Characterization of intestinal microbiota and response to dietary virginiamycin supplementation in the broiler chicken

Data analytics-based evaluation of blood indices and adaptation of medicated and non-medicated broiler chickens under humid tropical conditions

The growth performance and blood indices of medicated and non-medicated broiler chickens have been the subject of this research coupled with a paucity of comparative information on what can actually happen to broiler chickens if not medicated when reared under humid tropical conditions. One hundred unsexed day-old broilers were randomly and equally allotted into two treatment groups of TM (medicated) and TN (non-medicated) in a completely randomized design each treatment with five replicates having ten birds each. The birds were reared on deep litter system for 56 d which was divided into two phases of 28 d each (starter and finisher), during which data were collected with respect to daily feed intake, final body weight, body weight gained (BWG), mortality rate while blood analysis was carried out on 28th and 56th d for starter and finisher phases, respectively. Non-medicated group served as control. Feed conversion ratio (FCR) and feed conversion efficiency (FCE), were later calculated. Data collected were subjected to analysis of variance statistically. There was no significant difference between the medicated and non-medicated broilers for daily feed intake, final body weight, and BWG and also for the blood parameters investigated at starter phase. However, at finisher phase, no significant difference was observed in the daily feed intake of Tm and Tn but there was significant (P < 0.05) difference in the final body weight, BWG, FCR, FCE, and mortality rate between the two groups. Birds on Tm attained higher weight significantly (P < 0.05) than those on TN. BWG, FCR, and FCE followed the same trend and also the mortality rate. White blood cells count of TN was higher significantly (P < 0.05) than TM while TM birds recorded higher packed cell volume, red blood counts, and hemoglobin concentration (Hb) significantly (P < 0.05) than TM birds. Effect of medication was much noticeable at finisher phase as it improved the growth rate though mortality rate was close to that of TN group. These results suggest that broilers can be produced free of medication with good feeding without loss of birds while the growth rate can be enhanced with the use of prebiotics and prebiotics.

How did antibiotic growth promoters increase growth and feed efficiency in poultry?

It has been hypothesized that reducing the bioenergetic costs of gut inflammation as an explanation for the effect of antibiotic growth promoters (AGPs) on animal efficiency, framing some observations but not explaining the increase in growth rate or the prevention of infectious diseases. The host's ability to adapt to alterations in environmental conditions and to maintain health involves managing all physiological interactions that regulate homeostasis. Thus, metabolic pathways are vital in regulating physiological health as the energetic demands of the host guides most biological functions. Mitochondria are not only the metabolic heart of the cell because of their role in energy metabolism and oxidative phosphorylation, but also a central hub of signal transduction pathways that receive messages about the health and nutritional states of cells and tissues. In response, mitochondria direct cellular and tissue physiological alterations throughout the host. The endosymbiotic theory suggests that mitochondria evolved from prokaryotes, emphasizing the idea that these organelles can be affected by some antibiotics. Indeed, therapeutic levels of several antibiotics can be toxic to mitochondria, but subtherapeutic levels may improve mitochondrial function and defense mechanisms by inducing an adaptive response of the cell, resulting in mitokine production which coordinates an array of adaptive responses of the host to the stressor(s). This adaptive stress response is also observed in several bacteria species, suggesting that this protective mechanism has been preserved during evolution. Concordantly, gut microbiome modulation by subinhibitory concentration of AGPs could be the result of direct stimulation rather than inhibition of determined microbial species. In eukaryotes, these adaptive responses of the mitochondria to internal and external environmental conditions, can promote growth rate of the organism as an evolutionary strategy to overcome potential negative conditions. We hypothesize that direct and indirect subtherapeutic AGP regulation of mitochondria functional output can regulate homeostatic control mechanisms in a manner similar to those involved with disease tolerance.

Xylo-oligosaccharide-based prebiotics upregulate the proteins of the Sus-like system in caecal Bacteroidetes of the chicken: evidence of stimbiotic mechanism

The present study was conducted to investigate the stimbiotic mechanism of xylo-oligosaccharide (XOS) in degrading the complex polysaccharides by the caecal bacteria of the chicken, by applying a proteomic approach. A total of 800 as-hatched Ross 308 broiler chicks were equally divided into 4 experimental pens (200 chicks per pen) at a commercial poultry barn, allocating 2 pens per treatment. Birds were fed ad libitum with 2 dietary treatments; CON (without XOS) and XOS (with 0.1g XOS/kg diet) from d 0 to 35. From each pen, 60 Individual birds were weighed weekly whereas caecal content was obtained from 5 birds cervically dislocated on d 35. The caecal bacteria were lysed and their proteins were quantified using label-free quantitative proteomic mass spectrometry. The results showed that XOS significantly increased (P < 0.05) bird weight on d 7, 14, 21, and 28, and body weight gain on d 7, 14, 21, and 35 compared to CON. However, no difference (P > 0.05) in body weight gain was observed from d 0 to 35 between CON and XOS. The proteomic analysis of caecal bacteria revealed that 29 proteins were expressed differently between the CON and the XOS group. Out of 29, 20 proteins were significantly increased in the XOS group compared to CON and 9 of those proteins belonged to the starch-utilizing system (Sus)-like system of the gram-negative Bacteroidetes. Bacteroides thetaiotaomicron (Bt) is a significant constituent of the human gut microbiota, known for its remarkable ability to hydrolyze most glycosidic bonds of polysaccharides. This microorganism possesses a 5-protein complex in its outer membrane, named the starch utilization system (Sus), responsible for adhering to, breaking down, and transporting starch into the cell. Sus serves as an exemplar system for numerous polysaccharide utilization loci that target glycans found in Bt and other members of the Bacteroidetes phylum. The proteins of the Sus-like system are involved in the degradation of complex polysaccharides and transportation of the oligosaccharides into the periplasm of the caecal bacteria where they are further broken down into smaller units. These smaller units are then transported into the cytoplasm of the cell where they are utilized in metabolic pathways leading to potential generation of short-chain fatty acids, thus improving the nutritive value of residual feed. In conclusion, XOS supplementation upregulates the expression of the proteins of the Sus-like system indicating its role as a stimbiotic.

Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices

Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices. Four commercial farms (2 conventional and 2 NAE) were included in this study. On each farm, cecal (n = 224) and ileal (n = 224) contents were collected from birds at different stages during the grow out of a single flock and following transportation to the processing facility. Cecal microbiota was dominated by the genera Escherichia and Enterococcus upon hatching in both conventional and NAE flocks, shifting with time toward predominantly Faecalibacterium and Bacteroides. The composition of cecal microbial communities of NAE broilers was different than that of conventional chickens (P ≤ 0.05). Conventional broilers harbored a rich, but less diverse cecal microbiota than NAE, while the ileal microbiota was primarily populated with genera previously named Lactobacillus, which exhibited a higher abundance in NAE broilers (P ≤ 0.05). In both production systems, the microbiota followed a similar temporal succession that was more evident in the ceca. Transportation to the processing plant impacted the microbial composition of the ileum (P ≤ 0.05), characterized by an increase in the relative abundance of Psychrobacter. Finally, differential abundance analysis showed a positive correlation between Campylobacter and Enorma within the cecum microbiota, and a negative correlation with Salmonella.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Therapeutic effect of heat-killed Lactobacillus plantarum L-137 on the gut health and growth of broilers

Although some studies on the effects of para-probiotics on the immune system and intestinal health have been conducted independently of research on antibiotics ass growth promoters. This study investigated the effects of heat-killed Lactobacillus plantarumL-137 (L-137) and antibiotics as preventive and/or therapeutic substances for broilers against subclinical necrotic enteritis caused by Clostridium perfringens (CP). In total, 300 1-day-old broilers (46.13 ± 1.38 g) were randomly stocked at 10 birds pen^-1 in five replicates and divided into six groups, namely T1 and T2, positive and negative control of CP challenge; T3 and T4, prevention with basal diet plus 10 and 50 mg/kg L-137; T5 and T6, prevention and treatment with basal diet plus 50 mg/kg of L-137 and bacitracin at 50 ppm, respectively. Broilers administered L-137 in T4, T5 and bacitracin in T6 showed an improved (p < 0.05) villus height/crypt depth ratio than control groups, suggesting that it might significantly boost growth performance. In contrast to bacitracin, a high dosage of L-137 significantly increased (p < 0.05) the spleen index value and the cytokine levels, as well as the expression of intestinal β-defensin genes on day 28. During the 42-day production period, broilers in T4 and T5 showed a significantly enhanced (p < 0.05) expression of cytokines, AvBD-1 and AvBD-7 on day 42 compared to the control and bacitracin groups. In particular, broilers given the L-137 diets demonstrated no cumulative mortality following CP exposure, compared to a 2% mortality in T6. Our findings provide insight into eco-friendly alternatives to antibiotics for maximizing growth performance, feed efficiency and long-term disease protection in chickens; however, this has to be proven in larger-scale commercial experiments.

Intestinal Immune Development Is Accompanied by Temporal Deviation in Microbiota Composition of Newly Hatched Pigeon Squabs

Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease later in life. However, knowledge about this interaction during the early posthatch development period in altrices is limited. To fill this gap, samples of intestinal content and tissue were collected from newly hatched pigeon squabs at four time points (days 0, 7, 14, and 21) for microbial community analysis and genome-wide transcriptome profiling, respectively. We show that the first week after hatching seems to be the critical window for ileal microbiota colonization and that a potentially stable microbiota has not yet been well established at 21 days of age. Regional transcriptome differences revealed that the jejunum rather than the ileum plays a crucial role in immunity at both the innate and adaptive levels. In the ileum, temporal deviation in innate immune-related genes mainly occurs in the first week of life and is accompanied by a temporal change in microbiota composition, indicating that the ileal innate mucosal immune system development regulated by microbial colonization occurs mainly in this period. Furthermore, we provide evidence that colonization by Escherichia and Lactobacillus within the first week of life is likely one of the causative factors for the induction of proinflammatory cytokine expression in the ileum. We also demonstrate that cellular adaptive immune responses mediated by Th17 cells following commensal-induced proinflammatory cytokine production in the ileum begin as early as the first week posthatch, but this cellular immunity seems to be less effective in terms of maintaining the inflammatory response balance. Because the induction of high levels of mucosal secretory IgA (SIgA) seems to take approximately 3 weeks, we favor the idea that humoral adaptive immunity might be less active, at least, during the first 2 weeks of life. Our data may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period. IMPORTANCE The pigeon (Columba livia), an altricial bird, is one of the most economically important farmed poultry for table purposes. Identifying the interaction between intestinal mucosal immune system development and commensal microbiota colonization in neonates is of paramount importance for understanding how early life events affect resistance to disease and potential productivity later in life. However, knowledge about this interaction during the early posthatch development period in altricial birds is limited. The study described herein is the first to try to provide insights into this interaction. Our data provide evidence on the mutual relationship between intestinal mucosal immune system development and commensal microbiota colonization in pigeon squabs and may help to explain the phenomenon of the occurrence of intestinal infections mainly in the ileum of pigeon squabs during the early posthatch period.

Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes

Antimicrobial growth promoters (AGPs) are commonly used in broiler production. There is a huge societal concern around their use and their contribution to the proliferation of antimicrobial resistance (AMR) in food-producing animals and dissemination to humans or the environment. However, there is a paucity of comprehensive experimental data on their impact on poultry production and the AMR resistome. Here, we investigated the effect of five antimicrobial growth promoters (virginiamycin, chlortetracycline, bacitracin methyl disalicylate, lincomycin, and tylosin) used in the commercial broiler production in the Indian subcontinent and in the different parts of the world for three consecutive production cycles on performance variables and also the impact on gut bacteria, bacteriophage, and resistome profile using culture-independent approaches. There was no significant effect of AGPs on the cumulative growth or feed efficiency parameters at the end of the production cycles and cumulative mortality rates were also similar across groups. Many antibiotic resistance genes (ARGs) were ubiquitous in the chicken gut irrespective of AGP supplementation. In total, 62 ARGs from 15 antimicrobial classes were detected. Supplementation of AGPs influenced the selection of several classes of ARGs; however, this was not correlated necessarily with genes relevant to the AGP drug class; some AGPs favored the selection of ARGs related to antimicrobials not structurally related to the AGP. AGPs did not impact the gut bacterial community structure, including alpha or beta diversity significantly, with only 16-20 operational taxonomic units (OTUs) of bacteria being altered significantly. However, several AGPs significantly reduced the population density of some of the potential pathogenic genera of bacteria, such as Escherichia coli. Chlortetracycline increased the abundance of Escherichia phage, whereas other AGPs did not influence the abundance of bacteriophage significantly. Considering the evidence that AGPs used in poultry production can select for resistance to more than one class of antimicrobial resistance, and the fact that their effect on performance is not significant, their use needs to be reduced and there is a need to monitor the spread of ARGs in broiler chicken farms.

cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae

The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.

Metagenomics analysis of the fecal microbiota in Ring-necked pheasants (Phasianus colchicus) and Green pheasants (Phasianus versicolor) using next generation sequencing

Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.

Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli

Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2x5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), and AGPs monensin (MON), lincomycin (LCM), and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively.The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared to sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.

Comparative Microbial Conversion of Deoxynivalenol and Acetylated Deoxynivalenol in Different Parts of the Chicken Intestine as Detected In Vitro and Translated to the In Vivo Situation

To assess potential differences in the intestinal microbial metabolism of deoxynivalenol (DON) and its acetylated forms 3-Ac-DON and 15-Ac-DON, in vitro anaerobic incubations with intestinal contents from chickens were conducted. Quantitative microbiota characterization was obtained by 16S rRNA sequencing. The data showed substantial differences in the level of different toxin conversions by the microbiota from the different intestinal segments. The transformation rate of DON to its metabolite DOM-1 decreased in the order of cecum > ileum > jejunum, and caecum contents could completely transform DON to DOM-1 within 24 h. However, no transformation appeared in the duodenum. For 3-Ac-DON, the deacetylation rate decreased as follows: duodenum > caecum > ileum > jejunum, and 100% deacetylation was observed in the duodenum within 24 h. The deacetylation of 15-Ac-DON decreased in the order of cecum > duodenum > ileum with no transformation in the jejunum. Some genera may contribute to the transformation of the toxins. Based on the in vitro kinetic parameters and their scaling to the in vivo situation, it was concluded that in the chicken small intestine, the deconjugation of both 3-Ac-DON and 15-Ac-DON will not likely be completed upon full transit. Whether this also holds for humans remains to be established.

Antibiotic Resistance: One Health One World Outlook

Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.

Modulation of intestinal morphology and microbiota by dietary Macleaya cordata extract supplementation in Xuefeng Black-boned Chicken

Antibiotics are commonly overused to prevent livestock from diseases and to increase production performance. As potential substitutes of antibiotics, plant extracts have attracted the attention of researchers. It was known to all that addition of Macleaya cordata extract (MCE) to the food could advance immunity, intestinal health and animal performance. Thus, it was conducted to investigate the influence of MCE (0, 100, 150 and 200 mg/kg, with six replicate pens/treatment and 24 hens/pen) on intestinal morphology and microbial diversity in different intestinal segments in Xuefeng black-boned chicken in this study. The results showed that MCE supplement (100, 150 and 200 mg/kg) significantly diminished (P < 0.05) the crypt depth of the jejunum as compared to basal diet group. The 100 mg/kg group displayed a marked increase (P < 0.05), compared with 0 and 200 mg/kg group, in ileum microbial diversity as represented by the Shannon's index. In the cecum, treatment of MCE significantly decreased (P < 0.01) the Firmicutes, but Deferribacteres in 200 mg/kg MCE group were significantly raised (P < 0.05). In conclusion, we found that MCE improved intestinal morphology and reduced the crypt depth in jejunum. Together, addition of 200 mg/kg MCE modulated intestinal microbiota, increased beneficial bacteria such as Lactobacillus. Adding 100 mg/kg MCE to diet increased bacterial community diversity and relative abundance in jejunum and ileum, but had no effect on cecum microbial diversity.

Pharmaceuticals and alkylphenols in transplanted Pacific oysters (Crassostrea gigas): Spatial variation and growth effects

Pharmaceuticals and personal care products in wastewater discharge can be stressors to estuarine species. We transplanted juvenile Pacific oysters at varying distances within sites near wastewater treatment plant outfalls or oyster aquaculture control sites to assess small scale spatial variation in contaminant uptake and oyster condition. Oysters were transplanted to sites in Coos and Netarts Bays, Oregon and Grays Harbor, Washington, then collected after 9 and 12 months. Two pharmaceuticals (miconazole and virginiamycin M1) were detected in spring samples and four alkylphenols (NP1EO, NP2EO, NP and OP) were detected in summer samples, with more frequent detections at wastewater sites. Contaminant concentrations were similar across site types, indicating that even in sparsely populated coastal areas (<25,000 in the watershed), shellfish are exposed to and uptake wastewater contaminants. Additionally, oyster condition was lower at wastewater sites compared to aquaculture sites, indicating a need to better understand whether contaminant exposure affects oyster condition.

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.

Antibiotic resistance, antimicrobial residues, and bacterial community diversity in pasture-raised poultry, swine, and beef cattle manures

Animal manure can be a source of antibiotic-resistant genes (ARGs) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABRs) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine, and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARGs (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR (real-time PCR). Results indicated that the ARG abundances (Sul1 [P < 0.05] and TetA [P < 0.001]) were higher in layer hen manures (16.5 × 10-4 and 1.4 × 10-4 µg kg-1, respectively) followed by broiler chickens (2.9 × 10-4 and 1.7 × 10-4 µg kg-1, respectively), swine (0.22 × 10-4 and 0.20 × 10-4 µg kg-1, respectively) and beef cattle (0.19 × 10-4 and 0.02 × 10-4 µg kg-1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg-1) than for other animal species (1.8 to 0.06 µg kg-1), while chlortetracycline, lincomycin, and oxytetracycline ABRs were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic-resistant microorganisms (ARMs) and ARG.

Effects of exogenous β-glucanase on ileal digesta soluble β-glucan molecular weight, digestive tract characteristics, and performance of coccidiosis vaccinated broiler chickens fed hulless barley-based diets with and without medication

Introduction

Limited use of medication in poultry feed led to the investigation of exogenous enzymes as antibiotic alternatives for controlling enteric disease. The objective of this study was to evaluate the effects of diet β-glucanase (BGase) and medication on β-glucan depolymerization, digestive tract characteristics, and growth performance of broilers.

Materials and methods

Broilers were fed hulless barley (HB) based diets with BGase (Econase GT 200P from AB Vista; 0 and 0.1%) and medication (Bacitracin and Salinomycin Na; with and without) arranged as a 2 × 2 factorial. In Experiment 1, 160 broilers were housed in cages from d 0 to 28. Each treatment was assigned to 10 cages. In Experiment 2, broilers (2376) were housed in floor pens and vaccinated for coccidiosis on d 5. Each treatment was assigned to one floor pen in each of nine rooms.

Results

In Experiment 1, the soluble β-glucan weighted average molecular weight (Mw) in the ileal digesta was lower with medication in the 0% BGase treatments. Peak molecular weight (Mp) and Mw were lower with BGase regardless of medication. The maximum molecular weight for the smallest 10% β-glucan (MW-10%) was lower with BGase addition. In Experiment 2, Mp was lower with medication in 0% BGase treatments. Beta-glucanase resulted in lower Mp regardless of medication, and the degree of response was lower with medication. The MW-10% was lower with BGase despite antibiotic addition. Body weight gain and feed efficiency were higher with medication regardless of BGase use through-out the trial (except d 11–22 feed efficiency). Beta-glucanase resulted in higher body weight gain after d 11 and worsened and improved feed efficiency before and after d 11, respectively, in unmedicated treatments.

Conclusion

BGase and medication caused the depolymerization of soluble ileal β-glucan. Beta-glucanase acted as a partial replacement for diet medication by increasing growth performance in coccidiosis vaccinated broilers.

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Effects of Xylo-Oligosaccharides on Growth and Gut Microbiota as Potential Replacements for Antibiotic in Weaning Piglets

Xylo-oligosaccharides (XOS) is a well-known kind of oligosaccharide and extensively applied as a prebiotic. The objective of this study was to investigate the effect of XOS supplementation substituting chlortetracycline (CTC) on growth, gut morphology, gut microbiota, and hindgut short chain fatty acid (SCFA) contents of weaning piglets. A total of 180 weaned piglets were randomly allocated to three treatments for 28 days, as follows: control group (basal diet, CON), basal diet with 500 mg/kg (XOS500) XOS, and positive control (basal diet with 100 mg/kg CTC). Compared with the CON group, the piglets in the XOS500 group improved body weight (BW) on days 28, average daily gain (ADG) and reduced feed: gain ratio during days 1–28 (P < 0.05). The XOS500 supplementation increased Villus height and Villus height: Crypt depth ratio in the ileum (P < 0.05). Villus Height: Crypt Depth of the ileum was also increased in the CTC treatment group (P < 0.05). Meanwhile, the XOS500 supplementation increased significantly the numbers of goblet cells in the crypt of the cecum. High-throughput 16S rRNA gene sequencing revealed distinct differences in microbial compositions between the ileum and cecum. XOS500 supplementation significantly increased the bacterial diversity. However, CTC treatment markedly reduced the microbial diversity (P < 0.05). Meanwhile, XOS500 supplementation in the diet significantly increased the abundance of Lactobacillus genus compared to the CON and CTC group in the ileum and cecum (P < 0.01), whereas the level of Clostridium_sensu_stricto_1, Escherichia-Shigella, and Terrisporobacter genus in the XOS500 group were markedly lower than the CON and CTC group (P < 0.05). In addition, dietary supplementation with XOS500 significantly increased the total short-chain fatty acids, propionate and butyrate concentrations and decreased the acetate concentration compared to the CON group in the cecum (P < 0.05). In summary, dietary supplemented with XOS500 could enhance specific beneficial microbiota abundance and decrease harmful microbiota abundance to maintain the structure of the intestinal morphology and improve growth performance of weaned piglets. Thus, XOS may potentially function as an alternative to in-feed antibiotics in weaned piglets in modern husbandry.

Novel biotechnological approaches for monitoring and immunization against resistant to antibiotics Escherichia coli and other pathogenic bacteria

The application of next-generation molecular, biochemical and immunological methods for developing new vaccines, antimicrobial compounds, probiotics and prebiotics for zoonotic infection control has been fundamental to the understanding and preservation of the symbiotic relationship between animals and humans. With increasing rates of antibiotic use, resistant bacterial infections have become more difficult to diagnose, treat, and eradicate, thereby elevating the importance of surveillance and prevention programs. Effective surveillance relies on the availability of rapid, cost-effective methods to monitor pathogenic bacterial isolates. In this opinion article, we summarize the results of some research program initiatives for the improvement of live vaccines against avian enterotoxigenic Escherichia coli using virulence factor gene deletion and engineered vaccine vectors based on probiotics. We also describe methods for the detection of pathogenic bacterial strains in eco-environmental headspace and aerosols, as well as samples of animal and human breath, based on the composition of volatile organic compounds and fatty acid methyl esters. We explain how the introduction of these low-cost biotechnologies and protocols will provide the opportunity to enhance co-operation between networks of resistance surveillance programs and integrated routine workflows of veterinary and clinical public health microbiology laboratories.

Effect of Dietary Supplementation with Coarse or Extruded Oat Hulls on Growth Performance, Blood Biochemical Parameters, Ceca Microbiota and Short Chain Fatty Acids in Broiler Chickens

The purpose of this study was to determine the effect of dietary supplementation with coarse or extruded oat hulls on growth performance, blood biochemistry, cecal microbiota, and short chain fatty acids (SCFA) in broiler chickens. Chickens were randomly allotted to four dietary treatments consisting of a corn-wheat-soybean meal-based diet (Basal), Basal + Bacitracin methylenedisalicylate (BMD), Basal +3% coarse OH (COH), and basal +3% extruded OH (EOH). Feed intake (FI), body weight gain (BWG), and feed conversion ratio (FCR) were recorded weekly. On day 36, eight chickens/treatment were euthanized, blood samples were collected, and organ weights were determined. Cecal digesta samples were collected for the determination of SCFA concentration and microbial DNA sequence. Data were subjected to ANOVA using the mixed procedure of SAS. Alpha diversity was estimated with the Shannon index, and the significance of diversity differences was tested with ANOVA. Birds fed COH and EOH had reduced (p < 0.05) BWG, but there was no effect of treatment on FCR. There was a significant increase (p = 0.0050) in relative gizzard empty weight among birds that were fed COH, compared to the other treatments. Dietary treatments had no effect on blood biochemical parameters and SCFA concentration. Cecal microbial composition of chickens was mostly comprised of Firmicutes and Tenericutes. Seven OTUs that were differentially abundant among treatments were identified. In conclusion, supplementation of broiler chickens' diets with 3% COH or EOH did not affect the FCR, blood biochemical parameters and SCFA concentration, but modified few cecal microbiota at the species level. Dietary supplementation with COH but not EOH significantly increased the relative gizzard weight.

Phenomenal Bombardment of Antibiotic in Poultry: Contemplating the Environmental Repercussions

Antibiotics have constantly been added at an unprecedented rate in order to enhance poultry meat production. Such antibiotics impose a negative impact on human health directly through meat and egg consumption. On the other hand, they also affect humans indirectly by affecting the normal key microbial processes in the agricultural environments, when used as poultry compost. For many years, farmers have been turning poultry litter into compost for agricultural use. Very few studies have addressed the fate of the unmetabolized antibiotic residues in poultry litter that could potentially affect microbial communities when used as poultry compost. We have also questioned the fate of residual antibiotic in poultry waste which may create possible negative environmental pressure on microbial communities that are involved in microbial mediated poultry litter composting processes. The incorporation of antibiotic degrading environmental isolates in poultry litter at the initial stage of composting in order to accelerate the process is addressed in this review as a future perspective.

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.

Changes in cecum microbial community in response to total sulfur amino acid (TSAA: DL-methionine) in antibiotic-free and supplemented poultry birds

The effect of essential total sulfur amino acids (TSAA) like methionine and cysteine on the cecal microbiome of broilers was investigated at 2 different time points (days 21 and 42) of broiler rearing. A total of 360-day-old Cobb male broiler chicks were randomly distributed to 6 dietary treatments in a 2 × 3 factorial arrangement, with 2 levels of antibiotic growth promoters (AGP: 0 and 0.05%) and 3 levels of TSAA (DL-methionine) either for starter (0.7, 0.8, and 0.9%) or finisher chicks (0.52, 0.62, and 0.72%), labeled as diets 1 to 6. Cecal digesta from each replicate (n = 10) were sampled on days 21 and 42. DNA was extracted for the amplification of the V4 region of bacterial 16S rRNA genes and subjected to Illumina sequencing. Bioinformatic analyses were performed using QIIME, Mothur, and ad hoc tools and functional profiles of the inferred metagenome were analyzed using PICRUST. Statistical difference was determined by 2-way ANOVA and PERMANOVA. Clustering of cecal communities using PCoA showed clear separation of microbial communities based on age (P < 0.05) of birds and between low and medium/ high levels of TSAA (DL-methionine). At day 21, bacterial richness and diversity were higher than at day 42 where Clostridium cluster XI and Lactobacillus were found most abundant. No variability in taxonomic richness at the genus level was observed with AGP and DL-methionine supplementation. Interbird variation for richness was greater at day 42 compared to day 21. The mean fold difference of richness was greater (1.5 mean fold) with diets 1 and 6, suggesting interactive effects of AGP and TSAA (DL-methionine) in the diet. KEGG function profiles calculated by PICRUST suggest that the cecal microbiome increased glycolysis and energy generation correlated with increased dietary TSAA (DL-methionine) supplementation levels during the late broiler growth period (day 42). This study increases our knowledge of microbial dynamics and functions that are relevant to host nutrition and performance that may help us tailoring alternative strategies for raising poultry birds under antibiotic-free conditions.

Effect of prebiotic and synbiotic supplementation in diet on growth performance, small intestinal morphology, stress, and bacterial population under high stocking density condition of broiler chickens

The current study investigated the effect of prebiotic mannan-oligosaccharide (MOS) and synbiotic (MOS mixed with Bacillus subtilis and Bacillus licheniformis) on growth performance and bacterial population under high stocking density (HSD) conditions in broilers. A total of 605 one-day-old male Arbor Acres broiler chickens were randomly assigned to 4 treatments: normal stocking density (NSD; 30 kg/m2 fed basal diets), HSD (40 kg/m2 fed basal diets), HSD chickens fed 0.1% prebiotic (HSDp), and HSD fed 0.1% synbiotic (HSDs). At 35 D of age, the body weight of HSD and HSDp were poorer than NSD group (P < 0.01), whereas the feed conversion ratio (FCR) of the HSDs) group was better than the NSD group (P < 0.01). The HSDp and HSDs groups improved FCR (P < 0.01) and has cheaper feed cost per gain compared to the HSD group. Moreover, the body weight of HSDs group was heavier than the HSDp group (P < 0.05). The level of corticosterone and the heterophil to lymphocyte ratio were highest in the HSD group, whereas these indexes were reduced in both HSDp and HSDs groups (P < 0.05). Duodenal, jejunal, and ileal villus heights were shortest in the HSD group (P < 0.01), and the lowest ileal segment goblet cell counts were also observed in this group (P < 0.05). The HSDp and HSDs groups improved the morphology of gastrointestinal (GI) tract (P < 0.05). The Lactobacillus sp. and Clostridium sp. count in the GI tract of HSD group were low (P < 0.01), whereas Escherichia coli was high (P < 0.01), and Salmonella spp. in jejunum and cecum were detectable when compared with NSD group. Conversely, Bacillus sp., Lactobacillus sp., and Clostridium sp. in HSDp and HSDs groups were increased, and E. coli was reduced in the HSDs group (P < 0.01). Therefore, it is clear that stress from HSD negatively affected growth performance, gut morphology, and microbial population, whereas the supplementation of prebiotic or synbiotic can mitigate the effect of stress and microbial dysbiosis in gut of broiler chickens under HSD condition. Comparatively, under this condition, using synbiotic appears to have more beneficial effects than using the prebiotic.

Dietary Antibiotic Growth Promoters Down-Regulate Intestinal Inflammatory Cytokine Expression in Chickens Challenged With LPS or Co-infected With Eimeria maxima and Clostridium perfringens

Subtherapeutic levels of dietary antibiotics increase growth performance in domestic animals, but the mechanisms are poorly understood. Here, 1-week-old broiler chickens were challenged with LPS (experiment 1), or co-infected with Eimeria maxima and Clostridium perfringens as an experimental model of necrotic enteritis (experiment 2), and fed a standard basal diet or a basal diet supplemented with virginiamycin or bacitracin methylene disalicylate. In experiment 1, LPS-challenged chickens fed the unsupplemented diet had decreased body weight gains, compared with unsupplemented controls given the PBS control. In contrast, antibiotic supplementation increased body weight gains in both the LPS-challenged and PBS groups, compared with the antibiotic-free diet. LPS-challenged chickens fed the unsupplemented diet had increased expression levels of intestinal tight junction proteins (ZO1, JAM2), MUC2 gel-forming mucin, and inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-17A) at 24 h post-challenge, compared with unsupplemented chickens given the PBS control. However, LPS-challenged chickens fed the antibiotic-supplemented diets had decreased levels of intestinal inflammatory cytokine transcripts, compared with LPS-challenged chickens given the unsupplemented basal diet. In experiment 2, E. maxima/C. perfringens-co-infected chickens fed the antibiotic-supplemented diets had increased body weight gains, decreased intestinal pathology, and greater intestinal crypt depth, compared with co-infected chickens given the unsupplemented diet. Further, similar to LPS challenge, E. maxima/C. perfringens-co-infection of chickens fed the antibiotic-supplemented diets decreased expression levels of intestinal inflammatory cytokines, compared with co-infected chickens given the unsupplemented diet. These results support the hypothesis that dietary antibiotic growth promoters might increase poultry growth, in part, through down-regulation of pathogen-induced inflammatory responses.

Preliminary Study on the Effect of Bacillus amyloliquefaciens TL on Cecal Bacterial Community Structure of Broiler Chickens

Probiotics can promote the health and growth performance of animals through modulation of intestinal microbiota. When used as a feed additive, they have the potential to minimize or abolish the use of antibiotics. In this study, we investigated the effect of the probiotic strain Bacillus amyloliquefaciens TL on the growth performance and cecum microflora composition in Cobb 500 broiler chickens. In total, 180 broilers were randomly divided into three groups-each group comprised 4 pens, and each pen contained 15 chickens. The three groups were fed either a control diet, or a diet supplemented with either the antibiotic chlortetracycline or B. amyloliquefaciens TL. Broilers were weighed, and cecum contents were collected on days 7, 14, 21, and 35, respectively. The broilers in both the antibiotic and probiotic groups exhibited significant weight gain compared with controls, exhibiting increases of 16.02% and 13.40%, respectively, after 35 days (P < 0.01). Similarly, the feed conversion ratio (FCR, 1-35 days) of broilers in the chlortetracycline and B. amyloliquefaciens TL groups was lower than that of the controls. HiSeq high-throughput sequencing of 16S rRNA of the cecal microbiota was performed on days 7, 14, 21, and 35, respectively. The Firmicutes/Bacteroidetes ratio was higher in the chlortetracycline and B. amyloliquefaciens TL groups than in the control group on days 14, 21, and 35, and especially on day 21. The prevalence of genera Oscillospira, Ruminococcus, Butyricicoccus, and Faecalibacterium (Firmicutes) was higher in the antibiotic and probiotic groups, while that of Bacteroides, Parabacteroides (Bacteroidetes), and Lactobacillus was higher in the control group. In this study, the changes in the microbiota of the probiotic group were similar to those in the antibiotic group. These results suggest that the probiotic strain B. amyloliquefaciens TL can modulate the cecal microbiota of broilers similar to chlortetracycline.

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.

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota

Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11-87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54-0.71 and 0.71-0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = -0.2-0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.

A mutated rabbit defensin NP-1 produced by Chlorella ellipsoidea can improve the growth performance of broiler chickens

The demand for alternatives to antibiotics to improve the growth performance of food animals is increasing. Defensins constitute the first line of defence against pathogens in the innate immune system of animals and humans. A transgenic Chlorella ellipsoidea strain producing mNP-1 (a mutated rabbit defensin NP-1) was previously obtained in our laboratory. In this study, a process for producing the transgenic strain on a large scale was developed, and the C. ellipsoidea strain producing mNP-1 was used as a feed additive to improve the health and growth performance of chickens. The volume of C. ellipsoidea producing mNP-1 can be scaled up to 10,000 L with approximately 100 g/L dry biomass, and the mNP-1 content of transgenic microalgal powder (TMP) was 90–105 mg/L. A TMP-to-regular feed ratio of 1‰, as the optimal effective dose, can promote the growth of broiler chickens by increasing weight by 9.27–12.95%. mNP-1 can improve duodenum morphology by promoting long and thin villi and affect the microbial community of the duodenum by increasing the diversity and abundance of beneficial microbes. These results suggested that transgenic Chlorella producing mNP-1 can be industrially produced and used as an effective feed additive and an alternative to antibiotics for improving the health and growth performance of broiler chickens or other types of food animals/poultry.

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.

Differential Effects of Bacitracin Methylene Disalicylate (BMD) on the Distal Colon and Cecal Microbiota of Young Broiler Chickens

Antibiotics have been used extensively for growth promotion in poultry, along with other food production animals, as well as therapeutically to treat infectious diseases. However, with concerns over selection for drug antibiotic resistant bacteria the practice of using subtherapeutic doses of antibiotics is under increased scrutiny. Consequently, we assessed the impact of the commonly used antibiotic bacitracin methylene disalicylate (BMD) on the gastrointestinal microbiota of chickens. For this we administered therapeutic doses of BMD as a feed additive and 16s rRNA gene amplicon sequencing to measure changes in taxonomic abundance on the distal colon and cecal microbiota of young broiler chickens. While BMD treatment was found to impact the abundance of selected taxa and overall beta diversity, significant changes were, in general, limited to the colon of the treated birds. Selected taxa at the phylum, class, and genus levels that were most impacted were identified. The composition of the cecum remained relatively stable in BMD-treated animals. As poultry production practices seek alternatives to growth promoting antibiotic feed additives, manipulation of the gastrointestinal microbiota holds promise. These results suggest that targeting the cecum may offer a means to promote changes to the microbiota that maximize the benefits for the hosts.

Bioprospection of anti-inflammatory phytochemicals suggests rutaecarpine and quinine as promising 15-lipoxygenase inhibitors

15-Lipoxygenase (15-LOX) belongs to the family of nonheme iron containing enzymes that catalyzes the peroxidation of polyunsaturated fatty acids (PUFAs) to generate eicosanoids that play an important role in signaling pathways. The role of 15-LOX has been demonstrated in atherosclerosis as well as other inflammatory diseases. In the present study, drug-like compounds were first screened from a set of anti-inflammatory phytochemicals based on Lipinski's rule of five (ROF) and in silico toxicity filters. Two lead compounds-quinine (QUIN) and rutaecarpine (RUT) were shortlisted by analyzing molecular interactions and binding energies of the filtered compounds with the target using molecular docking. Molecular dynamics simulation studies indicate stable trajectories of apo_15-LOX and docked complexes (15-LOX_QUIN and 15-LOX_RUT). In vitro 15-LOX inhibition studies shows that both QUIN and RUT have lower inhibitory concentration (IC₅₀ ) value than the control (quercetin). Both QUIN and RUT exhibit moderate antioxidant activities. The cell viability study of these compounds suggests no significant toxicity in HEK-293 cell lines. Further, QUIN and RUT both did not show any inhibition against selected Gram-positive and Gram-negative bacterial species. Thus, based on our present findings, rutaecarpine and quinine may be suggested as promising 15-LOX inhibitor for the prevention of the atherosclerosis development.

Effects of spray-dried porcine plasma on fecal microbiota in nursery pigs

Spray-dried porcine plasma (SDPP) has been considered as an alternative for in-feed antibiotics to improve pig growth performance; however, the effect of SDPP on gut microbiota is unknown. The objective of this study was to evaluate effects of feeding SDPP on fecal microbial communities of nursery pigs. Ninety-six weaned pigs were assigned to 16 pens, which were allotted to two dietary treatments, including the control or the control + SDPP (5% and 2.5% SDPP inclusion in phase 1 and 2, respectively) diet. Fecal samples were collected at d 0, 7, 14, 21, and 28. Multiplex sequencing of V3 region of the 16S rRNA gene was used to characterize the bacterial community structure of fecal samples. Pearson's correlation tests were performed in Calypso to identify bacterial taxa that were either positively or negatively associated with overall growth performance. Feeding SDPP altered microbial structure at family, genus, and operational taxonomic unit (OTU) classifications; however, fecal microbes shifted with time. At the family level, Clostridiaceae increased (P < 0.001) on d 14, but decreased (P < 0.05) on d 28 in SDPP-fed pigs compared with control pigs. Decreased Veillonellaceae (P < 0.05; d 14) and Lachnospiraceae (P = 0.001; overall) were observed in SDPP-fed pigs compared with control pigs. Feeding SDPP increased lactic acid-producing bacteria (Lactobacillus delbrueckii, d 7) and cellulolytic bacteria (Ruminococcus albus, d 7; Clostridium thermocellum, d 7 and 14; and Clostridium saccharoperbutylacetonicum/beijerinckii, d 14; and Megasphaera elsdenii, d 21). On d 28, feeding SDPP decreased (P < 0.05) Clostridium difficile compared with control pigs. In conclusion, feeding SDPP altered fecal microbial communities in nursery pigs. The results of this study may provide information to help explain the positive effects associated with feeding SDPP on nutrient digestibility and gut health of nursery pigs.

Bile salt hydrolases: Structure and function, substrate preference, and inhibitor development

The worldwide trend of limiting the use of antibiotic growth promoters (AGPs) in animal production creates challenges for the animal feed industry, thus necessitating the development of effective non-antibiotic alternatives to improve animal performance. Increasing evidence has shown that the growth-promoting effect of AGPs is highly correlated with the reduced activity of bile salt hydrolase (BSH, EC 3.5.1.24), an intestinal bacteria-producing enzyme that has a negative impact on host fat digestion and energy harvest. Therefore, BSH inhibitors may become novel, attractive alternatives to AGPs. Detailed knowledge of BSH substrate preferences and the wealth of structural data on BSHs provide a solid foundation for rationally tailored BSH inhibitor design. This review focuses on the relationship between structure and function of BSHs based on the crystal structure, kinetic data, molecular docking and comparative structural analyses. The molecular basis for BSH substrate recognition is also discussed. Finally, recent advances and future prospectives in the development of potent, safe, and cost-effective BSH inhibitors are described.

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves

This study investigated the effect of supplementing the diet of calves with two direct fed microbials (DFMs) (Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) and Lactobacillus acidophilus BT1386 (LA)), and an antibiotic growth promoter (ATB). Thirty-two dairy calves were fed a control diet (CTL) supplemented with SCB or LA or ATB for 96 days. On day 33 (pre-weaning, n = 16) and day 96 (post-weaning, n = 16), digesta from the rumen, ileum, and colon, and mucosa from the ileum and colon were collected. The bacterial diversity and composition of the gastrointestinal tract (GIT) of pre- and post-weaned calves were characterized by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The DFMs had significant impact on bacteria community structure with most changes associated with treatment occurring in the pre-weaning period and mostly in the ileum but less impact on bacteria diversity. Both SCB and LA significantly reduced the potential pathogenic bacteria genera, Streptococcus and Tyzzerella_4 (FDR ≤ 8.49E-06) and increased the beneficial bacteria, Fibrobacter (FDR ≤ 5.55E-04) compared to control. Other potential beneficial bacteria, including Rumminococcaceae UCG 005, Roseburia and Olsenella, were only increased (FDR ≤ 1.30E-02) by SCB treatment compared to control. Furthermore, the pathogenic bacterium, Peptoclostridium, was reduced (FDR = 1.58E-02) by SCB only while LA reduced (FDR = 1.74E-05) Ruminococcus_2. Functional prediction analysis suggested that both DFMs impacted (p < 0.05) pathways such as cell cycle, bile secretion, proteasome, cAMP signaling pathway, thyroid hormone synthesis pathway and dopaminergic synapse pathway. Compared to the DFMs, ATB had similar impact on bacterial diversity in all GIT sites but greater impact on the bacterial composition of the ileum. Overall, this study provides an insight on the bacteria genera impacted by DFMs and the potential mechanisms by which DFMs affect the GIT microbiota and may therefore facilitate development of DFMs as alternatives to ATB use in dairy calf management.

Microbial community mapping in intestinal tract of broiler chicken

Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.

Use of antibiotics in broiler production: Global impacts and alternatives

Antibiotics are used to fight bacterial infections. However, a selective pressure gave rise to bacteria resistant to antibiotics. This leaves scientists worried about the danger to human and animal health. Some strategies can be borrowed to reduce the use of antibiotics in chicken farms. Much research has been carried out to look for natural agents with similar beneficial effects of growth promoters. The aim of these alternatives is to maintain a low mortality rate, a good level of animal yield while preserving environment and consumer health. Among these, the most popular are probiotics, prebiotics, enzymes, organic acids, immunostimulants, bacteriocins, bacteriophages, phytogenic feed additives, phytoncides, nanoparticles and essential oils.

Purification and Characterization of a Novel Anti-Campylobacter Bacteriocin Produced by Lactobacillus curvatus DN317

The lactic acid bacteria (LAB) microbiota of Saudi chicken ceca was determined. From 60 samples, 204 isolates of lactic acid bacteria were obtained. Three isolates produced antimicrobial activities against Campylobacter jejuni, Listeria monocytogenes, and Bacillus subtilis. The isolate DN317, which had the highest activity against Campylobacter jejuni ATCC 33560, was identified as Lactobacillus curvatus (GenBank accession numbers: KX353849 and KX353850). Full inhibitory activity was observed after a 2-h incubation with the supernatant at pH values between 4 and 8. Only 16% of the activity was conserved after a treatment at 121 °C for 15 min. The use of proteinase K, pepsin, chymotrypsin, trypsin, papain, and lysozyme drastically reduced the antimicrobial activity. However, lipase, catalase, and lysozyme had no effect on this activity. The active peptide produced by Lactobacillus curvatus DN317 was purified by precipitation with an 80% saturated ammonium sulfate solution, and two steps of reversed phase HPLC on a C18 column. The molecular weight of this peptide was 4448 Da as determined by MALDI-ToF. N-terminal sequence analysis using Edman degradation revealed 47 amino acid residues (UniProt Knowledgebase accession number C0HK82) revealing homology with the amino acid sequences of sakacin P and curvaticin L442. The antimicrobial activity of the bacteriocin, namely curvaticin DN317, was found to be bacteriostatic against Campylobacter jejuni ATCC 33560. The use of microbial antagonism by LAB is one of the best ways to control microorganisms safely in foods. This result constitutes a reasonable advance in the antimicrobial field because of its potential applications in food technology.

The sub-inhibitory theory for antibiotic growth promoters

Antibiotics have played a critical role in the prevention, control, and treatment of bacterial diseases in humans and animals, and as growth promoters (AGPs) when used at sub-therapeutic concentrations in animal production. Numerous hypotheses have been proposed for the effectiveness of AGPs, which have largely centered on the beneficial modulation of the intestinal microbiota. However, these hypotheses have been doubted by some researchers, as AGPs are fed at concentrations that would typically be below minimum inhibitory concentrations (sub-MIC) for the antibiotic used. More recently, pro-inflammatory immune responses have been associated with poor growth performance, and this, along with reported direct, anti-inflammatory effects of some antibiotics, have led to suggestions that reducing the nutrient cost of (intestinal) inflammation may explain the growth promoting or permitting effect of AGPs. However, doubts about antibacterial effects of AGPs, and the search for alternative explanations, overlook the sub-MIC effects of antibiotics. This paper summarizes some of the reported sub-MIC effects of antibiotics and considers these in the context of helping to explain the mode of action of AGPs and effects seen in studies in vivo. This leads to suggestions for the features that alternatives to AGPs could exhibit to achieve similar performance efficacy as AGPs.

Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

Emerging evidences have linked the gut microbiota to poultry physiology. Gut microbiota composition in Shaoxing ducks were profiled under different rearing conditions: raised on the litter floor and the plastic mesh floor. A total of 46 and 39 luminal content samples from the duodenum, ileum, and cecum of the ducks reared under the two conditions were analyzed by 16S rRNA gene amplicon sequencing analysis. Proteobacteria (48.66%), Proteobacteria (33.38%), and Bacteroidetes (55.35%) were the dominant phyla in the duodenum, ileum, and cecum of the ducks reared on the litter floor respectively, while Firmicutes (30.80%), Firmicutes (66.62%) and Bacteroidetes (47.15%) were the topmost phyla in the duodenum, ileum, and cecum of the ducks reared on the plastic mesh floor. Physiologically, the height of villi and the ratio of villus height to crypt depth in the ileum and duodenum were significantly greater in the ducks reared on plastic mesh floor. Furthermore, our results demonstrate that the gut microbiota was significantly associated with the duck phenotypes, such as chest depth and serum estradiol levels (p < 0.05), which were altered by the different rearing conditions. Collectively, our results showed that the rearing floor types have an important effect on the gastrointestinal microbial composition of ducks.

Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks

Background:

Livestock production should respond to societal, environmental and economic changes. Since 2006 and the ban on antibiotics as growth factors in European Union, the use of probiotics has become widespread and has demonstrated the effect of intestinal microbiota on the performance of farm animals.

Objective:

The aim of this study was to investigate the effect of supplementation with Lactobacillus salivarius (as a probiotics strain or combined with other strains) on zootechnical performance, metabolic and immune gene expression and intestinal microbiota diversity in mule ducks using high-throughput sequencing and real-time PCR.

Method:

The mule ducks were reared for 79 days and overfed for 12 days with or without probiotics. Samples were collected at 14 (starting period) and 91 days (end of overfeeding period), 3 hours post feeding.

Results:

Irrespective of digestive content, age, level of feed intake or supplementation with probiotics, Firmicutes, Proteobacteria and Bacteroidetes were the dominant phyla in the bacterial community in mule ducks. At 14 days, both the ileal and cecal samples were dominated by Firmicutes (in particular the Clostridiales order). Overfeeding induced a shift between Clostridiales and Lactobacillales in the ileal samples whereas in the cecal samples, the relative abundance of Firmicutes decreased. Overfeeding also induced hepatic over-expression of Fatty Acid Synthase (FAS) and of the lipid transporter gene Fatty Acid Binding Protein 4 (FABP4). This increase in lipid metabolism genes is associated with a decrease in inflammatory response.

Conclusion:

Finally, probiotic supplementation had only a slight impact on gene expression and microbiota diversity, both at 14 days and after overfeeding.