Development of the Caecal Microbiota in Three Broiler Breeds

Prebiotic galactooligosaccharide feed modifies the chicken gut microbiota to efficiently clear Salmonella

Chicken meat is contaminated with Salmonella from the gut of infected chickens during slaughter. Eradication of Salmonella from broiler chickens through hygiene measures and/or vaccination is not cost-effective; complementary approaches are required. A mature gut microbiota obstructs Salmonella infection in chickens, and deliberate fortification of colonization resistance through prebiotic feed formulations would benefit public health and poultry production. Prebiotic galactooligosaccharides hastens Salmonella clearance from the gut of infected chickens. To better understand the role of galactooligosaccharides in colonization resistance, broiler chickens were raised on a wheat-soybean meal-based feed, with or without galactooligosaccharides for the first 24 days of life. Chickens were orally challenged with Salmonella enterica serovar Enteritidis at 20 days and the effect of supplementary galactooligosaccharides characterized by profiling Salmonella colonization, gut microbiota, innate immune response, and cecal short-chain fatty acid concentrations. Exposure to dietary galactooligosaccharides shortened the time to clear S. Enteritidis from the ceca. Differential abundance analysis of the cecal microbiota associated Salmonella challenge with a bacterial taxon belonging to the Acidaminococcaceae family (P < 0.005). Increased cecal concentrations of the short-chain fatty acids propionate and valerate were measured in Salmonella-challenged chickens sustained on either control or galactooligosaccharide-supplemented feed relative to mock-challenged controls; but far greater concentrations were detected in chickens fed a galactooligosaccharide-supplemented diet in early life. The abundance of the Acidaminococcaceae taxon exhibited a positive correlation with the cecal concentrations of propionate (ρ = 0.724, P = 0.008) and valerate (ρ = 0.71, P = 0.013). The absence of cecal pro-inflammatory transcriptional responses suggest that the rapid Salmonella clearance observed for the galactooligosaccharide-supplemented diet was not linked to innate immune function.

IMPORTANCE

Work presented here identifies bacterial taxa responsible for colonization resistance to Salmonella in broiler chickens. Deliberate cultivation of these taxa with prebiotic galactooligosaccharide has potential as a straight-forward, safe, and cost-effective intervention against Salmonella. We hypothesize that catabolism of galactooligosaccharide and its breakdown products by indigenous microorganisms colonizing the chicken gut produce excess levels of propionate. In the absence of gross inflammation, propionate is inimical to Salmonella and hastens intestinal clearance.

Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers

BACKGROUND

Variations in body weight (BW) remain a significant challenge within broiler flocks, despite uniform management practices. Chicken growth traits are influenced by gut microbiota, which are in turn shaped by early-life events like different hatching environments and timing of first feeding. Chicks hatched in hatcheries (HH) experience prolonged feed deprivation, which could adversely impact early microbiota colonization. Conversely, hatching on-farm (HOF) allows early feeding, potentially fostering a more favorable gut environment for beneficial microbial establishment. This study investigates whether BW differences among broilers are linked to the disparities in gut microbiota characteristics and whether hatching systems (HS) impact the initial microbial colonization of broilers differing in BW, which in turn affects their growth patterns. Male Ross-308 chicks, either hatched in a hatchery or on-farm, were categorized into low (LBW) and high (HBW) BW groups on day 7, making a two-factorial design (HS × BW). Production parameters were recorded periodically. On days 7, 14, and 38, cecal volatile fatty acid (VFA) and microbiota composition and function (using 16 S rRNA gene sequencing and PICRUSt2) were examined.

RESULTS

HOF chicks had higher day 1 BW, but HH chicks caught up within first week, with no further HS-related performance differences. The HBW chicks remained heavier attributed to higher feed intake rather than improved feed efficiency. HBW group had higher acetate concentration on day 14, while LBW group exhibited higher isocaproate on day 7 and isobutyrate on days 14 and 38. Microbiota analyses revealed diversity and composition were primarily influenced by BW than by HS, with HS having minimal impact on BW-related microbiota. The HBW group on various growth stages was enriched in VFA-producing bacteria like unclassified Lachnospiraceae, Alistipes and Faecalibacterium, while the LBW group had higher abundances of Lactobacillus, Akkermansia and Escherichia-Shigella. HBW microbiota presented higher predicted functional potential compared to the LBW group, with early colonizers exhibiting greater metabolic activity than late colonizers.

CONCLUSIONS

Despite differences in hatching conditions, the effects of HS on broiler performance were transient, and barely impacting BW-related microbiota. BW variations among broilers are likely linked to differences in feed intake, VFA profiles, and distinct microbiota compositions and functions.

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

BACKGROUND

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS

Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS

The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.

Integrative Analysis of the Microbiome and Metabolome of Broiler Intestine: Insights into the Mechanisms of Probiotic Action as an Antibiotic Substitute

Antibiotic substitutes have become a research focus due to restrictions on antibiotic usage. Among the antibiotic substitutes on the market, probiotics have been extensively researched and used. However, the mechanism by which probiotics replace antibiotics remains unclear. In this study, we aimed to investigate this mechanism by comparing the effects of probiotics and antibiotics on broiler growth performance and intestinal microbiota composition. Results shown that both probiotics and antibiotics increased daily weight gain and reduced feed conversion rate in broilers. Analysis of ileum and cecum microorganisms via 16S rRNA gene sequencing revealed that both interventions decreased intestinal microbial diversity. Moreover, the abundance of Bacteroides increased in the mature ileum, while that of Erysipelatoclostridium decreased in the cecum in response to both probiotics and antibiotics. The main metabolites of probiotics and antibiotics in the intestine were found to be organic acids, amino acids, and sugars, which might play comparable roles in growth performance. Furthermore, disaccharides and trisaccharides may be essential components in the ileum that enable probiotics to replace antibiotics. These findings provide important insights into the mechanisms underlying the use of probiotics as antibiotic substitutes in broiler breeding.

Comparative analysis of reproductive tract microbiomes in modern and slower-growing broiler breeder lines

Introduction

The reproductive tract microbiome in hens is of interest because bacteria in the reproductive tract could potentially affect fertilization and egg production, as well as integrate into the forming egg and vertically transmit to progeny.

Methods

The reproductive tract microbiome of 37-week-old modern commercial Cobb breeding dams was compared with that of dams from a broiler Legacy line which has not undergone selection since 1986. All animals were kept together under the same management protocol from day of hatch to avoid confounders.

Results

In regards to reproductive abilities, Cobb dams' eggs weighed more and the magnum section of their reproductive tract was longer. In regards to microbiome composition, it was found that the reproductive tract microbiomes of the two lines had a lot in common but also that the two breeds have unique reproductive tract microbiomes. Specifically, the order Pseudomonadales was higher in the magnum of Legacy dams, while Verrucomicrobiales was lower. In the infundibulum, Lactobacillales were higher in the Legacy dams while Verrucomicrobiales, Bacteroidales, RF32 and YS2 were lower.

Discussion

our results show that breeding programs have modified not only the physiology of the reproductive tract but also the reproductive tract microbiome. Additional research is required to understand the implications of these changes in the reproductive tract microbiome on the chicken host.

Characteristics of gut microbiota and metabolomic of Hainan Tunchang pigs at various growth stages

Numerous gut microorganisms residing in the gut tract and their metabolites play an important role in animal growth. Diet, as the main factor, affects the changes of gut microbiota, and host genetics also have a significant impact on gut microbiota, including growth stages. However, the differences of gut microbiota and its metabolites at various growth stages in local pig breed remains unclear. We used 16S rRNA gene sequencing and untargeted metabolomics to investigate the fecal microbiota and metabolites in different developmental stages of Hainan Tunchang pigs. The relative proportions of dominant bacteria Firmicutes and Spirochaetes increased, Bacteroidetes and Proteobacteria decreased with the development. As age increased, different physiological states led to structural and functional changes in animal nutrition metabolism and immune needs, as well as changes in gut microbiota and its metabolites. We have detected several statistically different microbial and metabolic biomarkers at different growth stages. Meanwhile, through correlation analysis between differential bacteria and metabolites, it was found that the bacteria forming networks with their significant related metabolites were different at various growth stages, Holdemanella, Sharpea, Subdoligranulum, and uncultured_bacterium_o_Bacteroidales were enriched between preweaning piglets and weaning piglets, and they all positive correlated with related metabolites. We also found that the differential bacteria were significantly related to short-chain fatty acid. These findings might provide new insights into the developmental changes of gut microbiota in local pig breeds and the interaction mechanism between the body, and improve pig growth performance and efficiency by regulating the composition of gut microbiota and metabolites.

Stimbiotic supplementation and xylose-rich carbohydrates modulate broiler's capacity to ferment fibre

Stimbiotics are a new category of feed additives that can increase fibre fermentability by stimulating fibre-degrading microbiota in the gut. The aim of this study was to test, ex vivo, if the microbiota of broilers fed a stimbiotic are better able to ferment different xylose-rich substrates in an ileal and a caecal environment. The ileal and caecal contents from broiler chickens fed a stimbiotic or from a control group were used as an inoculum in the ex vivo fermentation experiment. Different xylose-rich substrates including monomeric xylose (XYL), XOS with DP 2 to 6 (XOS), short DP XOS of 2 to 3 (sDP-XOS), long DP XOS of 4 to 6 (lDP-XOS) and de-starched wheat bran (WB), were added to each ileal and caecal inoculum in fermentation vessels. Total gas, short-chain fatty acids (SCFA) production, bacterial quantification, and carbohydrate utilisation were monitored for 9 h post-inoculation. No significant interactions were observed in any of the parameters measured in either the ileal or caecal contents (p > 0.05). Stimbiotic ileal inocula resulted in higher total gas (p < 0.001) and volatile fatty acid (VFA) (p < 0.001) production, increased numbers of Lactobacillus spp. (p < 0.001), and decreased numbers of Enterococcus spp. (p < 0.01) after 9 h regardless of the xylose-rich substrate added. Stimbiotic caecal inocula resulted in a higher ratio of VFA to branched-chain fatty acids (BCFAs) by up to +9% (p < 0.05). Ileal microbiota were found to preferentially metabolise WB, while caecal microbiota favoured XOS substrates, particularly lDP-XOS. These results indicate that stimbiotics can promote the abundance of lactic acid bacteria involved in the establishment of fibre-degrading bacteria and VFA content in the gut, which could have beneficial effects on broiler performance. Further, ileal and caecal microbiota differ in their utilisation of different substrates which may impact the effectiveness of different stimbiotic products.

Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain

The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.

Exploring Gut Microbiome Variations between Popillia japonica Populations of Azores

Popillia japonica (Coleoptera: Scarabaeidae), is an emerging invasive pest in Europe and America. In the Azores, this pest was first found on Terceira Island during the sixties and soon spread to other islands. The rate of infestation differs between islands, and we hypothesized that microbiome composition could play a role. Therefore, we sampled 3rd instar larvae and soil from sites with high and low infestation rates to analyze the microbiome using next-generation sequencing. We analyzed twenty-four 16S DNA libraries, which resulted in 3278 operational taxonomic units. The alpha and beta diversity of the soil microbiome was similar between sites. In contrast, the larvae from high-density sites presented a higher bacterial gut diversity than larvae from low-density sites, with biomarkers linked to plant digestion, nutrient acquisition, and detoxification. Consequently, larvae from high-density sites displayed several enriched molecular functions associated with the families Ruminococcaceae, Clostridiaceae and Rikenellaceae. These bacteria revealed a supportive function by producing several CAZyme families and other proteins. These findings suggest that the microbiome must be one drive for the increase in P. japonica populations, thus providing a checkpoint in the establishment and spread of this pest.

Intestinal colonization with Campylobacter jejuni affects broiler gut microbiota composition but is not inhibited by daily intake of Lactiplantibacillus plantarum

Introduction

Lactobacilli may prevent broilers from colonization with Campylobacter spp. and other gram-negative zoonotic bacteria through lactic acid production and modulation of the intestinal microbiota. This study evaluated the effects of daily intake of Lactiplantibacillus plantarum 256 (LP256) on Campylobacter jejuni (C. jejuni) loads in ceca and feces of C. jejuni challenged broilers, together with the changes in the gut microbiota.

Methods

Two experiments were conducted using the broilers Ross 308 (R-308; Experiment 1) for 42 days and Rowan Ranger broilers (RR; Experiment 2) for 63 days. The LP256 strain was administered either via silage inoculated with LP256 or direct supplementation in the drinking water. Concurrently, haylage as a forage similar to silage but without any inoculum was tested. C. jejuni loads in fecal matter and cecal content were determined by plate counts and qPCR, respectively. The cecal microbiota, in response to treatments and the challenge, were assessed by 16S rRNA sequencing.

Results and Discussion

Culturing results displayed a significant reduction in C. jejuni colonization (2.01 log) in the silage treatment in comparison to the control at 1 dpi (day post-infection) in Experiment 1. However, no treatment effect on C. jejuni was observed at the end of the experiment. In Experiment 2, no treatment effects on C. jejuni colonization were found to be statistically significant. Colonization load comparison at the peak of infection (3 dpi) to that at the end of the trial (32 dpi) revealed a significant reduction in C. jejuni in all groups, regardless of treatment. Colonization dynamics of C. jejuni in the cecal samples analyzed by qPCR showed no difference between any of the treatments in Experiment 1 or 2. In both experiments, no treatment effects on the cecal microbiota were observed. However, proportional changes in the bacterial composition were observed after the C. jejuni challenge, suggesting that colonization affected the gut microbiota. Overall, the daily intake of LP256 was not effective in reducing C. jejuni colonization in either broiler type at the end of the rearing period and did not cause any significant changes in the birds' cecal microbiota composition.

Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks

BACKGROUND

Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive attention; however, the influence of early-day use of prophylactic antibiotics on the gut microflora and on the disease resistance ability in chicks has not been explored. Here, we comprehensively evaluate the growth performance, gut microbial dynamics, level of antibiotic resistance genes (ARGs) in the gut microbial community, and resistance to H9N2 avian influenza virus (AIV) in chickens following long-term and short-term early-day prophylactic antibiotic treatment.

RESULTS

Unexpectedly, long-term prophylactic enrofloxacin treatment slowed the growth rate of chickens, whereas short-term antibiotics treatments were found to increase the growth rate, but these changes were not statistically significant. Strikingly, expansions of Escherichia-Shigella populations were observed in early-life prophylactic antibiotics-treated groups of chickens, which is in contrast to the general perception that antibiotics should control their pathogenicity in chicks. The gut microbiota composition of chickens treated long term with antibiotics or received early-day antibiotics treatment tend to be more dramatically disturbed compared to the gut microbiome of chickens treated with antibiotics for a short term at a later date, especially after H9N2 AIV infection.

CONCLUSIONS

Our data provide evidence that early-day and long-term antibiotic treatments have a more adverse effect on the intestinal microbiome of chickens, compared to short-term late age antibiotic treatment. Furthermore, our metagenomic data reveal that both long-term and short-term antibiotic treatment increase the relative abundance of ARGs. Our findings highlight the adverse effects of prophylactic antibiotic treatment and provide a theoretical basis for the cautious administration of antibiotics in food-producing animal management. Video Abstract.

Diversity and Co-Occurrence Pattern Analysis of Cecal and Jejunal Microbiota in Two Rabbit Breeds

This study aimed to evaluate the productive performance and microbiota variation in the jejunum and cecum of two rabbit breeds with different growth rates. This study was carried out on Native Middle-Egypt Breed (NMER) and Giant Flanders (GF) rabbits from 5 weeks to 12 weeks of age. Twenty NMER (NM) and GF male rabbits were slaughtered, and the jejunum and cecum tracts were collected to assay gut microbiota composition via 16S ribosomal RNA (rRNA) gene sequencing and histology examination. At 12 weeks of age, daily weight gain, villus height in the jejunum, total protein, and albumin were higher in GF rabbits than in NMER rabbits. Also, the jejunal villi of GF were well arranged in their dense borders. The microbiota between the jejunum and cecum was significantly different in terms of Beta-diversity. A significant correlation between Enterococcus (jejunum NM samples) and Lactobacillus (cecum GF samples) with body weight and weight gain was found (p < 0.05). Moreover, Escherichia-Shigella in the cecum of NM was significantly correlated with weight gain (p < 0.05). The most abundant genera identified in the jejunal and cecal contents of GF were generally beneficial microbiota. They may also play a role in reducing the pathogenic effects of Escherichia coli in these rabbits.

Host genotype affects endotoxin release in excreta of broilers at slaughter age

Host genotype, early post-hatch feeding, and pre- and probiotics are factors known to modulate the gut microbiome. However, there is a knowledge gap on the effect of both chicken genotype and these dietary strategies and their interplay on fecal microbiome composition and diversity, which, in turn, can affect the release of endotoxins in the excreta of broilers. Endotoxins are a major concern as they can be harmful to both animal and human health. The main goal of the current study was to investigate whether it was possible to modulate the fecal microbiome, thereby reducing endotoxin concentrations in the excreta of broiler chickens. An experiment was carried out with a 2 × 2 × 2 factorial arrangement including the following three factors: 1) genetic strain (fast-growing Ross 308 vs. slower growing Hubbard JA757); 2) no vs. combined use of probiotics and prebiotics in the diet and drinking water; and 3) early feeding at the hatchery vs. non-early feeding. A total of 624 Ross 308 and 624 Hubbard JA757 day-old male broiler chickens were included until d 37 and d 51 of age, respectively. Broilers (N = 26 chicks/pen) were housed in a total of 48 pens, and there were six replicate pens/treatment groups. Pooled cloacal swabs (N = 10 chickens/pen) for microbiome and endotoxin analyses were collected at a target body weight (BW) of 200 g, 1 kg, and 2.5 kg. Endotoxin concentration significantly increased with age (p = 0.01). At a target BW of 2.5 kg, Ross 308 chickens produced a considerably higher amount of endotoxins (Δ = 552.5 EU/mL) than the Hubbard JA757 chickens (p < 0.01). A significant difference in the Shannon index was observed for the interaction between the use of prebiotics and probiotics, and host genotype (p = 0.02), where Ross 308 chickens with pre-/probiotics had lower diversity than Hubbard JA757 chickens with pre-/probiotics. Early feeding did not affect both the fecal microbiome and endotoxin release. Overall, the results suggest that the chicken genetic strain may be an important factor to take into account regarding fecal endotoxin release, although this needs to be further investigated under commercial conditions.

Research Note: Therapeutic effect of a Salmonella phage combination on chicks infected with Salmonella Typhimurium

Antibiotic treatment failure is increasingly encountered for the emergence of pandrug-resistant isolates, including the prototypical broad-host-range Salmonella enterica serovar (S.) Typhimurium, which mainly transmitted to humans through poultry products. In this study we explored the therapeutic potential of a Salmonella phage composition containing a virulent phage and a nonproductive phage that does not produce progeny phage against chicks infected with a pandrug-resistant S. Typhimurium strain of avian origin. After approximately 10⁷ CFU of S. Typhimurium strain ST149 were administrated to chicks by intraperitoneal injection, the phage combination (∼10⁸ PFU) was gavaged at 8-h, 32-h, and 54-h postinfection. At d 10 postinfection, phage treatment completely protected chicks from Salmonella-induced death compared to 91.7% survival in the Salmonella challenge group. In addition, phage treatment also greatly reduced the bacterial load in various organs, with Salmonella colonization levels decreasing more significantly in spleen and bursa than in liver and cecal contents, possibly due to higher phage titers in these immune organs. However, phages could not alleviate the decreased body weight gain and the enlargement of spleen and bursa of infected chicks. Further examination of the bacterial flora in the cecal contents of chicks found that S. Typhimurium infection caused a remarkable decrease in abundance of Clostridia vadin BB60 group and Mollicutes RF39 (the dominant genus in chicks), making Lactobacillus the dominate genus. Although phage treatment partially restored the decline of Clostridia vadin BB60 group and Mollicutes RF39 and increased abundance of Lactobacillus caused by S. Typhimurium infection, Fournierella that may aggravate intestinal inflammation became the major genus, followed by increased Escherichia-Shigella as the second dominate bacterial genus. These results suggested that successive phage treatment modulated the structural composition and abundance of bacterial communities, but failed to normalize the intestinal microbiome disrupted by S. Typhimurium infection. Phages need to be combined with other means to control the spread of S. Typhimurium in poultry.

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

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

Dietary folic acid addition reduces abdominal fat deposition mediated by alterations in gut microbiota and SCFA production in broilers

Intensive selective breeding for high growth rate and body weight cause excess abdominal fat in broilers. Gut microbiota and folic acid were reported to regulate lipid metabolism. A total of 210 one-day-old broilers were divided into the control (folic acid at 1.3 mg/kg) and folic acid groups (folic acid at 13 mg/kg) to illustrate the effects of folic acid on growth performance, abdominal fat deposition, and gut microbiota, and the experiment lasted 28 d. Results revealed that dietary folic acid addition decreased abdominal fat percentage (P < 0.05) and down-regulated genes expression related to cell proliferation and differentiation in abdominal fat including IGF1, EGF, C/EBPα, PPARγ, PLIN1, FABP4 and PCNA (P < 0.05). Folic acid addition decreased caecal Firmicutes-to-Bacteroidetes ratio (P < 0.01) and increased the proportions of Alistipes, Oscillospira, Ruminococcus, Clostridium, Dehalobacterium and Parabacteroides (P < 0.05). Caecal acetic acid, and propionic acid contents were found to be higher under folic acid treatment (P < 0.05), which were negatively related to genes expression associated with adipocyte proliferation and differentiation (P < 0.05). Ruminococcus was positively correlated with caecal acetic acid content, and the same phenomenon was detected between propionic acid and Oscillospira and Ruminococcus (P < 0.05). Acetic acid and Oscillospira were identified to be negatively associated with abdominal fat percentage (P < 0.05). In conclusion, our data demonstrated that dietary supplementation of folic acid reduced fat deposition in broilers by inhibiting abdominal adipocyte proliferation and differentiation, which might be mediated by changes in gut microbiota and short chain fatty acid production.

Timing and delivery route effects of cecal microbiome transplants on Salmonella Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions

BACKGROUND

Exposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. However, administration of microbiota transplant products in a hatchery setting may prove challenging. Effective administration strategies are dependent on key factors, such as; the age of chicks receiving interventions and mode of delivery. This study aimed to assess these two aspects to provide supporting evidence towards microbiome manipulation strategies for use in commercial hatcheries.

RESULTS

Manipulation of the microbiota between 4 and 72 h of hatch markedly reduced faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration of transplant material via spray or gel drop delivery systems had minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that all transplant groups had higher diversity and species richness than non-transplant groups during the first week of life and the early stages of infection with ST47/4.The relative abundance of the bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections.

CONCLUSIONS

This study demonstrated that administration of microbiome transplants, using methods that would align with hatchery practices, effectively reduced colonisation and shedding of Salmonella in chickens. Age of chicks at microbiome administration had limited effect on the diversity and composition of the microbiome and conferred protection against Salmonella infections. Traditional hatchery delivery systems, such as spray or gel-drop, are sufficient to transfer donor material, alter the microbiome and confer protection against Salmonella. This study helps highlight the opportunity for use of microbiome modification methods within the hatchery.

The effects of a Bacillus licheniformis and phytase mixture added to broiler diets on growth performance, nutrient digestibility, and cecal microecosystem

This study aims to evaluate the effects of Bacillus licheniformis and 6-phytase added alone or in combination to broiler chicken diets on the growth performance, apparent ileal digestibility coefficient (AID) of nutrients, microbial activity, and cecal bacterial communities. In total, 400 one-day-old female Ross 308 chicks were randomly allocated to 4 dietary treatments (10 replicate pens, 10 birds each). The following groups were defined: NC (negative control), basal diet without any feed additive supplementation; NC+Pro, basal diet with addition of the B. licheniformis preparation (500 g/t of diet); NC+Phy, basal diet with addition of phytase (200 g/t of diet); and NC+Pro+Phy, basal diet combined with both studied additives. B. licheniformis positively affected (P<0.05) the feed intake (FI) and feed conversion ratio (FCR) in the first 10 d of bird rearing. Moreover, phytase supplementation elevated the FCR from 21 to 35 d. In the entire experiment, an interaction between phytase and probiotic was observed only in terms of decreasing the bird FI (P=0.005) without a negative effect on the FCR (P>0.05). Furthermore, the AID of ether extract was improved by phytase supplementation. In terms of the cecal microecology, both separately administered factors promoted Lactobacillaceae in the ceca. Interactions between probiotic preparation and phytase were noted that indicated a decreased Clostridiales population and favored Ruminococcaceae proliferation. It can be concluded that for the first time in the available literature, the favorable interactions between B. licheniformis and phytase resulted in improved performance and cecal microbiota changes in broilers.

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.

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.

Differences in gut bacterial community composition between modern and slower-growing broiler breeder lines: Implications of growth selection on microbiome composition

In the last century broiler chicken lines have undergone an extensive breeding regime aimed primarily at growth and high meat yield. It is not known if breeding has also resulted in a change to the broiler breeder's associated gut microbiota. Here we compared the gut microbiota of 37-week-old commercial Cobb breeding dams with dams from a broiler Legacy line which has not undergone selection since 1986. The dams from both lines were kept together in the same shed under the same management protocol from day of hatch to avoid additional confounders. We chose this age to allow significant bacterial exchange, thus avoiding exposure dependent artifacts and so that we could compare dams at the same developmental state of adulthood and peak laying performance. Significant differences in the composition of the cecum bacterial communities were found. Bacteria of the genus Akkermansia, implicated in mucin degradation and associated with host metabolic health, accounted for 4.98% ± 5.04% of the Cobb cecum community, but were mostly absent from the ceca of the Legacy line dams. Inversely, Legacy dams had higher levels of Clostridiales, Lactobacillales and Aeromonadales. These results show that breeding has resulted in a change in the gut microbiota composition, likely by changing the physiological conditions in the mucosa. It remains unclear if changes in gut microbiota composition are a part of the mechanism affecting growth or are a secondary result of other physiological changes accelerating growth. Therefore, the identification of these changes opens the door to further targeted research.

Administration of a Multi-Genus Synbiotic to Broilers: Effects on Gut Health, Microbial Composition and Performance

In recent years, the applicability of prebiotics, probiotics and their mixtures, defined as synbiotics, in poultry production has received considerable attention. Following the increasing regulation of antibiotic use, these nutraceuticals are seen as an alternative way to sustain production efficiency and resistance to pathogens and stressors by modulating birds' gut health. The aim of this study was to evaluate the benefits provided under field conditions by administering the multi-species synbiotic PoultryStar^® sol to broilers in drinking water. To this purpose, three Ross 308 broiler flocks, representing separate progenies of a breeder flock which was treated with the same synbiotic, were housed in separate farms, divided into treatment and control groups, and followed throughout the productive cycle. Synbiotic administration was shown to improve gut health even in absence of a challenge, with limited changes in terms of macroscopic intestinal lesions and more overt differences related to histopathological scores and villi length. Synbiotic-fed chickens performed consistently better in terms of body weight gain, feed conversion ratio and survivability. Lastly, the evaluation of the caecal microbiome through next-generation sequencing highlighted the effects of synbiotic supplementation on the composition of the bacterial population, the implications of which will, however, require further studies to be better comprehended.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Early life microbiota transplantation from highly feed-efficient broiler improved weight gain by reshaping the gut microbiota in laying chicken

Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p < 0.01). Kyoto encyclopedia of genes and genomes (KEGG) pathways for microbial functions regarding amino acid metabolism, secondary metabolites biosynthesis, carbohydrate metabolism, energy metabolism, and enzyme families, cofactors, and vitamins were significantly annotated in the FMT group. Overall, FMT administration from the donor of highly feed-efficient broilers improved weight gain by reshaping a distinct gut microbiome, which may be related to the metabolism and health in the recipients laying chicks, providing new insight on the application of the FMT technique for early life programming of laying chickens.

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

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

Poor body condition is associated with lower hippocampal plasticity and higher gut methanogen abundance in adult laying hens from two housing systems

It is still unclear which commercial housing system provides the best quality of life for laying hens. In addition, there are large individual differences in stress levels within a system. Hippocampal neurogenesis or plasticity may provide an integrated biomarker of the stressors experienced by an individual. We selected 12 adult hens each with good and poor body condition (based on body size, degree of feather cover and redness of the comb) from a multi-tier free range system containing H&N strain hens, and from an enriched cage system containing Hy-Line hens (n = 48 total). Immature neurons expressing doublecortin (DCX) were quantified in the hippocampus, contents of the caecal microbiome were sequenced, and expression of inflammatory cytokines was measured in the spleen. DCX⁺ cell densities did not differ between the housing systems. In both systems, poor condition hens had lower DCX⁺ cell densities, exhibited elevated splenic expression of interleukin-6 (IL6) mRNA, and had a higher relative caecal abundance of methanogenic archea Methanomethylophilaceae. The findings suggest poor body condition is an indicator that individual hens have experienced a comparatively greater degree of cumulative chronic stress, and that a survey of the proportion of hens with poor body conditions might be one way to evaluate the impact of housing systems on hen welfare.

Alterations in bacterial metabolites, cytokines, and mucosal integrity in the caecum of broilers caused by feed additives and host-related factors

A total of 2,880 one-day-old male and female broiler chicks from two breeds, Ross308 and Cobb500 were randomly assigned to 72 pens. Broilers were offered three diets: a wheat-soybean diet without (CO), or with either a probiotic (probiotic; 2.4 x 10⁹ CFU/kg diet of Bacillus subtilis DSM32324 and DSM32325 and B. amyloliquefaciens DSM25840) or a phytobiotic (phytobiotic; grape extract with 165 ppm procyanidin and 585 ppm polyphenol) product. The trial was conducted with a 3 × 2 × 2 factorial arrangement of diet, breed and sex in a completely randomized design and consisted of 6 replicate-pens per treatment (40 birds per pen). At day 7, 21, and 35, one chicken per pen was slaughtered for caecal sampling to quantify bacterial metabolites (digesta) as well as evaluate mRNA abundance and histomorphology (tissue). Data were subjected to ANOVA using GLM procedure to evaluate age, diet, breed and sex and their interactions. Spearman’s correlation (r) was analyzed between metabolite concentration and mRNA abundance. Overall, the concentration of short chain fatty acids increased with age, while lactate decreased from day 7 to 21 (p < 0.05). The mRNA abundance of IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17α, IL-18, IFN-γ and TGF-β2 increased with age but IL-1β and TNF-α increased in abundance from day 7 to 21 and then decreased (p < 0.05). Abundance of MUC2 and CLDN5 increased after day 21 (p < 0.05). Caecal crypt depth increased with age (p < 0.05). Acidic goblet cell (GC) number peaked at day 21 (p < 0.05), while mixed GC number was not affected by age. A few impacts of breed, diet and interactions on the investigated variables showed no meaningful biological pattern. Propionate positively correlated with all cytokines investigated (r = 0.150–0.548), except TNF-α. Lactate negatively correlated with pro-inflammatory cytokines like IL-1β (r = −0.324). Aging affected caecal histomorphology, bacterial activity and genes responsible for barrier integrity and inflammatory response. This effect could be attributed to the interaction between gut microbiota and immune system as well as the direct effect of metabolites on gut histomorphology and cytokine mRNA abundance.

Integrated omics analysis reveals differences in gut microbiota and gut-host metabolite profiles between obese and lean chickens

Abdominal fat is the major adipose tissue in chickens. In chicken, the deposition of abdominal fat affects meat yield and quality. Previous reports suggest that gut microbiota composition and function are associated with lipid metabolism. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut-host metabolite profiles in Shouguang (SG; a Chinese chicken breed with low-fat deposition) and Luqin (LQ; a fatty-type chicken breed with a fast growth rate) chickens. The results showed that LQ chickens had higher body weight, eviscerated yield, abdominal fat yield, abdominal fat ratio, and triglyceride (TG) content in the breast muscle than SG chickens. Untargeted metabolomics analyses showed a total of 11 liver metabolites, 19 plasma metabolites, and 30 cecal metabolites differentially enriched in LQ and SG chickens based on variable importance in the projection (VIP) ≥ 1 and P ≤ 0.05. These metabolites are involved in lipid and amino acid metabolism. The relative abundance of bacteria in the microbiota differed significantly between the 2 chicken breeds. The functional prediction of microbiota abundant in LQ chickens was starch and lactose degradation. Erysipelatoclostridium was abundant in LQ chickens and significantly positively correlated to palmitoyl ethanolamide (PEA), a key regulator of lipid metabolism. Our findings revealed differences in liver and plasma metabolites between chicken breeds with different adipose deposition capacities. Long-chain acylcarnitines might be important markers of adipose deposition differences in chickens. The cecum's microbial communities and metabolome profiles significantly differed between LQ and SG chickens. However, the relationship between cecal microbiota and their metabolites and liver and plasma metabolites is not thoroughly understood. Future research will focus on relating tissue metabolite changes to intestinal microbiota and their effects on body fat deposition.

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.

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure

BACKGROUND

The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry to eliminate the use of antibiotic growth promotants (AGPs) as feed additives. To mitigate their removal, efficacious alternatives are required. AGPs are thought to operate through modulating the gut microbiome to limit opportunities for colonization by pathogens, increase nutrient utilization, and reduce inflammation. However, little is known concerning the underlying mechanisms. Previous studies investigating the effects of AGPs on the poultry gut microbiome have largely focused on 16S rDNA surveys based on a single gastrointestinal (GI) site, diet, and/or timepoint, resulting in an inconsistent view of their impact on community composition.

METHODS

In this study, we perform a systematic investigation of both the composition and function of the chicken gut microbiome, in response to AGPs. Birds were raised under two different diets and AGP treatments, and 16S rDNA surveys applied to six GI sites sampled at three key timepoints of the poultry life cycle. Functional investigations were performed through metatranscriptomics analyses and metabolomics.

RESULTS

Our study reveals a more nuanced view of the impact of AGPs, dependent on age of bird, diet, and intestinal site sampled. Although AGPs have a limited impact on taxonomic abundances, they do appear to redefine influential taxa that may promote the exclusion of other taxa. Microbiome expression profiles further reveal a complex landscape in both the expression and taxonomic representation of multiple pathways including cell wall biogenesis, antimicrobial resistance, and several involved in energy, amino acid, and nucleotide metabolism. Many AGP-induced changes in metabolic enzyme expression likely serve to redirect metabolic flux with the potential to regulate bacterial growth or produce metabolites that impact the host.

CONCLUSIONS

As alternative feed additives are developed to mimic the action of AGPs, our study highlights the need to ensure such alternatives result in functional changes that are consistent with site-, age-, and diet-associated taxa. The genes and pathways identified in this study are therefore expected to drive future studies, applying tools such as community-based metabolic modeling, focusing on the mechanistic impact of different dietary regimes on the microbiome. Consequently, the data generated in this study will be crucial for the development of next-generation feed additives targeting gut health and poultry production. Video Abstract.

Rapid Oxford Nanopore Technologies MinION Sequencing Workflow for Campylobacter jejuni Identification in Broilers on Site—A Proof-of-Concept Study

Campylobacter is recognised as one of the most important foodborne bacteria, with a worldwide health and socioeconomic impact. This bacterium is one of the most important zoonotic players in poultry, where efficient and fast detection methods are required. Current official culture methods for Campylobacter enumeration in poultry usually include >44 h of culture and >72 h for identification, thus requiring at least five working shifts (ISO/TS 10272-2:2017). Here, we have assembled a portable sequencing kit composed of the Bento Lab and the MinION and developed a workflow for on-site farm use that is able to detect and report the presence of Campylobacter from caecal samples in less than five hours from sampling time, as well as the relationship of Campylobacter with other caecal microbes. Beyond that, our workflow may offer a cost-effective and practical method of microbiologically monitoring poultry at the farm. These results would demonstrate the possibility of carrying out rapid on-site screening to monitor the health status of the poultry farm/flock during the production chain.

Salmonella Phages Affect the Intestinal Barrier in Chicks by Altering the Composition of Early Intestinal Flora: Association With Time of Phage Use

Phages show promise in replacing antibiotics to treat or prevent bacterial diseases in the chicken breeding industry. Chicks are easily affected by their environment during early growth. Thus, this study investigated whether oral phages could affect the intestinal barrier function of chicks with a focus on the cecal microbiome. In a two-week trial, forty one-day-old hens were randomly divided into four groups: (1) NC, negative control; (2) Phage 1, 10⁹ PFU phage/day (days 3–5); (3) Phage 2, 10⁹ PFU phage/day (days 8–10); and (4) AMX, 1 mg/mL amoxicillin/day (days 8–10). High-throughput sequencing results of cecal contents showed that oral administration of phages significantly affected microbial community structure and community composition, and increased the relative abundance of Enterococcus. The number of different species in the Phage 1 group was much higher than that in the Phage 2 group, and differences in alpha and beta diversity also indicated that the magnitude of changes in the composition of the cecal microbiota correlated with the time of phage use. Particularly in the first stage of cecal microbiota development, oral administration of bacteriophages targeting Salmonella may cause substantial changes in chicks, as evidenced by the results of the PICRUSt2 software function prediction, reminding us to be cautious about the time of phage use in chicks and to avoid high oral doses of phages during the first stage. Additionally, the Phage 2 samples not only showed a significant increase in the relative abundance of Bifidobacterium and Subdoligranulum, but also improved the intestinal morphology (jejunum) and increased the mRNA expression level of occludin and ZO-1. We concluded that phages do not directly interact with eukaryotic cells. The enhancement of intestinal barrier function by phages in chicks may be related to changes in the intestinal flora induced by phages. This implies that phages may affect intestinal health by regulating the intestinal flora. This study provides new ideas for phage prevention of intestinal bacterial infections and promotes large-scale application of phages in the poultry industry.

Dietary Bacitracin Methylene Disalicylate Improves Growth Performance by Mediating the Gut Microbiota in Broilers

The growth performance of livestock and poultry has always been a concern. However, much work is currently focused on the selection of breeds and diets to improve the growth performance of livestock and poultry. Furthermore, numerous studies have shown that the gut microbiota is closely related to the growth performance of livestock and poultry. At present, there are many reports on the impact of antibiotic intervention on the structure of gut microbiota. However, there are few reports on the influence of antibiotic intervention on the structure of intestinal microbes and the effect of this change on growth performance. Bacitracin methylene disalicylate (BMD) intervention changes the microbial structure in the caecum of broilers at different growth stages, as shown in this study. To further reveal the potential relationship between gut microbiota changes and growth performance caused by BMD intervention, correlation analysis was used for analysis. A total of 144 1-day-old male Cobb-Vantress were randomly divided into two groups. In addition to antibiotic-free starter mash diets, starter mash diets supplemented with 55 mg/kg BMD were also used, called the CON group and the BMD group, and lasted 28 days. (1) These study results showed that adding BMD to the diet had a significant effect on the growth performance of broilers. Compared with the CON group, the body weight of the BMD group increased significantly by 11.08% and 20.13% on Days 14 and 28, respectively (p < 0.05). Similarly, at 0−14, 14−28 and 0−28 days of age, the average daily gain of the BMD group increased significantly by 12.28%, 24.49% and 20.80%, respectively. The average daily feed intake of the BMD group increased significantly by 18.28%, 27.39% and 24.97% (p < 0.05). In addition, at 0−28 days of age, the feed conversion ratio increased significantly by 5.5% (p < 0.05). (2) Alpha diversity results show that BMD intervention has an impact on gut microbiota at different growth stages. (3) The early intervention significantly affected 7 taxa by Day 14, followed by 22 taxa by Day 28, which is similar to the results in the caecal flora. Compared with the CON group, the Christensenellaceae R-7 group had the highest linear discriminant analysis (LDA) score on Day 28. In addition, Pearson’s correlation analysis showed that the Lachnospiraceae FCS020 group was significantly negatively correlated with growth performance. In general, these results indicate that dietary supplementation of BMD has an effect on broiler gut microbiota structure and growth performance. However, changes in growth performance may be caused by the gut microbiota structure.

The Microalgae Phaeodactylum tricornutum Is Well Suited as a Food with Positive Effects on the Intestinal Microbiota and the Generation of SCFA: Results from a Pre-Clinical Study

Microalgae such as Phaeodactylum tricornutum (PT) are a sustainable source of nutrients, especially eicosapentaenoic acid (EPA), fucoxanthin (Fx), and chrysolaminarin (Chrl), the concentrations of which can vary depending on the culture conditions. We generated three types of diets containing either an EPA- and Fx-rich (EPA/Fx) or Chrl-rich microalgae (with 5, 15, or 25% added to the diet) or an isocaloric control diet (CD). These diets were evaluated over 14 days in young C57BL/6J mice for safety and bioavailability, short-chain fatty acid (SCFA) production, and microbiome analysis. Both microalgae diets increased body weight gain dose-dependently compared to the CD. Microalgae-derived EPA was well absorbed, resulting in increased liver and fat tissue levels and a decrease in the n-6:n-3 ratio in liver tissue. Both microalgae diets increased the production of selected SCFA and decreased the Firmicutes/Bacteriodota ratio, whereas the Chrl-rich diet led to an increase in Akkermansia. Doses of up to 4621 mg Chrl, 920 mg EPA, and 231 mg Fx per kg body weight daily were tolerated without adverse effects. This pre-clinical study shows that PT is suitable for mouse feed, with positive effects on microbiota composition and SCFA production, suggesting beneficial effects on gut health.

Intestinal microbiota of layer hens and its association with egg quality and safety

The intestinal microbiota has attracted tremendous attention in the field of the poultry industry due to its critical role in the modulation of nutrient utilization, immune system, and consequently the improvement of the host health and production performance. Accumulating evidence implies intestinal microbiota of laying hens is a potential mediator to improve the prevalent issues in terms of egg quality decline in the late phase of laying production. However, the regulatory effect of intestinal microbiota on egg quality in laying hens remains elusive, which requires consideration of microbial baseline composition and succession during their long lifespans. Notable, although Firmicutes, Bacteroidetes, and Proteobacteria form the vast majority of intestinal microbiota in layer hens, dynamic intestinal microbiota succession occurs throughout all laying periods. In addition to the direct effects on egg safety, intestinal microbiota and its metabolites such as short-chain fatty acids, bile acids, and tryptophan derivatives, are suggested to indirectly modulate egg quality through the microbiota-gut-liver/brain-reproductive tract axis. These findings can extend our understanding of the crosstalk between intestinal microbiota and the host to improve egg quality and safety. This paper reviews the compositions of intestinal microbiota in different physiological stages of laying hens and their effects on egg quality and proposes that intestinal microbiota may become a potential target for modulating egg quality and safety by nutritional strategies in the future.

The Microbiota-Gut-Brain Axis: Gut Microbiota Modulates Conspecific Aggression in Diversely Selected Laying Hens

The gut microbiota plays an important role in regulating brain function, influencing psychological and emotional stability. The correlations between conspecific aggression, gut microbiota, and physiological homeostasis were further studied in inbred laying chicken lines, 63 and 72, which were diversely selected for Marek’s disease, and they also behave differently in aggression. Ten sixty-week-old hens from each line were sampled for blood, brain, and cecal content. Neurotransmitters, cytokines, corticosterone, and heterophil/lymphocyte ratios were determined. Cecal microbiota compositions were determined by bacterial 16s rRNA sequencing, and functional predictions were performed. Our data showed that the central serotonin and tryptophan levels were higher in line 63 compared to line 72 (p < 0.05). Plasma corticosterone, heterophil/lymphocyte ratios, and central norepinephrine were lower in line 63 (p < 0.05). The level of tumor necrosis factor α tended to be higher in line 63. Faecalibacterium, Oscillibacter, Butyricicoccus, and Bacteriodes were enriched in line 63 birds, while Clostridiales vadin BB60, Alistipes, Mollicutes RF39 were dominated in line 72. From the predicted bacterial functional genes, the kynurenine pathway was upregulated in line 72. These results suggested a functional linkage of the line differences in serotonergic activity, stress response, innate immunity, and gut microbiota populations.

A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae

Simple Summary

Feeding poultry with insects could reduce production costs, but the impact of this diet on their gut microbiota and growth is little known because the network of relationships between their weights, the composition of their microbiota and their diet is complex and potentially biased by confounding factors (such as the gut compartment, age and sex of the birds). In this study, we were able to unravel these relationships in local breed chickens fed or not fed with black soldier fly larvae thanks to a technique of artificial intelligence (the probabilistic structural equation model). Bacteria were grouped into few entities with distinctive metabolic attributes and were probably linked nutritionally. Birds’ age influenced body weights and bacterial composition. The proposed methodology was thus able to simplify the complex dependencies among bacteria present in the gut and to highlight links potentially important in the response of chicken to insect feed.

Abstract

Feeding chicken with black soldier fly larvae (BSF) may influence their rates of growth via effects on the composition of their gut microbiota. To verify this hypothesis, we aim to evaluate a probabilistic structural equation model because it can unravel the complex web of relationships that exist between the bacteria involved in digestion and evaluate whether these influence bird growth. We followed 90 chickens fed diets supplemented with 0%, 5% or 10% BSF and measured the strength of the relationship between their weight and the relative abundance of bacteria (OTU) present in their cecum or cloaca at 16, 28, 39, 67 or 73 days of age, while adjusting for potential confounding effects of their age and sex. Results showed that OTUs (62 genera) could be combined into ten latent constructs with distinctive metabolic attributes. Links were discovered between these constructs that suggest nutritional relationships. Age directly influenced weights and microbiotal composition, and three constructs indirectly influenced weights via their dependencies on age. The proposed methodology was able to simplify dependencies among OTUs into knowledgeable constructs and to highlight links potentially important to understand the role of insect feed and of microbiota in chicken growth.

Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

BACKGROUND

Antibiotic growth promoters (AGPs) are commonly used within poultry production to improve feed conversion, bird growth, and reduce morbidity and mortality from clinical and subclinical diseases. Due to the association between AGP usage and rising antimicrobial resistance, the industry has explored new strategies including the use of probiotics and other microbial-based interventions to promote the development of a healthy microbiome in birds and mitigate against infections associated with food safety and food security. While previous studies have largely focused on the ability of probiotics to protect against Clostridium perfringens and Salmonella enterica, much less is known concerning their impact on Campylobacter jejuni, a near commensal of the chicken gut microbiome that nevertheless is a major cause of food poisoning in humans.

RESULTS

Here we compare the efficacy of four microbial interventions (two single strain probiotics, the bacterium-Pediococcus acidilactici, and the yeast-Saccharomyces cerevisiae boulardii; and two complex, competitive exclusion, consortia-Aviguard and CEL) to bacitracin, a commonly used AGP, to modulate chicken gut microbiota and subsequently impact C. jejuni infection in poultry. Cecal samples were harvested at 30- and 39-days post hatch to assess Campylobacter burden and examine their impact on the gut microbiota. While the different treatments did not significantly decrease C. jejuni burden relative to the untreated controls, both complex consortia resulted in significant decreases relative to treatment with bacitracin. Analysis of 16S rDNA profiles revealed a distinct microbial signature associated with each microbial intervention. For example, treatment with Aviguard and CEL increased the relative abundance of Bacteroidaceae and Rikenellaceae respectively. Furthermore, Aviguard promoted a less complex microbial community compared to other treatments.

CONCLUSIONS

Depending upon the individual needs of the producer, our results illustrate the potential of each microbial interventions to serve flock-specific requirements.

Influence of heat stress on intestinal integrity and the caecal microbiota during Enterococcus cecorum infection in broilers

Enterococcus cecorum (EC) is one of the most relevant bacterial pathogens in modern broiler chicken production from an economic and animal welfare perspective. Although EC pathogenesis is generally well described, predisposing factors are still unknown. This study aimed to understand the effect of heat stress on the caecal microbiota, intestinal integrity, and EC pathogenesis. A total of 373 1-day-old commercial broiler chicks were randomly assigned to four groups: (1) noninoculated, thermoneutral conditions (TN); (2) noninoculated, heat stress conditions (HS); (3) EC-inoculated, thermoneutral conditions (TN + EC); and (4) EC-inoculated, heat stress conditions (HS + EC). Birds were monitored daily for clinical signs. Necropsy of 20 broilers per group was performed at 7, 14, 21, and 42 days post-hatch (dph). A trend towards enhanced and more pronounced clinical disease was observed in the EC-inoculated, heat-stressed group. EC detection rates in extraintestinal tissues via culture were higher in the HS + EC group (~19%) than in the TN + EC group (~11%). Significantly more birds were colonized by EC at 7 dph in the HS + EC group (100%) than in the TN + EC group (65%, p < 0.05). The caecal microbiota in the two EC-inoculated groups was significantly more diverse than that in the TN group (p < 0.05) at 14 dph, which may indicate an effect of EC infection. An influence of heat stress on mRNA expression of tight junction proteins in the caecum was detected at 7 dph, where all six investigated tight junction proteins were expressed at significantly lower levels in the heat stressed groups compared to the thermoneutral groups. These observations suggest that heat stress may predispose broilers to EC-associated disease and increase the severity thereof. Furthermore, heat stress may impair intestinal integrity and promote EC translocation.

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

Effects of Xylanase in Corn- or Wheat-Based Diets on Cecal Microbiota of Broilers

Xylanase has been demonstrated to improve growth performance of broilers fed wheat- or corn-based diets due to its ability to degrade arabinoxylans (AX). However, content and structure of AX in corn and wheat are different, comparing effects of xylanase on cecal microbiota of broilers fed corn- or wheat-based diets could further elaborate the mechanism of the specificity of xylanase for different cereal grains. Thus, a total of 192 one-day-old broilers were randomly allotted into four dietary treatments, including wheat-soybean basal diet, wheat-soybean basal diet with 4,000U/kg xylanase, corn-soybean basal diet, and corn-soybean basal diet with 4,000U/kg xylanase to evaluate interactive effects of xylanase in corn- or wheat-based diets on broilers cecal microbiota during a 6-week production period. The results indicated that bacterial community clustering was mainly due to cereal grains rather than xylanase supplementation. Compared with broilers fed wheat-based diets, corn-based diets increased alpha-diversity and separated from wheat-based diets (p<0.05). Xylanase modulated the abundance of specific bacteria without changing overall microbial structure. In broilers fed wheat-based diets, xylanase increased the abundance of Lactobacillus, Bifidobacterium, and some butyrate-producing bacteria, and decreased the abundance of non-starch polysaccharides-degrading (NSP) bacteria, such as Ruminococcaceae and Bacteroidetes (p<0.05). In broilers fed corn-based diets, xylanase decreased the abundance of harmful bacteria (such as genus Faecalitalea and Escherichia-Shigella) and promoted the abundance of beneficial bacteria (such as Anaerofustis and Lachnospiraceae_UCG_010) in the cecum (p<0.05). Overall, xylanase supplementation to wheat- or corn-based diets improved broilers performance and cecal microbiota composition. Xylanase supplementation to wheat-based diets increased the abundance of butyrate-producing bacteria and decreased the abundance of NSP-degrading bacteria. Moreover, positive effects of xylanase on cecal microbiota of broilers fed corn-based diets were mostly related to the inhibition of potentially pathogenic bacteria, and xylanase supplementation to corn-based diets slightly affected the abundance of butyrate-producing bacteria and NSP-degrading bacterium, the difference might be related to lower content of AX in corn compared to wheat.

Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection

Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.

The Spatial and Temporal Characterization of Gut Microbiota in Broilers

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

Bacillus pumilus and Bacillus subtilis Promote Early Maturation of Cecal Microbiota in Broiler Chickens

Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious period before reaching mature configuration. Whether probiotics can play a role in the early maturation of intestinal microbiota is unknown. To address this, day-old chicks were assigned into six groups: NC (basal diet), PC (virginiamycin), low (BPL) and high-dose (BPH) of Bacillus pumilus, and low (BSL) and high-dose (BSH) of Bacillus subtilis. Cecal contents at days 7, 14, 28 and 42 were used to analyze the treatment and time effects on the diversity and composition of microbiota. Overall, the alpha diversity was significantly decreased in the NC group between days 7 and 14, while this decline was prevented in the Bacillus subtilis probiotic (BSL and BSH) and even reversed in the BPH group. The beta-diversity showed significant responses of microbial communities to probiotics in first two weeks of life. Analyses of the abundance of microbiota reflected that members of the family Ruminococcaceae (Ruminnococcus, Oscillospira, Faecalibacterium, Butyricicoccus, and Subdoligranulum), which were dominant in mature microbiota, were significantly higher in abundance at day 14 in the probiotic groups. Conversely, the abundance of genera within the family Lachnospiraceae (Ruminococcus, Blautia, and Coprococcus) was dominant in early dynamic microbiota but was significantly lower in the probiotic groups at day 14. The Lactobacillus and Bifidobacterium abundance was higher, while the Enterobacteriaceae abundance was lower in the probiotic groups. In summary, the probiotics efficiently helped the cecal microbiota reach mature configuration earlier in life. These results could be used for the future manipulation of microbiota from the perspective of improving poultry performance.

Relative Effects of Dietary Administration of a Competitive Exclusion Culture and a Synbiotic Product, Age and Sampling Site on Intestinal Microbiota Maturation in Broiler Chickens

In this research, the effects of early post-hatch inoculation of a competitive exclusion product (Br) and the continuous feeding of a synbiotic supplement (Sy) containing probiotic bacteria, yeast, and inulin on the production traits and composition of ileal chymus (IC), ileal mucosa (IM), and caecal chymus (CC) microbiota of broiler chickens were evaluated. The dietary treatments had no significant effects on the pattern of intestinal microbiota or production traits. The digestive tract bacteriota composition was affected mostly by the sampling place and age of birds. The dominant family of IC was Lactobacillaceae, without change with the age. The abundance of the two other major families, Enterococcaceae and Lachnospiraceae decreased with the age of birds. In the IM, Clostridiaceae was the main family in the first three weeks. Its ratio decreased later and Lactobacillaceae became the dominant family. In the CC, Ruminococcaceae and Lachnospiraceae were the main families with decreasing tendency in the age. In IC, Br treatment decreased the abundance of genus Lactobacillus, and both Br and Sy increased the ratio of Enterococcus at day 7. In all gut segments, a negative correlation was found between the IBD antibody titer levels and the ratio of genus Leuconostoc in the first three weeks, and a positive correlation was found in the case of Bifidobacterium, Rombutsia, and Turicibacter between day 21 and 40.

Comparison of Chicken Cecal Microbiota after Metaphylactic Treatment or Following Administration of Feed Additives in a Broiler Farm with Enterococcal Spondylitis History

Minimizing the clinical signs of Enterococcus cecorum infections causing enterococcal spondylitis in broiler herds is successful when initiated as metaphylaxis in the first week of life. Mechanistically, either the Enterococcus species present at that time are reduced by antibiotic treatment or antibiotic treatment might induce changes in intestinal microbiota composition with an indirect and subsequent influence. The aim of the present study was to examine the cecal microbiota of chickens after administering lincospectin or different additives to evaluate whether these additives have lincospectin-like effects on microbiota. Therefore, 157,400 broiler chickens were reared in four chicken houses (~40,000 birds each) on a broiler farm with history of enterococcal spondylitis. Each flock was treated either with lincospectin or water soluble esterified butyrins, Bacillus (B.) licheniformis or palm oil was added via drinking water during the first days of life. Ten birds per house were dissected at days 11, 20 and 33 of life and cecal microbiota were analyzed (16S rRNA gene sequencing). Lincospectin treatment elicited significant changes in the cecal microbiota composition until slaughter age. Among the tested additives, effects of B. licheniformis on cecal microbiota composition were most similar to those seen after the treatment with lincospectin at day 11.

The link between broiler flock heterogeneity and cecal microbiome composition

BACKGROUND

Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the commercial value. The purpose of this study was to investigate the role of the cecal microbiome in weight differences between animals. Understanding how the gut microbiome may contribute to flock heterogeneity helps to pave the road for identifying methods to improve flock uniformity and performance.

RESULTS

Two hundred eighteen male broiler chicks were housed in the same pen, reared for 37 days, and at study end the 25 birds with highest BW (Big) and the 25 birds with lowest BW (Small) were selected for microbiome analysis. Cecal contents were analyzed by a hybrid metagenomic sequencing approach combining long and short read sequencing. We found that Big birds displayed higher microbial alpha diversity, higher microbiome uniformity (i.e. lower beta diversity within the group of Big birds), higher levels of SCFA-producing and health-associated bacterial taxa such as Lachnospiraceae, Faecalibacterium, Butyricicoccus and Christensenellales, and lower levels of Akkermansia muciniphila and Escherichia coli as compared to Small birds.

CONCLUSION

Cecal microbiome characteristics could be linked to the size of broiler chickens. Differences in alpha diversity, beta diversity and taxa abundances all seem to be directly associated with growth differences observed in an otherwise similar broiler flock.

The Development of the Gut Microbiota and Short-Chain Fatty Acids of Layer Chickens in Different Growth Periods

A long-term observation of changes of the gut microbiota and its metabolites would be beneficial to improving the production performance of chickens. Given this, 1-day-old chickens were chosen in this study, with the aim of observing the development of the gut microbiota and gut microbial function using 16S rRNA gene sequencing and metabolites short-chain fatty acids (SCFAs) from 8 to 50 weeks. The results showed that the relative abundances of Firmicutes and genus Alistipes were higher and fiber-degradation bacteria were less at 8 weeks compared with 20 and 50 weeks (P < 0.05). Consistently, gut microbial function was enriched in ATP-binding cassette transporters, the energy metabolism pathway, and amino acid metabolism pathway at 8 weeks. In contrast, the abundance of Bacteroidetes and some SCFA-producing bacteria and fiber-degradation bacteria significantly increased at 20 and 50 weeks compared with 8 weeks (P < 0.05), and the two-component system, glycoside hydrolase and carbohydrate metabolism pathway, was significantly increased with age. The concentration of SCFAs in the cecum at 20 weeks was higher than at 8 weeks (P < 0.01), because the level of fiber and the number of dominant fiber-degradation bacteria and SCFA-producing bacteria were more those at 20 weeks. Notably, although operational taxonomic units (OTUs) and the gut microbial α-diversity including Chao1 and abundance-based coverage estimator (ACE) were higher at 50 than 20 weeks (P < 0.01), the concentration of SCFAs at 50 weeks was lower than at 20 weeks (P < 0.01), suggesting that an overly high level of microbial diversity may not be beneficial to the production of SCFAs.

Microbial Diversity and Community Variation in the Intestines of Layer Chickens

The intestinal microbiota is increasingly recognized as an important component of host health, metabolism and immunity. Early gut colonizers are pivotal in the establishment of microbial community structures affecting the health and growth performance of chickens. White Lohmann layer is a common commercial breed. Therefore, this breed was selected to study the pattern of changes of microbiota with age. In this study, the duodenum, caecum and colorectum contents of white Lohmann layer chickens from same environment control farm were collected and analyzed using 16S rRNA sequencing to explore the spatial and temporal variations in intestinal microbiota. The results showed that the diversity of the microbial community structure in the duodenum, caecum and colorectum increased with age and tended to be stable when the layer chickens reached 50 days of age and the distinct succession patterns of the intestinal microbiota between the duodenum and large intestine (caecum and colorectum). On day 0, the diversity of microbes in the duodenum was higher than that in the caecum and colorectum, but the compositions of intestinal microbes were relatively similar, with facultative anaerobic Proteobacteria as the main microbes. However, the relative abundance of facultative anaerobic bacteria (Escherichia) gradually decreased and was replaced by anaerobic bacteria (Bacteroides and Ruminococcaceae). By day 50, the structure of intestinal microbes had gradually become stable, and Lactobacillus was the dominant bacteria in the duodenum (41.1%). The compositions of dominant microbes in the caecum and colorectum were more complex, but there were certain similarities. Bacteroides, Odoribacter and Clostridiales vadin BB60 group were dominant. The results of this study provide evidence that time and spatial factors are important factors affecting the intestinal microbiota composition. This study provides new knowledge of the intestinal microbiota colonization pattern of layer chickens in early life to improve the intestinal health of layer chickens.