilers. In Exp. 1, 180 1-day-old Sanhuang broilers (male, 36.17 ± 2.47 g) were randomly allocated into 3 treatments, with 6 replicates in each treatment. The 3 experimental diets included 1 basal diet (control) and 2 PFP-added diets supplemented with 1 and 2% PFP, respectively. The trial lasted for 42 d. In Exp. 2, 144 Sanhuang broilers (male, 112-day-old, 1.62 ± 0.21 kg) were randomly allocated to 3 treatments. Each treatment was distributed among 6 pens, and each pen contained 8 broilers. The 3 treatment diets included: a control diet, a positive control diet supplementing 75 mg/kg chlortetracycline, and the experimental diet supplementing 3% EPF. The trial lasted for 56 d. Results showed that dietary 1 and 2% PFP addition did not affect growth performance in Exp. 1, and the 3% EPF supplementation had a negative effect on ADFI (P < 0.05) in Exp. 2. A decreased serum triglyceride (P < 0.05) in broilers was observed in Exp. 1. Broilers fed EPF had a higher glutathione peroxidase (GSH-Px) (P < 0.05), and lower levels of tumor necrosis factor-α (TNF-α) (P < 0.05) and glucose (P < 0.05) in Exp. 2. We also found that broilers from PFP or EPF-treated treatments had an increased butyrate content and higher microbial diversity in the cecum. The effects of antioxidation, anti-inflammatory function, and elevated SCFAs were confirmed after the microbe and untargeted metabolomic analysis. Dietary EPF supplementation significantly increased the SCFA-generating bacteria, anti-inflammatory-related bacteria, the antioxidant-related and anti-inflammatory-related metabolites. Moreover, dietary 3% EPF addition positively affects the biosynthesis of phenylpropanoids, which strongly correlate with the antioxidant and anti-inflammatory properties. In conclusion, the proper addition level did not affect the growth performance, and the PFP and EPF could improve the antioxidation state, anti-inflammatory activity, and intestinal functions of Sanhuang broilers to some extent.

Application of Organic Acids and Essential Oils as Alternatives to Antibiotic Growth Promoters in Broiler Chickens

This study was conducted to evaluate the effects of OAs and EOs on growth performance, serum biochemistry, antioxidant enzyme activities, intestinal morphology, and digestive enzyme activities to replace AGP in broilers. Six hundred one-day-old broilers were allotted to five treatments with six replicates: (1) negative control (NC; basal diet); (2) positive control (PC; NC + 50 mg/kg bacitracin methylene disalicylate); (3) organic acids (OA; NC + 2000 mg/kg OA); (4) essential oils (EO; NC + 300 mg/kg EO); and (5) OA + EO (NC + 2000 mg/kg OA + 300 mg/kg EO). In the starter phase, the PC, EO, and OA + EO groups had a significantly lower feed conversion ratio (FCR) compared to the NC group. While the final body weight (BW) of broilers fed OAs was similar compared to broilers fed PC (p > 0.1), the FCR of the OA group tended to be lower than the PC group on D 42 (p = 0.074). The OA group had the higher serum GLOB:ALB (albumin) and ileal villus height and crypt depth (VH:CD) ratios compared to the EO group. Thus, the supplementation of EOs and OAs could substitute AGP in the starter and finisher phase, respectively.

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Background

The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota.

Results

Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M.

Conclusions

These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02619-6.

An Investigation of the Effect of Water Additives on Broiler Growth and the Caecal Microbiota at Harvest

Campylobacter is the most common foodborne pathogen in developed countries and most cases are associated with poultry. This study investigated the effect of three anti-Campylobacter water additives on broiler growth and on the caecal microbiota at harvest using 16S rRNA amplicon sequencing. Mixtures of organic acids (OA) and essential oils (EO) were administered to broilers for the entirety of the production cycle (35 d) and medium-chain fatty acids (MCFA) for 5 d immediately before harvest, under commercial conditions. Bird weight gain was significantly (p < 0.001) reduced in broilers receiving the OA and EO treatments. While this was most likely due to reduced water intake and corresponding lower feed consumption, changes to the caecal microbiota may also have contributed. Firmicutes made up over 75% of the bacteria regardless of sample type, while the minor phyla included Bacteroidetes, Actinobacteria, Melainabacteria, and Proteobacteria. There were no significant (p > 0.05) differences in the alpha diversity as measured using ACE, Chao1, and Shannon indices, except for control (water) versus MCFA and OA versus MCFA, using the Wilcox test. In contrast, there was a significant (p < 0.05) difference in beta diversity when the treated were compared to the untreated control and main flock samples, while linear discriminant analysis effect size (LeFSe) identified three OTUs that were present in the control but absent in the treated birds. It was concluded that the water additives tested adversely affected broiler performance, which may, at least in part, be due to changes in the caecal microbiota, assuming that the altered microbiota at day 35 is indicative of a change throughout the production cycle.

The Effects of Agrimonia pilosa Ledeb, Anemone chinensis Bunge, and Smilax glabra Roxb on Broiler Performance, Nutrient Digestibility, and Gastrointestinal Tract Microorganisms

Poultry farming is growing globally, particularly in developing countries, to meet the demands of growing populations for poultry meat and eggs. This is likely to lead to an increase in the use of antibiotics in poultry feed, thus contributing to the development and spread of antibiotic resistance which, poses a serious threat to human and animal health worldwide. One way of reducing this threat is to reduce the use of antibiotics in poultry production by finding effective and sustainable antibiotic alternatives that can be used to support poultry health and productivity. Therefore, this study evaluates the incorporation of three medicinal plants, Anemone chinensis Bunge, Smilax glabra Roxb, and Agrimonia pilosa Ledeb, in poultry feed on production performance, nutrient digestibility, and bacteria in the chicken caecum in a 35-day performance trial with 420-day-old male Ross 308 broilers. Groups of randomly selected chicks received one of six dietary treatments. These included five experimental diets of reduced nutrient specifications as a negative control (NC); with amoxicillin as a positive antibiotic control (PC1); with A. pilosa Ledeb (NC1); with A. chinensis Bunge (NC2); and with S. glabra Roxb (NC3). One other positive control diet contained the recommended nutrient specification (PC2). Weight gain and feed intake were measured weekly and used to calculate the feed conversion ratio as performance parameters. Bacteria were enumerated from chicken caecum using a traditional plating method and selective agar. S. glabra Roxb and A. chinensis Bunge showed comparable effects to amoxicillin with significantly increased weight gain in birds offered these diets, compared to those offered the negative control from days 0 to 35 (p < 0.001). S. glabra Roxb exhibited effects similar to the amoxicillin control group with an improved feed conversion ratio (p < 0.001). In addition, S. glabra Roxb decreased numbers of E. coli and Campylobacter spp. on days 21 (p < 0.05) and 35 (p < 0.01) and increased numbers of lactic acid bacteria comparable to the antibiotic group on days 14 (p < 0.001) and 35 (p < 0.01). The findings of this in vivo trial highlight the potential of S. glabra Roxb and A. chinensis Bunge as beneficial feed material to promote poultry health and productivity in the absence of antibiotics.

Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens

This study evaluated the effect of the delivery of a commercial essential oil blend containing the phytonutrients star anise, cinnamon, rosemary, and thyme oil (via different routes) on broiler chickens’ ileal and ceca microbiota and liver transcriptome compared to an antibiotic growth promoter. Eggs were incubated and allocated into three groups: non-injected, in ovo saline, and in ovo essential oil. On day 18 of incubation, 0.2 mL of essential oil in saline (dilution ratio of 2:1) or saline alone was injected into the amnion. At hatch, chicks were assigned to post-hatch treatment combinations: (A) a negative control (corn-wheat-soybean diet), (B) in-feed antibiotics, (C) in-water essential oil (250 mL/1000 L of drinking water), (D) in ovo saline, (E) in ovo essential oil, and (F) in ovo essential oil plus in-water essential oil in eight replicate cages (six birds/cage) and raised for 28 days. On days 21 and 28, one and two birds per cage were slaughtered, respectively, to collect gut content and liver tissues for further analysis. Alpha and beta diversity differed significantly between ileal and ceca samples but not between treatment groups. In-feed antibiotic treatment significantly increased the proportion of specific bacteria in the family Lachnospiraceae while reducing the proportion of bacteria in the genus Christensenellaceae in the ceca, compared to other treatments. Sex-controlled differential expression of genes related to cell signaling and tight junctions were recorded. This study provides data that could guide the use of these feed additives and a foundation for further research.

Informal nutrition symposium: leveraging the microbiome (and the metabolome) for poultry production

Knowledge of gut microbiology of poultry has advanced from a limited ability to culture relatively few microbial species, to attempting to understand the complex interactions between the bird and its microbiome. The Informal Nutrition Symposium 2021 was intended to help poultry scientists to make sense of the implications of the vast amounts of information being generated by researchers. This paper represents a compilation of the talks given at the symposium by leading international researchers in this field. The symposium began with an overview of the historical developments in the field of intestinal microbiology and microbiome research in poultry. Next, the systemic effects of the microbiome on health in the context of the interplay between the intestinal microbiota and the immune system were presented. Because the microbiome and the host communicate and influence each other, the novel field of kinomics (the study of protein phosphorylation) as used in the study of the poultry microbiome was discussed. Protein phosphorylation is a rapid response to the complex of signals among the microbiome, intestinal lumen metabolites, and the host. Then, a description of why an understanding of the role of microbial endocrinology in poultry production can lead to new understanding of the mechanisms by which the gut microbiota and the host can interact in defined mechanisms that ultimately determine health, pathogenesis of infectious disease, and behavior was given. Finally, a view forward was presented underscoring the importance of understanding mechanisms in microbiomes in other organ systems and other species. Additionally, the importance of the development of new -omics platforms and data management tools to more completely understand host microbiomes was stressed.

Yeast β-Glucan Altered Intestinal Microbiome and Metabolome in Older Hens

The prebiotics- and probiotics-mediated positive modulation of the gut microbiota composition is considered a useful approach to improve gut health and food safety in chickens. This study explored the effects of yeast β-glucan (YG) supplementation on intestinal microbiome and metabolites profiles as well as mucosal immunity in older hens. A total of 256 43-week-old hens were randomly assigned to two treatments, with 0 and 200 mg/kg of YG. Results revealed YG-induced downregulation of toll-like receptors (TLRs) and cytokine gene expression in the ileum without any effect on the intestinal barrier. 16S rRNA analysis claimed that YG altered α- and β-diversity and enriched the relative abundance of class Bacilli, orders Lactobacillales and Enterobacteriales, families Lactobacillaceae and Enterobacteriaceae, genera Lactobacillus and Escherichia–Shigella, and species uncultured bacterium-Lactobacillus. Significant downregulation of cutin and suberin, wax biosynthesis, atrazine degradation, vitamin B6 metabolism, phosphotransferase system (PTS), steroid degradation, biosynthesis of unsaturated fatty acids, aminobenzoate degradation and quorum sensing and upregulation of ascorbate and aldarate metabolism, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, steroid biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, sesquiterpenoid and triterpenoid biosynthesis, lysine degradation, and ubiquinone and other terpenoid-quinone biosyntheses were observed in YG-treated hens, as substantiated by the findings of untargeted metabolomics analysis. Overall, YG manifests prebiotic properties by altering gut microbiome and metabolite profiles and can downregulate the intestinal mucosal immune response of breeder hens.

Effects of Clostridium butyricum on Growth Performance, Gut Microbiota and Intestinal Barrier Function of Broilers

This study was conducted to evaluate the effects of Clostridium butyricum dietary supplementation on the growth, antioxidant, immune response, gut microbiota, and intestinal barrier function of broilers under high stocking density (HSD) stress. A total of 324 1-day-old Arbor Acres male broilers were randomly assigned to three treatments with six replicates, each replicate including 18 chickens (18 birds/m²). The experiment lasted 6 weeks. The three treatments were basal diet (control, CON), basal diet supplemented with 1 × 10⁹ colony forming units (cfu)/kg C. butyricum (CB), and basal diet supplemented with 10 mg/kg virginiamycin (antibiotic, ANT). The results showed that the body weight (BW) and average daily gain (ADG) of broilers in the CB group were significantly higher than those in the CON group in three periods (p < 0.05). The total antioxidant capacity (T-AOC) and the superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity in serum of the CB group were significantly increased compared with those in the CON and ANT groups at 42 days (p < 0.05). At 42 days, the serum immunoglobulin M (IgM) and immunoglobulin G (IgG) levels of the CB group were significantly higher than those of the CON group. Compared with the CON group, interleukin-1β (IL-1β) in the CB group was significantly decreased in the starter and grower stages (p < 0.05), but there was no significant difference between the two treatment groups (p > 0.05). C. butyricum significantly decreased the high stocking density-induced expression levels of IL-1β and tumor necrosis factor-α (TNF-α) in the ileum of broilers at different stages. Additionally, C. butyricum could increase the expressions of claudin-1 and zonula occludens-1 (ZO-1) in intestinal tissue. Moreover, C. butyricum significantly increased the Sobs and Shannon indices in the CB group compared with the ANT group (p < 0.05), while the Ace index in the CB group was significantly higher than that of the CON group (p < 0.05). Furthermore, by using 16S rRNA gene sequencing, the proportion of Bacteroides in the CB group was increased compared to those in the CON and ANT groups at the genus level. In conclusion, C. butyricum supplemented into feed could improve the growth performance and feed utilization of broilers by promoting immune and intestinal barrier function and benefiting the cecal microflora.

Development of the in vitro Cecal Chicken ALIMEntary tRact mOdel-2 to Study Microbiota Composition and Function

The digestive system of the chicken plays an important role in metabolism, immunity, and chicken health and production performance. The chicken ceca harbor a diverse microbial community and play a crucial role in the microbial fermentation and production of energy-rich short-chain fatty acids (SCFA). For humans, dogs, and piglets in vitro digestive system models have been developed and are used to study the microbiota composition and metabolism after intervention studies. For chickens, most research on the cecal microbiota has been performed in in vivo experiments or in static in vitro models that may not accurately resemble the in vivo situations. This paper introduces an optimized digestive system model that simulates the conditions in the ceca of the chicken, i.e., the Chicken ALIMEntary tRact mOdel-2 (CALIMERO-2). The system is based on the well-validated TNO in vitro model of the colon-2 (TIM-2) and is the first dynamic in vitro digestion model for chickens species. To validate this model, the pH, temperature, and different types of microbial feeding were compared and analyzed, to best mimic the conditions in the chicken ceca. The bacterial composition, as well as the metabolite production at 72 h, showed no significant difference between the different microbial feedings. Moreover, we compared the CALIMERO-2 digestive samples to the original inoculum and found some significant shifts in bacterial composition after the fermentation started. Over time the bacterial diversity increased and became more similar to the original inoculum. We can conclude that CALIMERO-2 is reproducible and can be used as a digestive system model for the chicken ceca, in which the microbial composition and activity can be maintained and shows similar results to the in vivo cecum. CALIMERO-2 can be used to study effects on composition and activity of the chicken cecum microbiota in response to in-feed interventions.

A Review of the Effects and Production of Spore-Forming Probiotics for Poultry

Simple Summary

Spore-forming probiotics are widely used in the poultry industry for their beneficial impact on host health. The main feature that separates spore-forming probiotics from the more common lactic acid probiotics is their high resistance to external and internal factors, resulting in higher viability in the host and correspondingly, greater efficiency. Their most important effect is the ability to confront pathogens, which makes them a perfect substitute for antibiotics. In this review, we cover and discuss the interactions of spore-forming probiotic bacteria with poultry as the host, their health promotion effects and mechanisms of action, impact on poultry productivity parameters, and ways to manufacture the probiotic formulation. The key focus of this review is the lack of reproducibility in poultry research studies on the evaluation of probiotics’ effects, which should be solved by developing and publishing a set of standard protocols in the professional community for conducting probiotic trials in poultry.

Abstract

One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing.

Effects of Enteromorpha polysaccharide dietary addition on the diversity and relative abundance of ileum flora in laying hens

This experiment explored the effects of different levels of Enteromorpha polysaccharide dietary addition on the intestinal flora structure in laying hens. A total of 300 Hy-line brown laying hens aged 280 days old were selected according to the principle of equal weight and egg production rate. Group 1 was the blank control group fed with basic diet, Group 2 was the antibiotic control group supplemented with bacitracin zinc (0.005%) and basic diet, and Groups 3-5 were the experimental groups that received 0.1%, 0.2%, and 0.4% Enteromorpha polysaccharides in their diets, respectively. Four replicates per group and 15 repeats per replicate were prepared. The pretrial period was 10 days, and the normal trial period was 42 days. The ileum contents of laying hens were collected aseptically toward the end of the test to detect the diversity and relative abundance of the flora. Results were as follows. (1) Bacterial abundance (ACE and Chao1) and diversity (Simpson and Shannon) indexes were not significantly different between the control and test groups (P > 0.05). (2) Compared with that in group 1, the relative abundance of Firmicutes in groups 4 and 5 significantly increased by 14.13% (P < 0.05) and 13.70% (P < 0.05), respectively. The relative abundance of Bacilli in group 4 was significantly increased by 11.94% (P < 0.05) and 12.86% (P < 0.05) compared with those in groups 1 and 3, respectively. The relative abundance of Lactobacillales in group 4 was significantly increased by 27.02% (P < 0.05) compared with that in group 1. The relative abundance of Lactobacillaceae in group 4 was significantly increased by 22.92% (P < 0.05) and 11.4% (P < 0.05) compared with those in groups 1 and 3, respectively. The relative abundance of Lactobacillus in groups 4 and 5 was increased by 19.75% (P < 0.05) and 18.54% (P < 0.05), respectively. CONCLUSION: The dietary addition of 0.2% Enteromorpha polysaccharides can remarkably increase the relative abundance of Firmicutes phylum, Bacilli class, Lactobacillales order, Lactobacillaceae family, and Lactobacillus genus in the ileum of laying hens. This effect was equivalent to the action of bacitracin zinc and had no substantial influence on the diversity of ileum flora.

Current Perspectives and Potential of Probiotics to Limit Foodborne Campylobacter in Poultry

Poultry has been one of the major contributors of Campylobacter related human foodborne illness. Numerous interventions have been applied to limit Campylobacter colonization in poultry at the farm level, but other strategies are under investigation to achieve more efficient control. Probiotics are viable microbial cultures that can establish in the gastrointestinal tract (GIT) of the host animal and elicit health and nutrition benefits. In addition, the early establishment of probiotics in the GIT can serve as a barrier to foodborne pathogen colonization. Thus, probiotics are a potential feed additive for reducing and eliminating the colonization of Campylobacter in the GIT of poultry. Screening probiotic candidates is laborious and time-consuming, requiring several tests and validations both in vitro and in vivo. The selected probiotic candidate should possess the desired physiological characteristics and anti-Campylobacter effects. Probiotics that limit Campylobacter colonization in the GIT rely on different mechanistic strategies such as competitive exclusion, antagonism, and immunomodulation. Although numerous research efforts have been made, the application of Campylobacter limiting probiotics used in poultry remains somewhat elusive. This review summarizes current research progress on identifying and developing probiotics against Campylobacter and presenting possible directions for future research efforts.

Regional Differences in the Gut Microbiota and Gut-Associated Immunologic Factors in the Ileum and Cecum of Rats With Collagen-Induced Arthritis

Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation and a multifactorial etiology. We previously showed that gut microbiota dysbiosis in the rat ileum is involved in the development of collagen-induced arthritis (CIA). The gut microbiota in the distinct gastrointestinal tract (GIT) plays region-specific roles, but information on the different roles of the microbiota in distinct GIT compartments of CIA rats is limited. This study aimed to evaluate the region-specific differences in the gut microbial communities and certain gut-associated immunologic factors in the ileum and cecum of CIA rats. Ileal and cecal digesta were collected from CIA and control rats for microbiome analysis. We determined the microbial richness, diversity and taxa as well as the expression of interleukin (IL)-1β and IL-17A in the epithelium and lamina propria of the ileum and cecum mucosal layers. The CIA-induced microbiota alterations in the ileum differed from those in the cecum. The ileal microbiota were more markedly influenced in CIA, as revealed by sharp reductions in the abundances of the families Enterococcaceae, Lactobacillaceae and Streptococcaceae and the genera Lactobacillus and Lactococcus. Moreover, significant increases in IL-1β, and IL-17A mRNA expression were detected in only the ileal epithelium and lamina propria of the mucosal layer. Therefore, the microbial characteristics in the ileum were consistent with the immune-mediated inflammatory features of CIA, suggesting that the ileal microbiota might better represent the CIA-induced inflammatory responses than the cecal microbiota and that these responses might partially impact the progression of RA by regulating intestinal mucosal immunity.

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

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

Amino acid digestibility coefficient values of animal protein meals with dietary protease for broiler chickens

A digestibility experiment was conducted to evaluate the effects of dietary exogenous monocomponent protease on the coefficient of apparent total tract digestibility (ATTD) and coefficient apparent ileal digestibility (AID) of amino acids in meat and bones meal (MBM), poultry byproducts meal (PBPM), and feather meal (FM). A total of 512 Cobb-500 male broiler chickens (aged 14 d) were randomly placed into 64 metabolism cages (8 birds per pen) and were allocated to eight treatments with eight replicates in a semi-controlled environmental room. The experimental diets consisted of the basal diet (corn/SBM) and the replacement of 300 g/kg on a weight basis with MBM, PBPM, or FM. The excreta were collected during 3 d (19 to 21 d), and the ileal digesta (using Celite as an indigestible marker) only 1 d (21 d). The protease contained 75,000 PROT units/g. The use of the enzyme increased (P < 0.05) ATTD for alanine, cysteine, glycine, and threonine in the basal diet and AID for the amino acids alanine, cysteine, glycine, lysine, threonine, and valine for the basal diet (vegetable). Regarding meals, there was an increase (P < 0.05) in the amino acid digestibility in large part due to the amino acids of MBM (14) and PBPM (9), with only five amino acids for FM. The amino acids glycine and threonine showed increases (P < 0.05) in both total and ileal digestibility for all animal meals and for the diet based on corn and soybean meal, which indicates a high specificity of the enzyme for these amino acids. The overall results obtained in this study found satisfactory effectiveness of this exogenous protease. The total collection method was lower by 1.83% of amino acids digestibility than the ileal method.

Interactions between Gut Microbiota and Immunomodulatory Cells in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is one of the most common autoimmune diseases caused by abnormal immune activation and immune tolerance. Immunomodulatory cells (ICs) play a critical role in the maintenance and homeostasis of normal immune function and in the pathogenesis of RA. The human gastrointestinal tract is inhabited by trillions of commensal microbiota on the mucosal surface that play a fundamental role in the induction, maintenance, and function of the host immune system. Gut microbiota dysbiosis can impact both the local and systemic immune systems and further contribute to various diseases, such as RA. The neighbouring intestinal ICs located in distinct intestinal mucosa may be the most likely intermediary by which the gut microbiota can affect the occurrence and development of RA. However, the reciprocal interaction between the components of the gut microbiota and their microbial metabolites with distinct ICs and how this interaction may impact the development of RA are not well studied. Therefore, a better understanding of the gut microbiota, ICs, and their interactions might improve our knowledge of the mechanisms by which the gut microbiota contribute to RA and facilitate the further development of novel therapeutic approaches. In this review, we have summarized the roles of the gut microbiota in the immunopathogenesis of RA, especially the interactions between the gut microbiota and ICs, and further discussed the strategies for treating RA by targeting/regulating the gut microbiota.

The relationship among gut microbiota, short-chain fatty acids, and intestinal morphology of growing and healthy broilers

The gut microbiota play an important role in the growth and intestinal health of broilers. The present study was to investigate the gut microbiota, short-chain fatty acids, and intestinal morphology of broilers at different ages. A total of 320 one-day-old male broilers were raised in 8 replicates and fed the same corn–soybean diets for 42 D. The duodenal, jejunal, and ileal segments and their and cecal microbiota were collected on day 1, 7, 14, 21, and 42, respectively. The villous height (VH), crypt depth (CD), and their ratio of VH:CD in the duodenum, jejunum, and ileum all increased (P < 0.05) with age. Caecal acetate, propionate, butyrate, valerate, and isovalerate increased (P < 0.01), but isobutyrate decreased (P < 0.001) with age. The cecum had the greatest (P < 0.001) alpha diversity of bacterial community in broilers at different ages. Beta diversities showed distinct differences in gut microbial compositions among different ages (R = 0.55, P < 0.002) and different intestinal segments (R = 0.53, P < 0.002). Lactobacillus was the most abundant genus in the duodenum (36∼97%), jejunum (39∼72%), and ileum (24∼96%) at all ages, and in the ileum, it was positively correlated with VH (R = 0.559, P < 0.03), VH:CD (R = 0.55, P < 0.03), and acetate contents (R = 0.541, P < 0.04) but negatively correlated (R = -0.50, P < 0.05) with isobutyrate contents. Escherichia–Shigella and Salmonella dominated in the cecum of newly hatched broilers, and then the Bacteroides dominated in the cecum on day 42. In the cecum, Escherichia–Shigella was positively correlated (R = 0.577∼0.662, P < 0.05) with isobutyrate contents and Salmonella negatively correlated (R = -0.539∼-0.843, P < 0.05) with isovalerate, butyrate, and acetate contents. These aforementioned results indicated that the most abundant Lactobacillus from the small intestine and the most diversity of microflora community and short-chain fatty acids in the cecum might contribute to the development of intestinal structure in the whole growing period of broilers.

Effects of polysaccharides from Yingshan Yunwu tea on meat quality, immune status and intestinal microflora in chickens

The present study was aimed to investigate the effects of the addition of Yingshan Yunwu green tea polysaccharide conjugates (GTPC) on meat quality, immune response and gut microflora in chickens. A total of 200 chickens with average initial body weight were randomly allotted to 4 groups. Intestinal samples were collected at the end of experiment for bacterial culture and microbial community analysis by 16S rDNA gene sequencing using Illumina MiSeq. Chicken breast muscle and serum were also sampled for analysis of meat quality and immune function. The results showed that dietary GTPC addition increased (P < 0.05) chicken breast muscle pH and redness-greenness (a*) value and decreased (P < 0.05) the values of lightness (L*), yellowness-blueness (b*), hardness, toughness and adhesiveness. In addition, dietary supplementation of GTPC increased (P < 0.05) the weight of thymus and bursa and serum concentrations of IgA and IgG. Furthermore, of the 10 bacterial phyla, the predominant taxa across all sampling time-points were Bacteroidetes, Firmicutes, Proteobacteria, and Deferribacteres, representing >97% of all sequences. GTPC increased the abundance of Bacteroidetes and Lactobacillus, and decreased the abundance of Proteobacteria. These findings provided some references of the application of GTPC in the poultry industry.

Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

Comparison of Antimicrobial Resistance and Pan-Genome of Clinical and Non-Clinical Enterococcus cecorum from Poultry Using Whole-Genome Sequencing

Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol, suggesting possible new mechanisms of resistance to these drugs. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.

Development of the Ileal Microbiota in Three Broiler Breeds

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

Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes

The microbiome has entered the vernacular of the consumer as well as broiler production and is, therefore, becoming increasingly important to poultry producers to understand. The microbiome is, by definition, compositional and relates to how the microbiological organisms within the gut inhabit that ecological niche. The gut is diverse, flexible, and data acquired requires a greater understanding of the host-microbiome axes, as well as advanced bioinformatics and ecology. There are numerous microbial populations that define the gut microbiome; however, there are even more effects that can influence its composition. As management practices vary between producers, documenting these influences is an essential component of beginning to understand the microbiome. This review targets broiler production and concatenates the currently understood compositional ecology of the broiler gastrointestinal tract microbiome as well as its influences.

Heat shock protein 70 protects the quail cecum against oxidant stress, inflammatory injury, and microbiota imbalance induced by cold stress

The intent of this study was to investigate the effects of cold stress on oxidative indexes, inflammatory factors, and microbiota in the quail cecum. A total of 192 male quails (15-day-old) were randomly divided into 12 groups (16 in each group) and were exposed to acute (up to 12 h) and chronic (up to 20 D) cold stress at 12 ± 1°C. After cold stress treatment, we examined morphological damage, oxidative stress indexes, inflammatory factors, and intestinal microbiota. Results of morphological examination showed that both acute and chronic cold stress can lead to cecal tissue injury. In addition, both acute and chronic cold stress, especially chronic cold stress can influence the activity of oxidative stress mediators. Glutathione (GSH) and glutathione peroxidase (GSH-Px) activities decreased significantly (p < 0.05), while the nitric oxide (NO) content and inducible nitric oxide synthase (iNOS) activity increased significantly (p < 0.05). Moreover, mRNA levels of inflammatory factors cyclooxygenase-2 (COX-2), prostaglandin E synthase (PTGES), and heat shock protein 70 (Hsp70) were higher in both acute and chronic cold stress groups when compared with the control group (p < 0.05). Furthermore, the intestinal microbiota was changed in both the acute and chronic cold stress groups. These results suggested that cold stress caused oxidative stress and inflammatory injury in cecal tissues, influenced cecal microbiota, and increased expression of Hsp70, which may contribute in protecting the cecum against cold stress in quails.

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

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

Effects of wild blueberry (Vaccinium angustifolium) pomace feeding on gut microbiota and blood metabolites in free-range pastured broiler chickens

There is a need to develop cost-effective approaches to modulate gut microbiota, promote bird health, and prevent infections in pasture-raised broiler chickens. The present study evaluated the efficacy of organic wild blueberry (Vaccinium angustifolium) also called low-bush blueberry pomace (LBBP)-supplemented feed to modulate the chicken gut microbiota, and blood metabolites in order to improve bird health and productivity. Slow-growing broiler chickens were reared on pasture up to 64 D for sampling after 2 wk of treatment during brooding with 0, 1, and 2% LBBP in feed. Intestinal samples were collected at different time-points throughout the trial for bacterial culture and microbial community analysis by 16S rRNA gene sequencing using Illumina MiSeq. Blood sera were also analyzed for metabolites at each sampling time. Of the 14 bacterial phyla, the predominant taxa across all sampling time-points were Firmicutes, Proteobacteria, Bacteroidetes, and Tenericutes, representing >97% of all sequences. Bacteroidetes seemed to be replacing Firmicutes by LBBP supplementation, with the most noticeable effect at day 64 with 1% LBBP. LBBP inclusion enriched Lactobacillus, Bacteroides, and Bifidobacterium, while Escherichia coli, Clostridium_Clostridiaceae, Helicobacter, and Enterococcus showed higher abundances in control birds at the end of trial. Principal co-ordinate analysis showed a clear clustering of the intestinal samples from control and LBBP-treated groups at day 29. Application of LBBP resulted in a decrease (P < 0.05) in cholesterol at day 21, and an increase (P < 0.05) in high-density lipoprotein cholesterol in 14-day-old broilers. Higher (P < 0.05) levels of phosphorus, magnesium, and globulin at day 21 as well as iron and albumin at day 36 were also observed in 1% LBBP-fed birds. Despite limitations consisting essentially of low sampled birds for measurements, this study indicated that dietary supplementation of LBBP could positively influence gut microbiota and blood metabolites that may contribute to the overall health of pasture-raised broiler chickens.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan

Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock, also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the microbiome of chicken caeca in two different breeds and management systems throughout their whole productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa, as well as taxa associated with age were identified. Age was identified as the strongest influencing factor in caecal microbiota composition, and, in general, each age-group showed an age-associated community profile, with a transition period at the middle of their lifespan. However, substantial differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively correlated with Campylobacter relative abundance were also identified. Especially noteworthy was the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

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

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

Effects of antibiotic on microflora in ileum and cecum for broilers by 16S rRNA sequence analysis

An experiment was conducted to analyze and compare the microbial composition, abundance, dynamic distribution, and functions without and with antibiotic fed to broilers. A 16S rRNA-sequencing approach was used to evaluate the bacterial composition of the gut of male broilers under different groups. A total of 240 1-day old AA male broilers were randomly assigned to two groups, with 120 broilers per group. The treatment group was administered an antibiotic with their feed, while the control group was not administered antibiotic (control group). A total of 10 replicates were assessed per treatment. The control group was fed a basal diet containing corn, soybean meal, and cottonseed meal and met the nutritional requirement. The antibiotic group was fed 100 mg/kg aureomycin (based on the basal diet). The trial lasted 42 days. Operational taxonomic unit partition and classification, alpha diversity, taxonomic composition, beta diversity, and microflora comparative analyses along with key species screening were performed for all of the treatment groups. Our data indicate that aureomycin treatment in broilers is directly correlated with variations of the gut content of specific bacterial taxa, and herein provide insights into the impact of antibiotic on microbial communities in cecum and ileum of broiler chickens.

Chicken Gut Microbiota: Importance and Detection Technology

Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.

The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review

The microbiome of the broiler chicken gastrointestinal tract (GIT) has been extensively studied, and it has been amply demonstrated that it plays an important role in the health of the host, as it has a positive impact on the immune system, the physiology of the GIT, and productivity. Also, the microbiota is involved in reducing and preventing colonization by enteric pathogens through the process of competitive exclusion and the production of bacteriostatic and bactericidal substances. The taxonomic composition of the microbiota is affected by different factors, such as the organ, the age of the animal, diet and the use of antimicrobials.

Different kinds of additives that regulate the microbial community in feed include probiotics (live microorganisms that when administered in adequate amounts confer a health benefit on the host), prebiotics (ingredients that stimulate increased beneficial microbial activity in the digestive system in order to improve the health of the host) and phytobiotics (primary or secondary components of plants that contain bioactive compounds that exert a positive effect on the growth and health of animals). Phages may potentially provide an integrated solution to modulate the intestinal microbiome of chicken intestines, as they reduce specific pathogenic microbial populations, permitting the proliferation of beneficial microbiota. Studies have shown that the use of cocktails of phages, especially in high concentrations and with short lapses of time between exposure to the bacteria and treatment with phages, optimize the reduction of Salmonella in chickens. Each of these technologies has demonstrable positive effects on the health of the host and the reduction of the pathogen load in controlled assays.

This paper presents a comprehensive summary of the role of the microbiota in the broiler chicken gastrointestinal tract, and discusses the usefulness of different strategies for its modulation to control pathogens, with a particular emphasis on bacteriophages.

PLGA-encapsulated CpG ODN and Campylobacter jejuni lysate modulate cecal microbiota composition in broiler chickens experimentally challenged with C. jejuni

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. Reducing Campylobacter numbers in the intestinal tract of chickens will minimize transmission to humans, thereby reducing the incidence of infection. We have previously shown that oral pre-treatment of chickens with C. jejuni lysate and Poly D, L-lactide-co-glycolide polymer nanoparticles (PLGA NPs) containing CpG oligodeoxynucleotide (ODN) can reduce the number of C. jejuni in infected chickens. In the current study, the effects of these pre-treatments on the composition and functional diversity of the cecal microbiota, in chickens experimentally infected with C. jejuni, were investigated using next-generation sequencing. The taxonomic composition analysis revealed a reduction in cecal microbial diversity and considerable changes in the taxonomic profiles of the microbial communities of C. jejuni-challenged chickens. On the other hand, irrespective of the dose, the microbiota of PLGA-encapsulated CpG ODN- and C. jejuni lysate-treated chickens exhibited higher microbial diversity associated with high abundance of members of Firmicutes and Bacteroidetes and lower numbers of Campylobacter than untreated-chickens. These findings suggest that oral administration of encapsulated CpG ODN and C. jejuni lysate can reduce colonization by C. jejuni by enhancing the proliferation of specific microbial groups. The mechanisms that mediate these changes remain, however, to be elucidated.

Purification and Characterization of a Novel Anti-Campylobacter Bacteriocin Produced by Lactobacillus curvatus DN317

The lactic acid bacteria (LAB) microbiota of Saudi chicken ceca was determined. From 60 samples, 204 isolates of lactic acid bacteria were obtained. Three isolates produced antimicrobial activities against Campylobacter jejuni, Listeria monocytogenes, and Bacillus subtilis. The isolate DN317, which had the highest activity against Campylobacter jejuni ATCC 33560, was identified as Lactobacillus curvatus (GenBank accession numbers: KX353849 and KX353850). Full inhibitory activity was observed after a 2-h incubation with the supernatant at pH values between 4 and 8. Only 16% of the activity was conserved after a treatment at 121 °C for 15 min. The use of proteinase K, pepsin, chymotrypsin, trypsin, papain, and lysozyme drastically reduced the antimicrobial activity. However, lipase, catalase, and lysozyme had no effect on this activity. The active peptide produced by Lactobacillus curvatus DN317 was purified by precipitation with an 80% saturated ammonium sulfate solution, and two steps of reversed phase HPLC on a C18 column. The molecular weight of this peptide was 4448 Da as determined by MALDI-ToF. N-terminal sequence analysis using Edman degradation revealed 47 amino acid residues (UniProt Knowledgebase accession number C0HK82) revealing homology with the amino acid sequences of sakacin P and curvaticin L442. The antimicrobial activity of the bacteriocin, namely curvaticin DN317, was found to be bacteriostatic against Campylobacter jejuni ATCC 33560. The use of microbial antagonism by LAB is one of the best ways to control microorganisms safely in foods. This result constitutes a reasonable advance in the antimicrobial field because of its potential applications in food technology.

Effects of dietary fiber levels on cecal microbiota composition in geese

Objective

This study shows the effects of dietary fiber levels on cecal microbiota composition in geese at day 70 according to pyrosequencing of the 16S ribosomal RNA gene.

METHODS

A total of 468 1-day-old healthy male Yangzhou goslings with similar body weight were randomly divided into 3 groups with 6 replicates per group and 26 geese per replicate. Geese were fed diets with fiber levels of 2.5% (low fiber level diet, Group I) and 6.1% (Group III) during days 1-70, respectively, or 4.3% for days 1-28 and 6.1% for days 29-70 (Group II).

RESULTS

Low fiber level diet decreased body weight, average daily gain during, increased lower feed conversation rate of geese during day 1 to 70 (p&lt;0.05). Low fiber level diet decreased the total operational taxonomic units, Chao1 index and Shannon index, whereas increased the Simpson index of cecal microbiota in geese at day 70. Low fiber level diet decreased the relative abundance of Bacteroidetes, Firmicutes, Bacteroides, and Paraprevotella in cecum of geese at day 70. The similarity of cecal microbiota between low fiber level diet group and other groups was smaller.

CONCLUSION

This study indicates that the low fiber level diet decreased diversity of microbiota, and relative abundance of some beneficial microbiota in cecum of geese at day 70, implying that the low fiber level diet has negative influence on performance by altering the diversity and population of cecal microbiota in geese.

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens

Development of antibiotic resistance in foodborne pathogens, Salmonella spp. and Campylobacter, is a public health concern. Public demand to reduce the use of sub-therapeutic antibiotic growth promoters (AGP) in poultry feeding has resulted in greater adoption of antibiotic-free poultry production systems. There is a need to understand the effects of AGP removal from poultry feed on gut microbiota and its impact on prevalence of foodborne pathogens. The effect of antibiotic withdrawal from poultry feed on gut microbial community, host performance and immunity, and prevalence of Salmonella and Campylobacter was evaluated. Birds were raised on three phase diets (starter [d0-22], grower [d23-35] and finisher [d36-42]) with and without bacitracin dimethyl salicyclate (BMD). At early growth stage, bird performance was improved (P ≤ 0.05) with BMD treatment, whereas performance was better (P ≤ 0.05) in control group (no BMD in the feed) at the time of commercial processing. Acetate and butyrate production was affected (P ≤ 0.05) by age, whereas propionate production was affected (P ≤ 0.05) by both the treatment and age. The bacterial communities in the cecum were more diverse (P ≤ 0.001) and rich compared to the ileal communities, and they shifted in parallel to one another as the chicks matured. Differences in diversity and species richness were not observed (P > 0.05) between the BMD-fed and control groups. Comparing all ages, treatments and diets, the composition of cecal and ileal bacterial communities was different (P ≤ 0.001). Inclusion of BMD in the feed did not affect the bacterial phyla. However, predictable shift in the ileal and cecal bacterial population at lower taxonomic level was observed in control vs BMD-fed group. Cytokines gene expression (IL-10, IL-4, IFN-γ, beta-defensin, and TLR-4) was affected (P≤ 0.05) in the BMD-fed group at early stages of growth. The prevalence of foodborne pathogens, Campylobacter spp. and Salmonella spp. showed higher abundance in the ilea of BMD-fed chicks compared to control group. Overall, this study provided insight of the impact of AGP supplementation in the feed on gut microbial modulations, bird performance, host immunity and pathogen prevalence. This information can assist in designing alternative strategies to replace antibiotics in modern poultry production and for food safety.