Transition of microbiota in chicken cecal droppings from commercial broiler farms

Lack of consistency in poultry dust microbial taxa associated with high and low-performing commercial broiler flocks

The microbial communities of the gastrointestinal tract play an essential role in poultry health and productivity. Poultry dust has been used to investigate bacterial taxa associated with performance in commercial broiler farms. This study investigated the commonalities of poultry dust microbial taxa associated with performance in samples collected from three broiler integrator companies and their stability in a successive flock of the same companies using deep sequencing of the 16S rRNA gene. Poultry dust samples (n = 248) were collected on days 14 and 35 of the production cycle from 38 commercial broiler flocks (2 flocks from each of 19 farms). The farms were ranked as low or high performers based on the feed conversion ratio corrected for body weight. Permutational analysis of variance based on Bray-Curtis index using abundance data for bacterial community structure results showed that company explained the most variation in the bacterial community structure (7.5 %), followed by bird age (2 %) and the least variation was explained by performance (1.9 %), with significant interactions among these factors (P < 0.001). No bacterial taxa in high or low-performing farms overlapped in all three companies or successive flocks from the same company. Some taxa associated with high performance in a company were associated with low performance in another company (e.g., Bifidobacterium), corroborating other studies highlighting the lack of universal microbial markers of productivity. In conclusion, there were no consistent microbial taxa across companies and flocks within a company under the conditions of this study.

Effect of dietary fat source on the composition of the cecal microbiome in maturing broiler chicken

Diet has been found to significantly influence gut microbiota throughout various life stages, and gut microbiota have been increasingly shown to influence host physiology, health, and behavior. This study uses 16S rRNA sequencing to examine the effects of six different fat-supplemented diets (canola oil, coconut oil, fish oil, flaxseed oil, lard, and olive oil) on broiler chicken cecal microbial composition and predicted function in comparison with a common and inexpensive fat source (poultry fat). Groups of broilers were fed each of these diets and then evaluated on day 41 and day 55 of age. For both 41- and 55-day samples, Firmicutes and Bacteroidetes phyla were the dominant bacteria in the ceca accounting for 99% of the microbial community. Across the 41- and 55-day samples, treatment time was associated with a stronger and more significant microbiota shift (p < 0.001) than differences in dietary treatment alone (p = 0.117), but dietary treatment combined with treatment time is a significant factor as well (p = 0.047). Sparse partial least squares discriminant analysis was used to explore the more discriminating taxa for each treatment group. For identified species, butyrate production appears to be affected in a diet-specific manner, with many butyrate-producing species being evident for the fish-based diet at day 41 and a few of these species for the flaxseed-based diet at day 55. Predicted functions, as conducted with PICRUSt2, were significant for comparisons between the control and the flaxseed-based dietary treatment group at day 55, with indications of host health benefit for the flaxseed-based diet. Predicted functions found to be significant were for enzymes and pathways such as propionate CoA ligase, aminobutyraldehyde dehydrogenase, vitamin B12-transporting ATPase, thiamine kinase, acetylneuraminate epimerase, and L-tryptophan biosynthesis. This study provides insight surrounding specific dietary fat-based treatments to be investigated further and highlights the importance of polyunsaturated fat sources in poultry feed that may offer a favorable cecal microbial modulation compared to saturated fat sources.

Exploring the modulatory effects of brown seaweed meal and extracts on intestinal microbiota and morphology of broiler chickens challenged with heat stress

Brown seaweed (Ascophyllum nodosum) is known for its prebiotic roles and can improve animal intestinal health by enhancing the growth of beneficial microbes and inhibiting pathogenic ones. However, the gut health-modulatory roles of brown seaweed on chickens challenged with heat stress (HS) are rarely studied. The current study examined the effects of brown seaweed meal (SWM) and extract (SWE) on the ceca microbiota and small intestinal morphology of chickens challenged or unchallenged with HS. Three hundred and thirty-six 1-day-old Ross 308 broiler chicks were randomly assigned to either a thermoneutral (TN; 24 ± 1°C); or HS room (HS; 32-34°C, 8 h/d from d 21 to 27). All birds in each room were randomly allotted to 4 treatments - control (CON), CON + 1 mL/L seaweed extract (SWE) in drinking water, CON + 2 mL/L SWE in drinking water, and CON + 2% seaweed meal (SWM) in feed and raised for 28 d. On d 14 and 28, 12 and 24 birds per treatment group, respectively, were euthanized to collect the ceca content for gut microbiota analysis and small intestinal tissues for morphological examination. On d 14, 2% SWM increased (P = 0.047) the relative abundance of cecal Fecalibacterium and all brown seaweed treatments improved jejunal villus height (VH) and VH:CD compared to the CON diet. On d 28, HS significantly reduced (P < 0.05) ileal VH, VW, and VH:CD, and duodenal VH and VH:CD. Among the HS group, 2% SWM and 2 mL/L SWE significantly increased (P < 0.05) the relative abundance of Lactobacillus, Sellimonas, and Fournierella, compared to the CON diet. HS birds fed with 2% SWM had higher ileal VH and VH:CD compared to other treatments. In summary, SWM and SWE enhanced the abundance of beneficial microbes and improved small intestinal morphology among HS chickens. This implies that seaweed could potentially alleviate HS-induced intestinal impairment in chickens.

Detection of Klebsiella pneumoniae in healthy poultry: Insights and perspectives from culturing and metagenomics

Previously, Klebsiella pneumoniae was found to occur more frequently in healthy turkey flocks than in healthy broiler flocks in Norway. This study aimed to investigate whether this higher occurrence could be attributed to a greater abundance of K. pneumoniae in turkey flocks. We compared culturing, qPCR, and shotgun metagenomic sequencing for the detection and quantification of K. pneumoniae. Using qPCR, we found that 20.7% of broiler flock samples and 63.9% of turkey flock samples were positive for K. pneumoniae. Culturing revealed a significantly higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks. However, metagenomic analysis showed no difference in the relative abundance of Klebsiella spp. between broiler and turkey flocks, and no correlation between the results of culturing and metagenomic quantification. Interestingly, the differential abundance of K. quasipneumoniae was significantly different between the two hosts. Our results indicate that Klebsiella spp. are present in both turkey and broiler flocks at relatively low levels but with a higher abundance in turkey flocks. Our findings also suggest that shotgun metagenomic studies targeting low-abundance taxa such as Klebsiella have poor sensitivity when comparing groups, indicating that reliance on results from metagenomic analysis without experimental validation should be done with caution.

Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review

Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.

Prophylactic influences of prebiotics on gut microbiome and immune response of heat-stressed broiler chickens

Climatic changes and elevated ambient temperature are significant environmental stressors with a negative impact on birds' physiological, immunological, and behavioral status, increasing their susceptibility to stressors and immunosuppression and consequently increasing intestinal permeability (leaky gut). Prebiotics have been utilized to stop or diminish the harmful effects of stress in chickens. We aimed to evaluate the role of mannan-oligosaccharides, and beta-D-glucan prebiotics supplements in drinking water against experimentally induced heat stress (HS) on broiler chickens and study their impact on birds' performance, gut microbiome, and immune response. A total of 120 1-day-old Ross broiler chicks were allocated into four groups (30 birds/group), and each group was subdivided into triplicates (10 birds each). The experimental groups were classified as follows; the 1st (G1) control birds, the 2nd (G2) birds exposed experimentally to HS, the 3rd (G3) birds administered prebiotics in drinking water without exposure to HS, and the 4th (G4) birds exposed to HS and administered prebiotics in drinking water. After each vaccination, blood samples and serum samples were collected to evaluate the birds' immune status. Fecal samples were also collected for the molecular evaluation of the gut microbiome based on the genetic analyses and sequencing of 16S rRNA gene. The results showed that HS has reduced the birds' performance and badly affected the birds' immune response and gut microbiome. However, the addition of prebiotics to drinking water, with or without stress, enhanced the growth rate, maintained a normal gut microbiome, and improved immune parameters. Moreover, the usage of prebiotics improved the chicken gut microbiome and alleviated the negative effect of heat stress. Administering prebiotics significantly (p < 0.05) increased the relative abundance of beneficial bacteria and eradicated pathogenic ones in the birds' gut microbiome. Prebiotics showed a positive effect on the gut microbiome and the immune status of chickens under HS in addition to their efficacy as a growth promoter.

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.

Bacteroides-derived isovaleric acid enhances mucosal immunity by facilitating intestinal IgA response in broilers

BACKGROUND

The interaction between nutrition and immunity plays a vital role in nutrient digestion, absorption, and metabolism during poultry production. Recent studies showed that the gut microbiota contributes to the development of intestinal mucosal immunity. However, the mechanisms by which gut microbes regulate this process remain unclear.

METHODS

We compared the intestinal mucosal immunity and gut microbiota of Arbor Acre broilers (AA (lower mucosal immunity) and Chinese native Wuliang Mountain Black-bone chickens (WLMB) (higher mucosal immunity) using 16S rDNA sequencing, transcriptomic analysis, and immunoglobulin A (IgA) antibody repertoire sequencing. We then combined 16S rDNA sequencing with transcriptomics to identify the key microbes and found that they were positively correlated with IgA production. Next, we transplanted candidate microbes into 1-day-old broiler to explore their role in intestinal mucosal immunity. Finally, we verified the function of candidate microbial metabolites in regulating the immune function of macrophages and the intestinal-epithelial cells (IECs) using in vitro experiments.

RESULTS

WLMB performs stronger mucosal immunity than AA, including higher IgA levels, more diverse IgA antibody repertoire, and higher bacterial affinity. Bacteroides was identified as the key microbes related to the intestinal IgA response. Bacteroides transplantation could increase IgA concentration in the duodenal contents by enhancing the expression of IgA, polymeric immunoglobin receptor (PIgR), B cell-activating factor of the TNF family (BAFF), and activation-induced cytidine deaminase (AID) in the duodenum. Additionally, Bacteroides-derived isovaleric acid promoted M2 macrophage polarization of macrophage via mTOR/PPAR-γ/STAT3 signaling pathways and regulated the immunologic function of IECs to produce cytokines, including interleukin (IL)-10, IL-4, BAFF, and transforming growth factor-beta (TGF-β), thus promoting IgA production in B cells by facilitating AID expression.

CONCLUSION

Our study revealed that Bacteroides modulate the intestinal IgA response and maintain gut health in broilers. Bacteroides may be a promising alternative as an immunomodulatory microbial agent for developing next-generation probiotics for broiler production.

Succession in the caecal microbiota of developing broilers colonised by extended-spectrum β-lactamase-producing Escherichia coli

Background

Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has contributed to the appearance of resistant bacteria, such as extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiota of developing broilers in a commercial flock during their production life cycle (0–35 days). Broilers were categorised as ESBL-Ec colonised (ESBL-Ec⁺) or ESBL-Ec non-colonised (ESBL-Ec⁻) by selective culturing. Using 16S rRNA gene sequencing, we i. compared the richness, evenness and composition of the caecal microbiota of both broilers’ groups and ii. assessed the combined role of age and ESBL-Ec status on the broilers’ caecal microbiota.

Results

From day two, we observed an increasing linear trend in the proportions of ESBL-Ec throughout the broilers' production life cycle, X² (1, N = 12) = 28.4, p < 0.001. Over time, the caecal microbiota richness was consistently higher in ESBL-Ec⁻ broilers, but significant differences between both broilers’ groups were found exclusively on day three (Wilcoxon rank-sum test, p = 0.016). Bray–Curtis distance-based RDA (BC-dbRDA) showed no explanatory power of ESBL-Ec status, while age explained 14% of the compositional variation of the caecal microbiota, F (2, 66) = 6.47, p = 0.001.

Conclusions

This study assessed the role of ESBL-Ec in the successional dynamics of the caecal microbiota in developing broilers and showed that the presence of ESBL-Ec is associated with mild but consistent reductions in alpha diversity and with transient bacterial compositional differences. We also reported the clonal spread of ESBL-Ec and pointed to the farm environment as a likely source for ESBLs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00199-4.

A Complex Competitive Exclusion Culture Reduces Campylobacter jejuni Colonization in Broiler Chickens at Slaughter Age In Vivo

Diminishing Campylobacter prevalence in poultry flocks has proven to be extremely challenging. To date, efficacious control measures to reduce Campylobacter prevalence are still missing. A potential approach to control Campylobacter in modern poultry productions is to occupy its niche in the mucosal layer by administering live intestinal microbiota from adult chickens to dayold-chicks (competitive exclusion (CE)). Therefore, this in vivo study investigates the efficacy of a complex CE culture to reduce Campylobacter (C.) jejuni colonization in broiler chickens. For this purpose, the complex CE culture was applied twice: once by spray application to day-old chicks immediately after hatching (on the 1st day of life) and subsequently by an additional application via drinking water on the 25th day of life. We observed a consistent and statistically significant reduction of C. jejuni counts in cloacal swabs throughout the entire fattening period. At the end of the trial after necropsy (at 33 days of age), C. jejuni cecal counts also showed a statistically significant decrease of 1 log₁₀ MPN/g compared to the control group. Likewise, colon counts were reduced by 2.0 log₁₀ MPN/g. These results suggest that CE cultures can be considered a practically relevant control strategy to reduce C. jejuni colonization in broiler chickens on poultry farms.

Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress

The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.