In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner

16S rRNA and transcriptome analysis revealed the regulatory mechanism of Romboutsia lituseburensis on serum immunoglobulin levels in geese

Romboutsia is a dominant genus in the goose intestine. Recent studies have suggested that Romboutsia lituseburensis might regulate serum immunoglobulin levels in female geese, although the underlying mechanisms remain unclear. In this study, we administered Romboutsia lituseburensis (R. lituseburensis) orally to female geese, leading to successful colonization of the ileum. Subsequent analysis showed that the levels of IgM, IgA, and IgG in the serum significantly decreased after colonization (P < 0.01). 16S rRNA sequencing revealed that R. lituseburensis significantly altered the microbial composition and increased the relative abundance of Jeotgalicoccus (P < 0.01), Turicibacter, and Bacillus (P < 0.05) in the ileum. Transcriptome sequencing further identified 263 differentially expressed genes (DEGs) in the ileum (146 upregulated, 117 downregulated) and 725 DEGs in the spleen (300 upregulated, 425 downregulated). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these DEGs were enriched in 17 pathways in the ileum and 21 pathways in the spleen. Notably, the "Intestinal immune network for IgA production" pathway was significantly enriched in the spleen (P < 0.05). Further, Short Time-series Expression Miner (STEM) analysis grouped the DEGs in these 2 tissues into 49 clusters, with clusters 27 and 29 showing the highest significance and similar expression patterns. Pathway analysis confirmed that the "Intestinal immune network for IgA production" pathway was enriched in both clusters. Furthermore, a protein-protein interaction (PPI) network of these 2 clusters, along with correlation analysis between microbiota abundance and gene expression, highlighted KEL, SERPING1, CALR, and OSTN as key hub genes. Overall, R. lituseburensis significantly increased the abundance of Jeotgalicoccus, Turicibacter, and Bacillus in the ileum. Concurrently, it might downregulate the "Intestinal immune network for IgA production" pathway in the spleen (CCR9, TNFRSF13B, AICDA) via KEL, SERPING1, CALR, and OSTN, thereby contributing to the reduction of serum immunoglobulin levels. These findings offer new insights into how R. lituseburensis influences immune function in female geese and provide a theoretical basis for further research into its other physiological roles in geese.

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure

Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

Bacitracin Methylene Disalicylate (BMD) Treatment Affects Spleen Proteome in Broiler Chicks Infected with Salmonella enteritidis

Bacitracin Methylene Disalicylate (BMD), as a feed additive to poultry diets, enhances digestion, prevents Salmonella enteritidis (SE) colonization, and treats current infections. The objective of this study was to utilize a quantitative proteomic approach to determine the effect of BMD feed additive on broiler chickens challenged with SE in the spleen proteome. At 1 d of age, chicks were randomly allocated into four groups: control with and without SE challenge (CON, n = 60; CON-SE, n = 60), BMD with and without SE challenge (BMD, n = 60; BMD-SE, n = 60). Birds in the CON-SE and BMD-SE treatment were administered SE inoculum by oral gavage. On day three and day seven post-gavage, the spleen was collected aseptically from birds in each treatment group (CON, n = 4/day; CON-SE, n = 4/day; BMD, n = 4/day; BMD-SE, n = 4/day). Proteomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) showed an increased abundance of 115 proteins and decreased of 77 due to the BMD. Proteins that decreased in abundance were enriched for fibrinogen complex and extracellular space, whereas proteins that increased in abundance were enriched for proteasome-mediated ubiquitin-dependent protein catabolic process and mitochondrion. Analysis of the interaction between BMD and the Salmonella challenge found 230 differentially abundant proteins including proteins associated with RNA binding, spliceosome, protein transport, and cell adhesion among the upregulated proteins, and those associated with protein folding, carbon metabolism, biosynthesis of nucleotide sugars, response to oxidative stress, positive regulation of NIK/NF-kappaB signaling, and inflammatory response among the downregulated proteins. The impact of BMD treatment on spleen proteome indicates an anti-apoptotic effect. BMD also modified the response of the spleen to the SE challenge with a marked decrease in proteins that prompt cytokine synthesis and an increase in proteins involved in the selective removal of unfolded proteins.

The improvement of immunity and activation of TLR2/NF-κB signaling pathway by Romboutsia ilealis in broilers

This study was conducted to investigate the effects of Romboutsia ilealis on the immune function of broilers and the underlying mechanisms. A total of 48 one-day-old Arbor Acres broilers were allocated to 4 groups as follows: broilers treated daily with 1 mL live R. ilealis in general anaerobic medium broth media (0, 1 × 104, 1 × 106, and 1 × 108 CFU/mL) from days 1 to 7. Samples were collected on days 8 and 14. The results showed that R. ilealis had no negative effect on the body weight of broilers (P > 0.05). R. ilealis significantly increased the levels of lysozyme, IFN-γ, IFN-γ/IL-4, and IgG in the serum (P < 0.05). R. ilealis significantly increased the levels of IL-4, IFN-γ, sIgA, lysozyme, and iNOS in the ileal mucosa (P < 0.05). R. ilealis significantly increased the mRNA levels of TLR2, TLR4, NF-κB, IL-1β, TNF-α, IFN-γ, IgA, pIgR, iNOS, and MHC-II in the ileum (P < 0.05). R. ilealis significantly increased the relative abundance of Enterococcus and Paracoccus in the jejunum and ileum, ileal Candidatus Arthromitus, and cecal Romboutsia and Intestinimonas (P < 0.05). Correlation analysis showed that Enterococcus, Paracoccus, Romboutsia, and Intestinimonas were significantly positively correlated with humoral immune function (P < 0.05). In conclusion, R. ilealis boosted the immune system, activated the intestinal TLR2/NF-κB signaling pathway, and improved the gut microbiota in broilers.

Intestinal Damages by F18+Escherichia coli and Its Amelioration with an Antibacterial Bacitracin Fed to Nursery Pigs

This study investigated intestinal oxidative damage caused by F18⁺Escherichia coli and its amelioration with antibacterial bacitracin fed to nursery pigs. Thirty-six weaned pigs (6.31 ± 0.08 kg BW) were allotted in a randomized complete block design. Treatments were: NC, not challenged/not treated; PC, challenged (F18⁺E. coli at 5.2 × 10⁹ CFU)/not treated; AGP challenged (F18⁺E. coli at 5.2 × 10⁹ CFU)/treated with bacitracin (30 g/t). Overall, PC reduced (p < 0.05) average daily gain (ADG), gain to feed ratio (G:F), villus height, and villus height to crypt depth ratio (VH:CD), whereas AGP increased (p < 0.05) ADG, and G:F. PC increased (p < 0.05) fecal score, F18⁺E. coli in feces, and protein carbonyl in jejunal mucosa. AGP reduced (p < 0.05) fecal score and F18⁺E. coli in jejunal mucosa. PC reduced (p < 0.05) Prevotella stercorea populations in jejunal mucosa, whereas AGP increased (p < 0.05) Phascolarctobacterium succinatutens and reduced (p < 0.05) Mitsuokella jalaludinii populations in feces. Collectively, F18⁺E. coli challenge increased fecal score and disrupted the microbiota composition, harming intestinal health by increasing oxidative stress, and damaging the intestinal epithelium, ultimately impairing growth performance. Dietary bacitracin reduced reduced F18⁺E. coli populations and the oxidative damages they cause, thereby improving intestinal health and the growth performance of nursery pigs.

Identification and characterization of the causative agents of Focal Ulcerative Dermatitis in commercial laying hens

Focal Ulcerative Dermatitis (FUDS) is an emerging dermatological disease that affects cage-free laying flocks, it is characterized by the development of a lesion on the dorsum of the birds; FUDS is sporadic in nature and can result in a drop in egg production and up to 50% of cumulative mortality. A total of two cage-free flocks (flock 1: no history of FUDS; flock 2: birds affected with FUDS) from a commercial laying hen operation in the mid-west U.S. were sampled in this study. The microbial composition of skin, cloacal, cecal, and ileal samples from each bird was characterized through next generation sequencing (NGS). Results identified Staphylococcus aureus and Staphylococcus agnetis as the potential causative agents of FUDS, being the most predominant in FUDS positive birds. These results were confirmed by plating, with both staphylococci as the only pathogens isolated from lesions of FUDS positive birds. A total of 68 confirmed Staphylococcus isolates from skin and environmental samples were further analyzed by whole genome sequencing (WGS) for the presence of antimicrobial resistance (AMR) genes and virulence factors that could have contributed to the development of FUDS. Forty-four-point one-two percent of the isolates had between one and four acquired AMR genes encoding for macrolides, lincosamides, spectrogramines, and beta-lactams resistance. Six classes of virulence factors associated with adherence, enzyme, immune evasion, secretion system, toxin, and iron uptake were identified. The antimicrobial effect of 4 proprietary Bacillus Direct Fed Microbial (DFM) combinations was evaluated against the Staphylococcus aureus and Staphylococcus agnetis isolates, by agar well-diffusion (AWD) assay and competitive exclusion (CE) on broth culture. Through this antimicrobial screening, a particular two-strain combination of Bacillus pumilus was identified as the most effective inhibitor of both staphylococci. A customized Bacillus pumilus product is being used at different farms with history of FUDS resulting in the successful inhibition of both Staphylococcus aureus and Staphylococcus agnetis, decreasing FUDS mortalities, and improving harvestable eggs.

Probiotics as a Friendly Antibiotic Alternative: Assessment of Their Effects on the Health and Productive Performance of Poultry

Antibiotics have been used to maintain the overall health of poultry by increasing production efficiency, promoting growth, and improving intestinal function for more than 50 years. However, they have a number of side effects, such as antibiotic resistance, gut dysbiosis, destruction of beneficial bacteria, and the potential to spread diseases to humans. In order to address the aforementioned issues, a lot of effort is put into the development of antibiotic alternatives. One of them is the use of probiotics that can be added to the feed in order to increase poultry performance and avoid the aforementioned problems. Probiotics are live microorganisms consumed as feed additives or supplements. They function in the poultry gastrointestinal tract to benefit the host. Probiotics improve growth performance, bone health, meat and eggshell quality. The addition of probiotics to the diet also positively affects the immune response, intestinal microflora, and disease resistance. Careful selection of probiotic strains is of utmost importance. This review focuses on the significance of probiotics as a potential antibiotic-free alternative and the way in which they can be used as supplements in poultry feed for boosting production and safeguarding health.

How to employ metabolomic analysis to research on functions of prebiotics and probiotics in poultry gut health?

Gut health can be considered one of the major, manageable constituents of the animal immunity and performance. The fast spread of intestinal diseases, and increase of antimicrobial resistance have been observed, therefore the intestinal health has become not only economically relevant, but also highly important subject addressing the interest of public health. It is expected, that the strategies to control infections should be based on development of natural immunity in animals and producing resilient flocks using natural solutions, whilst eliminating antibiotics and veterinary medicinal products from action. Probiotics and prebiotics have been favored, because they have potential to directly or indirectly optimize intestinal health by manipulating the metabolism of the intestinal tract, including the microbiota. Studying the metabolome of probiotics and gut environment, both in vivo, or using the in vitro models, is required to attain the scientific understanding about the functions of bioactive compounds in development of gut health and life lasting immunity. There is a practical need to identify new metabolites being the key bioactive agents regulating biochemical pathways of systems associated with gut (gut-associated axes). Technological advancement in metabolomics studies, and increasing access to the powerful analytical platforms have paved a way to implement metabolomics in exploration of the effects of prebiotics and probiotics on the intestinal health of poultry. In this article, the basic principles of metabolomics in research involving probiotics and probiotics are introduced, together with the overview of existing strategies and suggestions of their use to study metabolome in poultry.

Health in poultry- immunity and microbiome with regard to a concept of one health

The overall concept of OneHealth focuses on health and infectious disease in the context of the relationship between humans, animals, and the environment. In poultry production, there are many opportunities to implement OneHealth by organizing work and introducing appropriate engineering solutions. It is recommended that future research directions include designing and testing solutions to improve air quality and the elimination of antibiotics in the poultry industry. For this to be possible, it is essential to understand the indigenous microbiota of poultry, which plays a crucial role in nutrients, but also restricts the growth of pathogenic organisms. In poultry production, the most important thing is disease control in the herd, high product quality, and product efficiency. Food safety is key for consumers, as some zoonoses are transmitted through the food chain. Moreover, antibiotic resistance of bacteria is becoming a growing threat. For this reason, it is essential to maintain the proper immune status in the herd. Virus disease control in poultry is based on vaccination programs and the maintenance of biosecurity. This chapter aims to present the current state of knowledge in the field of immunity and microbiome of poultry in the context of the OneHealth concept.

Biological units of antimicrobial resistance and strategies for their containment in animal production

The increasing prevalence of antimicrobial resistant bacterial infections has ushered in a major global public health crisis. Judicious or restricted antimicrobial use in animal agriculture, aiming to confine the use for the treatment of infections, is the most commonly proposed solution to reduce selection pressure for resistant bacterial strains and resistance genes. However, a multifaceted solution will likely be required to make acceptable progress in reducing antimicrobial resistance, due to other common environmental conditions maintaining antimicrobial resistance and limited executionary potential as human healthcare and agriculture will continue to rely heavily on antimicrobials in the foreseeable future. Drawing parallels from systematic approaches to the management of infectious disease agents and biodiversity loss, we provide examples that a more comprehensive approach is required, targeting antimicrobial resistance in agroecosystems on multiple fronts simultaneously. We present one such framework, based on nested biological units of antimicrobial resistance, and describe established or innovative strategies targeting units. Some of the proposed strategies are already in use or ready to be implemented, while some require further research and discussion among scientists and policymakers. We envision that antimicrobial resistance mitigation strategies for animal agriculture combining multiple tools would constitute powerful ecosystem-level interventions necessary to mitigate antimicrobial resistance.

Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome

Antimicrobial growth promoters (AGP) have played a decisive role in animal agriculture for over half a century. Despite mounting concerns about antimicrobial resistance and demand for antibiotic alternatives, a thorough understanding of how these compounds drive performance is missing. Here we investigate the functional footprint of microbial communities in the cecum of chickens fed four distinct AGP. We find relatively few taxa, metabolic or antimicrobial resistance genes similarly altered across treatments, with those changes often driven by the abundances of core microbiome members. Constraints-based modeling of 25 core bacterial genera associated increased performance with fewer metabolite demands for microbial growth, pointing to altered nitrogen utilization as a potential mechanism of narasin, the AGP with the largest performance increase in our study. Untargeted metabolomics of narasin treated birds aligned with model predictions, suggesting that the core cecum microbiome might be targeted for enhanced performance via its contribution to host-microbiota metabolic crosstalk.

This study compares the functional profiles of the cecal microbiome among chickens fed four different antimicrobial growth promoters. Chickens receiving narasin exhibited the largest performance increase via apparent nitrogen recycling by the core cecal microbiome.

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys

Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII, kpsIII) or siderophore (iroN, fyuA) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.

Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum

Three novel, anaerobic, Gram-positive bacteria were isolated from the eggshell of two separate white leghorn chicken flocks and the ileum of a healthy pig, and designated MMM721^T, ISU324 and PIG517 respectively. Cells were pleomorphic and capable of forming long chains of rods or coccoid clusters. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains to be within the genus Turicibacter, of which only one species, Turicibacter sanguinis, has been formally described. However, whole genome sequencing of novel isolates returned a digital DNA-DNA hybridization value of 22.5 % and average nucleotide identity (ANI) values of 76.4 % (ANIb) and 86.0 % (ANIm), indicating divergence between the type strain MMM721^T and T. sanguinis, suggesting the strains represented a novel species. The major fatty acid methyl esters of strain MMM721^T were C_16 : 0, C_18 : 1 ω7c and C_18 : 0. The strains mainly produced the volatile fatty acid lactate, along with smaller amounts of acetate and butyrate. Together, these data indicate that MMM721^T, along with ISU324 and PIG517, represent a novel species within the genus Turicibacter. We propose the name Turicibacter bilis sp. nov. for the species. The type strain is MMM721^T (=ATCC TSD-238^T=CCUG 74757^T).

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.

Typhlitis induced by Histomonas meleagridis affects relative but not the absolute Escherichia coli counts and invasion in the gut in turkeys

Unlike in chickens, dynamics of the gut microbiome in turkeys is limitedly understood and no data were yet published in context of pathological changes following experimental infection. Thus, the impact of Histomonas meleagridis-associated inflammatory changes in the caecal microbiome, especially the Escherichia coli population and their caecal wall invasion in turkeys was investigated. Birds experimentally inoculated with attenuated and/or virulent H. meleagridis and non-inoculated negative controls were divided based on the severity of macroscopic caecal lesions. The high throughput amplicon sequencing of 16SrRNA showed that the species richness and diversity of microbial community significantly decreased in severely affected caeca. The relative abundances of operational taxonomic units belonging to Anaerotignum lactatifermentans, E. coli, and Faecalibacterium prausnitzii were higher and paralleled with a decreased abundances of those belonging to Alistipes putredinis, Streptococcusalactolyticus, Lactobacillus salivarius and Lactobacillus reuteri in birds with the highest lesion scores. Although the relative abundance of E. coli was higher, the absolute count was not affected by the severity of pathological lesions. Immunohistochemistry showed that E. coli was only present in the luminal content of caecum and did not penetrate even severely inflamed and necrotized caecal wall. Overall, it was demonstrated that the fundamental shift in caecal microbiota of turkeys infected with H. meleagridis was attributed to the pathology induced by the parasite, which only led to relative but not absolute changes in E. coli population. Furthermore, E. coli cells did not show tendency to penetrate the caecal tissue even when the intestinal mucosal barriers were severely compromised.

Convergence of the turkey gut microbiota following cohabitation under commercial settings

Background

Microbiota development is a critical aspect of turkey poult maturation, and the succession of microbes in the turkey gut has been shown to correlate with poult performance. The purpose of this study was to determine the fate of the microbiota in turkey poults after movement of birds first raised in an isolated hatch brood system into a more traditional commercial brood facility with pre-existing birds. Turkey poults were first divided into groups raised in conventional brood pens from day-of-hatch and those raised in an experimental hatch brood system. After 11 days of growth, hatch brood birds were moved into pens within the conventional brood barn and monitored for an additional 18 days. Sampling of both hatch brood and conventional pen birds was performed at multiple timepoints throughout the study, and cecal content was used to analyze the bacterial microbiota using 16S rRNA gene amplicon sequencing.

Results

Alpha diversity tended to be higher in samples from conventional pen birds compared to those from hatch brood birds prior to the day 11 move, but the difference between systems was not observed post-move. Using beta diversity metrics, bacterial community succession appeared delayed in the hatch brood system birds pre-move, but post-move community composition quickly converged with that of the conventional pen birds. This was validated through assessment of significantly different genera between hatch brood system and conventional pen birds, where numbers of significantly different taxa quickly decreased following the move. Some key taxa previously associated with poult performance were delayed in their appearance and relative abundance in hatch brood birds.

Conclusions

Overall, this study demonstrates that the use of isolated hatch brood systems has an impact on the poult gut microbiota, but its impact is resolved quickly once the birds are introduced into a conventional brood environment. Therefore, the benefits of pathogen reduction with hatch brood systems may outweigh negative microbiota impacts due to isolation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00580-4.

Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions

The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.

Comparative efficacy of spray-dried plasma and bacitracin methylene disalicylate in reducing cecal colonization by Salmonella Enteritidis in broiler chickens

Spray-dried plasma (SDP) contains immunoglobulins and glycoproteins that possess antibacterial properties. Two floor-pen trials were conducted to determine the efficacy of dietary SDP and bacitracin methylene disalicylate (BMD) antibiotic in reducing intestinal colonization by Salmonella Enteritidis (SE) in broiler chickens. Experiment 1 was a 2-wk, 3 × 2 factorial design consisting of 6 treatments. Treatment CON consisted of chicks fed unmedicated corn-soybean meal (SBM) basal without SDP. Treatment BMD consisted of chicks given unmedicated corn-SBM basal into which BMD was added at 0.055g/kg diet. Treatment SDP consisted of chicks given unmedicated corn-SBM basal into which SDP was added at 30g/kg diet. Treatments CON-SE, BMD-SE, and SDP-SE consisted of chicks that were given diets similar to CON, BMD, and SDP, respectively, and were each inoculated with 7.46 × 10⁸ CFU SE /mL at 1 day of age. Experiment 2 was a 42-day trial that was similar to Experiment 1 in design, except that chicks were placed on fresh clean litter. On d 3, 7, 14, and 28 post-challenge (PC), ceca SE concentration was enumerated on xylose lysine tergitol-4 (XLT4) agar. Body weight gain (BWG) and feed conversion ratio (FCR) were also recorded. Results for d 3 showed that BMD- and SDP-fed chicks had similar (P > 0.05) cecal SE (3.39 log ₁₀ CFU / g and 3.58 log ₁₀ CFU / g, respectively), but these levels were lower (P < 0.05) than that of CON-fed chicks (5.68 log ₁₀ CFU / g). A similar trend was observed on d 7 and 14 PC. The BMD- and SDP-fed chicks also had higher BWG and FCR (P < 0.05) when compared with CON-fed chicks up to d 14. Thereafter, only BMD treatment sustained this growth-promoting effect till d 42 in SE-challenged birds. In conclusion, BMD and SDP showed similar efficacy in reducing cecal Salmonella and in mitigating consequent growth-depressing effect(s) in broiler chicks up to 2 wk of age.

A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni

The symptoms of infectious diarrheal disease are mediated by a combination of a pathogen's virulence factors and the host immune system. Campylobacter jejuni is the leading bacterial cause of diarrhea worldwide due to its near-ubiquitous zoonotic association with poultry. One of the outstanding questions is to what extent the bacteria are responsible for the diarrheal symptoms via intestinal cell necrosis versus immune cell initiated tissue damage. To determine the stepwise process of inflammation that leads to diarrhea, we used a piglet ligated intestinal loop model to study the intestinal response to C. jejuni. Pigs were chosen due to the anatomical similarity between the porcine and the human intestine. We found that the abundance of neutrophil related proteins increased in the intestinal lumen during C. jejuni infection, including proteins related to neutrophil migration (neutrophil elastase and MMP9), actin reorganization (Arp2/3), and antimicrobial proteins (lipocalin-2, myeloperoxidase, S100A8, and S100A9). The appearance of neutrophil proteins also corresponded with increases of the inflammatory cytokines IL-8 and TNF-α. Compared to infection with the C. jejuni wild-type strain, infection with the noninvasive C. jejuni ∆ciaD mutant resulted in a blunted inflammatory response, with less inflammatory cytokines and neutrophil markers. These findings indicate that intestinal inflammation is driven by C. jejuni virulence and that neutrophils are the predominant cell type responding to C. jejuni infection. We propose that this model can be used as a platform to study the early immune events during infection with intestinal pathogens.

Probiotics in poultry feed: A comprehensive review

The use of antibiotics to maintain animal well-being, promote growth and improve efficiency has been practised for more than 50 years. However, as early as the 1950s, researchers identified concern on the development of resistant bacteria for the antibiotics streptomycin and tetracycline used in turkeys and broilers respectively. These findings laid the groundwork for agricultural officials to impose stricter regulatory parameters on the use of antibiotics in poultry feeds. Probiotics are live micro-organisms included in the diet of animals as feed additives or supplements. Commonly known as a direct-fed microbial, probiotics provide beneficial properties to the host, primarily through action in the gastrointestinal tract (GIT) of the animal. Supplementation of probiotics in the diet can improve animal health and performance, through contributions to gut health and nutrient use. For instance, supplementation of probiotics has been demonstrated to benefit farm animals in immune modulation, structural modulation and increased cytokine production, which positively affect the intestinal mucosal lining against pathogens. Bacillus subtilis has been a popular bacterium used within the industry and was shown to improve intestinal villus height. Increasing the villus height and structure of the crypts in the GIT allows for the improvement of nutrient digestion and absorption. Tight junctions maintain important defences against pathogenic bacteria and cellular homeostasis. Heat stress can be a major environmental challenge in the poultry industry. Heat stress causes the bird to fluctuate its internal core temperature beyond their comfort zone. To overcome such challenges, poultry will attempt to balance its heat production and dissipation through behavioural and physiological adaptation mechanisms.

Complete Genome Sequence and Annotation for Turicibacter sanguinis MOL361T (DSM 14220)

Turicibacter sanguinis MOL361 (DSM 14220) is the reference and type strain for the Turicibacter genus, commonly found in the intestinal tract of animal species. Long-read sequencing was performed on this strain to complement publicly available Illumina HiSeq-based data, producing a complete annotated genome sequence.

Turicibacter sanguinis MOL361 (DSM 14220) is the reference and type strain for the Turicibacter genus, commonly found in the intestinal tract of animal species. Long-read sequencing was performed on this strain to complement publicly available Illumina HiSeq-based data, producing a complete annotated genome sequence.

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens

Background

The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell- and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch.

Results

Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well.

Conclusion

We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshell-only birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut. Further studies should explore the ability of eggshell- and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.

Complete Genome Sequence and Annotation for Romboutsia sp. Strain CE17

Here, we describe the complete genome sequence of Romboutsia sp. strain CE17, which was isolated during a screen for spore-forming anaerobic microorganisms that colonized the surface of chicken eggs.

Probiotics in Animal Husbandry: Applicability and Associated Risk Factors

Probiotics have been emerging as a safe and viable alternative to antibiotics for increasing performance in livestock. Literature was collated via retrieved information from online databases, viz, PubMed, MEDLINE, ScienceDirect, Scopus, Web of Science and Google Scholar. Besides improved immunomodulation and nutrient digestibility, in-feed probiotics have shown drastic reductions in gastrointestinal tract-invading pathogens. However, every novel probiotic strain cannot be assumed to share historical safety with conventional strains. Any strain not belonging to the wild-type distributions of relevant antimicrobials, or found to be harbouring virulence determinants, should not be developed further. Modes of identification and the transmigration potential of the strains across the gastrointestinal barrier must be scrutinized. Other potential risk factors include the possibility of promoting deleterious metabolic effects, excessive immune stimulation and genetic stability of the strains over time. Adverse effects of probiotics could be strain specific, depending on the prevailing immunological and physiological condition of the host. The most crucial concern is the stability of the strain. Probiotics stand a good chance of replacing antibiotics in animal husbandry. The possibility of the probiotics used in animal feed cross-contaminating the human food chain cannot be downplayed. Thus, the established safety measures in probiotic development must be adhered to for a successful global campaign on food safety and security.

The Microbial Pecking Order: Utilization of Intestinal Microbiota for Poultry Health

The loss of antibiotics as a tool to improve feed efficiency in poultry production has increased the urgency to understand how the microbiota interacts with animals to impact productivity and health. Modulating and harnessing microbiota-host interactions is a promising way to promote poultry health and production efficiencies without antibiotics. In poultry, the microbiome is influenced by many host and external factors including host species, age, gut compartment, diet, and environmental exposure to microbes. Because so many factors contribute to the microbiota composition, specific knowledge is needed to predict how the microbiome will respond to interventions. The effects of antibiotics on microbiomes have been well documented, with different classes of antibiotics having distinctive, specific outcomes on bacterial functions and membership. Non-antibiotic interventions, such as probiotics and prebiotics, target specific bacterial taxa or function to enhance beneficial properties of microbes in the gut. Beneficial bacteria provide a benefit by displacing pathogens and/or producing metabolites (e.g., short chain fatty acids or tryptophan metabolites) that promote poultry health by improving mucosal barrier function or immune function. Microbiota modulation has been used as a tool to reduce pathogen carriage, improve growth, and modulate the immune system. An increased understanding of how the microbiota interacts with animal hosts will improve microbiome intervention strategies to mitigate production losses without the need for antibiotics.