Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Effect of orally administered B. subtilis-cNK-2 on growth performance, immunity, gut health, and gut microbiome in chickens infected with Eimeria acervulina and its potential as an alternative to antibiotics

This study investigated the best oral delivery strategy (gavage or feed) for the B. subtilis expressing the chicken anti-microbial peptide cNK-2 (B. subtilis-cNK-2) in comparison to monensin, in chickens challenged with Eimeria acervulina (E. acervulina). A total of 120 broiler chickens were randomly allocated into 5 treatment groups in a completely randomized design: 1) uninfected chickens fed with basal diet (NC), 2) E. acervulina-infected chickens fed a basal diet (PC), 3) E. acervulina-infected chickens fed a basal diet supplemented with 90 mg monensin/kg feed (MO), 4) E. acervulina-infected chickens fed a basal diet and orally gavaged with B. subtilis-cNK-2 at 1 × 1010 cfu/d (CNK-O), and 5) E. acervulina-infected chickens fed a basal diet mixed with B. subtilis-cNK-2 at 1 × 1010 cfu/kg feed (CNK-F). The challenge consisted of 5,000 sporulated E. acervulina oocysts through oral gavage on d 15. Body weights were measured on d 7, 14, 21, and 23. Duodenal tissue and digesta samples were collected at 6 d postinfection (dpi) to assess the gut integrity, oxidative stress, mucosal immunity, and the gut microbiome. Fecal samples were collected from 6 to 8 dpi to enumerate the oocyst shedding. Chickens in the CNK-O group showed improved (P < 0.05) growth performance, gut integrity, and mucosal immunity compared to PC, comparable to chickens in the MO group. Chickens in the MO, CNK-F, and CNK-O treatment groups all showed lower (P < 0.05) oocyst shedding compared to PC chickens. Moreover, distinct cytokine profile, oxidative stress measures, tight junction proteins, and shifts in the gut microbiome with associated functional changes were observed in all challenge groups. In conclusion, we showed that the oral administration of B. subtilis-cNK-2 improved growth performance, enhanced local protective immunity, and reduced fecal oocyst shedding in broiler chickens infected with E. acervulina, demonstrating potential use of B. subtilis-cNK-2 as an alternative to antibiotics to protect chickens against coccidiosis.

Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study

BACKGROUND

Foodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter.

RESULTS

Analysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species.

CONCLUSIONS

These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.

Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens

BACKGROUND

Feed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.

METHODS

In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.

RESULTS

The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.

CONCLUSIONS

This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.

Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?

Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.

Dietary Chinese herbal mixture supplementation improves production performance by regulating reproductive hormones, antioxidant capacity, immunity, and intestinal health of broiler breeders

Chinese herbs have been used as feed additives and are commonly utilized in domestic intensive livestock farming. However, their impact on the production performance and intestinal health of broiler breeders has yet to be thoroughly explored. This study aimed to evaluate the effects of a Chinese herbal mixture (CHM) on the production performance of broiler breeders in terms of reproductive hormones, antioxidant capacity, immunity, and intestinal health of broiler breeders. A total of 336 thirty-wk-old hens were randomly allotted to 4 groups with 6 replicates of fourteen hens each, which fed a basal diet supplemented with 0 (CON), 500 (CHM500), 1,000 (CHM1000), and 1,500 (CHM1500) mg/kg CHM for 56 days, respectively. Our results showed that dietary supplementation with CHM1000 increased the laying rate and number of SYF and decreased the feed conversion ratio (P < 0.05). All CHM groups increased oviduct and ovarian indexes, serum E2 and T-AOC levels, and decreased serum TG and MDA levels compared with CON (P < 0.05). In comparison to the CON group, the CHM1000 and CHM1500 groups increased serum ALB, IgM, and IL-10 levels, whereas the CHM1000 group also increased serum TP and SOD levels, and the CHM1500 group increased serum P and decreased serum TNF-α (P < 0.05). The addition of CHM increased FSHR expressions in the ovary, Claudin-1 expressions in the jejunum, and SOD1 expressions in the liver and ovary, but decreased the mRNA expressions of INH in the ovary as well as IL-2 and IL-6 expressions in the jejunum (P < 0.05). Moreover, CHM500 and CHM1000 groups increased CAT, GPx, and HO-1 expression in the ovary, and SOD1 and GPx expression in the jejunum, while decreasing IL-17A expression in the jejunum (P < 0.05). In addition, CHM1000 and CHM1500 groups increased villus height, VCR, and the mRNA expressions of Nrf2, HO-1, Occludin, and MUC2 in the jejunum, and IL-10 expression in the ovary, while decreasing IL-2 and IL-17A expression in the ovary, in addition to increasing GPx, Nrf2, HO-1, NQO1, and IL-10 expression in the liver (P < 0.05). Supplementation with CHM1000 increased ESR-α, ESR-β, GnRH, Nrf2, and NQO1 expression in the ovary, but decreased IFN-γ expression in the ovary as well as crypt depth in the jejunum (P < 0.05). Supplementing CHM1500 increased NQO1 and ZO-1 expression in the jejunum and decreased IL-2 in the liver (P < 0.05). The high-throughput sequencing results showed that dietary CHM1000 supplementation altered the composition of the intestinal microbiota, as evidenced by the regulation of the genera Lactobacillus, Faecalibacterium, and Phascolarctobacterium. PICRUSt analysis revealed that metabolic pathways of bacterial chemotaxis, butanoate metabolism, and synthesis and degradation of ketone bodies were enriched in the CHM1000 group. Spearman's correlation analysis indicated that the differentiated genera were significantly associated with the production performance, serum hormone, and gut barrier-related genes. Taken together, supplementation of CHM, especially at 1,000 mg/kg, could improve production performance by regulating reproductive hormones, antioxidant capacity, immunity, and intestinal health of broiler breeders, and maybe provide insights into its application as a potential feed additive to promote the performance of broiler breeders.

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

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

Integrative analysis of microbiome and metabolome reveals the linkage between gut microbiota and carp growth

Gut microbiota and their metabolites are increasingly recognized for their crucial role in regulating the health and growth of the host. The mechanism by which the gut microbiome affects the growth rate of fish (Cyprinus carpio) in the rice-fish coculture system, however, remains unclear. In this study, the gut contents of the fast-growing and slow-growing (FG and SG) carp were collected from the rice-fish coculture system for both the fish gut microbiome and metabolome analyses. High throughput 16 S rRNA gene sequencing showed that the overall gut microbiota of FG group was distinct from that of SG group. For example, the cyanobacteria were highly enriched in the guts of SG carp (18.61%), in contrast, they only represented a minor fraction of gut microbiota for FG group (<0.20%). The liquid chromatography-mass spectrometry (LC-MS)-based metabolomics analysis revealed that 191 identified metabolites mostly located in 18 KEGG pathways were differentially present between the two groups, of which more than 50% of these metabolites were involved in lipid and amino acids metabolism. Compared with the FG group, the gut microbiota of SG group significantly enriched the metabolic pathways involved in the steroid (hormone) biosynthesis, whereas reducing those associated with beta-alanine metabolism, biosynthesis of unsaturated fatty acids and bile secretion. The enrichment and depletion of these metabolic pathways resulted in an increase in steroid metabolites and a decrease in the concentration of spermidine, which may have a major impact on the growth rate of carp. The metabolome results were further supported by the predicated KEGG functions of the gut microbiomes of the two groups, pointing out that the gut microbiota could substantially affect the growth of fish via their unique metabolic functions. Together, our integrated fish gut microbiome and metabolome analysis has substantial implications for the development of engineered microbiome technologies in aquaculture.

Orally delivered Bacillus subtilis expressing chicken NK-2 peptide stabilizes gut microbiota and enhances intestinal health and local immunity in coccidiosis-infected broiler chickens

We recently reported a stable Bacillus subtilis-carrying chicken NK-lysin peptide (B. subtilis-cNK-2) as an effective oral delivery system of an antimicrobial peptide to the gut with therapeutic effect against Eimeria parasites in broiler chickens. To further investigate the effects of a higher dose of an oral B. subtilis-cNK-2 treatment on coccidiosis, intestinal health, and gut microbiota composition, 100 (14-day-old) broiler chickens were allocated into 4 treatment groups in a randomized design: 1) uninfected control (CON), 2) infected control without B. subtilis (NC), 3) B. subtilis with empty vector (EV), and 4) B. subtilis with cNK-2 (NK). All chickens, except the CON group, were infected with 5,000 sporulated Eimeria acervulina (E. acervulina) oocysts on d 15. Chickens given B. subtilis (EV and NK) were orally gavaged (1 × 10¹² cfu/mL) daily from d 14 to 18. Growth performances were measured on d 6, 9, and 13 postinfection (dpi). Spleen and duodenal samples were collected on 6 dpi to assess the gut microbiota, and gene expressions of gut integrity and local inflammation makers. Fecal samples were collected from 6 to 9 dpi to enumerate oocyst shedding. Blood samples were collected on 13 dpi to measure the serum 3-1E antibody levels. Chickens in the NK group showed significantly improved (P < 0.05) growth performance, gut integrity, reduced fecal oocyst shedding and mucosal immunity compared to NC. Interestingly, there was a distinct shift in the gut microbiota profile in the NK group compared to that of NC and EV chickens. Upon challenge with E. acervulina, the percentage of Firmicutes was reduced and that of Cyanobacteria increased. In NK chickens, however, the ratio between Firmicutes and Cyanobacteria was not affected and was similar to that of CON chickens. Taken together, NK treatment restored dysbiosis incurred by E. acervulina infection and showed the general protective effects of orally delivered B. subtilis-cNK-2 on coccidiosis infection. This includes reduction of fecal oocyst shedding, enhancement of local protective immunity, and maintenance of gut microbiota homeostasis in broiler chickens.

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.

Metagenomic analysis of gut microbiota and antibiotic-resistant genes in Anser erythropus wintering at Shengjin and Caizi Lakes in China

Migratory birds are the primary source and reservoir of antibiotic-resistant genes (ARGs) related to their gut microbes. In this study, we performed metagenomics analysis to study the gut microbial communities and ARGs of Anser erythropus wintering at Shengjin (SJ) and Caizi (CZ) Lakes. The results showed that bacteria, fungi, viruses, and archaea were the dominant gut microbes. Principal component analysis (PCA) indicated that the microbiota compositions significantly differed between the two populations. Diet may be the most crucial driver of the gut microbial communities for A. erythropus. This species fed exclusively on Poaceae spp. at Shengjin Lake and primarily on Carex spp. at Caizi Lake. Tetracycline, macrolide, fluoroquinolone, phenicol, and peptide antibiotics were the dominant resistant types. ARGs had a significantly higher abundance of operational taxonomic units (OTUs) in the Shengjin Lake samples than in Caizi Lake samples. PCA indicated that most Shengjin Lake samples significantly differed in gut microbiota composition from those obtained at Caizi Lake. This difference in gut microbiota composition between the two lakes' samples is attributed to more extensive aquaculture operations and poultry farms surrounding Shengjin Lake than Caizi Lake. ARGs-microbes associations indicated that 24 bacterial species, commonly used as indicators of antibiotic resistance in surveillance efforts, were abundant in wintering A. erythropus. The results revealed the composition and structural characteristics of the gut microbiota and ARGs of A. erythropus, pointing to their high sensitivities to diet habits at both lakes. This study also provides primary data for risk prevention and control of potential harmful pathogens that could endanger public health and therefore are of major significance to epidemiological and public health.

Application of Baltic Pine (Pinus sylvestris) Needle Extract as a Gut Microbiota-Modulating Feed Supplement for Domestic Chickens (Gallus gallus)

The valorization of wood industry residues is very desirable from a circular economy perspective. Pine needle extracts are known for their health-promoting properties and therefore can be used as herbal remedies and nutritional supplements. Since the withdrawal of antibiotics as growth promoters in the European Union, natural feed additives that improve poultry health and production are needed. It was proposed that pine needle extract could be a good alternative to antibiotic usage at sub-therapeutic concentrations. The results relevant to our assumption could be obtained by using domestic chickens as an in vivo model for the evaluation of gut microbiota-altering properties of pine needle extract as an herbal supplement. We tested the antimicrobial effects of Baltic pine (Pinus sylvestris) needle extract. Then, we used chicken (Gallus gallus) that received feed supplemented with two different concentrations of the extract for 40 days to evaluate the changes in gut microbiota using 16S rRNA gene sequencing. This preliminary study demonstrated trends toward dose-dependent desirable changes in broiler microbiome, such as a reduction in the relative abundance of Campylobacter.

Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers

Despite the negative impacts of Salmonella intestinal colonization on human health, Salmonella is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of Salmonella across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between Salmonella enterica serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (n = 156/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators/room, 11 chicks/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators/breed, 108 total) were challenged with Salmonella Typhimurium (ST) (1 × 108 CFU/ml) via oral gavage while the remaining chicks (n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq. Salmonella Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7 days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (p < 0.05). Salmonella Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as Mollicutes RF39, Shuttleworthia, Flavonifractor, and Oscillibacter compared to broilers that were unchallenged with Salmonella Typhimurium (p < 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to Salmonella Typhimurium challenge. Thus, both broiler breed and Salmonella Typhimurium can impact the intestinal microbiota.

Metformin modulates the gut microbiome in broiler breeder hens

Broiler breeder hens, the parent stock of commercial broiler chickens, are genetically selected for rapid growth. Due to a longer production period and the focus of genetic selection on superior carcass traits in their progeny, these hens have the propensity to gain excess adipose tissue and exhibit severe ovarian dysfunction, a phenotype that is similar to human polycystic ovary syndrome (PCOS). Metformin is an antihyperglycemic drug approved for type 2 diabetes that is prescribed off-label for PCOS with benefits on metabolic and reproductive health. An additional effect of metformin treatments in humans is modulation of gut microbiome composition, hypothesized to benefit glucose sensitivity and systemic inflammation. The effects of dietary metformin supplementation in broiler breeder hens have not been investigated, thus we hypothesized that dietary metformin supplementation would alter the gut microbiome of broiler breeder hens. Broiler breeder hens were supplemented with metformin at four different levels (0, 25, 50, and 75 mg/kg body weight) from 25 to 65 weeks of age, and a subset of hens (n = 8-10 per treatment group) was randomly selected to undergo longitudinal microbiome profiling with 16S rRNA sequencing. Metformin impacted the microbial community composition in 75 mg/kg metformin compared to controls (adjusted PERMANOVA p = 0.0006) and an additional dose-dependent difference was observed between 25 mg/kg and 75 mg/kg (adjusted PERMANOVA p = 0.001) and between 50 mg/kg and 75 mg/kg (adjusted PERMANOVA p = 0.001) but not between 25 mg/kg and 50 mg/kg (adjusted PERMANOVA p = 0.863). There were few differences in the microbiome attributed to hen age, and metformin supplementation did not alter alpha diversity. Bacteria that were identified as differentially relatively abundant between 75 mg/kg metformin treatment and the control, and between metformin doses, included Ruminococcus and members of the Clostridia family that have been previously identified in human trials of PCOS. These results demonstrate that metformin impacts the microbiome of broiler breeder hens in a dose-dependent manner and several findings were consistent with PCOS in humans and with metformin treatment in type 2 diabetes. Metformin supplementation is a potentially promising option to improve gut health and reproductive efficiency in broiler breeder hens.

Dynamic Changes in the Gut Microbial Community and Function during Broiler Growth

During the entire growth process, gut microbiota continues to change and has a certain impact on the performance of broilers. Here, we used 16S rRNA gene sequencing to explore the dynamic changes in the fecal bacterial communities and functions in 120 broilers from 4 to 16 weeks of age. We found that the main phyla (Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides) accounted for more than 93.5% of the total bacteria in the feces. The alpha diversity of the fecal microbiota showed a downward trend with time, and the beta diversity showed significant differences at various time points. Then, the study on the differences of microbiota between high-weight (HW) and low-weight (LW) broilers showed that there were differences in the diversity and composition of microbiota between high- and low-weight broilers. Furthermore, we identified 22 genera that may be related to the weight change of broilers. The analysis of flora function reveals their changes in metabolism, genetic information processing, and environmental information processing. Finally, combined with microbial function and cecal transcriptome results, we speculated that microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect body weight (BW). Our results will help to expand our understanding of intestinal microbiota and provide guidance for the production of high-quality broilers. IMPORTANCE The intestinal microbiota has a certain impact on the performance of broilers. However, the change of intestinal microbiota after 4 weeks of age is not clear, and the mechanism of the effect of microorganisms on the weight change of broilers needs more exploration. After 4 weeks of age, the alpha diversity of microorganisms in broiler feces decreased, and the dominant bacteria were Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides. There were differences in microbiota diversity and composition between high- and low-weight broilers. Intestinal microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect the body weight. The results are helpful to increase the understanding of intestinal microbiota and provide reference for the production of high-quality broilers.

Development and Evaluation of a Commercial Direct-Fed Microbial (Zymospore®) on the Fecal Microbiome and Growth Performance of Broiler Chickens under Experimental Challenge Conditions

Simple Summary

Probiotics are recognized for their beneficial health-promoting properties, through competitive exclusion, promoting maintenance of intestinal epithelial integrity and host immune system homeostasis. The use of some spore-forming bacteria from the genus Bacillus has earned interest as a direct-fed microbial in recent years as a potential alternative to antibiotic growth promoters and growth enhancers. The present study evaluates the use of a Bacillus subtilis spore-based direct-fed microbial (Zymospore^®, Vetanco, Villa Martelli, Argentina) compared to an antibiotic growth promoter on the performance of broiler chickens under experimental intestinal challenge conditions. The results suggest that Zymospore^® increases the diversity of the broiler fecal microbiota and is an acceptable substitute for commonly used antibiotic growth promoters under defined and non-defined intestinal dysbiosis conditions.

Abstract

Direct-fed microbials (DFM) are added to broiler chicken diets in order to promote the proliferation of beneficial intestinal bacterial populations, which may lead to gains in performance efficiency and, potentially, reduce the level of enteric pathogens in the broiler chickens. The selection and laboratory evaluation of Bacillus subtilis strains as well as the experimental trial results of a novel Bacillus-based commercial DFM product are described. Fifteen wild-type Bacillus subtilis strains were characterized and assayed for their enzyme production capability, spore resistance to pH, salinity, and temperature, and ability to inhibit the growth of E. coli and Salmonella spp. The final DFM formulation was evaluated and compared to an antibiotic growth promoter (AGPs) in two experimental trials. In Experiment 1, broilers were given a defined challenge of Eimeria spp. and Clostridium perfringens to induce intestinal dysbiosis. The optimal dose of the DFM was determined to be 0.3 kg/ton of feed. At this dose, the broilers fed the DFM performed as well as the Flavomycin^®-fed broilers. Further, intestinal microbiome analysis indicates that the use of the DFM enhances bacterial diversity of the gut flora by day 5 of age, increasing levels of lactic acid bacteria (LAB) and Clostridiales by 25 days of age, which may enhance the digestion of feed and promote growth of the birds. In Experiment 2, the broilers were raised on recycled litter and given an undefined challenge orally to mimic commercial growth conditions. In this trial, the DFM performed as well as the bacitracin methylene disalicylate (BMD)-11%-fed birds. The results of the present studies suggest that this novel DFM, Zymospore^®, improves the performance of broiler chickens under experimental challenge conditions as effective as an AGP, providing a safe and effective substitute to the poultry industry.

Effect of Dietary Bacillus licheniformis Supplementation on Growth Performance and Microbiota Diversity of Pekin Ducks

This experiment was conducted to investigate the effects of different concentrations of Bacillus licheniformis (B. licheniformis) on growth performance and microbiota diversity of Pekin ducks. Three hundred 1-day-old healthy Pekin ducks were randomly divided into 5 groups with 6 replicates per group and 10 ducks per replicate. The five treatments supplemented with basal diets containing: either 0 (group CON), 200 (group LLB), 400 (group MLB), and 800 (group HLB) mg/kg B. licheniformis or 150 mg/kg aureomycin (group ANT) for 42 days, respectively, and were sacrificed and sampled in the morning of the 42nd day for detection of relevant indexes. The results showed as follows: The feed conversion ratio of the LLB group and MLB groups were lower than the CON group (P < 0.05). The body weight and average daily feed intake of the MLB group were significantly higher than that of the CON group and ANT group (P < 0.05). Compared with the CON group, the MLB group significantly increased the content of IgA (P < 0.05) and proinflammatory IL-6 were significantly decreased (P < 0.05), besides, the activity of SOD and T-AOC were also significantly increased in the MLB group (P < 0.05). The 16S rRNA analysis showed that B. licheniformis treatments had no effect (P > 0.05) on the alpha diversities of the intestine. The addition of B. licheniformis had a dynamic effect on the abundance of cecal microflora of Pekin ducks, and 1-21 d increased the diversity of microflora, while 21d-42 d decreased it. Compared with the CON group, the relative abundance of Epsilonbacteraeota in the MLB group was significantly increased on Day 21 (P < 0.05), and that of Tenericutes in the LLB group was significantly increased as well (P < 0.05). At 42 d, the relative abundance of Bacteroidetes in LLB, MBL, HBL, and ANT groups was significantly increased (P < 0.05). In addition, the addition of B. licheniformis increased the amount of SCAF-producing bacteria in the intestinal microbiota, such as Lachnospiraceae, Collinsella, Christensenellaceae, and Bilophila. The PICRUSt method was used to predict the intestinal microbiota function, and it was found that lipid transport and metabolism of intestinal microbiota in the MLB group were significantly affected. Overall, these results suggest diet supplemented with B. licheniformis improved growth performance, immune status, antioxidant capacity, and modulated intestinal microbiota in Pekin ducks. The optimal dietary supplement dose is 400 mg/kg.

Positive Influence of a Probiotic Mixture on the Intestinal Morphology and Microbiota of Farmed Guinea Fowls (Numida meleagris)

To understand the effectiveness of a probiotic mixture on intestinal morphology, mucus layer composition, and cecal microbiota diversity, 40 10-day-old Guinea fowls (Numida meleagris) were assigned to two groups: the control group (C), receiving drinking water, and the treated group (P), receiving water plus a commercial multi-strain probiotic (Slab51®, 2 × 10¹¹ CFU/L). Birds were slaughtered after 4 months, and the intestines were collected. Samples from the duodenum, ileum, and cecum were processed for morphological and morphometric studies, and conventional glycohistochemistry. Cecal samples were also used to assess the microbiota by 16S metataxonomic approach. Group P showed significant increase in the villus height (p < 0.001 in the duodenum and p < 0.05 in the ileum and cecum), villus width (p < 0.05 in all investigated tracts), depth of crypts (p < 0.001 in the duodenum and cecum; p < 0.05 in the ileum), and goblet cells per villus (p < 0.001 in all investigated tracts) compared with group C. Cecal microbiota of the birds varied considerably and comparing the relative abundance of the main observational taxonomic units (OTUs), a positive enrichment of several beneficial taxa, such as Oscillospira, Eubacterium, Prevotella, and members of the Ruminococcaceae, was observed. The enrichment of those taxa can improve microbiota stability and resilience facing environmental stresses, enhancing its resistance against invading pathogens. Ruminococcaceae, which represent the most important taxon in both groups, and Prevotella have a key role in the gut physiology due to the production of short-chain fatty acids (SCFAs), which are a vital energy source for enterocytes, improve glucose metabolism, and exert an overall anti-inflammatory effect. Probiotic administration enriches the presence of Coprococcus, Oscillospira, and Eubacterium taxa that produce butyrate, which exerts a beneficial effect on growth performance, structure of villi, and pathogen control and has anti-inflammatory properties too. This study indicates that Slab51® supplementation positively affects the morphology and microbiota diversity of the guinea fowl intestine.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency

The composition of the gut microbiome plays important roles in digestion, nutrient absorption, and health. Here, we analyzed the microbial composition in the duodenum and ileum of yellow broilers. Chickens were grouped based on feed efficiency (high feed efficiency [HFE] and low feed efficiency [LFE] groups; n = 22 each). Microbial samples from the duodenum and ileum were collected, and 16S rRNA sequencing of the V3–V4 region was performed. The dominant bacteria in the duodenum were from the phyla Firmicutes and Cyanobacteria and the genera Lactobacillus, Faecalibacterium, and Ruminococcus. In the ileum, the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, SMB53 and Enterococcus were predominant. Alpha diversity analysis showed that the microbiota diversity was significantly higher in the duodenum than in the ileum. The structure of the ileal microbiota was similar between groups, and the species richness of the microbiota in the HFE group was significantly higher than that in the LFE group. In the HFE and LFE groups, Firmicutes and Cyanobacteria were negatively correlated, and Lactobacillus had medium to high negative correlations with most other genera. Functional prediction analysis showed that the gluconeogenesis I pathway was the most abundant differential metabolic pathway and was significantly altered in the LFE group. Moreover, although the microbial community structures were similar in the duodenum and ileum, the diversity of the microbial community was significantly higher in the duodenum than in the ileum. Pearson correlation analysis revealed that the phylum Chloroflexi and genera Acinetobacter, Pseudomonas, Bacillus and Neisseria were with coefficients <−0.3 or >0.3. In the ileum, Ruminococcus may be associated with HFE whereas Faecalibacterium may be associated with LFE. These findings may provide valuable foundations for future research on composition and diversity of intestinal microbes and provide insights into the roles of intestinal microbes in improving feed efficiency and the industrial economic benefits of yellow broilers.

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.

The pelvic flexure separates distinct microbial communities in the equine hindgut

As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.

Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies

The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as “starch and sucrose metabolism,” “phenylalanine, tyrosine and tryptophan biosynthesis,” and “carbohydrate metabolism” were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.

Dietary supplementation with berberine improves growth performance and modulates the composition and function of cecal microbiota in yellow-feathered broilers

This study investigated the effect of berberine (BBR) on growth performance and composition and function of cecal microbiota in yellow-feathered broilers. A total of 360 1-day-old female broilers were assigned to 3 dietary treatments, each with 6 replicates of 20 birds. The dietary treatments consisted of a basal diet as negative control (NC), basal plus 200 mg/kg oxytetracycline calcium and 250 mg/kg nasiheptide as an antibiotic positive control (PC), and basal plus 250 mg/kg BBR. On day 21, 42, and 63, one chicken from each replicate was randomly selected for blood collection and cecal sampling. The 16S rRNA sequencing technology was used to analyze the community composition and function of cecal microbiota. Dietary supplementation with antibiotics or BBR increased the final body weight (BW) at day 63 and the average daily gain (ADG) during 1 to 21 d compared with the NC (P < 0.05). Supplementation with BBR improved the average daily feed intake (ADFI) at 22 to 42 d, 43 to 63 d, and 1 to 63 d (P < 0.05). Feed efficiency, indicated by feed to gain ratio (F/G), increased with PC during day 1 to 21 compared with NC (P < 0.05). The plasma concentrations of total protein at 42 d and uric acid at 21 d were increased, whereas creatine concentration at 63 d was decreased by BBR treatment (P < 0.05). The Chao 1 and Shannon index representing microbial α-diversity was reduced by BBR treatment (P < 0.05). The abundances of phylum Firmicutes and genera Lachnospiraceae, Lachnoclostridium, Clostridiales, and Intestinimonas were decreased, whereas the abundances of phylum Bacteroidetes and genus Bacteroides were increased with BBR treatment. Functional prediction of microbiota revealed that BBR treatment enriched pathways related to metabolism, organismal systems, and genetic information processing, especially DNA replication. The abundance of phylum Bacteroidetes, and genera Bacteroides and Lactobacillus in cecal contents were positively correlated with broiler growth performance. These results demonstrated dietary BBR supplementation improved the growth performance of yellow-feathered broilers, and was closely related to the significant changes in cecal microbiota composition.

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects

The concept of successional trajectories describes how small differences in initial community composition can magnify through time and lead to significant differences in mature communities. For many animals, the types and sources of early-life exposures to microbes have been shown to have significant and long-lasting effects on the community structure and/or function of the microbiome. In modern commercial poultry production, chicks are reared as a single age cohort and do not directly encounter adult birds. This scenario is likely to initiate a trajectory of microbial community development that is significantly different than non-industrial settings where chicks are exposed to a much broader range of environmental and fecal inocula; however, the comparative effects of these two scenarios on microbiome development and function remain largely unknown. In this work, we performed serial transfers of cecal material through multiple generations of birds to first determine if serial transfers exploiting the ceca in vivo, rather than the external environment or artificial incubations, can produce a stable microbial community. Subsequently, we compared microbiome development between chicks receiving this passaged, i.e. host-selected, cecal material orally, versus an environmental inoculum, to test the hypothesis that the first exposure of newly hatched chicks to microbes determines early GI microbiome structure and may have longer-lasting effects on bird health and development. Cecal microbiome dynamics and bird weights were tracked for a two-week period, with half of the birds in each treatment group exposed to a pathogen challenge at 7 days of age. We report that: i) a relatively stable community was derived after a single passage of transplanted cecal material, ii) this cecal inoculum significantly but ephemerally altered community structure relative to the environmental inoculum and PBS controls, and iii) either microbiome transplant administered at day-of-hatch appeared to have some protective effects against pathogen challenge relative to uninoculated controls. Differentially abundant taxa identified across treatment types may inform future studies aimed at identifying strains associated with beneficial phenotypes.

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)

Background

The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.

Results

In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.

Conclusions

Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.

Bacillus licheniformis-fermented products improve growth performance and the fecal microbiota community in broilers

This study investigated the effects of Bacillus licheniformis–fermented products on the growth performance and fecal microbial community of broilers. A total of 144 one-day-old male broiler chicks (Ross 308) were randomly assigned into 4 dietary treatments, with 6 replicate cages per treatment and 6 birds per cage. The dietary treatments comprised a basal diet as control, control plus 1 and 3 g/kg of B. licheniformis–fermented products, and control plus 10 mg/kg of enramycin. The results indicated that 3 g/kg of B. licheniformis–fermented products increased (P < 0.05) the BW and ADG of broilers relative to controls. No significant difference was observed in the growth performance of broilers fed enramycin and 3 g/kg of B. licheniformis–fermented products. However, principal coordinate analysis and a heatmap of species abundance indicated distinct clusters between the groups treated with enramycin and 3 g/kg of B. licheniformis–fermented products. The abundance of the phylum Firmicutes in feces increased (P < 0.05) in broilers fed 3 g/kg of B. licheniformis–fermented products, whereas the abundance of the phyla Verrucomicrobia and Bacteroidetes in feces decreased (P < 0.05) in response to treatment with 3 g/kg of B. licheniformis–fermented products. The abundance of the genera Enterococcus, Akkermansia, Ruminococcus torques group, Faecalibacterium, and Parabacteroides in feces decreased (P < 0.05) in broilers fed 3 g/kg of B. licheniformis–fermented products, whereas the abundance of the genus Lactobacillus in feces increased (P < 0.05) in response to treatment with 3 g/kg of B. licheniformis–fermented products. The average abundance of the genus Lactobacillus in feces was positively correlated with the growth performance of broilers. These results demonstrate that B. licheniformis–fermented products can improve the growth performance and fecal microflora composition of broilers.