Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome

Full-length 16S rRNA sequencing revealed an altered microbiome diversity and composition of the jejunum and cecum in chicken infected with Eimeria necatrix

Avian coccidiosis is an intestinal parasitic disease introduced by Eimeria spp., causing a major economic loss in the world poultry industry. Eimeria necatrix is the most pathogenic species that causes acute coccidiosis in chickens, leading to high mortality. Studies have shown that disruption of the gut environment due to Eimeria infection causes an imbalance in intestinal homeostasis. However, changes in the intestinal microbiota of chickens infected with E. necatrix remain unclear. In the present study, we performed full-length 16S ribosomal RNA amplicon sequencing to assess the effects of E. necatrix infection on jejunal and cecal microbiota at 4 and 10 days post-infection (dpi). The results showed that in both the infected and not infected groups at both time points, the most abundant phyla were Firmicutes, Proteobacteria and Bacteroidetes in the jejunum, and Firmicutes, Bacteroidetes and Proteobacteria in the cecum. The most common genera in the jejunum were Lactobacillus, Limosilactobacillus and Ligilactobacillus at 4 dpi, and Lactobacillus, Limosilactobacillus and Enterococcus in the infected group, and Lactobacillus, Limosilactobacillus and Streptococcus in the control group at 10 dpi. In the cecum, the most common genera were Phocaeicola, Lactobacillus and Alistipes at 4 dpi, and Lactobacillus, Phocaeicola and Alistipes in the infected group, and Lactobacillus, Phocaeicola and Bacteroides in the control group at 10 dpi. A total of 1528 species was annotated, and differences in relative abundance at the species level were analyzed using Lefse method. The results showed that the relative abundance of 23 species, including Acetilactobacillus jinshanensis, Anaerotruncus colihominis, Bacteroides heparinolyticus, Bacteroides ndongoniae, Bariatricus comes, Bifidobacterium gallinarum, Blautia coccoides, Butyricimonas paravirosa, Caproiciproducens galactitolivorans, Clostridioides difficile, Enterococcus cecorum, Escherichia coli, Intestinimonas timonensis, Lachnoanaerobaculum umeaense, Lactobacillus acetotolerans, Ligilactobacillus aviarius, Ligilactobacillus aviarius _B, Limosilactobacillus oris, Limosilactobacillus vaginalis, Megamonas funiformis, Plesiomonas shigelloides, Streptococcus pneumoniae, and Veillonella denticariosi, were significantly different between the infected and not infected groups. Our data reveal that E. necatrix infenction disrupts the integrity of gut microbiota, potentially promoting the establishment and growth of pathogenic bacteria; some species such as Bariatricus comes and Ligilactobacillus aviarius_B may be associated with the pathogenicity of the coccidian parasite and recovery of coccidiosis.

Impact of dietary polyphenols from shredded, steam-exploded pine on growth performance, organ indices, meat quality, and cecal microbiota of broiler chickens

The chicken's gastrointestinal tract is home to complex and diverse microbial communities that can be manipulated to enhance health and productivity. Although polyphenols have recently attracted the attention of researchers due to their potent antioxidant capabilities, their impact on the gut microbiota remains largely unexplored. Hence, in this study, we conducted a comprehensive analysis of the effects of dietary supplementation with polyphenol-rich extract from shredded, steam-exploded pine particles (PSPP) on growth, meat quality, and gut microbial dynamics in broiler chickens. Supplementation of PSPP was found to significantly improve birds' FCR until the third week of the trial but only marginally affected meat quality. Based on metataxonomic analyses of the cecal microbiotas of broilers fed increasing concentrations of PSPP, dietary PSPP modulated the composition of the cecal microbiota of the birds with a concomitant increase of Bacteroidetes and a decrease in the Firmicutes population. Similar trends were observed for the proportions of Alistipes and Faecalibacterium at the genus level. Additionally, 43 unique bacterial species were detected in the cecal microbiome of birds fed with PSPP. However, microbial diversity did not vary significantly among treatment groups. A particularly interesting finding was the specialization observed in the microbiome of birds receiving PSPP supplementation. Microbial co-occurrence network analyses revealed substantial modifications in their network structure when compared to control birds. Families like Rikenellaceae and Eubacteriaceae were notably absent, and the number of microbial interactions was drastically lower in the PSPP-fed group. Microbial taxa modeling revealed that the impact of increasing dietary PSPP levels primarily affected genus-level taxa, showing a decreasing trend. Overall, this offers compelling evidence that continuous PSPP supplementation may not only alter the composition of intestinal microbes but also have a profound effect on the interactions among different microbial species. Conversely, PSPP had minimal effects on broilers' performance and meat quality.

Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?

Bacteria are the major component of poultry gastrointestinal tract (GIT) microbiota and play an important role in host health, nutrition, physiology regulation, intestinal development, and growth. Bacterial community profiling based on the 16S ribosomal RNA (rRNA) gene amplicon sequencing approach has become the most popular method to determine the taxonomic composition and diversity of the poultry microbiota. The 16S rRNA gene profiling involves numerous steps, including sample collection and storage, DNA isolation, 16S rRNA gene primer selection, Polymerase Chain Reaction (PCR), library preparation, sequencing, raw sequencing reads processing, taxonomic classification, α- and β-diversity calculations, and statistical analysis. However, there is currently no standardized protocol for 16S rRNA gene analysis profiling and data deposition for poultry microbiota studies. Variations in DNA storage and isolation, primer design, and library preparation are known to introduce biases, affecting community structure and microbial population analysis leading to over- or under-representation of individual bacteria within communities. Additionally, different sequencing platforms, bioinformatics pipeline, and taxonomic database selection can affect classification and determination of the microbial taxa. Moreover, detailed experimental design and DNA processing and sequencing methods are often inadequately reported in poultry 16S rRNA gene sequencing studies. Consequently, poultry microbiota results are often difficult to reproduce and compare across studies. This manuscript reviews current practices in profiling poultry microbiota using 16S rRNA gene amplicon sequencing and proposes the development of guidelines for protocol for 16S rRNA gene sequencing that spans from sample collection through data deposition to achieve more reliable data comparisons across studies and allow for comparisons and/or interpretations of poultry studies conducted worldwide.

Application of Artificial Gastrointestinal Tract Models in Veterinary Medicine

Artificial gastrointestinal tract models have become essential tools in veterinary medicine, providing alternatives to in vivo studies, which are labor-intensive, costly, and under certain circumstances even ethically challenging. These in vitro models facilitate the study of digestion, enable disease and host-pathogen interaction modeling, and allow for the investigation of nutrient absorption, microbiota, and pharmacokinetics. Considering the One Health concept, the application of gastrointestinal tract systems in investigations for animals can clearly reflect human health, and thus, it is pointing to the relevance of the adaptation of already existing models and the development of new models to meet the needs of veterinary and animal farming practices. This review explores and compares the various types of gastrointestinal tract models, including static and dynamic systems, and their applications across different animal species. Specific technical and methodological considerations are discussed for core animal-developed and -tested artificial systems and their integration with common 'omics' techniques. Dynamic models, such as RUSITEC and PolyFermS, more accurately simulate in vivo processes, including peristalsis, enzymatic activity, and microbial fermentation. The studies employing tools for 'omics' approaches have been conducted with more understanding analysis and comprehensive discussion and results.

Exposure of broiler chickens to deoxynivalenol and Campylobacter jejuni induces substantial changes in intestinal gene expression

The mycotoxin deoxynivalenol (DON) is of high importance among feed contaminants because of its frequent occurrence in toxicologically relevant concentrations worldwide. Cereal crops, the main component of chicken diet, are commonly contaminated with DON, resulting in frequent exposure of chickens to DON. Likewise, Campylobacter (C.), a pathogen of major public and animal health concern, is frequently found in chicken flocks and poses a threat to the One Health approach. Campylobacter colonizes the gastrointestinal (GI) tract of poultry with a high bacterial load in the caeca. However, the mechanism of C. jejuni colonization in chickens is still not understood albeit it is well known that C. jejuni resides primarily in the mucosal layer of the chicken intestine. Therefore, in the actual study we focused on the effect of exposure to DON and/or C. jejuni on expression profiles of intestinal mucins (MUC1, MUC2), β-defensins (Gallinacin (GAL) 10, 12), cytokines (Toll-like receptor 2 (TLR2), Interleukin (IL) 6, 8, Interferon-γ (IFN)-γ), inducible nitric oxide synthase 2 (iNOS2), as well as selected tight junction proteins (Claudin 5 (CLDN5), Occludin (OCLN), and zonula occludens-1 (ZO1) via RT-qPCR. For this, a total of 150 one-day-old Ross 308 broiler chickens were randomly allocated to six different groups (n = 25 with 5 replicates/group) and were fed for 5 weeks with either contaminated diets (5 or 10 mg DON/kg feed) or basal diets (control). Following oral infection of birds with C. jejuni NCTC 12744 at 14 days of age, several changes in gene expression patterns were demonstrated. A significant (P ≤ 0.05) downregulation of MUC2 mRNA expression was observed in birds fed DON5 and DON10 diet, as well as in birds co-exposed to DON5 and C. jejuni at 7 dpi. Furthermore, at 14 dpi, MUC2 mRNA expression was significantly (P ≤ 0.05) downregulated in birds fed DON (5 mg and 10 mg/kg diet) with and without C. jejuni and in birds infected solely with C. jejuni. The actual study also demonstrated that co-exposure of broiler chickens to DON and C. jejuni resulted in a decreased barrier function via downregulation of OCLD mRNA expression. In addition, Campylobacter infection induced an increased expression of the antimicrobial peptide GAL12 and the IL8 gene, indicating that C. jejuni can initiate an immune response in the chicken gut in a proinflammatory manner. Similarly, DON with and without C. jejuni induced upregulation of GAL10 and GAL12 mRNA expression at 7 dpi. Moreover, no change in iNOS2 mRNA expression was observed in both the jejunum and the cecum at either 7 dpi or 14 dpi, suggesting unchanged NO production during exposure/infection. In conclusion, we confirmed that DON contamination corresponding to the currently applicable EU guidance value of 5 mg DON/kg feed affects the intestinal gene expression profiles of broilers, mainly in a dose-independent manner. Furthermore, DON exposure interacted synergistically with C. jejuni challenge regarding mucins, innate immunity gene expression in either the jejunum or the cecum, suggesting immunomodulatory activity of both foodborne agents (DON and C. jejuni).

Deep culturing the fecal microbiota of healthy laying hens

BACKGROUND

The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS

In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS

Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.

Probiotics/prebiotics effect on chicken gut microbiota and immunity in relation to heat-stress and climate-change mitigation

Heat stress is a serious hazard that threatens world poultry production. The avian gut microbiome plays a critical role in improving nutrient utilization, competing with pathogens, stimulating an immune response, and reducing inflammatory reactions. Hence, the gut microbiome has a positive impact on the host's health which appears in the shape of improved body weight, feed conversion rate, and increased birds' productivity (meat or eggs). Accordingly, this review shed light on the chicken gut microbiome, its correlation with the immunity of chicken, and how this affects the general health condition of the bird as well as, the role of prebiotics and probiotics in improving the gut health and increasing birds' productivity, especially under climate change and heat stress condition. The review aims to focus on the significance of maintaining healthy chickens in order to increase the production of poultry meat to satisfy human needs. A robust microbiota and a well-functioning immune system synergistically contribute to the optimal health and productivity of chickens.

Alternatives to antibiotics against coccidiosis for poultry production: the relationship between immunity and coccidiosis management – a comprehensive review

Avian coccidiosis is a protozoan infection caused by numerous Eimeria parasitic species and mainly affects the bird’s gastrointestinal tract and results in a reduction of the bird ‘ability to absorb nutrients, slower growth, with a higher mortality rate. According to recent research, immune-based treatments, such as dietary immunomodulating feed additives and recombinant vaccines, can help the hosts protect themselves from intracellular parasites and reduce inflammatory reactions caused by parasites. Coccidiosis control in the post-antiparasitic stage requires thoroughly investigation of the intricate relationships between the parasites, host defense system, enteroendocrine system, and gut microbiome contributing to coccidian infections. To produce a vaccine, it is crucial to explore the defense mechanism of the intestine’s immune machinery and to identify many effector molecules that act against intracellular parasites. Due to the massive usage of chemical anticoccidial drugs, coccidiosis developed resistant against most commonly used anticoccidials; therefore, numerous researches focused on the usage of safe natural anticoccidials such as probiotics, prebiotics, organic acids, and essential oils to counteract such resistance problem. This review describes how host immunity responds to coccidial infection in chickens and the use of some nonantiparasitic safe natural alternative controls to counter the disease. It would throw the light on the possibility of developing effective therapies against Eimeria to alleviate the detrimental effects of avian coccidiosis.

Enhancing poultry health and productivity through the liver-gut axis with integrated nutritional and immunological approaches: a mini-review

The liver-gut axis plays a central role in maintaining the health and productivity of poultry. In addition, the liver-gut axis serves as a key regulator of digestion, metabolism, immunity, and detoxification. The gut, with its diverse microbiota, is the primary site for nutrient absorption and immune modulation, while the liver metabolizes nutrients, detoxifies harmful substances, and acts as a frontline defense against pathogens translocated from the gut. Disruptions in this interconnected system, including gut dysbiosis or liver inflammation, can lead to compromised immunity and reduced productivity. This mini-review explores integrated nutritional and immunological strategies aimed at optimizing the liver-gut axis to enhance poultry performance. Nutritional interventions, such as the use of flavonoids, vitamins, amino acids, micronutrients, probiotics, prebiotics, and synbiotics, have demonstrated their potential to support liver and gut health. Dietary components such as phytogenic additives, fiber, and fatty acids further contribute to immune modulation and systemic health. Immunological approaches, such as beta-glucans and in ovo stimulation, and molecular approaches, including advanced genetic techniques, offer additional avenues for improving disease resistance and organ function. Despite notable advancements, challenges including antibiotic resistance, environmental stressors, and implementation costs persist. Emerging technologies like metagenomics, metabolomics, and precision breeding offer innovative solutions to enhance liver-gut interactions. This review underscores recent advancements in understanding the liver-gut axis and calls for holistic strategies to improve sustainable poultry production. Future research should integrate these approaches to enhance resilience, productivity, and sustainability in the poultry industry.

Impact of gut microbial diversity on egg production performance in chickens

Chickens are one of the most economically important poultry species, and their egg-laying performance is a crucial economic trait. The intestinal microbiome plays a significant role in the egg-laying performance. To clarify the diversity of chicken intestinal microbiota and its connection to egg-laying performance, this study utilized 16S rRNA sequencing technology to characterize the intestinal microbiomes of 101 chickens from 13 breeds with varying levels of egg production. The results reveal significant differences in gut microbiota structure among chicken groups with varying egg production levels. High egg-producing chickens showed significantly higher abundances of Firmicutes, Proteobacteria, and Lactobacillus, while low egg-producing chickens displayed greater microbial α-diversity and more complex community structures. These differences in gut microbiota influence key physiological functions, including nutrient absorption and hormone regulation through metabolic pathways, and directly affect egg production performance. The low and medium production groups partially overlapped on the principal coordinates analysis plot, whereas the high-production group was distinctly separate. This study provides a scientific basis and intestinal microbiome data for selecting probiotics related to high egg production in chickens.

IMPORTANCE

This study elucidates the critical role of gut microbiota in the egg-laying performance of chickens, a key economic indicator in the poultry industry. By employing 16S rRNA sequencing, we uncovered distinct microbial profiles associated with varying levels of egg production. High egg-producing chickens exhibit a higher abundance of specific bacterial taxa, such as Firmicutes and Proteobacteria, which are linked to enhanced nutrient absorption and metabolic efficiency. Conversely, lower and medium egg-producing chickens display greater microbial diversity, suggesting a more complex but less efficient gut ecosystem. Our findings provide valuable insights into the relationship between gut microbiota and egg production, offering a scientific foundation for the selection of probiotics that could potentially improve the egg-laying performance of chickens. This research not only advances our understanding of avian gut microbiology but also has practical implications for optimizing poultry farming practices and enhancing economic outcomes.

Optimizing male layer chicken performance and health with probiotic supplementation: A sustainable alternative to antibiotic growth promoters

Background

The rising global concern over antibiotic resistance has heightened scrutiny of antibiotic growth promoters (AGPs) in poultry farming, prompting a shift toward alternative feed additives to ensure sustainable and safe poultry production. This trend aligns with the increasing demand for free-range and naturally raised chicken meat in various regions, including Indonesia. In response, Indonesian breeders have turned to medium-sized male layer chickens (MLCs) as substitutes for traditional free-range chickens. This practice, coupled with the need to replace AGPs, highlights the critical importance of exploring innovative and natural solutions to enhance poultry growth and health.

Aim

This study investigated the effects of probiotics as an alternative to AGPs on the growth performance, carcass traits, and immune organs of male ISA Brown layer chickens.

Methods

The 180-day-old male ISA Brown layer chickens were used for the study. The intervention included six treatments. T1 basal feed, T2 2.5 g AGP/kg feed, T3 1 ml probiotic/kg feed, T4 3 ml probiotic/kg feed, T5 4 ml probiotic/kg feed, and T6 5 ml probiotic/kg feed. Probiotics used were Lactobacillus acidophilus, Bifidobacterium sp., and Lactobacillus plantarum at a concentration of 1.2 × 109 CFU/ml. The feeding trial lasted for 21 days for chickens aged 21-42 days, assessing growth performance [body weight, feed consumption, digestibility, and feed conversion ratio (FCR)], carcass traits, non-edible organs, and immune organs.

Results

The findings demonstrate that probiotic supplementation significantly outperformed the AGP-treated group (T2) in enhancing growth performance, carcass weight, pectoral weight development, FCR, internal and immune organ weights, nutrient intake, and digestibility. While AGPs showed improvements over the control (T1), probiotic- supplemented groups, particularly T6, achieved superior results across all parameters, indicating that probiotics are not only a viable alternative to AGPs but also a more effective and sustainable approach for poultry production.

Conclusion

The probiotics used in the study at 4 and 5 ml/kg of feed significantly enhanced the performance, immune organ development, and carcass attributes of MLCs, demonstrating their effectiveness as a viable alternative to AGPs. These findings highlight the potential of probiotics to improve poultry production sustainability by reducing reliance on antibiotics, enhancing growth and health outcomes, and promoting animal welfare through natural and efficient dietary interventions.

Impact of Chlorella vulgaris and probiotic supplementation on performance, immunity and intestinal microbiota of broiler chickens

Chlorella vulgaris has antioxidant, antimicrobial, and anti-inflammatory properties, as well as the probiotic that is important for keeping the intestinal microbiota balanced. The objective was to test the impact of supplementation with microalgae and/or probiotics on broiler chickens' performance, immunity, and intestinal microbiota. The experimental design was in randomized blocks in a 4x2 factorial scheme, with four levels of inclusion of C. vulgaris (0; 0.25; 0.50 and 1%) associated or not with a commercial probiotic with five replications of 26 chickens per experimental unit. The results showed that probiotics improved feed conversion. Probiotics increased the productivity index only at 0.25% C. vulgaris supplementation. There was a reduction in spleen weight at 42 days of age in chickens fed with probiotics, but the different treatments did not alter serum antibodies. Sampling age had a significant impact on richness addressed by the number of observed genera and diversity addressed by the Shannon index. The most abundant phylum in the chicken intestinal tract was Firmicutes followed by Bacteroidetes and Proteobacteria. Bifidobacterium spp. was found in animals receiving 1% microalgae and probiotics on day 42, suggesting that this genus has benefited from microalgae supplementation. It is concluded that the probiotic and C. vulgaris have the potential to improve performance without causing major changes in the immunity and cecal microbiota.

Insights into the gut microbiota characteristics between the organic and traditional feeding chickens based on amplicon and metagenomic sequencing

Intestinal microorganisms play a crucial role in chicken health and production performance, especially in the research of traditional and organic feeding methods. The intestinal contents of organic and feed chickens were analyzed by 16S rRNA gene and metagenome technology. The results showed that the microbial diversity of organic chickens was significantly higher than that of the feed chickens, especially the key microorganisms, such as Enterococcus, were more abundant in organic chickens. The functional analysis of metagenome revealed the significant difference in the metabolic function of intestinal microorganisms between them. The present study provides new insights into the gut microbiota characteristics of the organic and feed chicken based on amplicon and metagenomic sequencing. Our results are helpful to fully illustrate the effects of different feeding methods on intestinal microorganisms in chickens and can offer a more scientific basis for chicken production management.

Decoding the chicken gastrointestinal microbiome

Metataxonomic studies have underpinned a vast understanding of microbial communities residing within livestock gastrointestinal tracts, albeit studies have often not been combined to provide a global census. Consequently, in this study we characterised the overall and common 'core' chicken microbiota associated with the gastrointestinal tract (GIT), whilst assessing the effects of GIT site, bird breed, age and geographical location on the GIT resident microbes using metataxonomic data compiled from studies completed across the world. Specifically, bacterial 16S ribosomal DNA sequences from GIT samples associated with various breeds, differing in age, GIT sites (caecum, faeces, ileum and jejunum) and geographical location were obtained from the Sequence Read Archive and analysed using the MGnify pipeline. Metataxonomic profiles produced across the 602 datasets illustrated the presence of 3 phyla, 25 families and 30 genera, of which core genera (defined by presence in over 90% of datasets) belonged to Lactobacillus, Faecalibacterium, Butyricicoccus, Eisenbergiella, Subdoligranulum, Oscillibacter, Clostridium & Blautia. PERMANOVA analysis also showed that GIT site, bird breed, age and geographical location all had a significant effect on GIT microbial diversity, regardless of dietary factors, which were not considered in this study. On a genus level, Faecalibacterium was most abundant in the caeca, Lactobacillus was most abundant in the faeces, ileum and jejunum, with the data showing that the caeca and faeces were most diverse. AIL F8 progeny, Ross 308 and Cobb 500 breeds GIT bacteria were dominated by Lactobacillus, and Eisenbergiella, Megamonas and Bacteroides were most abundant amongst Sasso-T451A and Tibetan chicken breeds. Microbial communities within each GIT site develop with age, from a Lactobacillus and Streptococcus dominated community during the earlier stages of growth, towards a Faecalibacterium, Eisenbergiella, Bacteroides, Megamonas, and Lactobacillus dominated community during the later stages of life. Geographical locations, and thus environmental effectors, also impacted upon gastrointestinal tract microbiota, with Canadian and European datasets being dominated by Lactobacillus, whilst UK and Chinese datasets were dominated by Eisenbergiella and Bacteroides respectively. This study aids in defining what 'normal' is within poultry gastrointestinal tract microbiota globally, which is imperative to enhancing the microbiome for productive and environmental improvements.

Impact of Chlorella sorokiniana feed additive on poultry growth health and oxidative stress in erythrocytes

Microalgae, have emerged as a potentially promising feed additive option due to their beneficial nutritional profile rich in bioactive compounds. The present study examines the incorporation of Chlorella sorokiniana (at 0.1% and 1%) into chicken feed compared to control feed and its effect on growth and health parameters of poultry grown at pilot plant scale. Growth performance parameters (weight, feed conversion ratio (FCR), mortality, European Production Efficiency Index (EPEF)) and the immune system response are examined. In addition, it examines well-being gut health and nutrient absorption related variables via macroscopical and histological analysis. Finally, red blood cell (RBC) morphology and oxidative stress parameters (reactive oxygens species (ROS) and malondialdehyde level) in the whole blood as well as the lipid profile of the adipose tissue are determined. Addition of Chlorella sorokiniana at 0.1% resulted improved growth performance parameters whereas the ROS levels were significantly decreased indicating reduced oxidative stress. Finally, the results of histological analyses of the intestine on parameters related to nutrient absorption correlated with the results on growth performance. On the other hand, addition Chlorella sorokiniana at 1% did not affect significantly the growth performance parameters, resulted in increased footpad dermatitis, increased oxidative stress and alterations in RBC.

Effects of antibiotic growth promoter and its natural alternative on poultry cecum ecosystem: an integrated analysis of gut microbiota and host expression

Background

In-feed antibiotic growth promoters (AGPs) have been a cornerstone in the livestock industry due to their role in enhancing growth and feed efficiency. However, concerns over antibiotic resistance have driven a shift away from AGPs toward natural alternatives. Despite the widespread use, the exact mechanisms of AGPs and alternatives are not fully understood. This necessitates holistic studies that investigate microbiota dynamics, host responses, and the interactions between these elements in the context of AGPs and alternative feed additives.

Methods

In this study, we conducted a multifaceted investigation of how Bacitracin, a common AGP, and a natural alternative impact both cecum microbiota and host expression in chickens. In addition to univariate and static differential abundance and expression analyses, we employed multivariate and time-course analyses to study this problem. To reveal host-microbe interactions, we assessed their overall correspondence and identified treatment-specific pairs of species and host expressed genes that showed significant correlations over time.

Results

Our analysis revealed that factors such as developmental age substantially impacted the cecum ecosystem more than feed additives. While feed additives significantly altered microbial compositions in the later stages, they did not significantly affect overall host gene expression. The differential expression indicated that with AGP administration, host transmembrane transporters and metallopeptidase activities were upregulated around day 21. Together with the modulated kininogen binding and phenylpyruvate tautomerase activity over time, this likely contributes to the growth-promoting effects of AGPs. The difference in responses between AGP and PFA supplementation suggests that these additives operate through distinct mechanisms.

Conclusion

We investigated the impact of a common AGP and its natural alternative on poultry cecum ecosystem through an integrated analysis of both the microbiota and host responses. We found that AGP appears to enhance host nutrient utilization and modulate immune responses. The insights we gained are critical for identifying and developing effective AGP alternatives to advance sustainable livestock farming practices.

Metagenomic Analysis Reveals the Complex Microbial Landscape of Market Chicken Meat

The safety of meat from a microbiological standpoint is of paramount concern to public health, given the potential for bacterial contaminants to grow and persist during processing and storage. To address this issue, a culture-independent approach targeting the V3-V4 region of the 16S rRNA gene was utilized to investigate the inherent bacterial communities present in 10 chicken meat samples obtained from retail markets. Amplicons were sequenced using the Illumina MiSeq platform, and unique amplicon sequence variants (ASVs) were identified using the DADA2 pipeline. Results indicated the presence of 5 phyla, 7 classes, 16 orders, 33 families, 59 genera, and 273 unique ASVs. The dominant families were Flavobacteriaceae, Moraxellaceae, Enterobacteriaceae, Wohlfahrtiimonadaceae, Morganellaceae, and Pseudomonadaceae, comprising 27.03, 22.04, 15.67, 9.40, 7.92, and 5.02% of the identified families, respectively. Functional analysis using PICRUSt showed a diverse range of functional pathways. These findings have significant implications for policymaking regarding food safety and public health. Regular monitoring of bacterial communities in meat products is crucial to ensure their safety for consumption. This study demonstrates the utility of culture-independent approaches in characterizing microbial communities, which can provide valuable information for ensuring food safety and safeguarding public health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01249-y.

Research advancements on the diversity and host interaction of gut microbiota in chickens

The maintenance of host health and immune function is heavily dependent on the gut microbiota. However, the precise contribution of individual microbial taxa to regulating the overall functionality of the gut microbiome remains inadequately investigated. Chickens are commonly used as models for studying poultry gut microbiota, with high-throughput 16S rRNA sequencing has emerged as a valuable tool for assessing both its composition and functionality. The interactions between the gut's microbial community and its host significantly influence health outcomes, disease susceptibility, and various mechanisms affecting gastrointestinal function. Despite substantial research efforts, the dynamic nature of this microbial ecosystem has led to inconsistencies in findings related to chicken gut microbiota, which is largely attributed to variations in rearing conditions. Consequently, the interaction between the chickens' gut microflora and its host remains inadequately explored. This review highlights recent advances in understanding these relationships, with a specific focus on microbial composition, diversity, functional mechanisms, and their potential implications for improving poultry production.

Temporal Changes in Jejunal and Ileal Microbiota of Broiler Chickens with Clinical Coccidiosis (Eimeria maxima)

Coccidiosis in broiler chickens continues to be a major disease of the gastrointestinal tract, causing economic losses to the poultry industry worldwide. The goal of this study was to generate a symptomatic Eimeria maxima (1000 oocysts) infection to determine its effect on the luminal and mucosal microbiota populations (L and M) in the jejunum and ileum (J and IL). Samples were taken from day 0 to 14 post-infection, and sequencing of 16S rRNA was performed using Illumina technology. Infected birds had significantly (p < 0.0001) lower body weight gain (BWG), higher feed conversion ratio (FCR) (p = 0.0015), increased crypt depth, and decreased villus height (p < 0.05). The significant differences in alpha and beta diversity were observed primarily at height of infection (D7). Analysis of taxonomy indicated that J-L and M were dominated by Lactobacillus, and in IL-M, changeover from Candidatus Arthromitus to Lactobacillus as the major taxon was observed, which occurred quicky in infected animals. LEfSe analysis found that in the J-M of infected chickens, Lactobacillus was significantly more abundant in infected (IF) chickens. These findings show that E. maxima infection affects the microbiota of the small intestine in a time-dependent manner, with different effects on the luminal and mucosal populations.

Microbial community profiling in intestinal tract of indigenous chickens from different villages

Village chickens (Gallus gallus domesticus) are commonly reared in rural households of South Africa and other developing countries. They play a vital role as a primary source of protein through the provision of meat and eggs. The chicken gut microbiota plays an important role in chicken's immune system, its health, physiological development of the gut, digestion of food, nutrient absorption and productivity. Thus, it is imperative to critically investigate the chicken microbial composition in order to develop effective disease control measures and increase production. In this present study, microbial DNA was isolated from 34 non-descript mixed gender matured village chickens' intestinal contents followed by high throughput Illumina sequencing targeting 16S rRNA gene. Senwamokgope village had the largest microbiota composition as compared to Itieleni and Thakgalang villages. Overall, Firmicutes (74%) was the most abundant phylum observed, followed by Proteobacteria (8%), Actinobateria (5%), and Bacteroidota (3%). At the genus level, Lactobacillus was the dominant bacteria. Other genera found included Sphingomonas (7%), Cutibacterium (4%), and Clostridium_sensu_stricto_1 (2%). The richness of female intestinal microbiota was higher compared to the male microbiota. The findings of this study provide baseline information that can assist to better understand the chicken gut microbiota and its interaction with diseases and parasites.

Dual Regulation Mechanism of Obesity: DNA Methylation and Intestinal Flora

Obesity is a multifactorial chronic inflammatory metabolic disorder, with pathogenesis influenced by genetic and non-genetic factors such as environment and diet. Intestinal microbes and their metabolites play significant roles in the occurrence and development of obesity by regulating energy metabolism, inducing chronic inflammation, and impacting intestinal hormone secretion. Epigenetics, which involves the regulation of host gene expression without changing the nucleotide sequence, provides an exact direction for us to understand how the environment, lifestyle factors, and other risk factors contribute to obesity. DNA methylation, as the most common epigenetic modification, is involved in the pathogenesis of various metabolic diseases. The epigenetic modification of the host is induced or regulated by the intestinal microbiota and their metabolites, linking the dynamic interaction between the microbiota and the host genome. In this review, we examined recent advancements in research, focusing on the involvement of intestinal microbiota and DNA methylation in the etiology and progression of obesity, as well as potential interactions between the two factors, providing novel perspectives and avenues for further elucidating the pathogenesis, prevention, and treatment of obesity.

Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks

In this study, we sought to determine the effects of intestinal flora on the feed efficiency of meat ducks by evaluating the correlation between intestinal flora and residual feed intake. The F2 generation of Cherry Valley ducks × Runzhou Crested White ducks was used as the study subjects, and feed consumption being recorded from d 21 to 42. RFI was calculated based on growth performance, and 20 low RFI and 20 high RFI ducks were randomly selected to characterize the effect of RFI on growth performance. To analyze the intestinal flora affecting RFI, 16s rDNA sequencing was performed on the contents of 5 intestinal segments from the HR and LR groups, and macrogenomic sequencing was performed on the cecal contents. Feed intake, average daily feed intake, feed conversion ratio, and residual feed intake were lower in low RFI. Analysis of the intestinal flora revealed the cecum to be more highly enriched in the carbohydrate metabolism pathway and less enriched with potentially pathogenic taxa than the other assessed intestinal regions. Further analysis of the cecal microbiota identified nine significantly differentially enriched intestinal flora. In this study, we accordingly identified a basis for the mechanisms underlying the effects of the intestinal flora on meat duck feed efficiency.

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

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

Early-life factors shaping the gut microbiota of Common buzzard nestlings

BACKGROUND

Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.

RESULTS

We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.

CONCLUSION

Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken

Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870T=LMG 32876T), Limosilactobacillus galli sp. nov. (DSM 113833T=LMG 32623T), Limosilactobacillus avium sp. nov. (DSM 113849T=LMG 32671T), Limosilactobacillus pulli sp. nov. (DSM 115077T=LMG 32877T), Limosilactobacillus viscerum sp. nov. (DSM 113835T=LMG 32625T), Limosilactobacillus difficilis sp. nov. (DSM 114195T=LMG 32875T) and Clostridium butanoliproducens (DSM 115076T=LMG 32878T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Faecalispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860T=LMG 32675T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species Clostridium jeddahense and Clostridium sporosphaeroides to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.

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.

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.

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity

Recently, there has been considerable interest in the functions of gut microbiota in broiler chickens in relation to their use as feed additives. However, the gut-microbiota of chickens reared at different altitudes are not well documented for their potential role in adapting to prevailing conditions and functional changes. In this context, the present study investigates the functional diversity of gut-microbes in high-altitude (HACh) and low-altitude adapted chickens (LACh), assessing their substrate utilization profile through Biolog Ecoplates technology. This will help in the identification of potential microbes or their synthesized metabolites, which could be beneficial for the host or industrial applications. Results revealed that among the 31 different types of studied substrates, only polymers, carbohydrates, carboxylic acids, and amine-based substrates utilization varied significantly (p < 0.05) among the chickens reared at two different altitudes where gut-microbes of LACh utilized a broad range of substrates than the HACh. Further, diversity indices (Shannon and MacIntosh) analysis in LACh samples showed significant (p < 0.05) higher richness and evenness of microbes as compared to the HACh samples. However, no significant difference was observed in the Simpson diversity index in gut microbes of lowversus high-altitude chickens. In addition, the Principal Component Analysis elucidated variation in substrate preferences of gut-microbes, where 13 and 8 carbon substrates were found to constitute PC1 and PC2, respectively, where γ-aminobutyric acid, D-glucosaminic acid, i-erythritol and tween 40 were the most relevant substrates that had a major effect on PC1, however, alpha-ketobutyric acid and glycyl-L-glutamic acid affected PC2. Hence, this study concludes that the gut-microbes of high and low-altitudes adapted chickens use different carbon substrates so that they could play a vital role in the health and immunity of an animal host based on their geographical location. Consequently, this study substantiates the difference in the substrate utilization and functional diversity of the microbial flora in chickens reared at high and low altitudes due to altitudinal changes.

Does nest occupancy by birds influence the microbial composition?

Nest microbiota plays a vital role in the breeding and development of birds, which not only provides protection to bird hosts but also negatively affects the host. At present, it is unclear whether the composition of the microbes in the nests is affected by nesting. For this reason, we hung artificial nest boxes to simulate the natural nesting environment and combined 16S rRNA and ITS high-throughput sequencing technology to further study the differences in microbial composition and richness between used nests and control nests of Japanese tits (Parus minor). The study found that the bacteria in used nests and control nests showed significant differences at the phylum level (p < 0.05). It is also worth noting that the predominant bacteria in used nests were Proteobacteria (51.37%), Actinobacteria (29.72%), Bacteroidetes (6.59%), and Firmicutes (3.82%), while the predominant bacteria in control nests were Proteobacteria (93.70%), Bacteroidetes (2.33%), and Acidobacteria (2.06%). Both used nests and control nests showed similar fungi at the phylum level, which consisted mainly of Ascomycota and Basidiomycota, although significant differences were found in their relative abundance between both groups. The results of alpha diversity analysis showed significant differences in bacteria between the two groups and not in fungi. However, the beta diversity analysis showed significant differences between both bacteria and fungi. In summary, our results showed that the used nests had a higher abundance of beneficial microbiota and a lower presence of pathogenic microbiota. Therefore, we speculate that birds will change the characteristics of the nest microbial composition in the process of nest breeding to ensure their smooth reproductive development.

Enzymolytic soybean meal improves growth performance, economic efficiency and organ development associated with cecal fermentation and microbiota in broilers offered low crude protein diets

The objective of this experiment was to determine the effect of low crude protein (CP) diets containing increasing amounts of enzymolytic soybean meal (ESBM) on growth performance, economic benefit and organ development and the role of cecal fermentation and microbiota in broilers. A total of 360 one-day-old Arbor Acres chicks were randomly allocated into 6 groups with 6 replicates and 10 chicks each. The six dietary treatments consisted of a standard high-CP diet (PC), a low-CP diet (NC), and an NC diet with 0.5, 1.0, 1.5%, or 2.0% ESBM. The experiment lasted for 42 days. Compared to PC, NC showed decreased (p < 0.05) average daily gain (ADG) in broilers from 22 to 42 days and from 1 to 42 days, while increasing levels of ESBM quadratically increased (p < 0.05) ADG from 1 to 42 days. Feed cost and total revenue in the NC were lower (p < 0.05) than that in the PC, while supplementation with ESBM in the NC linearly increased (p < 0.05) net profit and economic efficiency in broilers. There were significant differences (p < 0.05) in the liver, proventriculus and gizzard indices between the PC and NC groups, and supplementation with ESBM linearly increased (p < 0.05) the relative weights of liver, pancreas, proventriculus and gizzard in broilers at 42 days of age. The PC group had a higher cecal acetic acid concentration at 21 days and propionic acid concentration at both 21 and 42 days than the NC group (p < 0.05). Cecal acetic acid and propionic acid concentrations linearly increased (p < 0.05) with increasing levels of ESBM in broilers at 42 days of age. No significant differences in ACE, Chao1, Shannon and Simpson indices were observed among groups (p > 0.05), while the cecal abundances of Bacteroides, Faecalibacterium and Clostridium IV increased (p < 0.05) with the increasing level of ESBM in the low-CP diets. In conclusion, feeding ESBM improved economic efficiency, digestive organ development, cecal fermentation and microbial community composition, and up to 2.0% ESBM addition had no negative effect on the growth performance in broilers fed low CP diets.

Characterizing the impact of Enterococcus cecorum infection during late embryogenesis on disease progression, cecal microbiome composition, and early performance in broiler chickens

Enterococcus cecorum (EC) has been associated with septicemia and early mortality in broiler chickens. There is limited research investigating the pathogenicity of EC field strains obtained from affected birds. The purpose of this study was to evaluate the effect of in-ovo administration into the amnion with different EC field isolates at d 18 of embryogenesis (DOE18). In Exp 1, 7 EC field isolates alone or in combination (EC1-EC3, EC4-EC5, EC6, and EC7) were selected based on phenotypic characteristics and evaluated at different concentrations (1 × 102, 1 × 104, and 1 × 106 CFU/200 µL/embryo) to assess the impact on early performance and macroscopic lesions. Three isolates (n = 3; EC2, EC5, EC7) were selected for additional evaluation based on the significant (P < 0.05) BWG reduction (d 0-21) compared to the negative control (NC) and the presence of macroscopic lesions observed during posting sessions at d 14 and d 21. An additional isolate associated with enterococcal spondylitis was included in Exp 2 (EC11B). Treatment groups for Exp 2 include: 1) NC, 2) EC2, 3) EC5, 4) EC7, and 5) EC11B (n = 90-120/embryos/group). Groups 2 to 5 were challenged at 1 × 102 CFU/200 µL/embryo by in-ovo injection into the amnion at DOE18. Chicks were placed in battery cages for the duration of the study (21 d), and pen weights were recorded at d 0, d 7, d 14, and d 21 to calculate average BW and BWG. At d 14 and d 21 posthatch, liver, spleen, free thoracic vertebrae (FTV), and femoral head (FH) were aseptically collected to enumerate Enterococcus spp. using Chromagar Orientation as the selective media. Cecal contents were collected at d 21 to evaluate the effect of EC challenge on the cecal microbiome composition. There was a significant (P < 0.05) reduction in BW at d 21, and BWG from d 14 to 21 and d 0 to 21, for EC7 and EC11B. Enterococcus cecorum was recovered from the FTV of all challenged groups at d 14 and d 21. The most representative lesions were pericarditis, hydropericardium, focal heart necrosis, and FH osteomyelitis. However, lesions were not uniform across challenged groups or ages (d 14 and d 21). Alpha diversity of the cecal contents was markedly lower in EC5 and EC11B compared to all treatment groups suggesting that EC exposure during late embryogenesis affect the cecal microbiome up to 21 d posthatch. Additionally, these results highlight the differences in pathogenicity of EC strains isolated from field cases and suggest that hatchery exposure to EC during late embryogenesis is a potential route of introduction into a flock.

Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy

Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.

Temporal stability and community assembly mechanisms in healthy broiler cecum

In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.

Ameliorative avian gut environment and bird productivity through the application of safe antibiotics alternatives: a comprehensive review

The avian digestive tract is an important system for converting ingested food into the nutrients their bodies need for maintenance, growth, and reproduction (meat, table eggs, and fertile eggs). Therefore, preserving digestive system integrity is crucial to bird health and productivity. As an alternative to antibiotics, the world has recently turned to the use of natural products to enhance avian development, intestinal health, and production. Therefore, the primary goal of this review is to explain the various characteristics of the avian digestive tract and how to enhance its performance with natural, safe feed additives such as exogenous enzymes, organic acids, photogenic products, amino acids, prebiotics, probiotics, synbiotics, and herbal extracts. In conclusion, the composition of the gut microbiome can be influenced by a number of circumstances, and this has important consequences for the health and productivity of birds. To better understand the connection between pathogens, the variety of therapies available, and the microbiome of the gut, additional research needs to be carried out.

Intestinal Immune Cell Populations, Barrier Function, and Microbiomes in Broilers Fed a Diet Supplemented with Chlorella vulgaris

This study aimed to evaluate the effects of dietary Chlorella vulgaris (CV) on the distribution of immune cells, intestinal morphology, intestinal barrier function, antioxidant markers, and the cecal microbiome in 10-day-old broiler chickens. A total of 120 day-old Ross 308 male broiler chicks were assigned to two dietary treatments using a randomized complete block design, with body weight as the blocking factor. Birds fed a diet containing CV showed an increase in CD4⁺ T cells (p < 0.05) compared to those fed the control diet. The relative mRNA expression of intestinal epithelial barrier function-related markers (occludin and avian β-defensin 5) was elevated (p < 0.05) in the CV-supplemented group compared to the control group. The alpha diversity indices (Chao1 and observed features) of the cecal microbiome in 10-day-old birds increased (p < 0.05), indicating higher richness within the cecal bacterial community. In the microbiome analysis, enriched genera abundance of Clostridium ASF356 and Coriobacteriaceae CHKCI002 was observed in birds fed the diet containing CV compared to those fed the control diet. Taken together, dietary CV supplementation might alter intestinal barrier function, immunity, and microbiomes in 10-day-old broiler chickens.

Effects of nonantibiotic growth promoter combinations on growth performance, nutrient utilization, digestive enzymes, intestinal morphology, and cecal microflora of broilers

Given the ban on antibiotic growth promoters, the effects of nonantibiotic alternative growth promoter combinations (NAGPCs) on the growth performance, nutrient utilization, digestive enzyme activity, intestinal morphology, and cecal microflora of broilers were evaluated. All birds were fed pellets of two basal diets-starter (0-21 d) and grower (22-42 d)-with either enramycin (ENR) or NAGPC supplemented. 1) control + ENR; 2) control diet (CON, basal diet); 3) control + mannose oligosaccharide (MOS) + mannanase (MAN) + sodium butyrate (SB) (MMS); 4) control + MOS + MAN + Bacillus subtilis (BS) (MMB); 5) control + MOS + fruit oligosaccharide (FOS) + SB (MFS); 6) control + FOS + BS (MFB); 7) control + MOS + FOS + MAN (MFM); 8) control + MOS + BS + phytase (PT) (MBP). ENR, MOS, FOS, SB, MAN, PT, and BS were added at 100, 2,000, 9,000, 1,500, 300, 37, and 500 mg/kg, respectively. The experiment used a completely random block design with six replicates per group: 2400 Ross 308 broilers in the starter phase and 768 in the grower phase. All NAGPCs significantly improved body weight gain (P < 0.01), utilization of dry matter, organic matter, and crude protein (P < 0.05), villus height and villus height/crypt depth in the jejunum and ileum (P < 0.01), and decreased the feed conversion ratio (P < 0.01) at d 21 and 42. MMS, MMB, MFB, and MFM duodenum trypsin, lipase, and amylase activities increased significantly (P < 0.05) at d 21 and 42. On d 21 and 42, MMS, MMB, and MBP increased the abundance of Firmicutes and Bacteroides whereas MMB, MFB, and MBP decreased the abundance of Proteobacteria, compared to ENR and CON. Overall, the NAGPCs were found to have some beneficial effects and may be used as effective antibiotic replacements in broilers.

Glucose oxidase as an alternative to antibiotic growth promoters improves the immunity function, antioxidative status, and cecal microbiota environment in white-feathered broilers

This study aimed to demonstrate the effects of glucose oxidase (GOD) on broilers as a potential antibiotic substitute. A total of four hundred twenty 1-day-old male Cobb500 broilers were randomly assigned into five dietary treatments, each with six replicates (12 chicks per replicate). The treatments included two control groups (a basal diet and a basal diet with 50 mg/kg aureomycin) and three GOD-additive groups involving three different concentrations of GOD. Analysis after the t-test showed that, on day 21, the feed:gain ratio significantly decreased in the 1,200 U/kg GOD-supplied group (GOD1200) compared to the antibiotic group (Ant). The same effect was also observed in GOD1200 during days 22-42 and in the 600 U/kg GOD-supplied group (GOD600) when compared to the control group (Ctr). The serum tests indicated that, on day 21, the TGF-β cytokine was significantly decreased in both GOD600 and GOD1200 when compared with Ctr. A decrease in malondialdehyde and an increase in superoxide dismutase in GOD1200 were observed, which is similar to the effects seen in Ant. On day 42, the D-lactate and glutathione peroxidase activity changed remarkably in GOD1200 and surpassed Ant. Furthermore, GOD upregulated the expression of the jejunal barrier genes (MUC-2 and ZO-1) in two phases relative to Ctr. In the aureomycin-supplied group, the secretory immunoglobulin A significantly decreased in the jejunum at 42 days. Changes in microbial genera were also discovered in the cecum by sequencing 16S rRNA genes at 42 days. The biomarkers for GOD supplementation were identified as Colidextribacter, Oscillibacter, Flavonifractor, Oscillospira, and Shuttleworthia. Except for Shuttleworthia, all the abovementioned genera were n-butyrate producers known for imparting their various benefits to broilers. The PICRUSt prediction of microbial communities revealed 11 pathways that were enriched in both the control and GOD-supplied groups. GOD1200 accounted for an increased number of metabolic pathways, demonstrating their potential in aiding nutrient absorption and digestion. In conclusion, a diet containing GOD can be beneficial to broiler health, particularly at a GOD concentration of 1,200 U/kg. The improved feed conversion ratio, immunity, antioxidative capacity, and intestinal condition demonstrated that GOD could be a valuable alternative to antibiotics in broiler breeding.

Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses

In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).

Metabolic and inflammatory linkage of the chicken cecal microbiome to growth performance

Introduction

Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production.

Methods

In the current study we examined whether the market weights of native chicken breeds were related to specific cecal bacteria, serum metabolites and inflammatory cytokines. We examined cecal bacterial taxa using 16S rDNA analysis along with untargeted serum metabolites and serum inflammatory cytokines.

Results

We found that the cecal microbiota could explain 10.1% of the individual differences in chicken weights and identified key cecal bacterial genera that influenced this phenotype. The presence of Sphaerochaeta spp. improved growth performance via bovinic acid metabolism. In contrast, Synergistes and norank_f_Desulfovibrionaceae had a negative effect on growth by inducing expression of the inflammatory cytokine IL-6.

Discussion

We were able to link specific bacterial genera with growth promotion in chickens and this study will allow further development of their use as probiotics in these animals.

Effects of dietary supplementation probiotic complex on growth performance, blood parameters, fecal harmful gas, and fecal microbiota in AA+ male broilers

In this study, Bacillus subtilis, Clostridium butyricum and Enterococcus faecalis were made into a probiotic complex (PC). The PC was supplemented in AA+ male broilers' diets to investigate the effects of PC on broiler growth performance, carcass traits, blood indicators, harmful gas emissions in feces and microbiota. Three hundred and sixty 1-day-old AA+ male broilers with an average initial body weight (data) were randomly divided into 3 dietary treatments of 6 replicates each, with 20 birds per replicate. The control group (T0) was fed a basal diet, while the test groups (T1 and T2) were supplemented with 0.025 and 0.05% PC in the basal diet, respectively. The trail was 42 days. The results showed that the supplementation of 0.05% PC significantly (p < 0.05) improved average daily gain (ADG) and average daily feed intake (ADFI) of broilers from 22 to 42 days and 1-42 days. Compared to the control group, the breast rate was significantly higher in T2, and the thymic index was significantly higher than that in T1 treatment (p < 0.05). The addition of PC had no significant effects on antibody potency in broiler serum (p > 0.05), but significantly increased albumin and total protein content in serum (p < 0.05). The addition of PC reduced H₂S and NH₃ emissions in the feces; the levels of Escherichia coli and Salmonella in the feces were significantly reduced and the levels of Lactobacillus were increased. And the most significant results were achieved when PC was added at 0.05%. Correlation analysis showed a significant positive correlation (p < 0.05) between the levels of E. coli and Salmonella and the emissions of H₂S and NH₃. Conclusion: Dietary supplementation with a 0.05% probiotic complex could improve the growth performance of broilers and also reduced fecal H₂S and NH₃ emissions, as well as fecal levels of E. coli and Salmonella, and increased levels of Lactobacillus. Thus, PC made by Bacillus subtilis, Clostridium butyricum and Enterococcus faecalis is expected to be an alternative to antibiotics. And based on the results of this trial, the recommended dose for use in on-farm production was 0.05%.

Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota

BACKGROUND

The broiler gastrointestinal microbiome is a potent flock performance modulator yet may also serve as a reservoir for pathogen entry into the food chain. The goal of this project was to characterise the effect of mannan rich fraction (MRF) supplementation on microbiome diversity and composition of the intestinum tenue and cecum of commercial broilers. This study also aimed to address some of the intrinsic biases that exist in microbiome studies which arise due to the extensive disparity in 16S rRNA gene copy numbers between bacterial species and due to large intersample variation.

RESULTS

We observed a divergent yet rich microbiome structure between different anatomical sites and observed the explicit effect MRF supplementation had on community structure, diversity, and pathogen modulation. Birds supplemented with MRF displayed significantly higher species richness in the cecum and significantly different bacterial community composition in each gastrointestinal (GI) tract section. Supplemented birds had lower levels of the zoonotic pathogens Escherichia coli and Clostridioides difficile across all three intestinum tenue sites highlighting the potential of MRF supplementation in maintaining food chain integrity. Higher levels of probiotic genera (eg. Lactobacillus and Blautia) were also noted in the MRF supplemented birds. Following MRF supplementation, the cecum displayed higher relative abundances of both short chain fatty acid (SFCA) synthesising bacteria and SCFA concentrations.

CONCLUSIONS

Mannan rich fraction addition has been observed to reduce the bioburden of pathogens in broilers and to promote greater intestinal tract microbial biodiversity. This study is the first, to our knowledge, to investigate the effect of mannan-rich fraction supplementation on the microbiome associated with different GI tract anatomical geographies. In addition to this novelty, this study also exploited machine learning and biostatistical techniques to correct the intrinsic biases associated with microbiome community studies to enable a more robust understanding of community structure.

Gut Microbiota, Intestinal Morphometric Characteristics, and Gene Expression in Relation to the Growth Performance of Chickens

this study aimed to investigate the growth mechanism in a local breed of chickens by comparing the highest weight (HW) and the lowest weight in their microbiota, histological characteristics, and gene expression. Golden Montazah chickens, an Egyptian breed, were reared until they were 49 days old. All of the birds were fed ad libitum by a starter diet from day 1 until day 21, followed by a grower diet from day 21 to the end of the study. At 49 days old, the forty-eight birds with the heaviest body weight (HW) and the lightest body weight (LW) were chosen. Blood biochemical and histological morphometric parameters, electron microscopy, and intestinal nutrient transporter gene expression were studied in the sampled jejunum. The microbial composition and functions of the content and mucosa in HW and LW chickens were studied using 16S rRNA gene sequencing. The histological morphometric parameters were all more significantly (p < 0.05) increased in the HW chickens than in the LW chickens. Total protein, albumin, and triglycerides in serum were significantly higher (p < 0.05) in the HW chickens than in the LW chickens. The microbiome profile in the gut showed that Microbacterium and Sphingomonas were positively correlated with the body weights. In the local breed, there were significant differences in the intestinal microstructure which could enhance the growth mechanism and body weight. Our findings showed that some microbial components were significantly associated with body weight and their interactions with the host could be inferred to explain why these interactions might alter the host’s metabolic responses. Further investigation into combining bioinformatics with lab experiments in chickens will help us to understand how gut bacteria can change the host’s metabolism by special metabolic features in the gastrointestinal system.

Yeast Probiotic and Yeast Products in Enhancing Livestock Feeds Utilization and Performance: An Overview

The intensive use of antibiotics as growth-promoting agents in animal production has resulted in the spread of animal antibiotic resistance and possibly human antibiotic resistance. Based on this premise, it is significant to explore an alternative approach to preventing infectious diseases and promoting animal growth and health. Yeast as the main natural growth promoter in livestock nutrition has been extensively studied for decades. Numerous yeasts and yeast-containing products are produced, marketed, and used in animal feed as providers of nutrient sources, probiotics, and nutrients or serve distinct nutritional functions. A large amount of scientific research suggests that yeasts and their derivatives may be good for animal growth performance and health, especially when animals are housed in poor sanitation or are suffering from disease. However, when yeasts are used as a surrogate for livestock antibiotics, the results vary according to several factors, including yeast species, yeast product components, feed ingredients, animal category, type of symptoms, and differences in the rearing environment. In this review, the effects of different yeasts on different animals will be reviewed. The types of widely used yeast products, their functional characteristics, and application effects will be discussed in order to provide a reference for the development and application of yeast feed products.

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species

The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host's own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal

The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.

Sodium humate alters the intestinal microbiome, short-chain fatty acids, eggshell ultrastructure, and egg performance of old laying hens

This study investigated the effect of sodium humate supplementation on changes in the intestinal microbiome, intestinal short-chain fatty acids production, and trace element absorption in older laying hens, with consequent effects on egg performance and shell quality. We used the same hens as their own control; a total of 720 laying hens aged 422 days were randomly divided into three replicates, with the CON group fed a commercial diet at 422–441 days of age and the HANa group fed a commercial diet supplemented with 0.05% sodium humate at 442–461 days of age. Compared with the CON group, in the HANa group, Bacteroidetes and Actinobacteria were significantly increased, whereas, Firmicutes was significantly decreased. Further, Veillonella, Enterococcus, Lactobacillus, and Turricibacter significantly decreased, and Peptoniphilus, Helcococcus, GW-34, Psychrobacter, Anaerococcus, Corynebacterium, Facklamia, Trichococcus, Gallicola, Clostridium, and Oscillospira were significantly increased. The results showed that sodium humate significantly altered the alpha and beta diversity and changed the structure of the intestinal microbiome. Acetic acid, isovaleric acid, and isobutyric acid, among short-chain fatty acids were significantly increased in the HANa group, whereas trace elements such as Mn, Zn, and Fe were significantly reduced. The eggshell strength and ultrastructure were significantly altered. In this study, sodium humate was found to alter the intestinal microbiome structure of aged hens, change the production of short-chain fatty acids, and promote the absorption of trace elements to keep aged hens from experiencing a decrease in egg production performance.

Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I

BACKGROUND

Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against systemic viral infections. Nephropathogenic infectious bronchitis virus (IBV) is a pathogenic coronavirus that causes high morbidity and multiorgan infection tropism in chickens.

RESULTS

In this study, we used broad-spectrum oral antibiotics (ABX) to treat specific pathogen free (SPF) chickens to deplete the microbiota before infection with nephropathogenic IBV to analyze the impact of microbiota on IBV infections in vivo. Depletion of the SPF chicken microbiota increases pathogenicity and viral burden following IBV infection. The gnotobiotic chicken infection model further demonstrated that intestinal microbes are resistant to nephropathogenic IBV infection. In addition, ABX-treated chickens showed a severe reduction in macrophage activation, impaired type I IFN production, and IFN-stimulated gene expression in peripheral blood mononuclear cells and the spleen. Lactobacillus isolated from SPF chickens could restore microbiota-depleted chicken macrophage activation and the IFNAR-dependent type I IFN response to limit IBV infection. Furthermore, exopolysaccharide metabolites of Lactobacillus spp. could induce IFN-β.

CONCLUSIONS

This study revealed the resistance mechanism of SPF chicken intestinal microbiota to nephropathogenic IBV infection, providing new ideas for preventing and controlling nephropathogenic IBV. Video abstract.

Luminal and mucosa-associated caecal microbiota of chickens after experimental Campylobacter jejuni infection in the absence of Campylobacter-specific phages of group II and III

Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between Campylobacter (C.) jejuni and the intestinal microbiota might influence Campylobacter colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with C. jejuni in Campylobacter-specific phage-free chickens under standardized conditions and special biosafety precautions.Therefore, 12 artificially infected (C. jejuni inoculum with a challenge dose of 7.64 log₁₀ c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No Campylobacter-specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between C. jejuni-negative and C. jejuni-positive chickens. The factor chickens' infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (P=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (P=0.015). The strongest difference between C. jejuni-non-infected and C. jejuni-infected birds was observed for the family Peptococcaceae whose presence in C. jejuni-infected birds could not be demonstrated. Further, several genera of the family Ruminococcaceae appeared to be depressed in its abundance due to Campylobacter infection. A negative correlation was found between Christensenellaceae R-7 group and Campylobacter in C. jejuni-colonised chickens, both genera potentially competing for substrate. This makes Christensenellaceae R-7 group highly interesting for further studies that aim to find control options for Campylobacter infections and assess the relevance of this finding for chicken health and Campylobacter colonization.

Effects of Macleaya cordata Extract on Blood Biochemical Indices and Intestinal Flora in Heat-Stressed Mice

Heat stress (HS) leads to disturbance of homeostasis and gut microbiota. Macleaya cordata extract (MCE) has anti-inflammatory, antibacterial, and gut health maintenance properties. Still, the specific effects of MCE on blood biochemical indices and gut microbiota homeostasis in heat-stressed mice are not entirely understood. This study aimed to investigate the impact of MCE on blood biochemical indices and gut microbiota in heat-stressed mice. A control group (CON) (25 °C, n = 6) and HS group (42 °C, n = 6) were gavaged with normal saline 0.2 mL/g body weight/day, and HS plus MCE group (HS-MCE) (42 °C, n = 6) was gavaged with 5 mg MCE/kg/day. HS (2 h/d) on 8–14 d. The experiment lasted 14 days. The results showed that HS increased mice’ serum aspartate transaminase, alanine transferase activities, heat shock protein 70 level, and malondialdehyde concentrations, and decreased serum catalase and superoxide dismutase activities. HS also disrupted microbiota diversity and community structure in mice, increasing the Bacteroidetes and decreasing Firmicutes and Lactobacillus; however, MCE can alleviate the disturbance of biochemical indicators caused by HS and regulate the flora homeostasis. Furthermore, MCE was able to moderate HS-induced metabolic pathways changes in gut microbiota. The Spearman correlation analysis implied that changes in serum redox status potentially correlate with gut microbiota alterations in HS-treated mice.