Characteristics of the intestinal flora of specific pathogen free chickens with age

In Vivo Expression of Chicken Gut Anaerobes Identifies Carbohydrate- or Amino Acid-Utilising, Motile or Type VI Secretion System-Expressing Bacteria

Complex gut microbiota increases chickens' resistance to enteric pathogens. However, the principles of this phenomenon are not understood in detail. One of the possibilities for how to decipher the role of gut microbiota in chickens' resistance to enteric pathogens is to systematically characterise the gene expression of individual gut microbiota members colonising the chicken caecum. To reach this aim, newly hatched chicks were inoculated with bacterial species whose whole genomic sequence was known. Total protein purified from the chicken caecum was analysed by mass spectrometry, and the obtained spectra were searched against strain-specific protein databases generated from known genomic sequences. Campylobacter jejuni, Phascolarctobacterium sp. and Sutterella massiliensis did not utilise carbohydrates when colonising the chicken caecum. On the other hand, Bacteroides, Mediterranea, Marseilla, Megamonas, Megasphaera, Bifidobacterium, Blautia, Escherichia coli and Succinatimonas fermented carbohydrates. C. jejuni was the only motile bacterium, and Bacteroides mediterraneensis expressed the type VI secretion system. Classification of in vivo expression is key for understanding the role of individual species in complex microbial populations colonising the intestinal tract. Knowledge of the expression of motility, the type VI secretion system, and preference for carbohydrate or amino acid fermentation is important for the selection of bacteria for defined competitive exclusion products.

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

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

Combined analysis of the microbiome, metabolome and transcriptome of silkie chickens in response to avian pathogenic E. coli (APEC)

Avian colibacillosis is a bacterial disease caused by avian pathogenic Escherichia coli (APEC) that results in great losses in the poultry industry every year. Individual Silkie chickens of the same breed that are given the same feed in the same feeding conditions have different levels of resistance or susceptibility to APEC. Differences in gut microbes, gut metabolites, and gene expression in the spleen of APEC-resistant and APEC-susceptible chickens were compared, and multiple omics associations were analyzed to explore the mechanism of resistance to APEC in Silkie chickens. Compared with those in the APEC-susceptible group, the APEC-resistant group showed significantly increased abundances of many gut microorganisms, including Bacillus, Thermoactinomyces, Arthrobacter, and Ureibacillus, which were positively correlated with norvaline, l-arginine, and valyl-glycine levels. Intestinal tryptophan, indole, and indole derivative-related differentially abundant metabolites played an active role in combatting APEC infection. In the spleen, "response to stimulus" was the most significantly enriched GO term, and "cytokine‒cytokine receptor interaction" was the most significantly enriched KEGG pathway. The arginine biosynthesis and PPAR signaling pathways were the KEGG pathways that were significantly enriched with differentially abundant metabolites and differentially expressed genes. This study provides new insight into the prevention and treatment of APEC infection in Silkie chickens and lays a foundation to study the mechanism of APEC infection in poultry.

Yupingfeng polysaccharide promote the growth of chickens via regulating gut microbiota

Introduction

Yupingfeng polysaccharide (YPF-P) is the main substance of alcohol deposition in Yupingfeng powder, which has many biological functions such as enhancing immunity, repairing intestinal barrier and enhancing antioxidant ability. This study employed in vitro growth-promoting drug feed additives and animal experiments to comprehensively evaluate the use of YPF-P in broiler production.

Methods

A total of 1,296 151 days-old Qingyuan Partridge chickens were randomly divided into four groups with six replicates and 54 hens per replicate: the control group was fed basal diet, and the experimental groups were fed diets supplemented with 4 g/kg, 8 g/kg, and 12 g/kg YPF-P for 14 days. Broilers were weighed before and at the end of the experiment to calculate total weight gain (GW), average daily gain (ADG), and feed compensation. At the end of the experiment, six chickens from each group were randomly selected for subwing vein blood sampling, which was used to measure serum biochemical indicators GHRH, GH, and IGF-1 by ELISA method. Randomly select chickens from control group and 8 g/kg group for slaughter, and cecal contents were collected for 16S high-throughput sequencing.

Results

Dietary supplementation of 8 g/kg YPF-P can significantly increase the final body weight, total weight gain, average daily gain and decrease the feed to gain ratio of chickens. During 151-165 days, serum IGF-1 concentrations increased significantly (p < 0.05). There were no significant changes in serum GH concentration (p > 0.05). In terms of gut microbiota, there was no significant difference between control group and test group in Shannon index and Simpson index. Compared with the control group,the addition of 8 g/kgYPF-P significantly increased the abundance of Firmicutes and significantly decreased the abundance of Bacteroides at the phylum level.At the genus level, the relative abundance of unclassified_Oscillospiraceae was significantly increased and the unclassified_Muribaculaceae, uncultured_Bacteroidales_bacterium, Lactobacillus, Alloprevotella, Ligilactobacillus, Prevotellaceae_UCG_001, and unclassified_Atopobiaceae was significantly decreased.

Conclusion

The above results showed that adding 8 mg/kg of YPF-P could increase the average daily gain of Qingyuan Partridge chickens, reduce the ratio of feed to meat, and affect the distribution proportion of intestinal microflora in chickens to some extent.

Improving broiler health through cecal microbiota transplantation: a comprehensive study on growth, immunity, and microbial diversity

Cecal microbiota has emerged as a prominent intervention target for improving the production and welfare of poultry. This is essential for the overall health and performance of broiler chickens. The current study focused on investigating the effect of cecal microbiota transplantation (CMT) from healthy donor chickens on the growth performance, immunity, and microbial composition of newly hatched chicks and evaluated the effect of sample storage on the microbial diversity of the cecal samples. A healthy "Wannan Yellow Chicken line" was selected as the donor, and 180 1-d-old chicks from the same line were used as recipients for a 60-d feed trial. The chicks were randomly allocated to three groups (60 birds per group) with three replicates in each group. The three treatment groups were CMT-0 (control, normal saline solution), CMT-I (1:12 cecal content, normal saline supplemented with 10% glycerol), and CMT-II (1:6 cecal content, normal saline supplemented with 10% glycerol). The results of weight gain and absolute organ weight showed significant improvements in the CMT-II group compared with the CMT-0 group. Serum IgG level was significantly improved (P < 0.05) in CMT-I compared with that in the CMT-0. However, IL-6 levels increased in CMT-I and then significantly decreased in CMT-II. The cecal microbial diversity of CMT treatment was compared between two groups, fresh samples (FS) and stored samples at-80 °C (SS). The results showed that beneficial taxa, such as Firmicutes and Verrucomicrobiota, were substantially more abundant in both CMT-I and CMT-II than in CMT-0 in both FS and SS. Microbial function analysis at levels 1, 2, and 3 showed improved metabolism, genetic information processing, cellular processes, environmental information processing, and organismal systems in CMT-I and CMT-II for both FS and SS groups. However, the SS group showed decreased microbial diversity and function. To conclude, cecal microbiota transplantation is a promising strategy for enhancing the productivity and health of broiler chickens.

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

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

Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta

The concept of competitive exclusion is well established in poultry and different products are used to suppress the multiplication of enteric pathogens in the chicken intestinal tract. While the effect has been repeatedly confirmed, the specific principles of competitive exclusion are less clear. The aim of the study was to compare metabolites in the cecal digesta of differently colonized chickens. Metabolites in the cecal contents of chickens treated with a commercial competitive exclusion product or with an experimental product consisting of 23 gut anaerobes or in control untreated chickens were determined by mass spectrometry. Extensive differences in metabolite composition among the digesta of all 3 groups of chickens were recorded. Out of 1,706 detected compounds, 495 and 279 were differently abundant in the chicks treated with a commercial or experimental competitive exclusion product in comparison to the control group, respectively. Soyasaponins, betaine, carnitine, glutamate, tyramine, phenylacetaldehyde, or 3-methyladenine were more abundant in the digesta of control chicks while 4-oxododecanedioic acid, nucleotides, dipeptides, amino acids (except for glutamate), and vitamins were enriched in the digesta of chickens colonized by competitive exclusion products. Metabolites enriched in the digesta of control chicks can be classified as of plant feed origin released in the digesta by degradative activities of the chicken. Some of these molecules disappeared from the digesta of chicks colonized by complex microbiota due to them being metabolized. Instead, nucleotides, amino acids, and vitamins increased in the digesta of colonized chicks as a consequence of the additional digestive potential brought to the cecum by microbiota from competitive exclusion products. It is therefore possible to affect metabolite profiles in the chicken cecum by its colonization with selected bacterial species.

A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production

OBJECTIVE

The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage.

METHODS

From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis.

RESULTS

Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05).

CONCLUSION

The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.

Comparison of the Gut Microbial Communities of Domestic and Wild Mallards (Anas platyrhynchos) Based on High-Throughput Sequencing Technology

Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

Plasmid DNA Prime/Protein Boost Vaccination against Campylobacter jejuni in Broilers: Impact of Vaccine Candidates on Immune Responses and Gut Microbiota

Campylobacter infections, traced to poultry products, are major bacterial foodborne zoonoses, and vaccination is a potential solution to reduce these infections. In a previous experimental trial using a plasmid DNA prime/recombinant protein boost vaccine regimen, two vaccine candidates (YP437 and YP9817) induced a partially protective immune response against Campylobacter in broilers, and an impact of the protein batch on vaccine efficacy was suspected. This new study was designed to evaluate different batches of the previously studied recombinant proteins (called YP437A, YP437P and YP9817P) and to enhance the immune responses and gut microbiota studies after a C. jejuni challenge. Throughout the 42-day trial in broilers, caecal Campylobacter load, specific antibodies in serum and bile, the relative expression of cytokines and β-defensins, and caecal microbiota were assessed. Despite there being no significant reduction in Campylobacter in the caecum of vaccinated groups, specific antibodies were detected in serum and bile, particularly for YP437A and YP9817P, whereas the production of cytokines and β-defensins was not significant. The immune responses differed according to the batch. A slight change in microbiota was demonstrated in response to vaccination against Campylobacter. The vaccine composition and/or regimen must be further optimised.

Dynamic Changes in the Gut Microbiota and Metabolites during the Growth of Hainan Wenchang Chickens

Gut microbiota and their metabolites play important roles in animal growth by influencing the host's intake, storage, absorption, and utilization of nutrients. In addition to environmental factors, mainly diet, chicken breed and growth stage also affect changes in the gut microbiota. However, little research has been conducted on the development of gut microbiota and its metabolites in local chickens. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With aging, the structure of gut microbiota tended to be more stable. The relative proportions of dominant bacteria phyla Firmicutes, Bacteroidetes, and Proteobacteria showed stage changes with the development. With aging, gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. Several microbial and metabolic biomarkers with statistical differences were detected in different development stages. The bacteria that form networks with their significant related metabolites were different in various growth stages, including uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, Faecalibacterium, uncultured_bacterium_o_Bacteroidales, and uncultured_bacterium_f_Lachnospiraceae. Partially differential bacteria were significantly correlated with short-chain fatty acids such as butyric acid. These findings may provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breeds, as well as resources for microbial and metabolic biomarker identification to improve growth efficiency.

Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard

The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.

Effect of Lactobacillus reuteri S5 Intervention on Intestinal Microbiota Composition of Chickens Challenged with Salmonella enteritidis

To understand the mechanism of lactic acid bacteria against Salmonella enteritidis infection; we examined how lactic acid bacteria regulated the intestinal microbiota to resist infection by pathogenic bacteria. The probiotic strain Lactobacillus reuteri S5 was used to construct an animal model of S. enteritidis infected broilers. A high-throughput sequencing technology was used to analyze the regulatory effects of L. reuteri S5 on the structure of the intestinal microbiota of broilers infected with S. enteritidis; and to examine the possible defense mechanism they used. Our results showed that the administration of L. reuteri S5 reduced colonization of S. enteritidis (p < 0.05), decreased intestinal permeability (p < 0.05), and reduced the bacterial displacement likely due by S. enteritidis colonization (p < 0.05), suggesting some enhancement of the intestinal barrier function. Furthermore, L. reuteri S5 increased the number of operational taxonomic units (OTUs) in the chicken cecal microflora and the relative abundance of Lactobacillaceae and decreased the relative abundance of Enterobacteriaceae. These results suggest that the lactic acid bacterium L. reuteri S5 protected the intestinal microbiota of chickens against S. enteritidis infection.

Integrated gut microbiota and metabolomic analysis reveals immunomodulatory effects of Echinacea extract and Astragalus polysaccharides

Immunosuppression in different animals increases the susceptibility of various infections caused by pathogenic microorganisms leading to increase risks posed by antibiotics in different animal farming sectors. Therefore, investigation of the interactions between natural medicines and the intestinal environmental ecosystem is of vital importance and crucial. This study for the first time investigated the effects of Echinacea Extract (EE) and Astragalus polysaccharide (APS) on the gut using 16S rRNA and metabolomic analysis approaches in immunosuppressed broiler chickens. There were four groups divided into control (C), immunosuppression (IS), EE, and APS groups. Sequencing of gut microbes showed that immunosuppression decreased the relative abundance of Anaerofustis, Anaeroplasma, Anaerotroncus, and Lachnospira in the gut while increasing that of c_115 and Holdemania. However, EE and APS diminished the effects on the immunosuppression on the microbiota. The results revealed up-regulation of the relative abundance of Enterococcus in broiler chickens. In addition, EE reduced the relative abundance of Ruminococcus and Blautia. The results on metabolomic analysis revealed that immunosuppression mainly affects cyanuric acid metabolism, starch and sucrose metabolism while interconversion of pentose and glucuronide. EE and APS, on the other hand mainly impact butyrate metabolism, alanine, aspartate and glutamate metabolism while the interconversion of pentose and glucuronide, and D-glutamine and D-glutamate metabolism. Results regarding correlation analysis revealed significantly metabolic pathways including TCA cycle, butyrate metabolism, glyoxylate and dicarboxylate metabolism, propionate metabolism, alanine, aspartate and glutamate metabolism associated with Ruminococcus and Blautia. Both EE and APS can antagonize the effects of immunosuppression by modulating the disrupted gut microbiota. Nevertheless, EE might have a bidirectional regulatory functions on the intestinal health and further studies are needed to know the exact and relevant mechanisms of action regarding the effects of EE and APS.

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation

Background

Intestinal inflammation is prevalent in chicken, which results in decreased growth performance and considerable economic losses. Accumulated findings established the close relationship between gut microbiota and chicken growth performance. However, whether gut microbiota impacts chicken growth performance by lessening intestinal inflammation remains elusive.

Results

Seven-weeks-old male and female chickens with the highest or lowest body weights were significantly different in breast and leg muscle indices and average cross-sectional area of muscle cells. 16S rRNA gene sequencing indicated Gram-positive bacteria, such as Lactobacilli, were the predominant species in high body weight chickens. Conversely, Gram-negative bacteria, such as Comamonas, Acinetobacter, Brucella, Escherichia-Shigella, Thermus, Undibacterium, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were significantly abundant in low body weight chickens. Serum lipopolysaccharide (LPS) level was significantly higher in low body weight chickens (101.58 ± 5.78 ng/mL) compared with high body weight chickens (85.12 ± 4.79 ng/mL). The expression of TLR4, NF-κB, MyD88, and related inflammatory cytokines in the jejunum was significantly upregulated in low body weight chickens, which led to the damage of gut barrier integrity. Furthermore, transferring fecal microbiota from adult chickens with high body weight into 1-day-old chicks reshaped the jejunal microbiota, mitigated inflammatory response, and improved chicken growth performance.

Conclusions

Our findings suggested that jejunal microbiota could affect chicken growth performance by mitigating intestinal inflammation.

Intestinal Immune Development Is Accompanied by Temporal Deviation in Microbiota Composition of Newly Hatched Pigeon Squabs

Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease later in life. However, knowledge about this interaction during the early posthatch development period in altrices is limited. To fill this gap, samples of intestinal content and tissue were collected from newly hatched pigeon squabs at four time points (days 0, 7, 14, and 21) for microbial community analysis and genome-wide transcriptome profiling, respectively. We show that the first week after hatching seems to be the critical window for ileal microbiota colonization and that a potentially stable microbiota has not yet been well established at 21 days of age. Regional transcriptome differences revealed that the jejunum rather than the ileum plays a crucial role in immunity at both the innate and adaptive levels. In the ileum, temporal deviation in innate immune-related genes mainly occurs in the first week of life and is accompanied by a temporal change in microbiota composition, indicating that the ileal innate mucosal immune system development regulated by microbial colonization occurs mainly in this period. Furthermore, we provide evidence that colonization by Escherichia and Lactobacillus within the first week of life is likely one of the causative factors for the induction of proinflammatory cytokine expression in the ileum. We also demonstrate that cellular adaptive immune responses mediated by Th17 cells following commensal-induced proinflammatory cytokine production in the ileum begin as early as the first week posthatch, but this cellular immunity seems to be less effective in terms of maintaining the inflammatory response balance. Because the induction of high levels of mucosal secretory IgA (SIgA) seems to take approximately 3 weeks, we favor the idea that humoral adaptive immunity might be less active, at least, during the first 2 weeks of life. Our data may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period. IMPORTANCE The pigeon (Columba livia), an altricial bird, is one of the most economically important farmed poultry for table purposes. Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease and potential productivity later in life. However, knowledge about this interaction during the early posthatch development period in altricial birds is limited. The study described herein is the first to try to provide insights into this interaction. Our data provide evidence on the mutual relationship between intestinal mucosal immune system development and commensal microbiota colonization in pigeon squabs and may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period.

Fecal Microbiota Transplantation Reshapes the Physiological Function of the Intestine in Antibiotic-Treated Specific Pathogen-Free Birds

The topic about the interactions between host and intestinal microbiota has already caught the attention of many scholars. However, there is still a lack of systematic reports on the relationship between the intestinal flora and intestinal physiology of birds. Thus, this study was designed to investigate it. Antibiotic-treated specific pathogen-free (SPF) bird were used to construct an intestinal bacteria-free bird (IBF) model, and then, the differences in intestinal absorption, barrier, immune, antioxidant and metabolic functions between IBF and bacteria-bearing birds were studied. To gain further insight, the whole intestinal flora of bacteria-bearing birds was transplanted into the intestines of IBF birds to study the remodeling effect of fecal microbiota transplantation (FMT) on the intestinal physiology of IBF birds. The results showed that compared with bacteria-bearing birds, IBF birds had a lighter body weight and weaker intestinal absorption, antioxidant, barrier, immune and metabolic functions. Interestingly, FMT contributed to reshaping the abovementioned physiological functions of the intestines of IBF birds. In conclusion, the intestinal flora plays an important role in regulating the physiological functions of the intestine.

Dietary aluminium intake disrupts the overall structure of gut microbiota in Wistar rats

Approximately, 40% of ingested dietary aluminium accumulates in the intestine, which has been considered a target organ for dietary aluminium exposure. The gut microbiota may be the first protective barrier against the toxic metal aluminium and a crucial mediator of the bioavailability of metal aluminium. We previously evaluated dietary aluminium intake and its health risks in a population from Jilin Province, China, and found that the average daily intake of aluminium in the diet of residents in Jilin Province was 0.163 mg/kg after the total diet survey. In the present study, the equivalent concentration of aluminium in rats was extrapolated by the average dietary aluminium intake in the population of Jilin Province based on body surface area. Furthermore, healthy adult Wistar rats were randomly divided into four groups (n = 15 for each group): a control group and three groups treated with aluminium solution (1, 10, and 100 mg/kg/day, intragastrically) for 28 days. Following treatment, necrosis of renal tubular epithelial cells, hyperplasia of bile ducts and hyperplasia of heart tissue, as well as fiber in the liver, kidney, and heart tissues of aluminium‐treated rats were observed, although there were no significant changes in the spleen and brain. Subsequently, fecal samples were withdrawn for 16S rRNA gene sequence analysis. It was found that aluminium decreased the microbiota diversity and changed the overall community structure of the gut microbiota, including three phyla and four genera, together with the regulation of 12 signaling pathways. Collectively, treatment with aluminium markedly altered the structure of the gut microbiota, suggesting that the disorders of intestinal flora induced by aluminium may be an important mechanism for aluminium toxicity.

Early Weaning Stress Induces Intestinal Microbiota Disturbance, Mucosal Barrier Dysfunction and Inflammation Response Activation in Pigeon Squabs

Early weaning stress has been reported to impair intestinal health in mammals. Like mammals, weaning of the pigeon squab, an altricial bird, is associated with social, environmental and dietary stress. However, understanding of weaning stress on intestinal functions is very limited in altricial birds, especially in squabs. This study was aimed to evaluate the effects of early weaning stress on intestinal microbiota diversity, architecture, permeability, the first line defense mechanisms, mucosal barrier functions, and immune cell responses. A total of 192 newly hatched squabs were randomly allocated into two groups, one weaned on day 7 and the other remained with the parent pigeons. Mucosal tissue and digesta in ileum, as well as blood samples, were collected from squabs (n = 8) on days 1, 4, 7, 10, and 14 postweaning. Our results showed that weaning stress induced immediate and long-term deleterious effects on both growth performance and intestinal barrier functions of squabs. Early weaning significantly increased ileal bacterial diversity and alters the relative abundance of several bacteria taxa. Weaning stress can also cause morphological and functional changes in ileum, including an atrophy in villi, an increase in permeability, and a variation in the mRNA expression of genes encoding mucins, immunoglobulins, tight junction proteins, toll-like receptors, and cytokines, as well as the concentration of secretory IgA. We concluded that the impaired intestinal barrier functions accompanied with early weaning stress seems to be the main reason for the poor growth rate after weaning in squabs. In addition, the disturbance of intestinal microbiota of early weaning stress in squabs coincided with dysfunction of intestinal mucosal barrier and activation of inflammation cell responses that were possibly mediated via the activation of toll-like receptors.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

BACKGROUND

Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.

RESULTS

Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.

CONCLUSIONS

Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

Oscillospira - a candidate for the next-generation probiotics

Oscillospira is a class of organism that often appears in high-throughput sequencing data but has not been purely cultured and is widely present in the animal and human intestines. There is a strong association between variation in Oscillospira abundance and obesity, leanness, and human health. In addition, a growing body of studies has shown that Oscillospira is also implicated in other diseases, such as gallstones and chronic constipation, and has shown some correlation with the positive or negative changes in its course. Sequencing data combined with metabolic profiling indicate that Oscillospira is likely to be a genus capable of producing short-chain fatty acids (SCFAs) such as butyrate, which is an important reference indicator for screening "next-generation probiotics ". Considering the positive effects of Oscillospira in some specific diseases, such as obesity-related metabolic diseases, it has already been characterized as one of the next-generation probiotic candidates and therefore has great potential for development and application in the future food, health care, and biopharmaceutical products.

Role of Physiology, Immunity, Microbiota, and Infectious Diseases in the Gut Health of Poultry

“Gut health” refers to the physical state and physiological function of the gastrointestinal tract and in the livestock system; this topic is often focused on the complex interacting components of the intestinal system that influence animal growth performance and host-microbial homeostasis. Regardless, there is an increasing need to better understand the complexity of the intestinal system and the various factors that influence gut health, since the intestine is the largest immune and neuroendocrine organ that interacts with the most complex microbiome population. As we face the post-antibiotic growth promoters (AGP) era in many countries of the world, livestock need more options to deal with food security, food safety, and antibiotic resilience to maintain agricultural sustainability to feed the increasing human population. Furthermore, developing novel antibiotic alternative strategies needs a comprehensive understanding of how this complex system maintains homeostasis as we face unpredictable changes in external factors like antibiotic-resistant microbes, farming practices, climate changes, and consumers’ preferences for food. In this review, we attempt to assemble and summarize all the relevant information on chicken gut health to provide deeper insights into various aspects of gut health. Due to the broad and complex nature of the concept of “gut health”, we have highlighted the most pertinent factors related to the field performance of broiler chickens.

Blautia-a new functional genus with potential probiotic properties?

Blautia is a genus of anaerobic bacteria with probiotic characteristics that occur widely in the feces and intestines of mammals. Based on phenotypic and phylogenetic analyses, some species in the genera Clostridium and Ruminococcus have been reclassified as Blautia, so to date, there are 20 new species with valid published names in this genus. An extensive body of research has recently focused on the probiotic effects of this genus, such as biological transformation and its ability to regulate host health and alleviate metabolic syndrome. This article reviews the origin and biological characteristics of Blautia and the factors that affect its abundance and discusses its role in host health, thus laying a theoretical foundation for the development of new functional microorganisms with probiotic properties.

Low pathogenic avian influenza virus infection retards colon microbiota diversification in two different chicken lines

BACKGROUND

A commensal microbiota regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiota population changes following a low pathogenicity avian influenza virus (AIV) of the H9N2 subtype infection of two different chicken breeds was conducted.

METHODS

Colon samples were taken from control and infected groups at various timepoints post infection. 16S rRNA sequencing on an Illumina MiSeq platform was performed on the samples and the data mapped to operational taxonomic units of bacterial using a QIIME based pipeline. Microbial community structure was then analysed in each sample by number of observed species and phylogenetic diversity of the population.

RESULTS

We found reduced microbiota alpha diversity in the acute period of AIV infection (day 2-3) in both Rhode Island Red and VALO chicken lines. From day 4 post infection a gradual increase in diversity of the colon microbiota was observed, but the diversity did not reach the same level as in uninfected chickens by day 10 post infection, suggesting that AIV infection retards the natural accumulation of colon microbiota diversity, which may further influence chicken health following recovery from infection. Beta diversity analysis indicated a bacterial species diversity difference between the chicken lines during and following acute influenza infection but at phylum and bacterial order level the colon microbiota dysbiosis was similar in the two different chicken breeds.

CONCLUSION

Our data suggest that H9N2 influenza A virus impacts the chicken colon microbiota in a predictable way that could be targeted via intervention to protect or mitigate disease.

Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period

Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.

The Spatial and Temporal Characterization of Gut Microbiota in Broilers

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

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.

The Succession of the Gut Microbiota in Insects: A Dynamic Alteration of the Gut Microbiota During the Whole Life Cycle of Honey Bees (Apis cerana)

The Asian honey bee Apis cerana is a valuable biological resource insect that plays an important role in the ecological environment and agricultural economy. The composition of the gut microbiota has a great influence on the health and development of the host. However, studies on the insect gut microbiota are rarely reported, especially studies on the dynamic succession of the insect gut microbiota. Therefore, this study used high-throughput sequencing technology to sequence the gut microbiota of A. cerana at different developmental stages (0 days post emergence (0 dpe), 1 dpe, 3 dpe, 7 dpe, 12 dpe, 19 dpe, 25 dpe, 30 dpe, and 35 dpe). The results of this study indicated that the diversity of the gut microbiota varied significantly at different developmental stages (ACE, P = 0.045; Chao1, P = 0.031; Shannon, P = 0.0019; Simpson, P = 0.041). In addition, at the phylum and genus taxonomic levels, the dominant constituents in the gut microbiota changed significantly at different developmental stages. Our results also suggest that environmental exposure in the early stages of development has the greatest impact on the gut microbiota. The results of this study reveal the general rule of gut microbiota succession in the A. cerana life cycle. This study not only deepens our understanding of the colonization pattern of the gut microbiota in workers but also provides more comprehensive information for exploring the colonization of the gut microbiota in insects and other animals.

Preliminary study on theory of spleen injury caused by exogenous cold and dampness based on intestinal microecology

Exogenous cold and dampness is most likely to damage spleen Yang, which affects the spleen's function of governing transportation and dispersing essence. Human intestinal flora is widely involved in the regulation of gastrointestinal digestive functions. Therefore, based on the general understanding of the correlation between intestinal microecology and the spleen in modern research, this paper discusses the response mechanism of intestinal microflora to random exposure to cold and dampness environment in the process of gastrointestinal digestive dysfunction, and suggests that intestinal microecology imbalance may be one of the mechanisms of spleen injury caused by exogenous cold and dampness in traditional Chinese medicine.

Assessment of Microbiota Modulation in Poultry to Combat Infectious Diseases

Simple Summary

This research was designed to evaluate the differences in caecal microbiota in broilers reared under two different farm conditions (commercial vs. optimal) during the growing period, using 16 rRNA sequencing analysis. Microbiota composition is affected by stress; for this reason, it could be considered a biomarker of poultry welfare and health. The main results demonstrated that no statistically significant differences were found between groups on microbiota composition from the beginning to the mid-period. However, significant differences were found at the end of growing, when a higher level of microbiota diversity was observed in the optimal farm conditions group. In conclusion, microbiota composition could be an interesting tool to evaluate new management conditions at field level, and could be developed to improve animal welfare during the growing period.

Abstract

Poultry is one of the main agricultural sub-sectors worldwide. However, public concern regarding animal welfare and antimicrobial resistance has risen in recent years. Due to the influence of management practices on microbiota, it might be considered to evaluate poultry welfare and health. Therefore, the objective of this research was to analyse the influence on microbiota balance of broilers under commercial and optimal farm conditions, using 16S rRNA sequencing analysis. The research was performed in two identical poultry houses (commercial vs. optimal). Results showed a higher level of microbiota complexity in the group reared under optimal farm conditions at the end of rearing. Regarding microbiota composition, Firmicutes was the dominant phylum during the entire growing period. However, the second most prevalent phylum was Proteobacteria at the arrival day, and Bacteroidetes from the mid-period onward in both groups. Moreover, the most predominant genera identified were Oscillospira, Ruminococcus, Bacteroides, and Coprococcus. In conclusion, it is necessary to optimize farm management as much as possible. Using gut microbiota diversity and composition as biomarkers of animal health could be an important tool for infectious disease control, with the aim of reducing the administration of antibiotics at field level.

Effect of fermentation bed on bacterial growth in the fermentation mattress material and cecum of ducks

The composition of microorganisms in the gastrointestinal tract is closely related to the intestinal microenvironments and the exterior growth environments of host. In this study, 16S rDNA sequencing technology was adopted to investigate the influence of fermentation bed on the cecum microorganisms of ducks. Two feeding density treatment groups were set up, including group A (n = 4brids/m²) and group B (n = 6brids/m²). Samples were collected from the intermediate core fermentation layer (10-20 cm) of the fermented mattress materials and from the intestinal contents of ducks at 4, 6 and 8 weeks, respectively. Results showed that Bacteroidetes (20.12-27.17%) and Ruminococcaceae UCG-014 (2.97-10.1%) were the predominant microorganisms in duck cecum, while the Truepera (5.08-6.29%), Pricia (4.44-5.44%) and Luteimonas (3.62-4.99%) were the dominant microorganisms in fermentation mattress material. The cecum bacteria exhibited great difference among different growth periods of the ducks. Increasing the stocking density of ducks had a negative effect on the beneficial bacteria in the cecum. The microbial populations in fermentation mattress material were very different from that in the cecal. In summary, our findings can provide a scientific data for the rational use of fermentation bed feeding mode in poultry production.

Characterization of fecal branched-chain fatty acid profiles and their associations with fecal microbiota in diarrheic and healthy dairy calves

Branched-chain fatty acids (BCFA) have recently been reported to play a role in human gut health during early life. However, little information is available on the fecal BCFA profiles in young ruminants and whether they are associated with the development of neonatal calf diarrhea. The objectives of this study were to (1) characterize BCFA profiles in feces collected from young calves, (2) compare the fecal BCFA composition between diarrheic and nondiarrheic dairy calves, and (3) explore the potential relationships between BCFA and microbiota in the feces. A total of 32 male Holstein dairy calves (13 ± 3 d old) with the same diet management were grouped as diarrheic (n = 16) or healthy (n = 16) based on fecal score (determined by liquid fecal consistency with some solid particles); diarrhea cases were defined as fecal score ≥2 for at least 2 d. Fecal samples were collected on the seventh day after calf arrival, and the fecal BCFA and microbial profiles were assessed using gas chromatograph and amplicon sequencing, respectively. In total, 7 BCFA were detected in the feces of all dairy calves; however, the concentrations of fecal BCFA differed between diarrheic and nondiarrheic calves. Specifically, the concentrations of iso-C16:0, iso-C17:0, anteiso-C17:0, and total even-chain BCFA were significantly higher in the feces of diarrheic calves. When the associations between BCFA and bacteria were studied, the relative abundance of Eggerthella was positively correlated with the concentrations of iso-C16:0 (ρ = 0.67), iso-17:0 (ρ = 0.77), anteiso-C17:0 (ρ = 0.73), and iso-C18:0 (ρ = 0.65), whereas the relative abundance of Subdoligranulum was positively correlated with the concentrations of iso-C14:0 (ρ = 0.62), iso-C15:0 (ρ = 0.78), and anteiso-C15:0 (ρ = 0.63). Use of random forest algorithm showed that BCFA such as anteiso-C15:0, iso-C16:0, iso-C17:0, iso-C18:0, and total even-chain BCFA could be used as biomarkers to differentiate diarrheic calves from healthy ones. Our findings generated fundamental knowledge on the potential roles of BCFA in neonatal calf gut health. Follow-up studies with larger animal populations are warranted to validate the feasibility of using BCFA as indicators of health status in neonatal calves.

Early Life Inoculation With Adult-Derived Microbiota Accelerates Maturation of Intestinal Microbiota and Enhances NK Cell Activation in Broiler Chickens

Studies in mammals, including chickens, have shown that the development of the immune system is affected by interactions with intestinal microbiota. Early life microbial colonization may affect the development of innate and adaptive immunity and may contribute to lasting effects on health and resilience of broiler chickens. We inoculated broiler chickens with adult-derived-microbiota (AM) to investigate their effects on intestinal microbiota composition and natural killer (NK) cells, amongst other immune cells. We hypothesized that AM inoculation directly upon hatch (day 0) would induce an alteration in microbiota composition shortly after hatch, and subsequently affect (subsets of) intestinal NK cells and their activation. Microbiota composition of caecal and ileal content of chickens of 1, 3, 7, 14, 21, and 35 days of age was assessed by sequencing of 16S ribosomal RNA gene amplicons. In parallel, subsets and activation of intestinal NK cells were analyzed by flow cytometry. In caecal content of 1- and 3-day-old AM chickens, a higher alpha-diversity (Faith's phylogenetic diversity) was observed compared to control chickens, whereas ileal microbiota were unaffected. Regarding beta-diversity, caecal microbiota profiles could be clustered into three distinct community types. Cluster A represented caecal microbiota of 1-day-old AM chickens and 1- and 3-day-old control chickens. Cluster B included microbiota of seven of eight 3- and 7-day-old AM and 7-day-old control chickens, and cluster C comprised microbiota of all chickens of 14-days and older, independent of inoculation. In 3-day-old AM chickens an increase in the percentages of intestinal IL-2Rα+NK cells and activated NK cells was observed compared to control chickens of the same age. In addition, an increase in relative numbers of intestinal cytotoxic CD8αα+T cells was observed in 14- and 21-day-old AM chickens. Taken together, these results indicate that early exposure to AM shapes and accelerates the maturation of caecal microbiota, which is paralleled by an increase in IL-2Rα+NK cells and enhanced NK cell activation. The observed association between early life development of intestinal microbiota and immune system indicates possibilities to apply microbiota-targeted strategies that can accelerate maturation of intestinal microbiota and strengthen the immune system, thereby improving the health and resilience of broiler chickens.

Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period

Simple Summary

This study was conducted to characterise the caecal microbiota in two broiler management systems (fast and slow-growing) during the growing period, using 16S rRNA sequencing analysis. Because of the essential role of the caecal bacteria in poultry health and productivity, these data could be considered as a biomarker of health status and will make it possible to evaluate different treatments applied in animals. The main results demonstrated that microbiota is in constant development throughout the growing period for both management systems, and the most abundant bacteria groups are related to better productive performance and intestinal health.

Abstract

Caecal microbiota and its modulation play an important role in poultry health, productivity and disease control. Moreover, due to the emergence of antimicrobial-resistant bacteria, society is pressing for a reduction in antibiotic administration by finding effective alternatives at farm level, such as less intensified production systems. Hence, the aim of this study was to characterise the caecal microbiota in two different broiler management systems, fast and slow-growing, using 16S rRNA sequencing analysis. To this end 576 broilers were reared in two different management systems (fast and slow-growing). Results showed that Firmicutes represented the dominant phylum for both systems. At the onset, Proteobacteria was the second prevalent phylum for fast and slow-growing breeds, outnumbering the Bacteroidetes. However, during the rest of the production cycle, Bacteroidetes was more abundant than Proteobacteria in both groups. Finally, regardless of the management system, the most predominant genera identified were Oscillospira spp., Ruminococcus spp., Coprococcus spp., Lactobacillus spp. and Bacteroides spp. In conclusion, fast and slow-growing broiler microbiota are in constant development throughout rearing, being relatively stable at 21 days of age. Regarding the genus, it should be noted that the three most abundant groups for both systems, Ruminococcus spp., Lactobacillus spp. and Bacteroides spp., are related to better productive performance and intestinal health.

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

Background

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

Results

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

Conclusion

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

Composition and Function of Chicken Gut Microbiota

Simple Summary

Chickens evolved for millions of years to be hatched in a nest in contact with an adult hen. However, current commercial production of chickens is based on hatching chicks in a clean hatchery environment in the absence of adult hens. The ancestors of domestic chickens inhabited a living environment different from that used for current commercial production. Currently, the lifespan of broilers is around 5 weeks, the lifespan of egg layers is around one year while chickens can live for 15–20 years. This means that studies on chicken–microbiota interactions are of specific importance. The intestinal tract of commercially hatched chicks is gradually colonised from environmental sources only, however, if the chicks are provided experimentally with microbiota from a hen they can be colonised by adult-type microbiota from the very first days of life and become resistant to infections with pathogenic Escherichia coli, Clostridium perfringens, or Salmonella. Because of such specificities in the interactions of chickens with their gut microbiota, current knowledge in this area is critically presented in this review.

Abstract

Studies analyzing the composition of gut microbiota are quite common at present, mainly due to the rapid development of DNA sequencing technologies within the last decade. This is valid also for chickens and their gut microbiota. However, chickens represent a specific model for host–microbiota interactions since contact between parents and offspring has been completely interrupted in domesticated chickens. Nearly all studies describe microbiota of chicks from hatcheries and these chickens are considered as references and controls. In reality, such chickens represent an extreme experimental group since control chicks should be, by nature, hatched in nests in contact with the parent hen. Not properly realising this fact and utilising only 16S rRNA sequencing results means that many conclusions are of questionable biological relevance. The specifics of chicken-related gut microbiota are therefore stressed in this review together with current knowledge of the biological role of selected microbiota members. These microbiota members are then evaluated for their intended use as a form of next-generation probiotics.

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

Background

The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare.

Results

In this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identified significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterised the development of the microbiota at each intestinal site over time.

Conclusions

Our study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

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

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

Rearing pattern alters porcine myofiber type, fat deposition, associated microbial communities and functional capacity

BACKGROUND

The Chinese believe that the meat of pigs reared in the past with free range tastes better than that of the pigs reared indoor on a large scale today. Gastrointestinal microflora is closely associated with the main factor of meat flavour, including fibre characteristics and lipid metabolism. Our method in this study involved different raising patterns within the semi free-grazing farm (FF) or indoor feeding farm (DF), the measurement of fat deposition and myofiber type by paraffin section and reverse transcription polymerase chain reaction and the identification of microbiome and functional capacities associated with meat quality through metagenomic sequencing.

RESULTS

Results showed that the fat area in muscle and adipose tissue and the myofiber density significantly increased in the pigs of the FF group. The relative abundance of bacteria associated with lipid metabolism, such as g_Oscillibacter, in the feces of the FF group was higher than that in DF group, and the relative abundance of some bacteria with probiotic function, including g_Lactobacillus and g_Clostridium, was lower than that in DF group. The abundance of g_Clostridium was significantly positively correlated with the intramuscular fat area, whereas health-related bacteria, such as g_Butyricicoccus, g_Eubacterium, g_Phascolarctobacterium and g_Oribacterium, was significantly negatively correlated with abdominal fat area, myofiber density and adipose triglyceride lipase (ATGL) mRNA expression. KEGG analysis showed that pigs raised in semi free-grazing farm can activate the pathway of inosine monophosphate (IMP) biosynthesis, glycolysis/gluconeogenesis and alanine, aspartate and glutamate metabolism.

CONCLUSIONS

Free range feeding improves meat quality by changing the fibre type, myofiber density and metabolic pathways related to flavour amino acids, IMP or glycolysis/gluconeogenesis in muscle. However, prolonged feeding cycle increases fat deposition and associated microbial communities.