Cecal microbiome profile of Hawaiian feral chickens and pasture-raised broiler (commercial) chickens determined using 16S rRNA amplicon sequencing

The impact of dietary supplementation of polysaccharide derived from Polygonatum sibiricum on growth, antioxidant capacity, meat quality, digestive physiology, and gut microbiota in broiler chickens

Polygonatum sibiricum polysaccharide (PSP) has demonstrated diverse medicinal properties, extensively researched for human applications. Nonetheless, there is a lack of studies investigating the potential advantages of PSP in poultry farming. The present study investigated the impact of incorporating PSP into broiler diets on their growth performance, meat quality, blood metabolites, antioxidative status, and ileal histomorphology. Two hundred and forty-one-day-old male Ross-308 broiler chicks (44.98 ± 0.79 g) were randomly assigned to 3 experimental groups, with 8 replicates of 10 birds each. The birds were fed diets supplemented with PSP at 0, 400, and 800 mg/kg (control, PSP400, and PSP800, respectively). The results revealed a linear (P > 0.05) improvement in body weight gain, European production efficiency index, and feed conversion ratio during the grower (22-35 d) and overall periods (1-35 d). The pH levels in the ingluvies, ileum, and cecum exhibited a linear reduction (P > 0.05) in the PSP800 group at d 21 and d 35, respectively. Villus height and crypt depth were increased in the PSP400 and PSP800 groups compared to the control group. PSP400 and PSP800 groups exhibited decreased hydrogen peroxide (H2O2) levels and increased total antioxidant capacity (TAC) at 21 d, while at 35 d, TAC and sulfhydryl concentrations were elevated, and H2O2 was reduced only in the PSP800 group compared to the untreated one. No significant variations between the groups at the phylum and genus levels were observed, with Bacteroidetes and Firmicutes being the dominant phyla. However, PSP supplementation notably augmented Firmicutes and Verrucomicrobiota while reducing Euryarchaeota and Proteobacteria. At the genus level, there was an increase in Akkermansia, Alistipes, CHKCI001, Erysipelatoclostridium, and a decrease in Methanobrevibacter. Conclusively, incorporating PSP into broiler diets, particularly at a dosage of 800 mg/kg, improved growth performance, antioxidant capacity, and intestinal architecture and resulted in alterations in cecal microbiota without discernible impacts on digestive function and meat quality criteria.

Identification of a microbial sub-community from the feral chicken gut that reduces Salmonella colonization and improves gut health in a gnotobiotic chicken model

A complex microbial community in the gut may prevent the colonization of enteric pathogens such as Salmonella. Some individual or a combination of species in the gut may confer colonization resistance against Salmonella. To gain a better understanding of the colonization resistance against Salmonella enterica, we isolated a library of 1,300 bacterial strains from feral chicken gut microbiota which represented a total of 51 species. Using a co-culture assay, we screened the representative species from this library and identified 30 species that inhibited Salmonella enterica subspecies enterica serovar Typhimurium in vitro. To improve the Salmonella inhibition capacity, from a pool of fast-growing species, we formulated 66 bacterial blends, each of which composed of 10 species. Bacterial blends were more efficient in inhibiting Salmonella as compared to individual species. The blend that showed maximum inhibition (Mix10) also inhibited other serotypes of Salmonella frequently found in poultry. The in vivo effect of Mix10 was examined in a gnotobiotic and conventional chicken model. The Mix10 consortium significantly reduced Salmonella load at day 2 post-infection in gnotobiotic chicken model and decreased intestinal tissue damage and inflammation in both models. Cell-free supernatant of Mix10 did not show Salmonella inhibition, indicating that Mix10 inhibits Salmonella through either nutritional competition, competitive exclusion, or through reinforcement of host immunity. Out of 10 species, 3 species in Mix10 did not colonize, while 3 species constituted more than 70% of the community. Two of these species were previously uncultured bacteria. Our approach could be used as a high-throughput screening system to identify additional bacterial sub-communities that confer colonization resistance against enteric pathogens and its effect on the host.IMPORTANCESalmonella colonization in chicken and human infections originating from Salmonella-contaminated poultry is a significant problem. Poultry has been identified as the most common food linked to enteric pathogen outbreaks in the United States. Since multi-drug-resistant Salmonella often colonize chicken and cause human infections, methods to control Salmonella colonization in poultry are needed. The method we describe here could form the basis of developing gut microbiota-derived bacterial blends as a microbial ecosystem therapeutic against Salmonella.

Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella, were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella. Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

Effect of Bacillus subtilis Supplemented Diet on Broiler's Intestinal Microbiota and TLRs Gene Expression

This study aimed to investigate the effects of dietary Bacillus subtilis supplementation on gut microbiota diversity, digestive enzyme activity, and Toll-like receptor (TLR) expression in broiler chickens. A total of 240 "817" crossbred broiler chickens were randomly assigned to four groups: control (basal diet, BD), group I (BD + 300 g/d B. subtilis at 1.08 × 107 CFU/kg), group II (BD + 600 g/d B. subtilis at 2.16 × 107 CFU/kg), and group III (BD + 900 g/d B. subtilis at 3.24 × 107 CFU/kg). Gut microbiota analysis revealed significant improvements in the abundance of specific microorganisms in the treatment groups, with distinct variations in the core microorganisms between the groups. Notably, protease activity in the ileum was significantly increased in groups II (22.59%; p < 0.01) and III (14.49%; p < 0.05) compared to that in the control group. Moreover, significant up-regulation of TLR1A and TLR7 expression was observed in jejunum and cecum of the treated groups. Additionally, the TLR1B expression in the ileum was significantly increased. Furthermore, TLR2A and MyD88 transcription levels were significantly elevated in the jejunum, liver, spleen, and kidneys of experimental groups. Modulations in the expression of various TLR's (TLR2B, TLR3, TLR4, TLR15, and TLR21) were also observed in different organs. The spleen and kidney of B. subtilis-supplemented chickens exhibited upregulated expression of the proinflammatory cytokine IL-1β. Dietary supplementation with B. subtilis in broiler chickens improved the gut microbiota diversity and significantly upregulated TLR's expression in various organs. B. subtilis could be a valuable feed additive, contributing to improved disease management and overall health in broiler chickens.

Dietary supplementation of solubles from shredded, steam-exploded pine particles modulates cecal microbiome composition in broiler chickens

This study evaluated the effects of supplementing solubles from shredded, steam-exploded pine particles (SSPP) on growth performances, plasma biochemicals, and microbial composition in broilers. The birds were reared for 28 days and fed basal diets with or without the inclusion of SSPP from 8 days old. There were a total of three dietary treatments supplemented with 0% (0% SSPP), 0.1% (0.1% SSPP) and 0.4% (0.4% SSPP) SSPP in basal diets. Supplementation of SSPP did not significantly affect growth or plasma biochemicals, but there was a clear indication of diet-induced microbial shifts. Beta-diversity analysis revealed SSPP supplementation-related clustering (ANOSIM: r = 0.31, p < 0.01), with an overall lower (PERMDISP: p < 0.05) individual dispersion in comparison to the control group. In addition, the proportions of the Bacteroides were increased, and the relative abundances of the families Vallitaleaceae, Defluviitaleaceae, Clostridiaceae, and the genera Butyricicoccus and Anaerofilum (p < 0.05) were significantly higher in the 0.4% SSPP group than in the control group. Furthermore, the linear discriminant analysis effect size (LEfSe) also showed that beneficial bacteria such as Ruminococcus albus and Butyricicoccus pullicaecorum were identified as microbial biomarkers of dietary SSPP inclusion (p < 0.05; | LDA effect size | > 2.0). Finally, network analysis showed that strong positive correlations were established among microbial species belonging to the class Clostridia, whereas Erysipelotrichia and Bacteroidia were mostly negatively correlated with Clostridia. Taken together, the results suggested that SSPP supplementation modulates the cecal microbial composition of broilers toward a "healthier" profile.

Spatial distribution of airborne bacterial communities in caged poultry houses

Microbial aerosols in intensive broiler houses whose species and concentrations are closely related to human health are ubiquitous. Based on 16S rRNA gene sequencing, the aim of this study was to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. Significant spatial variations in airborne bacterial concentrations were observed inside the poultry farmhouse. The results indicated that bacteria in the air samples could be grouped into a total of 1,674 OTUs. Alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (p < 0.01). The Sankey diagram illustrated species dynamic changes in Proteobacteria, Firmicutes, and Actinobacteria among the different locations. From the aspect of LEfSe (LDA Effect Size) analysis, we discovered that the abundance of Planctomycetes was significantly higher in the entry than in the rear and middle. This study shows the spatial distribution of the entire bacterial community in intensive broiler houses, which offers a new perspective for studying airborne total bacteria in those environments.Implications: The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. The results observed that bacterial aerosol concentrations in the examined broilers house varied greatly at different positions, and a significantly higher exposure to bacterial aerosol was observed at the middle than at the other positions (p < 0.05). The alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (P<0.01). Sankey diagram illustrated species dynamic changes of Proteobacteria, Firmicutes and Actinobacteria among the different locations. The microbial communities in genus level in the samples of entry and rear were closer, while the species diversity of middle and rear samples in chicken house was highly similar (P>0.05). Altogether, results revealed that the effects of spatial factors on the diversity and abundance of bacteria in the air of closed-cage broiler houses, which poses a potential threat to the health of animals and workers in those environments.

Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.

Heat Stress Affects Jejunal Immunity of Yellow-Feathered Broilers and Is Potentially Mediated by the Microbiome

In the perspective of the global climate change leading to increasing temperature, heat stress (HS) has become a severe issue in broiler production, including the indigenous yellow-feathered broilers. The present study aimed to investigate the effects of HS on jejunal immune response, microbiota structure and their correlation in yellow-feathered broilers. A total of forty female broilers (56-days-old) were randomly and equally divided into normal treatment group (NT group, 21.3 ± 1.2°C, 24 h/day) and HS group (32.5 ± 1.4°C, 8 h/day) with five replicates of each for 4 weeks feeding trial. The results showed that HS exposure increased the contents of TNF-α, IL-1β, and IL-6 in jejunal mucosa (p < 0.05). The HS exposure up-regulated the relative fold changes of NF-κB, TNF-α, IL-1β, and IL-6 (p < 0.01) while down-regulated the relative fold change of IFN-γ in jejunal mucosa (p < 0.05). Meanwhile, HS had no significant impacts on alpha diversity of jejunal microbiota such as Simpson, Chao1 richness estimator (Chao 1), abundance-based coverage estimators (ACE), and Shannon index (p > 0.10). Broilers exposed to HS reduced the jejunal microbial species number at the class and order level (p < 0.05). Moreover, HS decreased the relative abundance of Ruminococcus, Bdellovibrio, and Serratia at the genus level in jejunum (p < 0.05). At the phylum level, four species of bacteria (Bacteroidetes, Cyanobacteria, Thermi, and TM7) were significantly associated with immune-related genes expression (p < 0.05). At the genus level, ten species of bacteria were significantly correlated with the expression of immune-related genes (p < 0.05), including Caulobacteraceae, Actinomyces, Ruminococcaceae, Thermus, Bdellovibrio, Clostridiales, Sediminibacterium, Bacteroides, Sphingomonadales and Ruminococcus. In particular, the microbial with significantly different abundances, Ruminococcus and Bdellovibrio, were negatively associated with pro-inflammatory cytokines expression (p < 0.05). These findings demonstrated that HS exposure promoted the production of pro-inflammatory cytokines in yellow-feathered broilers’ jejunum. The detrimental effects of HS on jejunal immune response might be related to dysbiosis, especially the reduced levels of Ruminococcus and Bdellovibrio.

Effects of Heat Stress on Production Performance, Redox Status, Intestinal Morphology and Barrier-Related Gene Expression, Cecal Microbiome, and Metabolome in Indigenous Broiler Chickens

This study was done to evaluate the effects of heat stress (HS) on production performance, redox status, small intestinal barrier-related parameters, cecal microbiota, and metabolome of indigenous broilers. A total of forty female indigenous broilers (56-day-old) were randomly and equally divided into normal treatment group (NT group, 21.3 ± 1.2°C, 24 h/day) and HS group (32.5 ± 1.4°C, 8 h/day) with five replicates of each for 4 weeks feeding trial. The results showed that the body weight gain (BWG) of broilers in HS group was lower than those in NT group during 3–4 weeks and 1–4 weeks (p &lt; 0.05). The HS exposure increased the abdominal fat rate (p &lt; 0.05) but decreased the thigh muscle rate (p &lt; 0.01). Besides, broilers in HS group had higher drip loss of breast muscle than NT group (p &lt; 0.01). Broilers exposed to HS had lower total antioxidant capacity (T-AOC) in serum and jejunum, activities of total superoxide dismutase (T-SOD) in the jejunum, glutathione peroxidase (GSH-Px) in the thigh muscle, duodenum, and jejunum; and catalase (CAT) in breast muscle, duodenum, and jejunum (p &lt; 0.05). Whereas the malondialdehyde (MDA) contents in breast muscle, duodenum, and jejunum was elevated by HS exposure (p &lt; 0.05). Moreover, the relative mRNA expression of Occludin and ZO-1 in the duodenum, Occludin, Claudin-1, Claudin-4, ZO-1, Mucin-2 in the jejunum, and the Claudin-4 and Mucin-2 in the ileum was down-regulated by HS exposure (p &lt; 0.05). The 16S rRNA sequencing results showed that the HS group increased the relative abundance of Anaerovorax in the cecum at the genus level (p &lt; 0.05). Cecal metabolomics analysis indicated 19 differential metabolites between the two groups (p &lt; 0.10, VIP &gt;1). The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the differential metabolites mainly enriched in 10 signaling pathways such as the Citrate cycle (TCA cycle) (p &lt; 0.01). In summary, chronic HS exposure caused a decline of production performance, reduced antioxidant capacity, disrupted intestinal barrier function, and negatively affected cecal microbiota and metabolome in indigenous broilers.

Multi-Omics Revealed the Protective Effects of Rhamnolipids in Lipopolysaccharide Challenged Broilers

Rhamnolipid (RL) is a glycolipid biosurfactant and exhibits the following outstanding characteristics: strong antibacterial properties, low toxicity, and high biodegradability. The present research was conducted to explore the protective effects and mechanisms of rhamnolipids as an alternative to antibiotics in LPS (lipopolysaccharide)-challenged broilers. 16S rRNA gene sequencing and metabolomics were used for analyzing the cecal microbial composition and serum metabolites. Dietary antibiotics and RLS supplementation decreased the weight loss rate, enhanced serum immunoglobulin levels, reduced serum diamine oxidase and D-lactate acid concentration, and improved the symptoms of intestinal bleeding and villus height, when broilers were challenged with LPS. The addition of RLS in the diet enhanced serum interleukin-4 and interleukin-10 contents and reduced serum interleukin-6 and tumor necrosis factor-α levels in LPS-challenged broilers compared with the antibiotics group. Spearman’s correlation analysis revealed that RLS may alleviate LPS-induced inflammatory responses through altering the 6-methoxymellein level in broilers. The genus Bacteroides may contribute to the decreased weight loss rate via regulating the serum lysoPC [20:5(5Z,8Z,11Z,14Z,17Z)] secretion. RLS alleviates LPS-induced intestinal injury, enhances the growth and immunity, ameliorates intestinal microflora, and improves serum metabolites in LPS-challenged broilers. RLS exhibited better protective effect than antibiotic supplementation in the diet of LPS-challenged broilers. These findings provide potential regulation strategies and novel insights for RLS enhancing its protective effect in LPS-challenged broilers.

Effects of in ovo delivered xylo- and mannan- oligosaccharides on growth performance, intestinal immunity, cecal short-chain fatty acids, and cecal microbiota of broilers

Background

This study investigated a novel in ovo feeding strategy to determine the prebiotic effects of xylo- and mannan- oligosaccharides (XOS and MOS) differing in the degree of polymerization. A total of 192 fertilized eggs were divided into 6 treatment groups: i) normal saline control (NSC), ii) xylotriose (XOS3), iii) xylotetraose (XOS4), iv) mannotriose (MOS3), v) mannotetraose (MOS4), and vi) no injection control (NIC), each containing 4 replicate trays with 8 eggs per replicate. On d 17 of incubation, 3 mg of oligosaccharides (except for controls) dissolved in 0.5 mL of 0.85% normal saline were injected into the amnion of Cobb 500 broilers eggs. After hatch, the chicks were raised for 28 d under standard husbandry practices and were fed a commercial broilers diet ad libitum, and samples were collected periodically.

Results

The hatchability, growth performance, and relative weights of breast, drumstick, liver, and proventriculus were not different among the treatments (P > 0.05). The XOS3 injection increased the total short-chain fatty acid production at d 28 compared with both control groups (P < 0.05). The villus height to crypt depth ratio was significantly higher in the XOS4 group than both controls on the hatch day (P < 0.01) but were not different among any treatments on d 7 and 28 (P > 0.05). On the hatch day, the expression level of the CD3 gene (a T cell marker) was increased by XOS3, while the IL-10 gene (a marker of anti-inflammatory cytokine) was reduced by MOS4 (P < 0.05) compared with both controls. Compared with both controls, XOS3 exhibited a trend of reduction for IL-10 (P = 0.074). No cytokines or lymphocyte markers were affected by the treatments on d 7 (P > 0.05), except XOS4 increased IL-4 compared with NSC (P < 0.05). The broilers in the MOS4 group had higher operational taxonomic units (OTUs) and had more differentially abundant taxa, including order Lactobacillales and family Leuconostocaceae (P < 0.05) than both controls on d 28. The predictive functional profiling indicated that the linoleic acid metabolism pathway was enriched in the cecal microbiota of the XOS3 group compared with both controls (P < 0.05).

Conclusion

The effects of these XOS and MOS on ileal mucosa and immunity are transient, but the effects on fermentation and cecal microbiota are prolonged, and further research is warranted to determine their use as a gut health promoter in poultry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00666-z.

The digestive and reproductive tract microbiotas and their association with body weight in laying hens

Body weight at the onset of egg production is a major factor influencing hen productivity, as suitable body weight is crucial to laying performance in laying hens. To better understand the association between body weight and microbial community membership and structure in different sites of the digestive and reproductive tracts in chickens, we performed 16S rRNA sequencing surveys and focused on how the microbiota may interact to influence body weight. Our results demonstrated that the microbial community and structure of the digestive and reproductive tracts differed between low and high body weight groups. In particular, we found that the species Pseudomonas viridiflava was negatively associated with body weight in the 3 digestive tract sites, while Bacteroides salanitronis was negatively associated with body weight in the 3 reproductive tract sites; and further in-depth studies are needed to explore their function. These findings will help extend our understanding of the influence of the bird digestive and reproductive tract microbiotas on body weight trait and provide future directions regarding the control of body weight in the production of laying hens.