Chicken Gut Microbiota: Importance and Detection Technology

Age-dependent development trends (models) of intestinal significant microbiota species and Eimeria oocysts in coccidia-challenged broiler chickens as affected by dietary encapsulated organic acids and anticoccidial drugs

ABSTRACTThe study was conducted to investigate the effect of dietary encapsulated organic acids (EOAs) and anticoccidials on the age-dependent development trend of intestinal Lactobacillus, E. coli, coliforms, and Eimeria in Eimeria spp.-infected broiler chickens from reused litter. In total, 525 mixed-sex 1-day-old broiler chickens were used in an uninfected/un-supplemented control plus a 2 (no EOA or 0.1% EOA) × 3 (no anticoccidial, 0.05% maduramicin, and 0.02% diclazuril) factorial arrangement of treatments as a completely randomized design with five replicates of 15 chickens. Results indicated that the cubic model is the best model for explaining the development trends of the intestinal microbial population in uninfected and infected chickens (affected by the EOAs and anticoccidials). Based on the cubic models, the microbial populations had development trends with a decreasing slope from 1-day-old until the early or middle finisher period. EOAs and anticoccidials, especially their simultaneous usage, improved (P < 0.05) the linear and cubic models' slope (affected negatively by Eimeria infection). A polynomial model (order = 6) was determined as the best model for explaining the EOAs and anticoccidial effects on the trend of intestinal Eimeria oocysts in infected chickens. The infection peak (which happened at 25 days) was reduced by EOAs and anticoccidials, especially their simultaneous usage. In conclusion, cubic and polynomial (order = 6) regressions are the best models fitted for explaining the microbiota and Eimeria oocysts trends, respectively. EOAs and anticoccidials, especially their simultaneous usage, had beneficial effects on the microbiota and Eimeria development trends and gastrointestinal health in coccidia-infected broiler chickens.‏RESEARCH HIGHLIGHTSCubic regression is the best model for explaining intestinal microbiota development.Polynomial regression is the best model for intestinal Eimeria oocysts development.Age-development trends are affected by dietary encapsulated organic acids and anticoccidials.

Evaluation of Clostridium autoethanogenum protein as a new protein source for broiler chickens in replacement of soybean meal

OBJECTIVE

The object of this study was to investigate the effect of replacing soybean meal with Clostridium autoethanogenum protein (CAP) in broiler diets on growth performance, blood indicators, antioxidant capacity, and immune function.

METHODS

A total of 180 Arbor Acres broilers were randomly divided into three treatments, each treatment with six replicates and 10 broilers per replicate for a 42-day feeding trial. The control group (CON) was fed corn-soybean meal based diet. The CAP-1 and CAP-2 groups were considered to use CAP to replace 25% or 50% of soybean meal in the diet, respectively. The average daily gain and average daily feed intake of broilers at 1 to 21 d, 22 to 42 d, and 1 to 42 d were measured, and the feed conversion ratio was calculated. At the 42nd day of age, two broilers with similar weights and fasted for 12 h were selected in each replicate for blood collection from the brachial wing vein. The blood routine indicators, serum biochemical indicators, serum antioxidant capacity, and immunoglobulin content of broiler chickens were measured.

RESULTS

Replacement of soybean meal with 25% (CAP-1) and 50% (CAP-2) CAP significantly increased the average daily gain of 22 to 42 d and 1 to 42 d and decreased the average daily feed intake and feed conversion rate (p<0.05). The CAP-1 group, and CAP-2 group significantly increased hemoglobulin in the blood of broilers, while the CAP-2 group increased hematocrit content (p<0.05). Compared with the control group, the contents of superoxide dismutase and immunoglobulin A in serum of the CAP-2 group were significantly increased, while the contents of malondialdehyde in CAP group were significantly decreased (p<0.05).

CONCLUSION

Replacing soybean meal with CAP led to significant improvements in the growth performance, antioxidant capacity, and immunoglobulin content of broilers.

Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders

1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.

Lactococcus G423 improve growth performance and lipid metabolism of broilers through modulating the gut microbiota and metabolites

This study aimed to explore whether Lactococcus G423 could improve growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites. A total of 640 1-day-old AA broilers were randomly divided into 4 groups [Control (CON), Lac_L, Lac_H, and ABX]. Average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 days of age. Serum was obtained by centrifuging blood sample from jugular vein (10 mL) for determining high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), and triglyceride (TG) using ELISA. The ileal contents were harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, FCR significantly decreased in the Lac_H group (p < 0.05) in 1-21 days; ADG significantly increased and FCR significantly decreased in the Lac_H group (p < 0.05) in 22-42 days. 42 days weight body and ADG significantly increased in the Lac_H group (p < 0.05) in 42 days. Abdominal fat percentage was significantly decreased by Lactococcus G423 (p < 0.05), the high dose of Lactococcus G423 significantly decreased the serum of TG, TC, and LDL level (p < 0.05), and the low dose of Lactococcus G423 significantly decreased the serum of TG and TC level (p < 0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly increased (p < 0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (p < 0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, N-Acetyl-l-phenylalanine, and kynurenine), and these metabolites were involved in four metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (p < 0.05). Lactococcus G423 could ameliorate growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites.

Dietary Kluyveromyces marxianus hydrolysate alters humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broiler chickens raised under a high stocking density

This study investigated the impact of dietary supplementation with hydrolyzed yeast (Kluyveromyces marxianus) on growth performance, humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broilers raised at 45 kg/m2. A total of 1,176 mixed sex 1-day-old Ross 308 broilers were distributed into 42 pens and randomly assigned to either the control group, the control + 250 g hydrolyzed yeast (HY)/ton, 250HY group, or the control + 500 g HY/ton, 500HY group for 42 d. HY did not affect growth performance. However, HY reduced (P < 0.05) mortality at 25 to 35 d. Dietary HY lowered the heterophil/lymphocyte ratio and enhanced the villus height/crypt depth ratio and Newcastle disease titer (P < 0.05). Compared with HY250 and the control, HY500 upregulated (P < 0.05) IL-10. HY enhanced the α diversity, inferring the richness and evenness of the ceca microbiota. HY500 had greater β diversity than the control (P < 0.05). Six bacterial phyla, namely, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, and Cyanobacteria, were found. The relative abundance of Firmicutes was greater in the HY500 treatment group than in the HY250 and control groups. HY decreased the abundance of Actinobacteria. HY supplementation altered (P < 0.05) the abundance of 8 higher-level taxa consisting of 2 classes (Bacilli and Clostridia), 1 order (Lactobacillales), 1 family (Streptococcaceae), and five genera (Streptococcus, Lachnospiraceae_uc, Akkermansiaceae, PACO01270_g, and LLKB_g). HY500 improved (P < 0.05) the abundance of Bacilli, Clostridia, Lactobacillales, Streptococcaceae, Streptococcus, PACO01270_g, and Lachnospiraceae_uc, while HY250 enhanced (P < 0.05) the abundance of Akkermansiaceae and LLKB_g. HY improved the abundance of Lactobacillus and Akkermansia spp. Minimal set of pathway analyses revealed that compared with the control, both HY250 and HY500 regulated 20 metabolic pathways. These findings suggest that dietary K. marxianus hydrolysate, especially HY500, improved humoral immunity and jejunal morphology and beneficially altered the composition and metabolic pathways of the cecal microbiota in broilers raised at 45 kg/m2.

The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model

Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.

Significant Differences in Intestinal Bacterial Communities of Sympatric Bean Goose, Hooded Crane, and Domestic Goose

The host's physiological well-being is intricately associated with the gut microbiota. However, previous studies regarding the intestinal microbiota have focused on domesticated or captive birds. This study used high-throughput sequencing technology to identify the gut bacterial communities of sympatric bean geese, hooded cranes, and domestic geese. The results indicated that the gut bacterial diversity in domestic geese and hooded cranes showed considerably higher diversity than bean geese. The gut bacterial community compositions varied significantly among the three hosts (p < 0.05). Compared to the hooded crane, the bean goose and domestic goose were more similar in their genotype and evolutionary history, with less difference in the bacterial community composition and assembly processes between the two species. Thus, the results might support the crucial role of host genotypes on their gut microbiota. The gut bacteria of wild hooded cranes and bean geese had a greater capacity for energy metabolism compared to domestic geese, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Moreover, the intestines of the three hosts were identified as harboring potential pathogens. The relative abundance of pathogens was higher in the hooded crane compared to the other two species. The hooded crane gut bacterial community assemblage revealed the least deterministic process with the lowest filtering/selection on the gut microbiota, which might have been a reason for the highest number of pathogens result. Compared to the hooded crane, the sympatric bean goose showed the least diversity and relative abundance of pathogens. The intestinal bacterial co-occurrence network showed the highest stability in the bean goose, potentially enhancing host resistance to adverse environments and reducing the susceptibility to pathogen invasion. In this study, the pathogens were also discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Overall, the current findings have the potential to enhance the understanding of gut bacterial and pathogenic community structures in poultry and wild birds.

Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics

RESEARCH HIGHLIGHTS

RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.

Phytogenic feed additives as natural antibiotic alternatives in animal health and production: A review of the literature of the last decade

The use of antibiotics in animal production raises great public safety concerns; therefore, there is an urgent need for the development of substitutes for antibiotics. In recent decades, plant-derived feed additives have been widely investigated as antibiotic alternatives for use in animal health and production because they exert multiple biological functions and are less likely to induce resistance development. This review summarizes the research history and classification of phytogenic feed additives and their main functions, potential modes of action, influencing factors, and potential negative effects. Further, we highlight the challenges in developing sustainable, safe, and affordable plant-derived antibiotic alternatives for use in livestock production.

Measuring the impact of dietary supplementation with citrus or cucumber extract on chicken gut microbiota using 16s rRNA gene sequencing

This study investigated the effects of dietary supplements, citrus (CTS) and cucumber (CMB), on the jejunum and cecum microbiota of 14- and 28-days old broiler chickens to evaluate their impact on the gut health and assess their role as alternatives to antibiotic growth promoters (ABGPs). 16SrRNA gene sequencing revealed the overall bacterial microbiota composition was significantly affected by the gut site (p? Collapse

Key Words

• 16SrRNA gene sequencing
• Broiler chicken
• Citrus
• Cucumber
• Gut microbiota
• Novel plant extracts

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MESH Headings Collapse

Grants

• 765423 Horizon 2020
• 765423 Horizon 2020
• 765423 Horizon 2020
• 765423 Horizon 2020
• 765423 Horizon 2020

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Affiliation(s)

Francesca Riva School of Health and Life Sciences, University of the West of Scotland, High St, PA1 2BE, Paisley, UK School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK Faculty of Veterinary Medicine, University of Zagreb, Radoslava Cimermana, 10000, Zagreb, Croatia
David H McGuinness Glasgow Polyomics, University of Glasgow, Switchback Rd, G61 1BD, Bearsden, Glasgow, UK
Dorothy E F McKeegan School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
Jorge Peinado-Izaguerri School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Ko?ice, Komensk?ho, 041 81, Ko?ice, Slovakia School of Biological Sciences, The University of Manchester, Oxford Rd, M13 9PT, Manchester, UK
Geert Bruggeman Nutrition Sciences N. V, B-9031, Booiebos, Ghent, Belgium
David Hermans Nutrition Sciences N. V, B-9031, Booiebos, Ghent, Belgium
Peter D Eckersall School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK
Mark McLaughlin School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK.
Maureen Bain School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Bearsden Rd, G61 1QH, Glasgow, UK

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Identification of novel probiotic lactic acid bacteria from soymilk waste using the 16s rRNA gene for potential use in poultry

Background and Aim

In-feed antibiotics have been used as antibiotic growth promoters (AGPs) to enhance the genetic potential of poultry. However, the long-term use of AGPs is known to lead to bacterial resistance and antibiotic residues in poultry meat and eggs. To address these concerns, alternatives to AGPs are needed, one of which is probiotics, which can promote the health of livestock without having any negative effects. In vitro probiotic screening was performed to determine the ability of lactic acid bacteria (LAB) isolated from soymilk waste to be used as a probiotic for livestock.

Materials and Methods

Four LAB isolates (designated F4, F6, F9, and F11) isolated from soymilk waste were used in this study. In vitro testing was performed on LAB isolates to determine their resistance to temperatures of 42°C, acidic pH, bile salts, hydrophobicity to the intestine, and ability to inhibit pathogenic bacteria. A promising isolate was identified using the 16S rRNA gene.

Result

All LAB isolates used in this study have the potential to be used as probiotics. On the basis of the results of in vitro testing, all isolates showed resistance to temperatures of 42°C and low pH (2.5) for 3 h (79.87%-94.44%) and 6 h (76.29%-83.39%), respectively. The survival rate at a bile salt concentration of 0.3% ranged from 73.24% to 90.39%, whereas the survival rate at a bile salt concentration of 0.5% ranged from 56.28% to 81.96%. All isolates showed the ability to attach and colonize the digestive tract with a hydrophobicity of 87.58%-91.88%. Inhibitory zones of LAB against pathogens ranged from 4.80-15.15 mm against Staphylococcus aureus, 8.85-14.50 mm against Salmonella enteritidis, and 6.75-22.25 mm against Escherichia coli. Although all isolates showed good ability as probiotics, isolate F4 showed the best probiotic ability. This isolate was identified as Lactobacillus casei strain T22 (JQ412731.1) using the 16S rRNA gene.

Conclusion

All isolates in this study have the potential to be used as probiotics. However, isolate F4 has the best probiotic properties and is considered to be the most promising novel probiotic for poultry.

Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota

The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.

Isolation and Identification of Chicken-Derived Lactic Acid Bacteria: In Vitro Probiotic Properties and Antagonistic Effects against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli

The development of probiotics capable of quickly colonizing the intestines of animals is important in promoting the healthy growth of livestock. The aim of this study was to screen lactic acid bacteria (LAB) from the intestinal microbiota of chickens with potential applications, and to evaluate their probiotic properties and antagonistic abilities against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli. The results showed that a total of 79 strains with the characteristics of LAB were isolated from the chicken cecum microbiota, of which 7 strains exhibited strong inhibitory activity against S. pullorum, S. aureus, and E. coli. Performing 16s rDNA sequencing revealed that these seven strains were Lactiplantibacillus pentosus (n = 1), Lactiplantibacillus plantarum (n = 3), Lactiplantibacillus paraplantarum (n = 1), Lactiplantibacillus argentoratensis (n = 1), and Lactiplantibacillus fabifermentans (n = 1). Among them, L. pentosus R26 and L. plantarum R32 exhibited superior antibacterial activity. These two strains demonstrated high lactic acid production ability, with survival rates of 86.29% and 87.99% after 3 h of treatment at pH 1.5, 86.66% and 85.52% after 3 h of treatment with 0.5% bile salts, 90.03% and 88.16% after 2 h of treatment with simulated gastric fluid, and 98.92% and 98.22% after 2 h of treatment with simulated intestinal fluid, respectively. Co-cultivation with L. pentosus R26 for 24 h resulted in 50% of the pathogens being antagonized, while almost complete inhibition was observed following 72 h of co-cultivation. In conclusion, L. pentosus R26 and L. plantarum R32 exhibited high antibacterial activity and acid production capability, while also demonstrating satisfactory tolerance to low pH values and high concentrations of bile salts and digestive fluid. The probiotic characteristics and stress resistance of L. pentosus R26 were slightly superior to those of L. plantarum R32, indicating its potential for development as a probiotic.

Mulberry branch fiber improved lipid metabolism and egg yolk fatty acid composition of laying hens via the enterohepatic axis

BACKGROUND

The utilization of mulberry branch fiber (MF), the largest by-product of the sericulture industry, is an important issue. Supplementation with MF as a dietary fiber for poultry may serve as a useful application. However, little is known about the effects of MF on liver lipid metabolism and egg yolk fatty acid composition of laying hens and their underlying mechanisms. In this study, we performed a multi-omics investigation to explore the variations in liver lipid metabolism, egg yolk fatty acid composition, gut microbiota, and the associations among them induced by dietary MF in laying hens.

RESULTS

Dietary MF had no harmful effects on the laying performance or egg quality in laying hens. The enzyme activities associated with lipid metabolism in the liver were altered by the addition of 5% MF, resulting in reduced liver fat accumulation. Furthermore, dietary 5% MF induced the variation in the fatty acid profiles of egg yolk, and increased the polyunsaturated fatty acid (PUFA) content. We observed a significant reduction in the diversity of both gut bacteria and changes in their compositions after the addition of MF. Dietary MF significantly increased the abundance of genes involved in fatty acid biodegradation, and short-chain fatty acids biosynthesis in the gut microbiota of laying hens. The significant correlations were observed between the liver lipid metabolism enzyme activities of hepatic lipase, lipoprotein lipase, and total esterase with gut microbiota, including negative correlations with gut microbiota diversity, and multiple correlations with gut bacteria and viruses. Moreover, various correlations between the contents of PUFAs and monounsaturated fatty acids in egg yolk with the gut microbiota were obtained. Based on partial-least-squares path modeling integrated with the multi-omics datasets, we deduced the direct effects of liver enzyme activities and gut bacterial compositions on liver fat content and the roles of liver enzyme activities and gut bacterial diversity on egg yolk fatty acid composition.

CONCLUSIONS

The results indicate that dietary MF is beneficial to laying hens as it reduces the liver fat and improves egg yolk fatty acid composition through the enterohepatic axis. Video Abstract.

Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis

The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.

The Impact of Essential Amino Acids on the Gut Microbiota of Broiler Chickens

The research involving the beneficial aspects of amino acids being added to poultry feed pertaining to performance, growth, feed intake, and feed conversion ratio is extensive. Yet currently the effects of amino acids on the gut microbiota aren't fully understood nor have there been many studies executed in poultry to explain the relationship between amino acids and the gut microbiota. The overall outcome of health has been linked to bird gut health due to the functionality of gastrointestinal tract (GIT) for digestion/absorption of nutrients as well as immune response. These essential functions of the GI are greatly driven by the resident microbiota which produce metabolites such as butyrate, propionate, and acetate, providing the microbiota a suitable and thrive driven environment. Feed, age, the use of feed additives and pathogenic infections are the main factors that have an effect on the microbial community within the GIT. Changes in these factors may have potential effects on the gut microbiota in the chicken intestine which in turn may have an influence on health essentially affecting growth, feed intake, and feed conversion ratio. This review will highlight limited research studies that investigated the possible role of amino acids in the gut microbiota composition of poultry.

Effects of Dietary Terminalia chebula Extract on Growth Performance, Immune Function, Antioxidant Capacity, and Intestinal Health of Broilers

Terminalia chebula extract (TCE) has many physiological functions and is potentially helpful in maintaining poultry health, but its specific effect on the growth of broilers is not yet known. This research investigated the effects of dietary Terminalia chebula extract (TCE) supplementation on growth performance, immune function, antioxidant capacity, and intestinal health in yellow-feathered broilers. A total of 288 one-day-old yellow-feathered broilers were divided into four treatment groups (72 broilers/group), each with six replicates of 12 broilers. The broilers were given a basal diet of corn-soybean meal supplemented with 0 (control), 200, 400, and 600 mg/kg TCE for 56 d. The results demonstrated that, compared with the basal diet, the addition of TCE significantly increased (linear and quadratic, p < 0.05) the final body weight and overall weight gain and performance and decreased (linear and quadratic, p < 0.05) the feed-to-gain ratio in the overall period. Dietary TCE increased (linear, p < 0.05) the levels of IgM, IL-4, and IL-10 and decreased (linear and quadratic, p < 0.05) the level of IL-6 in the serum. Dietary TCE increased (linear and quadratic, p < 0.05) the levels of IL-2 and IL-4, decreased (linear and quadratic, p < 0.05) the level of IL-1β, and decreased (linear, p < 0.05) the level of IL-6 in the liver. Dietary TCE increased (linear and quadratic, p < 0.05) the level of IgM and IL-10, increased (linear, p < 0.05) the level of IgG, and decreased (linear and quadratic, p < 0.05) the levels of IL-1β and IL-6 in the spleen. Supplementation with TCE linearly and quadratically increased (p < 0.05) the catalase, superoxide dismutase, glutathione peroxidase, and total antioxidant capacity activities while decreasing (p < 0.05) the malonic dialdehyde concentrations in the serum, liver, and spleen. TCE-containing diets for broilers resulted in a higher (linear and quadratic, p < 0.05) villus height, a higher (linear and quadratic, p < 0.05) ratio of villus height to crypt depth, and a lower (linear and quadratic, p < 0.05) crypt depth compared with the basal diet. TCE significantly increased (linear, p < 0.05) the acetic and butyric acid concentrations and decreased (quadratic, p < 0.05) the isovaleric acid concentration. Bacteroidaceae and Bacteroides, which regulate the richness and diversity of microorganisms, were more abundant and contained when TCE was added to the diet. In conclusion, these findings demonstrate that supplementing broilers with TCE could boost their immune function, antioxidant capacity, and gut health, improving their growth performance; they could also provide a reference for future research on TCE.

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties

BACKGROUND

Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens' health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host.

RESULTS

The bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential.

CONCLUSIONS

This study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host. Video Abstract.

Isolation, identification, and molecular characterization of probiotic bacteria from locally selected Ethiopian free range chickens gastrointestinal tract

The poultry industry is facing continuous challenges with regard to increased feed costs and loss due to infectious disease. To overcome this challenge, several antibiotics have been used along with chicken feeds to promote growth. Nevertheless, the use of antibiotics as growth promoter has been banned in many countries, due to the concerns associated with potential risks of emerging and horizontal transfer of multidrug resistant genes to bacteria in animal tissues. The objective of this study was to identify and characterize potential probiotic bacteria strains from the gastrointestinal tract of free-range locally selected chickens. The bacterial isolates were screened, purified and characterized based on morphological, biochemical and molecular characteristics from 12 well-adopted free-range healthy young chickens. Low pH and bile salt tolerance, antagonistic activity, antibiotic activity, hemolysis activity, adhesion to the chicken intestine and carbohydrate fermentation tests was conducted to identify potential probiotic bacteria. Twelve bacterial isolates were screened based on their ability for their tolerance to low pH and bile salt. The isolates were identified by using 16S rRNA gene partial sequencing method. All screened isolates showed great survival percentage at low pH, that is (89.2 ± 0.75 to 97.1 ± 0.64) survived at 3 h and (83.6 ± 0.75 to 95.2 ± 0.63) at 6 h challenge at pH2. Isolate GCM112 was the least tolerant strain in 6.0% salt concentration at 12 and 24 h exposure time (82.1 ± 1.28 and 79.9 ± 1.96%) respectively. The result revealed no strain tests in this study exhibited α- and β-hemolytic activity when cultured in sheep blood agar. Most isolated strains showed best growth at 37°C temperature and up to 4% NaCl concentration. Based on the reported result from in vitro data, GCH212 and GCM412 isolates were recognized as best potential probiotic bacteria for chicken against pathogens but further studies are needed on in vivo assessment on the health benefits in the real life situation.

Association Between Escherichia coli Load in the Gut and Body Weight Gain in Broiler Chickens: A Systematic Review and Meta-Analysis

Escherichia coli is one of the first commensal bacteria to colonize the chicken gut, where it predominates at an early stage of broiler chick life. Escherichia coli can potentially cause colibacillosis in chickens, spreading to extraintestinal systemic organs, which results in high economic losses in poultry industry, as well as a potential risk to public health. Many studies conducted to investigate the effectiveness of natural products as alternatives to antibiotics and to enhance the production performance in broiler chickens have assessed E. coli load in the chicken gut, but it is still unknown how the E. coli count is linked to broiler growth performance. A systematic search of published research articles, including key terms of interest such as broiler chickens, growth performance, and E. coli count, was conducted using two main databases (PubMed and the Web of Science). A random effects metaregression model was built to evaluate the association between E. coli count and weight gain in untreated groups of broilers (negative controls) from eligible studies. Of 2108 articles in the initial screening, 60 were included in the final meta-analysis. After data extraction, records from the ileum and cecum at 21, 35, and 42 days of age were considered for the meta-analysis. The meta-analysis showed that the average E. coli count in both the ileum and cecum at 21 days of age was positively associated with the average weight gain in the studied broiler chickens, while no statistically significant associations were found at 35 and 42 days of age. In conclusion, the positive association between E. coli load and body weight gain in young broiler chickens may be attributed to the relative dominance of E. coli in the gut of this age group when the microbial population is less diverse. The dynamic association between the production performance and the load of E. coli that has dubious pathogenic potential suggests the importance of careful assessment of commensal E. coli to develop strategies to enhance production, particularly in young broiler chickens.

The antioxidative influence of dietary creatine monohydrate and L-carnitine on laying performance, egg quality, ileal microbiota, blood biochemistry, and redox status of stressed laying quails

The experiment was implemented to assess the influence of dietary supplementation of laying quails with creatine monohydrate (CrM), L-carnitine (CAR) and their mixture (CrMCAR) as antioxidants against oxidative stress (OS) induced by 2.5 ppm lead acetate (LA) in drinking water on productive, physiological and microbial aspects. In total, 400 laying quail females at 10 wk of age were divided into a randomized design with 5 groups and 4 replicates of 20 birds each. Birds were fed ad libitum with a balanced diet for 8 wk. The control group was kept under no-stress conditions and was given fresh water without any additives (G1). While birds in other groups were exposed to OS induced experimentally by 2.5 ppm LA in drinking water with no feed additive (G2) or supplemented with 500 mg/kg CrM (G3) or 500 mg/kg CAR (G4) or combination of 250 mg/kg each of CrM and CAR (CrMCAR, G5) to feed mixture. Compared to G2, G5 demonstrated the reduction (P ≤ 0.05) of feed conversion ratio, feed intake, mortality and ileal total coliform, as well as serum and egg malondialdehyde and serum lipid hydroperoxide, uric acid, glucose, cholesterol, enzymatic activities (alanine aminotransferase, aspartate transaminase, alkaline phosphatase, creatine phosphokinase, γ-glutamyl transferase), and heterophils/lymphocytes ratio. In the meanwhile, there was an increase (P ≤ 0.05) in egg production, egg mass, and weight with the improvement of egg quality, serum sex hormones level and ileal lactic acid bacteria for G5 followed by G4 and G3. Moreover, G5 enhanced (P ≤ 0.05), the total antioxidant capacity of egg and serum glutathione, superoxide dismutase, catalase, glutathione peroxidase, protein and calcium levels. Therefore, dietary CrMCAR, CAR and CrM have analogous influence to control by improving the antioxidant and physiological parameters which resulted in better productive performance and egg characteristics of stressed quails. These antioxidants, especially in their equal combination, are beneficial to alleviate oxidative stress incidence and can be recommended for poultry feeding under various aspects of environmental stresses.

Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains

Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.

Interactions between the helminth and intestinal microbiome in smallholder chicken farming systems

Helminth parasite infections are widespread in smallholder farming systems affecting farmers and livestock animals. There are pathogenic parasites that populate the gut of their host and coexist closely with the gut microbiota. The physical and immunological environment of the gut can be modified by parasites and microbiota creating a wide range of interactions. These interactions modify the development of infection, affects overall host health, and can modify the way a host interacts with its bacterial microbiota. In addition, where there is a high worm burden parasites will affect the health of the host and intestinal tract colonization. This review highlights key studies on the interaction between helminth parasites and the intestinal microbiome to understand the relationship between parasitic worm infections and gut microbiome health in chickens. Finally, the review discusses modulations, molecular changes, and the importance of helminth-microbiome interactions for the host.

Glycerol and reuterin-producing Limosilactobacillus reuteri enhance butyrate production and inhibit Enterobacteriaceae in broiler chicken cecal microbiota PolyFermS model

BACKGROUND

Administering probiotic strains of Limosilactobacillus reuteri to poultry has been shown to improve poultry performance and health. Some strains of L. reuteri taxa can produce reuterin, a broad-spectrum antimicrobial compound from glycerol conversion, with high inhibitory activity against enterobacteria. However, little is known about the metabolism of glycerol in the complex chicken cecal microbiota nor the effect of glycerol, either alone or combined with L. reuteri on the microbiota. In this study, we investigated the effect of L. reuteri PTA5_F13, a high-reuterin-producing chicken strain and glycerol, alone or combined, on broiler chicken cecal microbiota composition and activity using the continuous PolyFermS model recently developed to mimic chicken cecal fermentation.

METHODS

Three independent PolyFermS chicken cecal microbiota models were inoculated with immobilized cecal microbiota from different animals and operated continuously. The effects of two additional levels of glycerol (50 and 100 mM) with or without daily supplementation of chicken-derived L. reuteri PTA5_F13 (107 CFU/mL final concentration) were tested in parallel second-stage reactors continuously inoculated with the same microbiota. We analyzed the complex chicken gut microbiota structure and dynamics upon treatment using 16S rRNA metabarcoding and qPCR. Microbiota metabolites, short-chain and branched-chain fatty acids, and glycerol and reuterin products were analyzed by HPLC in effluent samples from stabilized reactors.

RESULTS

Supplementation with 100 mM glycerol alone and combined with L. reuteri PTA5_F13 resulted in a reproducible increase in butyrate production in the three modelled microbiota (increases of 18 to 25%). Glycerol alone resulted also in a reduction of Enterobacteriaceae in two of the three microbiota, but no effect was detected for L. reuteri alone. When both treatments were combined, all microbiota quantitatively inhibited Enterobacteriaceae, including in the last model that had very high initial concentrations of Enterobacteriaceae. Furthermore, a significant 1,3-PDO accumulation was measured in the effluent of the combined treatment, confirming the conversion of glycerol via the reuterin pathway. Glycerol supplementation, independent of L. reuteri addition, did not affect the microbial community diversity.

CONCLUSIONS

Glycerol induced a stable and reproducible butyrogenic activity for all tested microbiota and induced an inhibitory effect against Enterobacteriaceae that was strengthened when reuterin-producing L. reuteri was spiked daily. Our in vitro study suggests that co-application of L. reuteri PTA5_F13 and glycerol could be a useful approach to promote chicken gut health by enhancing metabolism and protection against Enterobacteriaceae.

Microbiome Changes in Layer Pullets Reared in Floor Pens along the Growth Period

The gastrointestinal tract microbiome is essential for regulating nutrient absorption, gut immune function, and host growth and development. In the present study, we characterized the development of ileum and cecum microbiota in pullets throughout the rearing period, encompassing a period from the day of hatching to 18 weeks of age. The growth performance and intestinal microbiome (ileum and cecum) of pullets were analyzed at 1, 5, 11, and 18 weeks of age. The richness of the ileum and cecum bacterial communities (alpha diversity) was higher in pullets at 18 weeks of age than in those at 1 and 5 weeks of age. Microbiota from weeks 1, 5, 11, and 18 were distinctly grouped in a NMDS plot, representing beta diversity within the ileum. However, the results for cecum microbiota did not reveal evident separation among the different age groups in the weighted UniFrac. In conclusion, our findings demonstrate variations and diversification in ileum and cecum microbiota across different rearing stages in pullets. These insights have the potential to inform the development of nutritional strategies that promote gut health and contribute to the improved development of pullets.

Biophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks

Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.

In vitro and in vivo evaluation of tannic acid as an antibacterial agent in broilers infected with Salmonella Typhimurium

This study was conducted to evaluate tannic acid (TA) as an antibacterial agent against Salmonella Typhimurium in in vitro and in vivo chicken models. The TA formed an inhibitory zone against Salmonella enterica serotypes including S. Typhimurium, S. Enteritidis, and S. Infantis. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of TA against Salmonella Typhimurium nalidixic acid resistant strain (STNR) were determined as 40 and 700 μg/mL, respectively. Sublethal doses of TA (5, 10, and 20 μg/mL) restricted swimming and swarming motility and biofilm formation of STNR compared to the control group (0 μg/mL) (P < 0.05). The TA-bovine serum albumin (BSA) complex formed at simulated gastric pH (pH 3.75) was hydrolyzed at pH 6.75 and 7.25 (P < 0.05), and the hydrolysis of the TA-BSA complex was stronger at pH 7.25 compared to the pH 6.75 (P < 0.05). The inhibitory zone of the TA-BSA complex against STNR at pH 6.75 was lower than TA without BSA at 30 and 60 min (P < 0.05), but not at 120 min (P > 0.1). The inhibitory zone of the TA-BSA complex against STNR at pH 7.25 was not decreased at 0, 30, and 60 min compared to TA without BSA (P > 0.1). The recovery rate of TA was 83, 54.8, 10.5, and 19.6% in the gizzard, jejunum, ileum, and ceca, respectively, in broiler chickens. The STNR-infected broilers fed 0.25 g/kg of TA had significantly lower unweighted beta diversity distance compared to the sham-challenged control (SCC) and challenged controlled (CC) group on D 21. TA supplementation linearly (P < 0.05) and quadratically (tendency; P = 0.071) reduced relative abundance of the family Peptostreptococcaceae in broilers infected with STNR on D 7. TA supplementation linearly (P < 0.05) and quadratically (tendency; P = 0.06) increased the relative abundance of the family Erysipelotrichaceae in broilers infected with STNR on D 21. Therefore, TA has potential to be used as an antibacterial agent against the S. Typhimurium infection in broilers.

Interactions between enzyme preparations and trace element sources on growth performance and intestinal health of broiler chicks

This experiment was conducted to explore the interactions between enzyme preparations and trace element sources on growth performance and intestinal health of broilers chicks. A total of 480 one-day-old healthy male yellow-feather broilers with similar weight were randomly arranged in a 2  ×  2 factorial design with 2 kinds of compound trace element sources (inorganic [I] and organic [O] trace element supplemented with 80, 8, 60, 40, 0.15 mg/kg of Fe, Cu, Mn, Zn, and Se, respectively) and 2 levels of enzyme preparations (0 and 200 mg/kg). The 4 groups named I, O, IE, and OE with 6 replicates and 20 birds per replicate. The trail lasted for 28 days. Results showed that the average weight (ABW), average daily gain (ADG) of broilers in IE and OE groups significantly increased while the F/G significantly decreased as compared with group I and O (P < 0.05). Enzyme preparation supplementation, regardless of the trace element sources, significantly increased the duodenal and jejunal endogenous enzyme (e.g., Try and AACT) activity, and improved the morphology and jejunal barrier function evidenced by the increased villus height and MUC-2 mRNA expression (P < 0.05). Sequencing data manifested that enzyme preparations favorably modulated the cecal microflora by increasing bacterial diversity and abundance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Anaerostipes, Anaerofusis, and Pygmaioactor), while decreasing the abundance of harmful bacteria (e.g., Desulfovibrio). Factorial analysis indicated that there were no interactions between enzyme preparation and trace element sources on growth performance and intestinal health of broiler chicks. In conclusion, dietary supplementation with enzyme preparations, regardless of the trace element sources, could enhance endogenous enzyme activity, improve intestinal morphology and barrier functions, and favorably modulate the cecal microflora, thereby improving the intestinal health and growth performance of broiler chicks.

Effects of different levels of Citri Sarcodactylis Fructus by-products fermented feed on growth performance, serum biochemical, and intestinal health of cyan-shank partridge birds

This research aimed to investigate the effects of supplements containing fermented feed made from Citri Sarcodactylis Fructus by-products (CSFBP-Fermented feed) on the growth performance, immunological function, and gut health of broilers. 1080 cyan-shank partridge birds aged 47 days were chosen and casually distributed to four groups, each with 6 replicates and 45 birds per replicate. The experimental groups were provided with 1% (group T2), 3% (group T3) and 5% (group T4) of CSFBP-fermented feed in the basic diet, while the control group (group T1) received the basic diet. The findings revealed that supplementation with CSFBP-Fermented feed reduced ADFI and FCR and improved ADG in birds (P < 0.05). MDA levels in the serum of birds fed CSFBP-fermented feed were lower than in the control group (P < 0.05). The CAT activity in the serum of broilers increased after supplementation with 3% CSFBP-Fermented feed (P < 0.05). Supplementing broilers with CSFBP-fermented feed enhanced VH in the ileum, jejunum, and duodenum (P < 0.05). The addition of 3% CSFBP-Fermented feed decreased CD in the jejunum (P < 0.05). The addition of 3% and 5% CSFBP-Fermented feed increased the mRNA expression of ZO-1 and Occludin in the jejunum of broiler chickens and reduced the mRNA expression of IL-6 (P < 0.05). The addition of 3% CSFBP-Fermented feed increased the mRNA expression of Claudin in the jejunum of broiler chickens and reduced IL-1β mRNA expression (P < 0.05). Compared to the control group, all experimental groups exhibited decreased mRNA expression of TNF-α and INF-γ in the jejunal mucosa of the birds (P < 0.05). According to research using high-throughput sequencing of microorganisms' 16S rDNA, and an analysis of α-diversity found that supplementing broilers with 3% CSFBP-Fermented feed decreased the number of bacteria in their cecum (P < 0.05). Bacteroidota was higher in all groups after supplementation with CSFBP-Fermented feed. At the genus level, after addition with 3% CSFBP-Fermented feed, the abundance of Bacteroide and Prevotellaceae_Ga6A1_group were higher than the control group (33.36% vs 29.95%, 4.35% vs 2.94%). The abundance of Rikenellaceae_RC9_gut_group and Fusobacterium were lower than the control group (5.52% vs. 7.17%,0.38% vs. 1.33%). In summary, supplementing the diet with CSFBP-Fermented feed can promote the growth of performance by enhancing intestinal morphology, and barrier function, as well as modulating intestinal inflammatory factors and microbial composition in broilers.

Identification and evaluation of probiotic potential of Bifidobacterium breve AHC3 isolated from chicken intestines and its effect on necrotizing enterocolitis (NEC) in newborn SD rats

Necrotizing enterocolitis (NEC) is a severe intestinal disease of the newborn infants, associated with high morbidity and mortality. It has been reported that Bifidobacterium could protect the intestinal barrier function and reduce the risk of NEC. This study aimed to evaluate the probiotic potential of Bifidobacterium strains isolated from the chicken intestines and its effect on necrotizing enterocolitis in newborn SD rats. Out of 32 isolates, B. breve AHC3 not only exhibited excellent probiotic potential, including tolerance to artificial simulated gastric conditions, adhesion to HT-29 cells, antioxidant capacity and antibacterial activity, but also possessed reliable safety. Additionally, NEC model was established to further investigate the effect of B. breve AHC3 on necrotizing enterocolitis in newborn SD rats. It was illustrated that administration of B. breve AHC3 significantly not only reduced the incidence of NEC (from 81.25% to 34.38%) (P< 0.05), but also alleviated the severity of ileal injury (P< 0.05). Compared with NEC model, B. breve AHC3 could significantly decrease the level of proinflammatory factor TNF-α (P< 0.05) and increase the level of antiinflammatory factor IL-10 (P< 0.05) in the ileum of NEC rats. Through the intervention of B. breve AHC3, the gray value of inducible nitric oxide synthase (iNOS) in intestinal tissue of NEC rats was significantly reduced (P< 0.05). It was indicated that B. breve AHC3 exhibited prominent probiotic potential and reliable safety. In the neonatal SD rat model of NEC, B. breve AHC3 had an available protective effect on the intestinal injury of NEC, which might be related to reducing the inflammatory reaction in the ileum and inhibiting the expression of iNOS in intestinal tissue cells. B. breve AHC3 could be used as a potential treatment for human NEC.

Evaluation of the Immunoprotective Capacity of Five Vaccine Candidate Proteins against Avian Necrotic Enteritis and Impact on the Caecal Microbiota of Vaccinated Birds

Avian necrotic enteritis is an enteric disease of broiler chickens caused by certain pathogenic strains of Clostridium perfringens in combination with predisposing factors. A vaccine offering complete protection against the disease has not yet been commercialized. In a previous study, we produced five recombinant proteins predicted to be surface-exposed and unique to necrotic enteritis-causing C. perfringens and the immunogenicity of these potential vaccine candidates was assessed in broiler chickens. In the current work, the relative contribution of the antibodies raised by these putative antigens to protect broiler chickens was evaluated using an experimental necrotic enteritis induction model. Additionally, the link between the immune response elicited and the gut microbiota profiles in immunized birds subjected to infection with virulent C. perfringens was studied. The ELISA results showed that the IgY antibody titers in vaccinated birds on days 21 and 33 were significantly higher than those on days 7 and 14 and those in birds receiving the adjuvant alone, while the relative contribution of the specific immunity attributed to these antibodies could not be precisely determined using this experimental necrotic enteritis induction model. In addition, 16S rRNA gene amplicon sequencing showed that immunization of birds with recombinant proteins had a low impact on the chicken caecal microbiota.

The digestive tract histology and geographical distribution of gastrointestinal microbiota in yellow-feather broilers

Exhaustive understanding of intestinal physiological characteristics is the critical precondition for the improvement of intestinal health and growth performance of yellow-feather broilers (YFB). As a vital part of gastrointestinal tract, the symbiotic, complex, and variable microbiota have a profound effect on the nutrition, immunity, health, and production of broilers. Hence, the development status of proventriculus, jejunum, and cecum, and spatial heterogeneity of bacterial community in crop, proventriculus, gizzard, jejunum, cecum, and rectum of adult YFB were detected in our study. The results revealed that proventriculus, jejunum, and cecum of broilers are well-developed based on morphological observation. The Chao and Shannon indexes in cecum and rectum are notably higher than other sections and their microbiota structure is also distinct from foregut. Firmicutes and Lactobacillus are the predominant phylum and genus in all gastrointestinal sections, respectively. As feature species of crop, Lactobacillus spp. mainly settle in foregut, whereas some Clostridia species (unclassified Lachnospiraceae, Faecalibacterium, Romboutsia and so on) are characteristic and more abundant in cecum and rectum. Interestingly, there are 2 Ruminococcus torques strains positively and negatively correlated with cecum development, respectively. In a whole, our findings reveal the specialized digestive physiology and regional distribution of intestinal microbiota in YFB, which provides a reference for the future study on the improvement of growth performance and intestinal development through microbiota manipulation in yellow-feather broilers.

Effect of in-water administration of quorum system inhibitors in broilers' productive performance and intestinal microbiome in a mild necrotic enteritis challenge

The poultry industry has been facing the impact of necrotic enteritis (NE), a disease caused by the bacterium Clostridium perfringens producing the haemolytic toxin NetB. NE severity may vary from mild clinical to prominent enteric signs causing reduced growth rates and affecting feed conversion ratio. NetB production is controlled by the Agr-like quorum-sensing (QS) system, which coordinates virulence gene expression in response to bacterial cell density. In this study, the peptide-containing cell-free spent media (CFSM) from Enterococcus faecium was tested in NE challenged broilers in two battery cage and one floor pen studies. Results showed a significant reduction of NE mortality. Metagenomic sequencing of the jejunum microbiome revealed no impact of the CFSM on the microbial community, and growth of C. perfringens was unaffected by CFSM in vitro. The expression of QS-controlled virulence genes netB, plc and pfoA was found to be significantly repressed by CFSM during the mid-logarithmic stage of C. perfringens growth and this corresponded with a significant decrease in haemolytic activity. Purified fractions of CFSM containing bioactive peptides were found to cause reduced haemolysis. These results showed that bioactive peptides reduce NE mortality in broilers by interfering with the QS system of C. perfringens and reducing bacterial virulence. Furthermore, the microbiome of C. perfringens-challenged broilers is not affected by quorum sensing inhibitor containing CFSM.

Supplementation of ginger root extract into broiler chicken diet: effects on growth performance and immunocompetence

Ginger contains bioactive compounds that possess anti-inflammatory and antimicrobial properties. In this study, 432-day-old Ross 708 broiler male chicks were randomly allocated to 6 dietary treatments to investigate the effect of ginger root extract (GRE) on immunocompetence and growth performance to 6 wk of age. Treatment 1 (CON) consisted of chicks fed a corn-soybean meal (SBM), a base diet without GRE. Treatment 2 (MX) chicks were given basal diets containing bacitracin methylene disalicylate (BMD) at 0.055 g/kg. Treatments 3 (GRE-0.375%), 4 (GRE-0.75%), 5 (GRE-1.5%), and 6 (GRE-3%) were fed similar diet to control with GRE supplemented at 0.375%, 0.75%, 1.5%, and 3%, respectively. Moreover, HPLC analysis of GRE was carried out to determine the concentration of bioactive compounds found in GRE. Each treatment consisted of 6 replicate pens with 12 chicks/pen. Bodyweight (BW) and feed conversion ratio (FCR) were recorded. Results show that the concentration of bioactive compounds increased with increasing GRE supplementation. Likewise, dietary GRE supplementation did not have any detrimental effect on growth performance parameters up to 1.5%, as values for BWG was not different from CON and MX; however, 3% GRE had the poorest FCR and a lower BWG as compared to other treatments. On d 27 and d 41, fecal and cecal concentrations of total bacteria count (TBC), Escherichia coli, Lactobacillus spp., and Bifidobacterium spp enumerated using selective plating media showed that GRE supplementation significantly reduced (P < 0.05) the amount of TBC and E. coli but increased the number of beneficial microorganisms such as Lactobacillus spp. and Bifidobacterium spp. On d 20, no significant differences were observed (P > 0.05) among all treatments for antibody titer against Newcastle disease virus and total IgY antibodies; however, on d 27, GRE-0.75% had the highest value for both immune indicators and was not different from MX. Dietary supplementation of GRE up to 1.5% enhanced the immune system and suppressed E. coli while promoting the growth of healthy bacteria, without any detrimental effect on growth performance.

Variations in the Intestinal Microbiota of the Chinese Soft-Shelled Turtle (Trionyx sinensis) between Greenhouse and Pond Aquaculture

The microbial community structure in aquaculture water plays an important role in the intestinal microbial diversity of aquatic animals. The Chinese soft-shelled turtle (SST) (Trionyx sinensis) is an important aquaculture species of high economic value in the Asia-Pacific region. An intuitive understanding of the microbial diversity and abundances of SST aquaculture is crucial for comprehending these ecosystems. Herein, the evolutionary characteristics of the bacterial communities in the SST and its aquaculture water systems were investigated using Illumina MiSeq sequencing. This experiment sampled nine SSTs from a pond outside a greenhouse and was repeated three times. The sequencing results revealed significant differences in the microflora composition at the phylum and genus levels in both the intestine and aquaculture water of the SSTs in the greenhouse and pond aquaculture environments. A total of 1039 genera belonging to 65 phyla were identified. At the phylum level, the relative abundances of Chloroflexi (24%), Acidobacteria (5%), and Nitrospira (3%) were higher in the greenhouse water than in the pond water. The relative abundances of Bacteroidetes (35%), Actinobacteria (8%), and Cyanobacteria (4%) were higher in the pond water than in the greenhouse water. The intestinal microorganisms in the SSTs experienced significant changes after the SSTs were transferred from a greenhouse culture to a pond culture environment for 28 days. After the SSTs were cultured in the ponds, we observed decreases in the relative abundances of Actinobacteria (39% to 25%), Cyanobacteria (24% to 0.8%), Chlorobacteria (9% to 3%), and Firmicutes (5.5% to 0.8%. However, we observed increases in the relative abundances of Bacteroidetes (2% to 35%) and Acidobacteria (0.3% to 25%). These results showed that the bacterial diversity and richness compositions in the intestinal tract and aquaculture water were the same. However, the relative abundances of bacterial communities varied. The results of this study are of great significance in understanding how the environment affects SST cultures. These data may provide valuable instructions for Chinese soft-shelled turtle aquaculture management.

Heat stress exposure cause alterations in intestinal microbiota, transcriptome, and metabolome of broilers

Introduction

Heat stress can affect the production of poultry through complex interactions between genes, metabolites and microorganisms. At present, it is unclear how heat stress affects genetic, metabolic and microbial changes in poultry, as well as the complex interactions between them.

Methods

Thus, at 28  days of age a total of 200 Arbor Acres broilers with similar body weights were randomly divided into the control (CON) and heat stress treatment (HS). There were 5 replicates in CON and HS, respectively, 20 per replication. From the 28-42  days, the HS was kept at 31 ± 1°C (9:00-17:00, 8 h) and other time was maintained at 21 ± 1°C as in the CON. At the 42nd day experiment, we calculated the growth performance (n = 8) of broilers and collected 3 and 6 cecal tissues for transcriptomic and metabolomic investigation and 4 cecal contents for metagenomic investigation of each treatment.

Results and discussion

The results indicate that heat stress significantly reduced the average daily gain and body weight of broilers (value of p < 0.05). Transcriptome KEGG enrichment showed that the differential genes were mainly enriched in the NF-kB signaling pathway. Metabolomics results showed that KEGG enrichment showed that the differential metabolites were mainly enriched in the mTOR signaling pathway. 16S rDNA amplicon sequencing results indicated that heat stress increased the relative abundance of Proteobacteria decreased the relative abundance of Firmicutes. Multi-omics analysis showed that the co-participating pathway of differential genes, metabolites and microorganisms KEGG enrichment was purine metabolism. Pearson correlation analysis found that ornithine was positively correlated with SULT1C3, GSTT1L and g_Lactobacillus, and negatively correlated with CALB1. PE was negatively correlated with CALB1 and CHAC1, and positively with g_Alistipes. In conclusion, heat stress can generate large amounts of reactive oxygen and increase the types of harmful bacteria, reduce intestinal nutrient absorption and antioxidant capacity, and thereby damage intestinal health and immune function, and reduce growth performance indicators. This biological process is manifested in the complex regulation, providing a foundational theoretical basis for solving the problem of heat stress.

Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review

Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.

A culture-based assessment of the microbiota of conventional and free-range chicken meat from Irish processing facilities

Chicken meat is the most popularly consumed meat worldwide, with free-range and ethically produced meat a growing market among consumers. However, poultry is frequently contaminated with spoilage microbes and zoonotic pathogens which impact the shelf-life and safety of the raw product, constituting a health risk to consumers. The free-range broiler microbiota is subject to various influences during rearing such as direct exposure to the external environment and wildlife which are not experienced during conventional rearing practices. Using culture-based microbiology approaches, this study aimed to determine whether there is a detectable difference in the microbiota from conventional and free-range broilers from selected Irish processing plants. This was done through analysis of the microbiological status of bone-in chicken thighs over the duration of the meat shelf-life. It was found that the shelf-life of these products was 10 days from arrival in the laboratory, with no statistically significant difference (P > 0.05) evident between free-range and conventionally raised chicken meat. A significant difference, however, was established in the presence of pathogenesis-associated genera in different meat processors. These results reinforce past findings which indicate that the processing environment and storage during shelf-life are key determinants of the microflora of chicken products reaching the consumer.

Microbiological Quality and Safety of Fresh Quail Meat at the Retail Level

The objective of this study was to evaluate the microbiological quality and safety of 37 fresh quail meats. Mesophiles, Pseudomonas spp., Enterobacteriaceae, and staphylococci counts were 5.25 ± 1.14, 3.92 ± 1.17, 3.09 ± 1.02, and 2.80 ± 0.64 log CFU/g, respectively. Listeria monocytogenes was detected in seven samples (18.92%). Campylobacter jejuni was detected in one sample (2.70%). Clostridium perfringens was not detected in any sample. The dominant bacteria were Pseudomonas spp. (30.46%), Micrococcaceae (19.87%), lactic acid bacteria (14.57%), and Enterobacteriaceae (11.92%). Brochotrix thermosphacta and enterococci were isolated to a lesser extent, 7.28% and 1.99%, respectively. The dominant Enterobacteriaceae found were Escherichia coli (42.53%). ESBL-producing E. coli was detected in one sample (2.70%), showing resistance to 16 antibiotics. Sixteen different Staphylococcus spp. and three Mammaliicoccus spp. were identified, the most common being S. cohnii (19.86%) and M. sciuri (17.02%). S. aureus and S. epidermidis were also found in one and four samples, respectively. Methicillin-resistant M. sciuri and S. warneri were found in 13.51% and 10.81% of quail samples, respectively. These bacteria showed an average of 6.20 and 18.50 resistances per strain, respectively. The high resistance observed in ESBL-producing E. coli and methicillin-resistant S. warneri is of special concern. Measures should be adopted to reduce the contamination of quail meat.

Effects of Traditional Chinese Herbal Feed Additive on Production Performance, Egg Quality, Antioxidant Capacity, Immunity and Intestinal Health of Laying Hens

Chinese herbs have been used as feed additives in animal production. This study investigated the effects of a Chinese herbal feed-additive (TCM, which contained Elsholtzia ciliate, Atractylodes macrocephala, Punica granatum pericarpium, and Cyperus rotundus) on the production performance, egg quality, antioxidant capacity, immunity, and intestinal health of Roman laying hens. A total of 720 28-week-old hens were randomly allotted to three groups with six replicates of forty hens each. The groups were fed a basal diet (CON group), a basal diet with 50 mg/kg zinc bacitracin (ABX group), or a basal diet with 400 mg/kg TCM (TCM group) for 56 days. The results showed that the TCM group increased egg production, egg mass, albumen height, and Haugh unit compared with the CON group (p < 0.05). There were no significant differences in egg weight, feed intake, feed conversion rate, and eggshell strength among all three groups (p > 0.05). Compared with the CON group, the TCM group enhanced the activities of glutathione peroxidase, total antioxidant capacity, and superoxide dismutase in serum and liver, and reduced malondialdehyde content (p < 0.05). The TCM also increased the levels of interleukin-2, interferon-γ, immunoglobulin A, immunoglobulin M, and immunoglobulin G, and decreased the levels of interleukin-6 and interleukin-8 compared with the CON group (p < 0.05). Furthermore, the TCM group increased jejunal goblet cell density and decreased ileal crypt depth and lymphocyte density compared with the CON group (p < 0.05). The results of 16S rRNA demonstrated that the TCM can change the diversity and composition of intestinal microbiota. At the phylum level, the abundance of Bacteroides increased while that of Firmicutes decreased in the TCM group (p > 0.05). At the genus level, the abundance of Lactobacillus, Rikenellaceae_RC9_gut_group, and Phascolarctobacterium increased while that of Bacteroides and unclassified_o__Bacteroidales decreased in the TCM group (p > 0.05). The effects of ABX were weaker than those of the TCM. In conclusion, the TCM has positive effects on production performance and the intestinal health of hens.

Amino acid digestibility of insect meals and effects on key bacterial groups in excreta of caecectomised laying hens

The chemical composition and amino acids (AA) digestibility were determined in insect meals from mealworms, crickets, black soldier fly (BSF) larvae and BSF prepupae, and soybean meal. Six caecectomised laying hens were individually housed in metabolism cages and fed either a basal diet or one of five assay diets. Diets and hens were arranged in a 6 × 6 Latin square design with 6 subsequent periods. In each period, the laying hens were fed their respective diet for 9 d, and excreta samples were quantitatively collected twice daily from day 5 to 8. On day 9, a sterile plastic bag was attached to the cloaca of each hen to collect excreta for microbiota analysis. The AA digestibility of the insect meals and soybean meal were calculated using a linear regression approach. Crude protein (CP) concentrations in crickets and mealworms were higher than the value in soybean meal, BSF prepupae and BSF larvae. Ether extract concentrations were high in the insect meals and low in the soybean meal. The digestibility of most essential AA in soybean meal was higher (p < 0.05) than in crickets and BSF prepupae and not different from AA digestibility in mealworms and BSF larvae (except for arginine and histidine). The gene copy number of Escherichia coli in excreta from hens fed with BSF prepupae was lower (p < 0.05) than those fed with BSF larvae, whereas the gene copy number of Bacillus spp. and Clostridium spp. in excreta from hens fed with crickets was lower (p < 0.05) than those fed with BSF larvae. In conclusion, the chemical composition and AA digestibility varied among insect meals based on insect species and life stage. The high level of AA digestibility of insect meals supports the assessment that insect meals are a suitable feed component for laying hens, but differences in AA digestibility should be considered in diet formulation.

Impact of antimicrobial use on abundance of antimicrobial resistance genes in chicken flocks in Vietnam

Objectives

We investigated longitudinally Vietnamese small-scale chicken flocks in order to characterize changes in antimicrobial resistance gene (ARG) content over their life cycle, and the impact of antimicrobial use (AMU) on an intervention consisting of veterinary advice provision.

Methods

AMU data and faecal samples were collected from 83 flocks (25 farms) at day-old, mid- and late-production (∼4 month cycle). Using high-throughput real-time PCR, samples were investigated for 94 ARGs. ARG copies were related to 16S rRNA and ng of DNA (ngDNA). Impact of AMU and ARGs in day-olds was investigated by mixed-effects models.

Results

Flocks received a mean (standard error, SE) animal daily dose (ADD) of 736.7 (83.0) and 52.1 (9.9) kg in early and late production, respectively. Overall, ARGs/16S rRNA increased from day-old (mean 1.47; SE 0.10) to mid-production (1.61; SE 0.16), further decreasing in end-production (1.60; SE 0.1) (all P > 0.05). In mid-production, ARGs/16S rRNA increased for aminoglycosides, phenicols, sulphonamides and tetracyclines, decreasing for polymyxins β-lactams and genes that confer resistance to mutiple classes (multi-drug resistance) (MDR). At end-production, aminoglycoside resistance decreased and polymyxin and quinolone resistance increased (all P < 0.05). Results in relation to ngDNA gave contradictory results. Neither AMU nor ARGs in day-olds had an impact on subsequent ARG abundance. The intervention resulted in 74.2% AMU reduction; its impact on ARGs depended on whether ARGs/ngDNA (+14.8%) or ARGs/16S rRNA metrics (-10.7%) (P > 0.05) were computed.

Conclusions

The flocks' environment (contaminated water, feed and residual contamination) is likely to play a more important role in transmission of ARGs to flocks than previously thought. Results highlight intriguing differences in the quantification of ARGs depending on the metric chosen.

Segmented filamentous bacteria-based treatment to elicit protection against Enterobacteriaceae in Layer chickens

Introduction

Gut microbes like segmented filamentous bacteria (SFB) play a key role in gut maturation during early life, as demonstrated in humans and mice. Our previous study demonstrated oral inoculation of ileum-spores containing SFB to chickens after hatch increases early SFB gut colonization, which increases immune maturation and resistance to bacteria, like Salmonella, as tested in vitro; however, more studies are needed for treatment optimization and in vivo testing. The objectives of this study were to (1) test a treatment that includes both spores and filamentous SFB, (2) validate antimicrobial ability of the treatment in layer hens in vivo, and (3) elucidate its molecular mechanism.

Methods

One-day-old specific pathogen-free layers (n = 12 per group) were orally treated with either PBS (CON) or SFB-based treatment (SFB). At 4 days post-inoculation (DPI), both CON and SFB groups were orally challenged with Salmonella Typhimurium. Total Enterobacteriaceae and Salmonella were examined by plating and enumeration in feces at 7,10 and 14 dpi; and in the ileum, cecum, and spleen at 16 dpi in euthanized birds. The presence and levels of SFB were determined from ilea scrapings via microscopy and qPCR, respectively. Relative gene expression of host-derived antimicrobial peptides and cytokines in the distal ileum was determined by RT-qPCR.

Results

At 10 and 14 dpi, a significant decrease in total Enterobacteriaceae was observed in the feces of the SFB group. At necropsy, the level of SFB was significantly higher in the SFB group than in the CON group, while a significant decrease in total Enterobacteriaceae and Salmonella was observed in the ceca of the SFB group. RT-qPCR revealed increased expression of β-defensin 14, and cytokines IL-10 and IFNγ.

Discussion

The introduction of SFB at hatch as a prophylactic treatment may benefit commercial partners as well as consumers by reducing the incidence of Enterobacteriaceae in food animals. Reduction of these bacteria in animals would, in turn, increase animal health, productivity, and safety for consumers. Studies to optimize the treatment for poultry industry applications are ongoing in our lab.

Review: Composition and utilisation of feed by monogastric animals in the context of circular food production systems

Food production has a major impact on environmental emissions, climate change and land-use. To reduce this impact, the circularity of future food production systems is expected to become increasingly important. In a circular food system, crop land is primarily used for plant-based food production, while low-opportunity cost feed materials (LCF), i.e. crop residues, co-products of the food industry, grass from marginal land and food waste form the basis of future, animal feeds. Animal diets thus contain much less cereals and soybean meal and include a higher proportion of diverse co-products, residues and novel human-inedible ingredients. These diets are characterised by a lower starch content, and a higher content of fibre, protein, fat, and phytate compared to present diets. In this review, possible consequences of the development towards a more circular food system for the type, volume and nutritional characteristics of feed materials and complete feeds are addressed and related research questions in the area of animal nutrition, physiology and metabolism are discussed. Additional attention is given to possible effects on intestinal health and gut functionality and to (bio)technological processing of LCF to improve their suitability for feeding farm animals, with a focus on the effects in pigs and poultry. It is concluded that an increased use of LCF may limit the use of presently used criteria for the efficiency of animal production and nutrient utilisation. Development of characteristics that reflect the efficacy and efficiency of the net contribution of animal production in a circular food system is required. Animal scientists can have an important role in the development of more circular food production systems by focussing on the optimal use of LCF in animal diets for the production of animal-source food, while minimising the use of human-edible food in animal feed.

Deciphering the Association between Campylobacter Colonization and Microbiota Composition in the Intestine of Commercial Broilers

Campylobacter is a major food safety concern and is transmitted mainly via poultry meat. We previously found that some commercial broiler farms consistently produced Campylobacter-negative flocks while others were consistently Campylobacter-positive for consecutive production cycles although the farms operated under similar management practices. We hypothesized that this difference in Campylobacter colonization might be associated with the gut microbiota composition. To address this, six commercial broiler farms were selected based on their Campylobacter status (three negative and three positive) to evaluate the microbiota differences between each farm category. For each farm on each production cycle (2-3 cycles), 40 ceca collected from five-week-old broilers were processed for microbiota analysis via 16S rRNA gene sequencing. Cecal microbiota species richness, phylogenetic diversity, community structure, and composition of Campylobacter-positive farms were noticeably different from those of Campylobacter-negative farms. Rikenella, Methanocorpusculum, Barnesiella, Parasutterella, and Helicobacter were significantly more abundant among Campylobacter-positive farms. In contrast, Ruminococcaceae, Streptococcus, Escherichia, Eggerthellaceae, Lactobacillus, Monoglobus, and Blausia were more abundant in Campylobacter-negative farms. Eggerthellaceae, Clostridia, Lachnospiraceae, Lactobacillus, Monoglobus, and Parabacteroides were significantly negatively correlated with Campylobacter abundance. These findings suggest that specific members of cecal microbiota may influence Campylobacter colonization in commercial broilers and may be further explored to control Campylobacter in poultry.

Influence of Live Attenuated Salmonella Vaccines on Cecal Microbiome Composition and Microbiota Abundances in Young Broiler Chickens

Salmonellosis is a global food safety challenge caused by Salmonella, a gram-negative bacterium of zoonotic importance. Poultry is considered a major reservoir for the pathogen, and humans are exposed through consumption of raw or undercooked products derived from them. Prophylaxis of Salmonella in poultry farms generally mainly involves biosecurity measures, flock testing and culling, use of antibiotics, and vaccination programs. For decades, the use of antibiotics has been a common practice to limit poultry contamination with important pathogenic bacteria such as Salmonella at the farm level. However, due to an increasing prevalence of resistance, non-therapeutic use of antibiotics in animal production has been banned in many parts of the world. This has prompted the search for non-antimicrobial alternatives. Live vaccines are among the developed and currently used methods for Salmonella control. However, their mechanism of action, particularly the effect they might have on commensal gut microbiota, is not well understood. In this study, three different commercial live attenuated Salmonella vaccines (AviPro^® Salmonella Vac T, AviPro^® Salmonella DUO, and AviPro^® Salmonella Vac E) were used to orally vaccinate broiler chickens, and cecal contents were collected for microbiomes analysis by 16S rRNA next generation sequencing. Quantitative real-time PCR (qPCR) was used to study the cecal immune-related genes expression in the treatment groups, while Salmonella-specific antibodies were analyzed from sera and cecal extracts by enzyme-linked immunosorbent assay (ELISA). We show that vaccination with live attenuated Salmonella vaccines had a significant influence on the variability of the broiler cecal microbiota (p = 0.016). Furthermore, the vaccines AviPro^® Salmonella Vac T and AviPro^® Salmonella DUO, but not AviPro^® Salmonella Vac E, had a significant effect (p = 0.024) on microbiota composition. This suggests that the live vaccine type used can differently alter the microbiota profiles, driving the gut colonization resistance and immune responses to pathogenic bacteria, and might impact the overall chicken health and productivity. Further investigation is, however, required to confirm this.

Effects of dosing non-toxigenic Clostridia on the bacterial populations and immunological responses in the intestinal tract of lactating dairy cows

Understanding the effects of dosing non-toxigenic Clostridia to cows is rare and has received little attention so far. In the present study, a total of eight lactating dairy cows were divided in two groups: control (n = 4) or Clostridia challenged (oral supplementation of five diverse strains of Paraclostridium bifermentans, n = 4). Bacterial communities were analyzed by qPCR and next-generation sequencing (NGS) in the buccal mucosa as well as digesta and mucosal samples of the gastrointestinal (GI) tract from rumen to rectum (10 compartments), as well as fecal samples. Transcriptomic analysis of barrier and immune-related gene expression was performed on rumen, jejunum, and liver samples. We observed increased microbial populations with the Clostridial challenge in the buccal tissues and the proximal GI tract (forestomach), correlating with Clostridial loads in the feed. Otherwise, there were no significant differences in microbial populations (p > 0.05) throughout the distal part of the GI tract. The NGS approach, however, revealed that the Clostridial challenge changed the relative abundance of gut and fecal microbiota. In particular, in the challenge group, no Bifidobacterium was observed in the mucosa-associated microbiota and abundance of Pseudomonadota increased in the feces. These results indicated potential adverse effects of Clostridia to cow health. In general, immune responses to the Clostridial challenge were weak. However, transcriptional analysis revealed the down-regulation of junction adhesion molecule encoding gene (-1.44 of log₂ fold-change), which might impact intestinal permeability.

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

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

Impact of Eimeria meleagrimitis and intermittent amprolium treatment on performance and the gut microbiome composition of Turkey poults

Introduction

Drug-sensitive live coccidiosis vaccines have been used to control coccidiosis and renew drug sensitivity in commercial chicken operations. However, only limited species coverage vaccines have been available for commercial turkey producers. This study aimed to assess the effect of an E. meleagrimitis vaccine candidate, with and without amprolium intervention, on performance and oocyst shedding. Additionally, the effect of vaccination, amprolium treatment, and E. meleagrimitis challenge on intestinal integrity and microbiome composition was evaluated.

Methods

Experimental groups included: (1) NC (non-vaccinated, non-challenged control); (2) PC (non-vaccinated, challenged control); (3) VX + Amprol (E. meleagrimitis candidate vaccine + amprolium); and 4) VX (E. meleagrimitis candidate vaccine). For VX groups, 50% of the direct poults were orally vaccinated at DOH with 50 sporulated E. meleagrimitis oocysts and were comingled with contact or non-vaccinated poults for the duration of the study. From d10-14, VX + Amprol group received amprolium (0.024%) in the drinking water. All groups except NC were orally challenged with 95K E. meleagrimitis sporulated oocysts/mL/poult at d23. At d29, ileal and cecal contents were collected for 16S rRNA gene-based microbiome analysis.

Results and Discussion

VX did not affect performance during the pre-challenge period. At d23-29 (post-challenge), VX groups had significantly (P < 0.05) higher BWG than the PC group. Contacts and directs of VX groups in LS had significantly reduced compared to PC. As anticipated, amprolium treatment markedly reduced fecal and litter OPG for the VX + Amprol group compared to the VX group which did not receive amprolium. The ileal and cecal content results showed that the PC group had different bacterial diversity and structure, including alpha and beta diversity, compared to NC. Linear discriminant analysis Effect Size (LEfSe) identified that Lactobacillus salivarius (ASV2) was enriched in PC's ileal and cecal content. Compared to NC and PC, the vaccinated groups showed no distinct clusters, but there were similarities in the ileal and cecal communities based on Bray-Curtis and Jaccard distances. In conclusion, these results indicate that vaccination with this strain of E. meleagrimitis, with or without amprolium intervention, caused a very mild infection that induced protective immunity and challenge markedly affected both the ileal and cecal microbiome.

Strategies to Assess the Impact of Sustainable Functional Food Ingredients on Gut Microbiota

Nowadays, it is evident that food ingredients have different roles and distinct health benefits to the consumer. Over the past years, the interest in functional foods, especially those targeting gut health, has grown significantly. The use of industrial byproducts as a source of new functional and sustainable ingredients as a response to such demands has raised interest. However, the properties of these ingredients can be affected once incorporated into different food matrices. Therefore, when searching for the least costly and most suitable, beneficial, and sustainable formulations, it is necessary to understand how such ingredients perform when supplemented in different food matrices and how they impact the host's health. As proposed in this manuscript, the ingredients' properties can be first evaluated using in vitro gastrointestinal tract (GIT) simulation models prior to validation through human clinical trials. In vitro models are powerful tools that mimic the physicochemical and physiological conditions of the GIT, enabling prediction of the potentials of functional ingredients per se and when incorporated into a food matrix. Understanding how newly developed ingredients from undervalued agro-industrial sources behave as supplements supports the development of new and more sustainable functional foods while scientifically backing up health-benefits claims.