Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens

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

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

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

Modulation of Gut Microbiota, and Morphometry, Blood Profiles and performance of Broiler Chickens Supplemented with Piper aduncum, Morinda citrifolia, and Artocarpus altilis leaves Ethanolic Extracts

Bioactive plants such as P. aduncum, M. citrifolia, and A. altilis might improve intestinal health as an alternative to antibiotic growth promoters. The objective of this study was to determine the effect of the ethanolic extracts (EEs) of these plants on the intestinal health of broiler chickens. Cobb 500 chickens (n = 352) were distributed into eight treatments with four replicates and 11 chickens each. T1 received a base diet, and T2 received a base diet with 0.005% zinc bacitracin. T3, T5, and T7 were supplemented with 0.005% of P. aduncum, M. citrifolia, and A. altilis EE in the diet while T4, T6, and T8 with 0.01% of the extract. The EEs were supplemented with drinking water from 1 to 26 days of age. The following parameters were evaluated: hematological profiles at 28 days of age, blood metabolites profiles at 14, 21, and 28 days; Escherichia coli, Staphylococcus aureus, and Lactobacillus sp. abundance in the ileum mucosa and content at 21 and 28 days, and histomorphometry of the duodenum, jejunum, and ileum mucosa at 14, 21, and 28 d. Final weight (FW), weight gain (WG), feed intake (FI), and feed conversion rate (FCR) were evaluated at seven, 21, and 33 days of age. M. citrifolia and A. altilis EE at 0.01% increased blood glucose levels at 21 and 28 days of age, respectively, and P. aduncum and M. citrifolia EE at 0.01% increased triglycerides at 28 days of age; in addition, this EE did not have any effect on the AST and ALT profiles. The depths of the Lieberkühn crypts and the villi length to the crypt's depth ratio increased with age on supplementation with 0.01% M. citrifolia and A. altilis EE at 21 days of age (p < 0.05). In addition, the depth of the crypts increased at 28 days of age (p < 0.05) in chickens supplemented with 0.01% A. altilis EE. The 0.01% M. citrifolia EE in diet decreased in the Staphylococcus aureus population in the ileal microbiota (p < 0.05). The FW and WG during the fattening and in the three stages overall increased, and the FCR decreased; however, the FI and the carcass yield did not change in the broiler chickens supplemented with 0.01% M. citrifolia EE (p < 0.05). Conclusively, the M. citrifolia EE at 0.01% of the diet improved intestinal health and thus the performance indices of the broiler chickens and did not have a detrimental effect on any of the parameters evaluated, so it is postulated as a potential alternative to AGP in poultry.

Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs

This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.

Integrated multi-omics reveals the roles of cecal microbiota and its derived bacterial consortium in promoting chicken growth

IMPORTANCE

The improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis. We also verified that a specific bacterial consortium consisting of isolates from the HBW chickens has the potential to be used as chicken growth promoters. These findings provide new insights into the potential links between gut microbiota and chicken phenotypes, shedding light on future manipulation of chicken gut microbiota to improve chicken growth performance.

Integrated Analysis of the Effects of Cecal Microbiota and Serum Metabolome on Market Weights of Chinese Native Chickens

The gut microbiota plays an important role in the physiological activities of the host and affects the formation of important economic traits in livestock farming. The effects of cecal microbiota on chicken weights were investigated using the Guizhou yellow chicken as a model. Experimental cohorts from chickens with high- (HC, n = 16) and low-market-weights (LC, n = 16) were collected. Microbial 16S rRNA gene sequencing and non-targeted serum metabolome data were integrated to explore the effect and metabolic mechanism of cecal microbiota on market weight. The genera Lachnoclostridium, Alistipes, Negativibacillus, Sellimonas, and Ruminococcus torques were enriched in the HC group, while Phascolarctobacterium was enriched in the LC group (p < 0.05). Metabolomic analysis determined that pantothenic acid (vitamin B5), luvangetin (2H-1-benzopyran-6-acrylic acid), and menadione (vitamin K3) were significantly higher in HC serum, while beclomethasone dipropionate (a glucocorticoid) and chlorophene (2-benzyl-4-chlorophenol) were present at higher levels in the LC group. The microbes enriched in HC were significantly positively correlated with metabolites, including pantothenic acid and menadione, and negatively correlated with beclomethasone dipropionate and chlorophene. These results indicated that specific cecal bacteria in Guizhou yellow chickens alter the host metabolism and growth performance. This study provides a reference for revealing the mechanism of cecal microbe actions that affect chicken body weight.

Cecal microbiota composition differs under normal and high ambient temperatures in genetically distinct chicken lines

Modern broilers, selected for high growth rate, are more susceptible to heat stress (HS) as compared to their ancestral jungle fowl (JF). HS affects epithelia barrier integrity, which is associated with gut microbiota. The aim of this study was to determine the effect of HS on the cecal luminal (CeL) and cecal mucosal (CeM) microbiota in JF and three broiler populations: Athens Canadian Random Bred (ACRB), 1995 Random Bred (L1995), and Modern Random Bred (L2015). Broiler chicks were subjected to thermoneutral TN (24 °C) or chronic cyclic HS (8 h/day, 36 °C) condition from day 29 until day 56. HS affected richness in CeL microbiota in a line-dependent manner, decreasing richness in slow-growing JF and ACRB lines, while increasing richness in faster-growing L1995 and L2015. Microbiota were distinct between HS and TN conditions in CeL microbiota of all four lines and in CeM microbiota of L2015. Certain bacterial genera were also affected in a line-dependent manner, with HS tending to increase relative abundance in CeL microbiota of slow-growing lines, while decreases were common in fast-growing lines. Predictive functional analysis suggested a greater impact of HS on metabolic pathways in L2015 compared to other lines.

Guar gum as galactomannan source induces dysbiosis and reduces performance in broiler chickens and dietary β-mannanase restores the gut homeostasis

Galactomannans are abundant nonstarch polysaccharides in broiler feed ingredients. In broilers, diets with high levels of galactomannans have been associated with innate immune response stimulation, poor zootechnical performance, nutrient and lipid absorption, and excessive digesta viscosity. However, data about its effects on the gut microbiome are scarce. β-Mannanases are enzymes that can hydrolyze β-mannans, resulting in better nutrient utilization. In the current study, we have evaluated the effect of guar gum, a source of galactomannans, supplemented to broiler diets, either with or without β-mannanase supplementation, on the microbiota composition, in an attempt to describe the potential role of the intestinal microbiota in β-mannanase-induced gut health and performance improvements. One-day-old broiler chickens (n = 756) were randomly divided into 3 treatments: control diet, guar gum-supplemented diet (1.7%), or guar gum-supplemented diet + β-mannanase (Hemicell 330 g/ton). The zootechnical performance, gut morphometry, ileal and cecal microbiome, and short-chain fatty acid concentrations were evaluated at different time points. The guar gum supplementation decreased the zootechnical performance, and the β-mannanase supplementation restored performance to control levels. The mannan-rich diet-induced dysbiosis, with marked effects on the cecal microbiota composition. The guar gum-supplemented diet increased the cecal abundance of the genera Lactobacillus, Roseburia, Clostridium sensu stricto 1, and Escherichia-Shigella, and decreased Intestinimonas, Alistipes, Butyricicoccus, and Faecalibacterium. In general, dietary β-mannanase supplementation restored the main microbial shifts induced by guar gum to levels of the control group. In addition, the β-mannanase supplementation reduced cecal isobutyric, isovaleric, valeric acid, and branched-chain fatty acid concentrations as compared to the guar gum-supplemented diet group, suggesting improved protein digestion and reduced cecal protein fermentation. In conclusion, a galactomannan-rich diet impairs zootechnical performance in broilers and results in a diet-induced dysbiosis. β-Mannanase supplementation restored the gut microbiota composition and zootechnical performance to control levels.

Anaerobutyricum and Subdoligranulum Are Differentially Enriched in Broilers with Disparate Weight Gains

The intestinal microbiota is critically important for animal health and productivity. However, the influence of the intestinal microbiota on animal growth efficiency remains elusive. This current study was aimed at identifying the intestinal bacteria that are associated with the growth rate of broilers in a commercial production setting. Ross 708 broilers with extremely high, medium, and extremely low body weight (BW) were separately selected for each sex from a house of approximately 18,000 chickens on day 42. The cecal content of each animal was subjected to 16S rRNA gene sequencing for microbiota profiling. Our results indicate that a number of bacteria were differentially enriched among different groups of broilers, with several showing a significant correlation (p < 0.05) with BW in both sexes or in a sex-specific manner. Subdoligranulum was drastically diminished in high-BW birds with a strong negative correlation with BW in both males and females. While one Anaerobutyricum strain showed a positive correlation with BW in both sexes, another strain of Anaerobutyricum was positively correlated with BW only in females. These sex-dependent and -independent bacteria could be targeted for improving the growth efficiency and may also be explored as potential biomarkers for the growth rate of broiler chickens.

Compound probiotics can improve intestinal health by affecting the gut microbiota of broilers

Probiotics, as a widely used additive, have played a unique advantage in replacing antibiotic products. As a result, the probiotic effects on broiler development, intestinal flora, intestinal barrier, and immunity were assessed by this investigation. Four hundred and eighty 1-day-old Arbor Acres broilers were randomly allotted to 4 groups of 5 replicates with 24 broilers each. The control was fed only a basal corn-soybean meal diet. Probiotics I, probiotics II, and probiotics III were fed basal diet and 1, 5, and 10 g/kg compound probiotics (Lactobacillus casei: Lactobacillus acidophilus: Bifidobacterium = 1:1:2), respectively. We found that broilers in the compound probiotic group exhibited better growth performance and carcass characteristics compared with control, especially among probiotics III group. The intestinal barrier-related genes relative expression of Claudin, Occludin, MUC2, and ZO-1 mRNA in the probiotic group increased at 21 and 42 d compared with control, especially among probiotics III group (P < 0.05). The early gut immune-related genes (TLR2, TLR4, IL-1β, and IL-2) mRNA increased compared with control, while the trend at 42 d was completely opposite to that in the earlier stage (P < 0.05). Among them, probiotics III group showed the most significant changes compared to probiotics II group and probiotics I group. Select probiotics III group and control group for 16S rDNA amplicon sequencing analysis. The 16S rDNA amplicon sequencing results demonstrated that probiotics increased the relative abundance of beneficial microbes such as o_Bacteroidales, f_Rikenellaceae, and g_Alistipes and improved the cecum's gut microbiota of 42-day-old broilers. Additionally, adding the probiotics decreased the relative abundance of harmful microbes such as Proteobacteria. PICRUSt2 functional analysis revealed that most proteins were enriched in DNA replication, transcription, and glycolysis processes. Therefore, this study can provide theoretical reference value for probiotics to improve production performance, improve intestinal barrier, immunity, intestinal flora of broilers, and the application of probiotics.

16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations

16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2–4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6–10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract—even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

Conserved developmental trajectories of the cecal microbiota of broiler chickens in a field study

There is great interest in identifying gut microbiota development patterns and underlying assembly rules that can inform strategies to improve broiler health and performance. Microbiota stratification using community types helps to simplify complex and dynamic ecosystem principles of the intestinal microbiota. This study aimed to identify community types to increase insight in intestinal microbiota variation between broilers and to identify factors that explain this variation. A total of 10 well-performing poultry flocks on four farms were followed. From each flock, the cecal content of nine broilers was collected at 7, 14, and 35 days posthatch. A total of two robust community types were observed using different clustering methods, one of which was dominated by 7-day-old broilers, and one by 35-day-old broilers. Broilers, 14-day-old, were divided across both community types. This is the first study that showed conserved cecal microbiota development trajectories in commercial broiler flocks. In addition to the temporal development with age, the cecal microbiota variation between broilers was explained by the flock, body weight, and the different feed components. Our data support a conserved development of cecal microbiota, despite strong influence of environmental factors. Further investigation of mechanisms underlying microbiota development and function is required to facilitate intestinal health promoting management, diagnostics, and nutritional interventions.

Assessment of Feed Value of Chicory and Lucerne for Poultry, Determination of Bioaccessibility of Their Polyphenols and Their Effects on Caecal Microbiota

Chicory and lucerne possess high feed value for poultry being good sources of protein and fiber. In addition, they are rich in polyphenols that help the body build an integrated antioxidant system to prevent damage from free radicals and positively modulate microbial populations in the gastrointestinal tract. These health-promoting effects of polyphenols depend on their bioaccessibility and absorption in the animal body. The present paper aimed to study the bioaccessibility of polyphenols from chicory and lucerne after subjecting the samples to gastric and intestinal phases of digestion in an in vitro model of chicken gut and assessment of their feed value by measuring the presence of fermentable substrates (in terms of gas production), SCFAs produced and their effects on gut microbiota population during in vitro cecal fermentation. Results revealed that the bioaccessibility of polyphenols varied with different polyphenol compounds. The highest bioaccessibility was recorded for p-hydroxybenzoic acid (90.8%) from chicory following the intestinal phase of digestion. The lowest bioaccessibility was observed for quercetin-3-rhamnoside (12.6%) from chicory after the gastric phase of digestion. From lucerne, the highest bioaccessibility was recorded for kaempferol-3-glucoside (77.5%) after the intestinal phase of digestion. Total gas production was higher for lucerne (39.9 mL/g) than chicory (28.1 mL/g). Similarly, total SCFAs production was higher after 24 h of cecal fermentation with lucerne (42.2 mmol L−1) as compared to chicory (38.1 mmol L−1). Results also revealed that the relative abundance of Clostridium was reduced with chicory (0.225%) and lucerne (0.176%) as compared to the control (0.550%) after 24 h of cecal fermentation. The relative abundance of Streptococcus was reduced by lucerne (4.845%) but was increased with chicory (17.267%) as compared to the control (5.204%) after 24 h of fermentation. These findings indicated that chicory and lucerne differentially affected the microbial populations during in vitro cecal fermentation.

Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens

Simple Summary

The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, metabolism, and health status of the host animal. Previous studies exploring the relationship between chicken growth performance and gut microbiota focused mostly on gut content and excreta samples, neglecting the mucosa that promotes colonisation by distinct groups of microorganisms. These observations emphasised the importance of studying the variations between the bacterial communities of the lumen and mucosa throughout the different sections of the GIT. The novelty of this study is that we have evaluated the microbial communities of the jejunum chymus, jejunum mucosa, and caecum chymus of broiler chickens with different growth rates. Besides the bacteriota composition, the interactions between the bacteria were also evaluated. We have confirmed that the microbiota composition is influenced mostly by the sampling place. However, some body weight (BW)-related changes and interactions have also been found. In these cases, the mucosa seems to play a crucial role.

Abstract

The study reported here aimed to determine whether correlations can be found between the intestinal segment-related microbiota composition and the different growing intensities of broiler chickens. The bacterial community structures of three intestinal segments (jejunum chymus—JC, jejunum mucosa—JM, caecum chymus—CC) from broiler chickens with low body weight (LBW) and high body weight (HBW) were investigated. Similar to the previous results in most cases, significant differences were found in the bacteriota diversity and composition between the different sampling places. However, fewer body weight (BW)-related differences were detected. In the JM of the HBW birds, the Bacteroidetes/Firmicutes ratio (B/F) was also higher. At the genus level significant differences were observed between the BW groups in the relative abundance of Enterococcus, mainly in the JC; Bacteroides and Ruminococcaceae UCG-010, mainly in the JM; and Ruminococcaceae UCG-013, Negativibacillus, and Alistipes in the CC. These genera and others (e.g., Parabacteroides and Fournierella in the JM; Butyricoccus, Ruminiclostridium-9, and Bilophila in the CC) showed a close correlation with BW. The co-occurrence interaction results in the JC revealed a correlation between the genera of Actinobacteria (mainly with Corynebacterium) and Firmicutes Bacilli classes with different patterns in the two BW groups. In the JM of LBW birds, two co-occurring communities were found that were not identifiable in HBW chickens and their members belonged to the families of Ruminococcaceae and Lachnospiraceae. In the frame of the co-occurrence evaluation between the jejunal content and mucosa, the two genera (Trichococcus and Oligella) in the JC were found to have a significant positive correlation with other genera of the JM only in LBW chickens.

Cecal Microbiota of Free-Range Hens Varied With Different Rearing Enrichments and Ranging Patterns

Free-range pullets are reared indoors but the adult hens can go outside which is a mismatch that may reduce adaptation in the laying environment. Rearing enrichments might enhance pullet development and adaptations to subsequent free-range housing with impact on behavior and health measures including gut microbiota. Adult free-range hens vary in range use which may also be associated with microbiota composition. A total of 1,700 Hy-Line Brown^® chicks were reared indoors across 16 weeks with three enrichment treatment groups: “control” with standard litter housing, “novelty” with weekly changed novel objects, and “structural” with custom-designed perching structures in the pens. At 15 weeks, 45 pullet cecal contents were sampled before moving 1,386 pullets to the free-range housing system. At 25 weeks, range access commenced, and movements were tracked via radio-frequency identification technology. At 65 weeks, 91 hens were selected based on range use patterns (“indoor”: no ranging; “high outdoor”: daily ranging) across all rearing enrichment groups and cecal contents were collected for microbiota analysis via 16S rRNA amplicon sequencing at V3-V4 regions. The most common bacteria in pullets were unclassified Barnesiellaceae, Prevotella, Blautia and Clostridium and in hens Unclassified, Ruminococcus, unclassified Lachnospiraceae, unclassified Bacteroidales, unclassified Paraprevotellaceae YRC22, and Blautia. The microbial alpha diversity was not significant within the enrichment/ranging groups (pullets: P ≥ 0.17, hen rearing enrichment groups: P ≥ 0.06, hen ranging groups: P ≥ 0.54), but beta diversity significantly varied between these groups (pullets: P ≤ 0.002, hen rearing enrichment groups: P ≤ 0.001, hen ranging groups: P ≤ 0.008). Among the short-chain fatty acids (SCFAs), the propionic acid content was higher (P = 0.03) in the novelty group of pullets than the control group. There were no other significant differences in the SCFA contents between the rearing enrichment groups (all P ≥ 0.10), and the ranging groups (all P ≥ 0.17). Most of the genera identified were more abundant in the indoor than high outdoor hens. Overall, rearing enrichments affected the cecal microbiota diversity of both pullets and adult hens and was able to distinguish hens that remained inside compared with hens that ranging daily for several hours.

Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear.

Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail.

Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

The structure of the cereal leaf beetle (Oulema melanopus) microbiome depends on the insect's developmental stage, host plant, and origin

Cereal leaf beetle (CLB, Oulema melanopus, Coleoptera, Chrysomelidae) is a serious agricultural pest that causes considerable damages to agricultural production. The aim of this study was to characterize the bacterial communities associated with larvae and imagoes of CLB collected from various cereal host species and locations. The bacterial profile was characterized by 16S rRNA gene sequencing at the V3-V4 hypervariable region. Using taxonomy-based analysis, the bacterial community of CLB containing 16 phyla, 26 classes, 49 orders, 78 families, 94 genera, and 63 species of bacteria was identified. The abundance of Wolbachia, Rickettsia, and Lactococcus genus was significantly higher in CLB imagoes than in larvae. Statistical analysis confirmed that the bacterial community of the larvae is more diverse in comparison to imagoes and that insects collected from spring barley and wheat are characterized by a much higher biodiversity level of bacterial genera and species than insects collected from other cereals. Obtained results indicated that the developmental stage, the host plant, and the insect's sampling location affected the CLB's microbiome. Additionally, the CLB core microbiome was determined. It consists of 2 genera (Wolbachia and Rickettsia) shared by at least 90% tested CLB insects, regardless of the variables analysed.

Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing

BACKGROUND

Antibiotic resistance poses a grave threat to One-Health. By replacing antibiotics with non-antibiotic additives (are alternatives to antibiotics, ATAs) like phytogenic feed additives and organic acids in poultry feed. ATAs are a potential alternative as these decline the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. In this study, we use 16S rRNA amplicon sequencing of the V3-V4 region to evaluate phytogenic feed additives and organic acids on the cecal microbial diversity of broiler chickens.

METHODS AND RESULTS

Two hundred & forty broiler chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG), and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with increased microbial diversity in AB, ORG, and COM (p < 0.05). The synergistic effects of PHY and ORG increased bacterial population of phyla: Firmicutes, Bacteroides, and Proteobacteria in the cecum. The presence of species, Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups.

CONCLUSIONS

Treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens, led to healthy and economical broiler meat.

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

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

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

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

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.

Assessing the Impact of Flavophospholipol and Virginiamycin Supplementation on the Broiler Microbiota: a Prospective Controlled Intervention Study

The antibiotic growth promoters (AGPs) flavophospholipol and virginiamycin have been widely used for decades in food animal production. AGP activity is believed to be partly modulated by gut microbial composition although exact AGP-induced changes remain unclear. In a controlled intervention study, we studied the effect of flavophospholipol and virginiamycin on the broiler chicken ileal microbiota spanning from birth to 39 days. Using 16S rRNA gene profiling and prediction of metabolic activity, we show that both AGPs result in dynamic microbial shifts that potentially increase anti-inflammatory mechanisms and bioavailability of several essential nutrients by decreasing degradation (flavophospholipol) or increasing biosynthesis (virginiamycin). Further, virginiamycin-supplemented broilers showed increased colonization with potentially pathogenic bacteria, Clostridium perfringens, Campylobacter, and Escherichia/Shigella spp. Overall, we show that both AGPs induce microbial changes potentially beneficial for growth. However, the increase in (foodborne) pathogens shown here with virginiamycin use could impact not only broiler mortality but also human health. IMPORTANCE Antibiotic growth promoters (AGPs) are commonly used within poultry farming to increase muscle growth. Microbial composition in the gut is known to be influenced by AGP use although exact AGP-induced changes remain unclear. Utilizing 16S rRNA gene profiling, this study provides a first head-to-head comparison of the effect of the two most commonly used AGPs, flavophospholipol and virginiamycin, on the broiler chicken ileum microbiota over time. We found that supplementation with both AGPs altered ileal microbial composition, thereby increasing potential bioavailability of essential nutrients and weight gain. Flavophospholipol showed a slight benefit over virginiamycin as the latter resulted in more extensive microbial perturbations including increased colonization by enteropathogens, which could impact broiler mortality.

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.

Composition of the Fecal Microbiota of Piglets at Various Growth Stages

Gastrointestinal (GI) microbiota play an important role in promoting growth in piglets. However, studies on microbiota composition at various growth stages are lacking. We measured body weights of Jinfen White and Mashen piglets every 7 days and collected their fecal samples by rectal swabbing at nine time points during suckling (1–28 days) and nursery (35–70 days) stages to gain insight into microbiota variability during piglet growth. The fecal microbiota were characterized via 16S rRNA gene sequencing to analyze the effects of microbial diversity on piglet growth and development preliminarily. The results showed that although the two breeds of piglets have similar body weights at birth, weaned Jinfen White piglets demonstrated a significantly greater body weight and daily weight gain than weaned Mashen piglets (P < 0.01). A total of 1,976 operational taxonomic units (OTUs) belonging to 27 phyla and 489 genera were uncovered, in which the highest numbers of OTUs belong to the phyla Firmicutes and Bacteroidetes. Lactobacillus, Bacteroides, and Prevotellaceae NK3B31 groups accounting for 12.4, 8.8, and 5.8% of OTUs, respectively, showed relatively high abundance at the genus level. Nine sampling time points were divided into three growth stages, namely, immediate postfarrowing (1 day old), suckling (7, 14, and 21 days old), and nursery (28, 35, 49, 63, and 70 days old), on the basis of the results of microbial diversity, principal coordinate, and co-occurrence network analyses. In addition, it identified 54 discriminative features in the microbiota between two breeds of piglets by LEfSe analysis, in which 17 genera enriched the microbiota community of Jinfen White piglets. Finally, abundances of 29 genera showed significant positive correlations with body weights and daily weight gain of piglets. Conversely, abundances of 12 genera demonstrated significant negative correlations with body weights of piglets. The results of our study will provide a theoretical basis for succession patterns in fecal microbiota of piglets and suggest the need for meticulous management of piglets in pig production.

A Review of the Effects and Production of Spore-Forming Probiotics for Poultry

Simple Summary

Spore-forming probiotics are widely used in the poultry industry for their beneficial impact on host health. The main feature that separates spore-forming probiotics from the more common lactic acid probiotics is their high resistance to external and internal factors, resulting in higher viability in the host and correspondingly, greater efficiency. Their most important effect is the ability to confront pathogens, which makes them a perfect substitute for antibiotics. In this review, we cover and discuss the interactions of spore-forming probiotic bacteria with poultry as the host, their health promotion effects and mechanisms of action, impact on poultry productivity parameters, and ways to manufacture the probiotic formulation. The key focus of this review is the lack of reproducibility in poultry research studies on the evaluation of probiotics’ effects, which should be solved by developing and publishing a set of standard protocols in the professional community for conducting probiotic trials in poultry.

Abstract

One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing.

Comparative analysis of the gut microbiota of mice fed a diet supplemented with raw and cooked beef loin powder

We used 16S ribosomal RNA sequencing to evaluate changes in the gut microbiota of mice fed a diet supplemented with either raw or cooked beef loin powder for 9 weeks. Male BALB/c mice (n = 60) were randomly allocated to five groups: mice fed AIN-93G chow (CON), chow containing 5% (5RB) and 10% (10RB) raw beef loin powder, and chow containing 5% (5CB) and 10% (10CB) cooked beef loin powder. Dietary supplementation with both RB and CB increased the relative abundance of Clostridiales compared to the CON diet (p < 0.05). Mice fed 10RB showed a significantly higher relative abundance of Firmicutes (p = 0.018) and Lactobacillus (p = 0.001) than CON mice, and the ratio of Firmicutes/Bacteroidetes showed an increasing trend in the 10RB mice (p > 0.05). Mice fed 10CB showed a higher abundance of Peptostreptococcaceae and a lower abundance of Desulfovibrionaceae compared with the CON mice (p < 0.05). Genes for glycan biosynthesis, which result in short-chain fatty acid synthesis, were enriched in the CB mice compared to the RB mice, which was correlated to a high abundance of Bacteroides. Overall, dietary RB and CB changed the gut microbiota of mice (p < 0.05).

Cecal microbiota contribute to the development of woody breast myopathy

The objective of this study was to characterize the bacterial diversity of cecal microbiota in broilers related to breast phenotype, diet, and genetic strain. Broilers from 2 genetic strains (120 birds/strain) were fed a control diet (15 birds/pen) and an amino acid reduced diet (15 birds/pen, digestible lysine, total sulfur amino acids, and threonine reduced by 20% compared to the control diet). At 8 wk of age, 4 male broilers with normal breast (NB, 1 chick per pen) and 4 male broilers with woody breast (WB, 1 chick per pen) were selected for each treatment (strain × diet). The DNA of cecal samples was extracted and the 16S rRNA genes were sequenced and analyzed. There were no differences (P > 0.05) in the alpha diversity of gut microbiota between 2 phenotypes (NB vs. WB), 2 strains, or 2 diets (control vs. reduced). However, principal coordinate analysis plots (beta diversity) revealed that there were composition differences in samples between the 2 phenotypes (P = 0.001) and the 2 diets (P = 0.024). The most abundant phyla in all samples were Firmicutes, followed by Bacteroidetes and Proteobacteria. There were differences (false discovery rate, FDR < 0.05) in bacterial relative abundance between phenotypes and between diet treatments, but not (FDR > 0.05) between the 2 genetic strains. Selenomonas bovis (12.6%) and Bacteroides plebeius (12.3%) were the top 2 predominant bacteria in the ceca of WB birds; however, the relative abundances of these 2 bacteria were only 5.1% and 1.2% in NB birds, respectively. Function analysis predicted that the metabolic activities differed (q < 0.05) only between phenotypes. The microbiota of WB birds was characterized as reduced glycolysis and urea cycle but increased tricarboxylic acid (TCA) cycles, sugar degradation, and purine and pyrimidine nucleotides biosynthesis. Further studies are needed to investigate if WB incidence could be reduced by regulating gut microbiota and the potential mechanism that leads to decreased WB incidence.

Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective

Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.

Allium-Based Phytobiotic Enhances Egg Production in Laying Hens through Microbial Composition Changes in Ileum and Cecum

Phytobiotics (bioactive compounds extracted from plants) are one of the explored alternatives to antibiotics in poultry and livestock due to their antimicrobial activity and its positive effects on gut microbiota and productive properties. In this study, we supplemented a product based on garlic and onion compounds in the diet to laying hens at the beginning of their productive life (from 16 to 20 weeks post-hatching). The experimental group showed a significant increase in the number of eggs laid and in their size, produced in one month compared to the control. This increase in production was accompanied by microbiota changes in the ileum and cecum by means of high throughput sequencing analyses. These bacterial shifts in the ileum were mainly the result of compositional changes in the rare biosphere (unweighted UniFrac), while in the cecum, treatment affected both majority and minority bacterial groups (weighted and unweighted UniFrac). These changes in the microbiota suggest an improvement in food digestibility. The relative abundance of Lactococcus in the ileum and Lactobacillus in the cecum increased significantly in the experimental group. The relative abundance of these bacterial genera are known to have positive effects on the hosts. These results are very promising for the use of these compounds in poultry for short periods.

Bacterial meta-analysis of chicken cecal microbiota

Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.

Efects of Coconut Oil (Cocos nucifera), Avocado Oil (Persea americana), Melon Seed Oil (Citrullus colocynthis L.) on Growth Performance, Blood, Biochemical, Haematological Parameters, and Total Microbial Loads of Noiler Birds

This study was carried out to examine the comparative effects of coconut oil (CO), avocado oil (AO), and melon seed oil (MSO) on the growth performance, blood, biochemical, hematological parameters, and total microbial loads of Noiler birds. A total of 120 Noiler birds with an average weight of 50.3 ± 0.13 g were randomized into four treatment groups with 3 replications (10 per pen) for six weeks of fattening. Weekly body weight gain and daily feed intake of the birds were recorded for six weeks, after which average weight gain and feed conversion ratios were calculated. At the end of the feeding trials, blood samples were collected for biochemical and hematological parameter assessments, and the digesta from the colon and ileum were collected for their intestinal total microbial load analysis. The average weight gains and feed conversion ratios (FCR) of the birds supplemented with CO (1229.40 ± 15.00) and MSO (1232.66 ± 43.18) were observed to be significantly higher (P < 0.05), compared to the birds supplemented with AO (1110.73 ± 18.29) and the birds fed feed only (1034.79 ± 2.04) having the least weight gained. The biochemical parameters of the birds across the treatment were not significantly different (P > 0.05). White blood cells, packed cell volume, red blood cells and lymphocytes were significantly higher in the CO group compared to the birds supplemented with the avocado oil and melon seed oil. There was no significant difference (P > 0.05) in the weight of the spleen, bursa and gall bladder among the birds. The Lactobacillus spp. in the colon of birds supplemented with coconut oil (6.43 ± 0.56) and melon oil (6.25 ± 0.65) were significantly higher. It can be concluded that coconut oil and melon seed oil have the potential to serve as growth promoters for chicken production.

Divergence in Gut Bacterial Community Structure between Male and Female Stag Beetles Odontolabis fallaciosa (Coleoptera, Lucanidae)

Simple Summary

Intestinal microbiota play crucial roles for their hosts. Odontolabis fallaciosa shows striking sexual dimorphism and male trimorphism, which represents an interesting system to study their gut microbiota. We have compared the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa. The gut bacterial community structure was significantly different between males and females. The females were associated with higher bacterial alpha-diversity relative to males. Large males had a higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which contributed to nutritional efficiency. The results increased our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among three male morphs, which might reveal the relationship among the gut microbiota, nutrition level, and phenotypic evolution of the stag beetle.

Abstract

Odontolabis fallaciosa (Coleoptera: Lucanidae) is a giant and popular stag beetle with striking sexual dimorphism and male trimorphism. However, little is known about their intestinal microbiota, which might play an indispensable role in shaping the health of their hosts. The aim of this study was to investigate the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa from China using high-throughput sequencing (Illumina MiSeq). The gut bacterial community structure was significantly different between males and females, suggesting that sex appeared to be the crucial factor shaping the intestinal bacterial community. Females had higher bacterial alpha-diversity than males. There was little difference in gut bacterial community structure among the three male morphs. However, compared to medium and small males, large individuals were associated with the higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which might contribute to nutritional efficiency. Overall, these results might help to further our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among the three male morphs.

Effects of Wheat Bran and Clostridium butyricum Supplementation on Cecal Microbiota, Short-Chain Fatty Acid Concentration, pH and Histomorphometry in Broiler Chickens

Simple Summary

Antimicrobial resistance issues and growing consumer demand promote the need for antibiotic-free meat production. Fostering animal productivity without antibiotic growth promoters accelerates the use of non-antibiotic feed additives and encourages researchers to gain a deeper understanding of diet-gut microbiota interactions. Little information is available about the effects of single strain probiotic bacteria Clostridium butyricum and wheat bran on the gut microbiota of chickens using next-generation sequencing. Therefore, these components were evaluated in the present study on gut microbiota composition and other gut health characteristics of broiler chickens. Results showed that probiotic supplementation decreased cecal Akkermansia spp. abundance, whereas wheat bran supplementation increased the relative abundance of Akkermansia spp. compared to the control and symbiotic groups, respectively. Dietary treatment also altered cecal crypt depth and had a trend to modify cecal fermentation profiles. Besides, the combination of probiotic and wheat bran supplementation did not have further effects on any investigated parameters. Members of the Akkermansia genus have several beneficial health effects in mammals, but less is known about its role in chicken health. The results of the present study expand our understanding of diet-gut microbiota interaction in chickens, which helps to approximate antibiotic-free meat production.

Abstract

Feed additives that can improve intestinal health and maintain a diverse and resilient intestinal microbiota of poultry are of great importance. Thus, the current study investigated the effects of a single strain butyric acid-producing Clostridium (C. butyricum) with (symbiotic) or without wheat bran supplementation on cecal microbiota composition and gut health characteristics of broiler chickens. In total, 384 male Ross 308 day-old chickens were divided into four dietary treatment groups and fed ad libitum until day 37 of life. Cecal samples were taken for Illumina sequencing and pH and short-chain fatty acid analyses, as well as for histological analysis at the end of the experimental period. Neither of the supplemented diets improved chicken growth performance. Caecum was dominated by the members of Bacteroidetes phyla followed by Firmicutes in each dietary group. At the genus level, Bacteroides, Oscillospira, Akkermansia, Faecalibacterium, Ruminococcus and Streptococcus genera exceeded 1% relative abundance. Dietary treatment influenced the relative abundance of the Akkermansia genus, which had a lower relative abundance in the C. butyricum group than in the other groups and in the symbiotic group compared to the wheat bran supplemented group. Dietary treatment also altered cecal crypt depth and had a trend to modify the cecal fermentation profile. Additive effects of wheat bran and C. butyricum supplementation were not detected. Our results suggest that Akkermansia muciniphila colonization in chicken can be influenced by diet composition.

Effect of dietary n-3 polyunsaturated fatty acids on the composition of cecal microbiome of Lohmann hens

Supplementation of n-3 fatty acids to poultry diets is widely acknowledged for its role in enhancing poultry products, however, little is known about the compositional responses of gut microbial communities to type and dosage of these supplements.  Here, we compared the effects of n-3 polyunsaturated fatty acids (PUFA), supplied as alpha-linolenic acid (ALA) or docosahexaenoic acid (DHA), on the composition of bacterial communities in ceca of laying hens.  Corn-soybean basal diets were supplemented with either flaxseed oil (FO, ALA-rich) or marine algal biomass (MA, DHA-rich), and each supplied 0.20 and 0.60% of total n-3 PUFA in the diet.  Lohmann LSL-Classic laying hens (n = 10/treatment) were randomly allocated to one of the 4 diets.  After 8 weeks of feeding, blood, liver and cecal digesta samples were obtained for plasma glucose, fatty acids, and short chain fatty acids analyses, respectively.  The gut bacterial communities were characterized using genomic DNA extracted from cecal contents, whereby the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina Miseq® platform.  Firmicutes and Bacteroidetes were the predominant phyla in both the FO- and MA-fed groups.  The relative abundance of Tenericutes, often associated with immunomodulation, was relatively higher (P<0.0001) in the FO than MA group.  Although the relative abundance of Bacteroides was greater for the FO- than the MA-fed group, this genus was negatively correlated (P<0.05) with total n-3 PUFA in the liver at higher dosages of both FO- and MA-fed hens.  Higher dose of FO (0.60%) and both dosages of MA (0.20 and 0.60%) substantially enriched several members of Firmicutes (e.g., Faecalibacterium, Clostridium and Ruminococcus) which are known to produce butyrate.  Moreover, co-occurrence network analysis revealed that, in the FO 0.60- and MA 0.20-fed hens, Ruminococcaceae was the most influential taxon accounting for about 31% of the network complexity.  These findings demonstrate that supplementation of different type and level of n-3 PUFA in hens' diets could enrich microbial communities with potential role in lipid metabolism and health.

Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: A field study

Disturbances in intestinal health are a common problem affecting commercial broiler chickens worldwide. Several studies have revealed associations between health, production performance, and intestinal microbiota. This study aimed to describe the development of the intestinal microbiota of broilers within a production cycle to evaluate to what extent clinical parameters and phenotypic characteristics can explain the intestinal microbiota variation. Of four well-performing flocks within two farms, the cecal content was collected of nine broilers at 0, 2, 4, or 5, 7, 11, or 12, 14, 21, 28, 35, and 40 days of the production cycle. In total, 342 samples were analyzed using 16S ribosomal RNA gene amplicon sequencing. Variables as macroscopic gut abnormalities, gut lesions, age, individual body weight, sex, footpad integrity, the color of ceca, and foam in cecal content were determined. Ileum tissue was collected for histological quantification of villus length and crypt depth. Flock infection levels of the intestinal disease coccidiosis were measured in pooled feces from the poultry house. Increases in phylogenetic diversity were observed from hatch until day 21 of age. Constrained multivariate analysis indicated that age, farm, body weight, ileum crypt depth, cecal color, and the coccidiosis lesion score were important variables to describe the variation in cecal microbiota. These results contribute to determining relevant variables in flocks that may be indicative of the intestinal microbiota composition. Moreover, this knowledge increases the awareness of interactions between the intestinal microbiota and broiler health as well as their relative importance.

Gut microbiota in a host-brood parasite system: insights from common cuckoos raised by two warbler species

An animal's gut microbiota (GM) is shaped by a range of environmental factors affecting the bacterial sources invading the host. At the same time, animal hosts are equipped with intrinsic mechanisms enabling regulation of GM. However, there is limited knowledge on the relative importance of these forces. To assess the significance of host-intrinsic vs environmental factors, we studied GM in nestlings of an obligate brood parasite, the common cuckoo (Cuculus canorus), raised by two foster species, great reed warblers (Acrocephalus arundinaceus) and Eurasian reed warblers (A. scirpaceus), and compared these with GM of the fosterers' own nestlings. We show that fecal GM varied between cuckoo and warbler nestlings when accounting for the effect of foster/parent species, highlighting the importance of host-intrinsic regulatory mechanisms. In addition to feces, cuckoos also expel a deterrent secretion, which provides protection against olfactory predators. We observed an increased abundance of bacterial genera capable of producing repulsive volatile molecules in the deterrent secretion. Consequently, our results support the hypothesis that microbiota play a role in this antipredator mechanism. Interestingly, fosterer/parent identity affected only cuckoo deterrent secretion and warbler feces microbiota, but not that of cuckoo feces, suggesting a strong selection of bacterial strains in the GM by cuckoo nestlings.

Changes in the Microbial Community of the Mottled Skate (Beringraja pulchra) During Alkaline Fermentation

Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkalinefermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.

Effects of Laetiporus sulphureus-Fermented Wheat Bran on Growth Performance, Intestinal Microbiota and Digesta Characteristics in Broiler Chickens

Simple Summary

This study investigated the effects of a Laetiporussulphureus-fermented wheat bran (LS) supplementation on the microbiota and digesta characteristics of broiler chickens. Results showed that a 5% LS supplementation could potentially enhance the feed conversion ratio and European Broiler Index (EBI) of the broilers by elevating the family Lactobacillaceae and suppressing the phylum Proteobacteria’s population. This could also change the intestinal environments by elevating the ileal and cecal lactic acid concentrations as well as lowering the pH and ammonium nitrate, thereby potentially favoring the growth and health of the broilers.

Abstract

This study investigated the effects of a Laetiporus sulphureus-fermented wheat bran (LS) supplementation on the microbiota and digesta characteristics of broiler chickens. Two hundred and forty male broilers (Ross 308) were randomly allocated into three groups fed with a corn–soybean-based diet (control), and the control diet being replaced with 5% wheat bran (WB) and 5% LS, respectively. Each group had four replicates and 20 birds per pen. Metagenomics analysis results of the ileum microbiota showed that, at the family level, the 5% LS groups had over 40% higher Lactobacillaceae compared to the control group in a mean difference comparison. Heat maps showed that, at the phylum level, the population of Firmicutes was higher and Proteobacteria was lower in the ileum of 5% LS compared to the control group. Results of the stack column plots of the top ten OTUs at the family level showed that a 5% LS and 5% WB supplementation altered the broiler microbiota distribution by increasing the relative abundance of Lactobacillaceae. Cecal microbiota analysis showed that the 5% LS-supplemented group had approximately 5% and 3% higher Veillonellaceae and Lactobacillaceae, respectively. Stack column plots of the top ten OTUs indicated that the distribution of cecal bacteria in each group was not markedly different. Both the ileum and cecum digesta in the 5% LS supplementation group had a slight and not significant elevation on the total VFA, while the pH values and ammonia nitrogen were significantly lowered compared to the control and 5% WB groups (p < 0.05). In addition, the 5% LS supplementation group had a significantly higher lactic acid concentration in both the ileum and cecum compared to the control and 5% WB groups (p < 0.05). In conclusion, a 5% LS supplementation could potentially enhance the feed conversion ratio and European Broiler Index (EBI) of broilers by elevating the family Lactobacillaceae and suppressing the phylum Proteobacteria’s population, thus creating changed intestinal environments that may potentially favor the growth and health of the broilers.

Gut Microbiota-Polyphenol Interactions in Chicken: A Review

The gastrointestinal tract of the chicken harbors very complex and diverse microbial communities including both beneficial and harmful bacteria. However, a dynamic balance is generally maintained in such a way that beneficial bacteria predominate over harmful ones. Environmental factors can negatively affect this balance, resulting in harmful effects on the gut, declining health, and productivity. This means modulating changes in the chicken gut microbiota is an effective strategy to improve gut health and productivity. One strategy is using modified diets to favor the growth of beneficial bacteria and a key candidate are polyphenols, which have strong antioxidant potential and established health benefits. The gut microbiota-polyphenol interactions are of vital importance in their effects on the gut microbiota modulation because it affects not only the composition of gut bacteria but also improves bioavailability of polyphenols through generation of more bioactive metabolites enhancing their health effects on morphology and composition of the gut microbiota. The object of this review is to improve the understanding of polyphenol interactions with the gut microbiota and highlights their potential role in modulation of the gut microbiota of chicken.

Enhanced modulation of gut microbial dynamics affecting body weight in birds triggered by natural growth promoters administered in conventional feed

This study explored the effects of natural growth promoters (phytogenic feed additives and organic acids) on animal performance, carcass characteristics, blood parameters, gut microflora composition, and microbe–host interactions in broiler chickens over a 42-day feeding period. Two-hundred-fifty-day-old chicks were randomly assigned to one of five treatments: (i) control diets (CON); (ii) control diets + 40 g/tons antibiotic growth promoter (AB); (iii) control diets + 3 kg/tons organic acids (ORG); (iv) control diets + 3 kg/tons phytogenic feed additives (PHY); (v) control diets + 3 kg/tons organic acids + phytogenic feed additive combination (COM). A non-significant differences (p > 0.05) were observed in broiler performance among treatments at 21 days of age; however, a gradually increasing body weight gain and reduced feed conversion ratio were observed at 42 days in treatments versus control group. Biochemical indices were non-significant (p > 0.05) except for decreased cholesterol (p < 0.05) and increased A/G ratio (p < 0.05) recorded in the treatment groups. The addition of PHY and ORG improved total counts of Enterococcus spp. and Lactobacillus spp. (p < 0.05) as well as reduced caecal and ileal Campylobacter spp. and Escherichia coli (p < 0.05). Correlation analysis elucidated beneficial bacteria (Enterococcus spp. and Lactobacillus spp.) were positively and pathogenic bacteria (Campylobacter spp. and E. coli) were negatively correlated (p < 0.05) with host weight gain. The findings indicated that dietary supplementation of PHY and ORG sustained balanced gut microflora, which in turn improved body weight. This study broadens the significance of using PHY and ORG as safe alternatives to antibiotic growth promoters for achieving healthier and economical broiler production.

Microbiota and metabolome responses in the cecum and serum of broiler chickens fed with plant essential oils or virginiamycin

This study investigated the cecal microbiota and serum metabolite profile of chickens fed with plant essential oils (PEO) or virginiamycin (VIRG) using high-throughput 16S rRNA gene sequencing and untargeted metabolomics approach. The main aim of this work was to explore the biochemical mechanisms involved in the improved growth performance of antibiotics and their alternatives in animal production. The results showed that both PEO and VIRG treatment significantly increased the relative abundance of phyla Bacteroidetes and decreased the abundance of phyla Firmicutes and genus of Lactobacillus in cecal microbiota of chickens. Compared to the control group (CT group), the relative abundance of genus of Alistipes, unclassified Rikenellaceae, Roseburia, and Anaeroplasma was enriched in the PEO group; that of genus Bacteroides, Lachnospiraceae, and unclassified Enterobacteriaceae was enriched in the cecal microbiota of the VIRG group. Untargeted metabolomics analyses revealed that the PEO treatment modified 102 metabolites and 3 KEGG pathways (primary bile acid biosynthesis and phenylalanine metabolism) in the cecal microbiota, and 81 metabolites and relevant KEGG pathways (fructose and mannose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid.) in the serum of the chicken. Compared to the CT group, VIRG treatment group differed 217 metabolites and 10 KEGG pathways in cecal contents and 142 metabolites and 7 KEGG pathways in serum of chickens. Pearson’s correlation analysis showed that phyla Bacteroidetes and genus of Bacteroides, Alistipes, and unclassified Rikenellaceae (in the VIRG and PE group) were positively correlated with many lipid metabolites. However, phyla Firmicutes and genera Lactobacillus (higher in the CT group) were negatively correlated with the lipid and thymine metabolism, and positively correlated with hydroxyisocaproic acid, cytosine, and taurine. This study shows that dietary supplementation with PEO and VIRG altered the composition and metabolism profile of the cecal microbiota, modified the serum metabolism profile.

Effects of Alternative Administration Programs of a Synbiotic Supplement on Broiler Performance, Foot Pad Dermatitis, Caecal Microbiota, and Blood Metabolites

This research investigated the effects of different synbiotic administration programs on broiler productive performance and foot pad dermatitis (FPD). Molecular insights on caecal microbiota and plasma metabolomics were also performed. - A total of 1000 one-day-old male chicks were grouped by the synbiotic treatment. The synbiotic was either sprayed as gel droplets onto newly hatched chicks at the hatchery (100 g/10,000 birds) or supplemented in-feed during the entire rearing period (1000, 500, and 250 g/ton according to feeding phase), or both. Only the treatments' combination produced significant results in comparison with the control group (untreated), improving feed conversion ratio from 14 to 29 d and in the overall period of the trial (1.570 vs. 1.509 and 1.643 vs. 1.596, respectively; p < 0.05) while lowering FPD occurrence at slaughter (17% vs. 5%; p < 0.05). These findings can be related to significant variations of caecal microbiota, like higher Firmicutes to Bacteroidetes ratio (with favorable implications for host's energy-harvesting potential from the diet) and more beneficial microbial consortium presumably sustaining eubiosis. Overall, these results indicate that administering synbiotics through gel droplets at the hatchery combined to in-feed supplementation for the whole growing cycle positively affects broiler feed efficiency and welfare.

Analysis of high-throughput sequencing for cecal microbiota diversity and function in hens under different rearing systems

Rearing systems play an important role in animal welfare, health and the composition of the gut microbiome. Therefore, the purpose of this study was to investigate the effects of different rearing systems on the composition and function of cecal microbiota in chickens. The 120-day-old Lohmann hens of cage rearing systems (CRS) and free-range systems (FRS) were studied. The cecal bacterial populations of hens were surveyed by high-throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3-V4 combined with metagenomic sequencing analysis. The 16S rRNA sequencing analysis showed that the cecal microbiota differed between the FRS and CRS. The three most abundant bacteria phyla in the two systems were the Bacteroidetes (> 48%), Firmicutes (> 37%), and Proteobacteria (> 6%), the Deferribacteres (> 2.4%) were found in FRS and almost absent in CRS (< 0.01%). The three most abundant genera were the Bacteroides, Rikenellaceae_RC9, and Faecalibacterium, and we found relative abundance of the Parabacteroides (P < 0.05), Prevotellaceae_Ga6A1 (P < 0.01), unclassified Proteobacteria (P < 0.05), and unclassified Spirochaetaceae (P < 0.01) was greater in FRS, whereas abundance of Faecalibacterium, Ruminococcaceae, and Helicobacter was greater in CRS (P < 0.05). Functional gene classification of metagenomic sequencing suggested that energy production and conversion, carbohydrate transport and metabolism, as well as amino acid transport and metabolism were significantly more abundant in FRS, and we identified a range of antibiotic resistance categories in gut microbes of hens reared under both systems. We confirmed differences in microbe gut composition and function in hens reared using two contrasting systems, and ARGs were also identified in the microbiota of these hens. This work has produced new data for laying hens in different production systems and increased the understanding of intestinal microorganisms in laying hens.

Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken

An obligately anaerobic, non-motile, Gram-positive coccobacillus strain SW451 was isolated from pooled caecum contents of feral chickens. Based on taxono-genomic, and biochemical analyses, the strain SW451 represents a new species of the genus Sellimonas, for which the name Sellimonas caecigallum sp. nov. is proposed. The type strain of Sellimonas caecigallum is SW451 (=DSM 109473^T = CCOS 1879^T).

Effects of yeast cultures with different fermentation times on the growth performance, caecal microbial community and metabolite profile of broilers

The objective of this study was to investigate the effects of yeast culture (YC) on the growth performance, caecal microbial community and metabolic profile of broilers. A total of 350 1-day-old healthy Arbor Acres broilers were randomly assigned to seven treatment groups. The first group received a basal diet without YC supplementation, whereas the remaining groups received a basal diet supplemented with either YC fermented for 12, 24, 36, 48 or 60 hr, or a commercial YC product (SZ2). MiSeq 16S rRNA high-throughput sequencing was used to investigate the bacterial community structure, and gas chromatography-mass spectrometry was used to identify the metabolites in the caeca of broilers. The broilers that received a diet supplemented with YC had a higher average daily gain and average daily feed intake than those received YC-free or SZ2-enriched diets. The feed conversion ratio (FCR) of YCs fermented for 24 hr resulted in the best feed efficiency, whereas the FCR of YC fermented for 60 hr resulted in poor feed efficiency (p < .05). In the caeca of broilers, the bacterial communities were well separated, as determined by principal component analysis, and the proportions of the eight genera were significantly different among the seven groups (p < .05). The genus Akkermansia was the most abundant when the diet supplemented with YC fermented for 24 hr (p < .05). Furthermore, the Firmicutes/Bacteroidetes ratio was positively correlated with the FCR in the caecum (r = .47, p < .005). Five differentially expressed metabolites (i.e., L-alanine, benzeneacetic acid, D-mannose, D-arabitol and cholesterol) were identified in the caeca of broilers that received diets supplemented with YCs fermented for 24 or 60 hr. In summary, the different fermentation times of the YCs can markedly improve the growth performance and FCR of broilers by altering the caecal microbial community, and the growth performance which is related to the changes in key metabolic pathways.

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

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

Microbiota, Gut Health and Chicken Productivity: What Is the Connection?

Gut microbiota and its relationship to animal health and productivity in commercial broiler chickens has been difficult to establish due to high variability between flocks, which derives from plenty of environmental, nutritional, and host factors that influence the load of commensal and pathogenic microbes surrounding birds during their growth cycle in the farms. Chicken gut microbiota plays a key role in the maintenance of intestinal health through its ability to modulate host physiological functions required to maintain intestinal homeostasis, mainly through competitive exclusion of detrimental microorganisms and pathogens, preventing colonization and therefore decreasing the expense of energy that birds normally invest in keeping the immune system active against these pathogens. Therefore, a “healthy” intestinal microbiota implies energy saving for the host which translates into an improvement in productive performance of the birds. This review compiles information about the main factors that shape the process of gut microbiota acquisition and maturation, their interactions with chicken immune homeostasis, and the outcome of these interactions on intestinal health and productivity.

Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers

Antimicrobial growth promoters (AGPs) are commonly used in the livestock industry at subtherapeutic levels to improve production efficiency, which is achieved mainly through modulation of the intestinal microbiota. However, how different classes of AGPs, particularly ionophores, regulate the gut microbiota remains unclear. In this study, male Cobb broiler chickens were supplemented for 14 days with or without one of five commonly used AGPs including three classical antibiotics (bacitracin methylene disalicylate, tylosin, and virginiamycin) and two ionophores (monensin and salinomycin) that differ in antimicrobial spectrum and mechanisms. Deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed that two ionophores drastically reduced a number of rare bacteria resulting in a significant decrease in richness and a concomitant increase in evenness of the cecal microbiota, whereas three antibiotics had no obvious impact. Although each AGP modulated the gut microbiota differently, the closer the antibacterial spectrum of AGPs, the more similarly the microbiota was regulated. Importantly, all AGPs had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggestive of enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest, which may collectively be responsible for the growth-promoting effect of AGPs.