Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities

In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.

The Impact of Essential Amino Acids on the Gut Microbiota of Broiler Chickens

The research involving the beneficial aspects of amino acids being added to poultry feed pertaining to performance, growth, feed intake, and feed conversion ratio is extensive. Yet currently the effects of amino acids on the gut microbiota aren't fully understood nor have there been many studies executed in poultry to explain the relationship between amino acids and the gut microbiota. The overall outcome of health has been linked to bird gut health due to the functionality of gastrointestinal tract (GIT) for digestion/absorption of nutrients as well as immune response. These essential functions of the GI are greatly driven by the resident microbiota which produce metabolites such as butyrate, propionate, and acetate, providing the microbiota a suitable and thrive driven environment. Feed, age, the use of feed additives and pathogenic infections are the main factors that have an effect on the microbial community within the GIT. Changes in these factors may have potential effects on the gut microbiota in the chicken intestine which in turn may have an influence on health essentially affecting growth, feed intake, and feed conversion ratio. This review will highlight limited research studies that investigated the possible role of amino acids in the gut microbiota composition of poultry.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.

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.

Plasmid DNA Prime/Protein Boost Vaccination against Campylobacter jejuni in Broilers: Impact of Vaccine Candidates on Immune Responses and Gut Microbiota

Campylobacter infections, traced to poultry products, are major bacterial foodborne zoonoses, and vaccination is a potential solution to reduce these infections. In a previous experimental trial using a plasmid DNA prime/recombinant protein boost vaccine regimen, two vaccine candidates (YP437 and YP9817) induced a partially protective immune response against Campylobacter in broilers, and an impact of the protein batch on vaccine efficacy was suspected. This new study was designed to evaluate different batches of the previously studied recombinant proteins (called YP437A, YP437P and YP9817P) and to enhance the immune responses and gut microbiota studies after a C. jejuni challenge. Throughout the 42-day trial in broilers, caecal Campylobacter load, specific antibodies in serum and bile, the relative expression of cytokines and β-defensins, and caecal microbiota were assessed. Despite there being no significant reduction in Campylobacter in the caecum of vaccinated groups, specific antibodies were detected in serum and bile, particularly for YP437A and YP9817P, whereas the production of cytokines and β-defensins was not significant. The immune responses differed according to the batch. A slight change in microbiota was demonstrated in response to vaccination against Campylobacter. The vaccine composition and/or regimen must be further optimised.

Recent Trends on Mitigative Effect of Probiotics on Oxidative-Stress-Induced Gut Dysfunction in Broilers under Necrotic Enteritis Challenge: A Review

Gut health includes normal intestinal physiology, complete intestinal epithelial barrier, efficient immune response, sustained inflammatory balance, healthy microbiota, high nutrient absorption efficiency, nutrient metabolism, and energy balance. One of the diseases that causes severe economic losses to farmers is necrotic enteritis, which occurs primarily in the gut and is associated with high mortality rate. Necrotic enteritis (NE) primarily damages the intestinal mucosa, thereby inducing intestinal inflammation and high immune response which diverts nutrients and energy needed for growth to response mediated effects. In the era of antibiotic ban, dietary interventions like microbial therapy (probiotics) to reduce inflammation, paracellular permeability, and promote gut homeostasis may be the best way to reduce broiler production losses. The current review highlights the severity effects of NE; intestinal inflammation, gut lesions, alteration of gut microbiota balance, cell apoptosis, reduced growth performance, and death. These negative effects are consequences of; disrupted intestinal barrier function and villi development, altered expression of tight junction proteins and protein structure, increased translocation of endotoxins and excessive stimulation of proinflammatory cytokines. We further explored the mechanisms by which probiotics mitigate NE challenge and restore the gut integrity of birds under disease stress; synthesis of metabolites and bacteriocins, competitive exclusion of pathogens, upregulation of tight junction proteins and adhesion molecules, increased secretion of intestinal secretory immunoglobulins and enzymes, reduction in pro-inflammatory cytokines and immune response and the increased production of anti-inflammatory cytokines and immune boost via the modulation of the TLR/NF-ĸ pathway. Furthermore, increased beneficial microbes in the gut microbiome improve nutrient utilization, host immunity, and energy metabolism. Probiotics along with biosecurity measures could mitigate the adverse effects of NE in broiler production.

Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens

Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log₁₀/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log₁₀/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae)

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

An In Vitro Model of the Chicken Gastrointestinal Tract with Special Emphasis to the Cecal Microbiota

An in vitro model of the upper gastrointestinal tract as well as the chicken cecum was developed to have a predictive tool for estimating the production performance of animals by analyzing the feeding value of a certain diet. The upper gastrointestinal tract consists of a batch type model, whereas the cecal model is comprised of 4 semi-continuous connected vessels inoculated with cecal or fecal microbes. The upper gastrointestinal tract and cecal simulations were both run with a corn- and a wheat-based diet to simulate 2 typical feed types. Samples were collected after the 5-h cecal simulations and aliquots were frozen to assess inoculum stability. The microbiota was analyzed by 16S rRNA gene sequencing, whereas short chain fatty acids as microbial metabolites were analyzed by using gas chromatography. As expected, some significant differences in microbial abundance after simulation between the cecal and fecal slurry samples (P = 0.001) were detected, as well between the fresh and frozen status (P = 0.001), hence simulations inoculated with cecal and fresh samples being more diverse. For the measured metabolites, almost all of them increased (P < 0.05) significantly when comparing fresh and frozen inoculum. The present chicken intestinal in vitro model represents a rapid systematic screening system for studying dietary related microbial changes and reducing the need of animal sacrifice for experimentation.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Deoxynivalenol damages the intestinal barrier and biota of the broiler chickens

Background

In the livestock feed industry, feed and feed raw materials are extremely susceptible to mycotoxin contamination. Deoxynivalenol (DON) is one of the main risk factors for mycotoxin contamination in broiler feed and feedstuff, however, there is still little knowledge about this. Hence, the purpose of this study was to explore the toxicity effect of DON on the intestinal barrier and the microecological balance of the biota in broiler chickens.

Results

In our present study, we compared the pathological scores of the small intestines of broilers on the 5^th, 7^th, and 10^th day, and chose the 7^th day to analyze the small intestine histomorphology, tight junctions, and cecal biota of the broilers. The results showed the damage to the small intestine worsened over time, the small intestinal villi of broilers were breakage, the tight junctions of the small intestine were destroyed, the cecal biota was unbalanced, and the growth performance of broilers was reduced on the 7^th day.

Conclusions

DON could damage the functional and structural completeness of the intestinal tract, disorder the Intestinal biota, and finally lead to declined broiler performance. Our study provided a basis for the prevention and treatment of DON in broiler production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03392-4.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Virioplankton assemblages from challenger deep, the deepest place in the oceans

Hadal ocean biosphere, that is, the deepest part of the world’s oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

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The unique virioplankton assemblages of the Challenger Deep were revealed

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Virus encoded auxiliary metabolic genes relating to the biogeochemical cycling

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Viruses in deep and hadal zone tend to be lysogenic, and potentially mediate the horizontal gene transfer

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

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

Impact of DNA Prime/Protein Boost Vaccination against Campylobacter jejuni on Immune Responses and Gut Microbiota in Chickens

Campylobacteriosis is reported to be the leading zoonosis in Europe, and poultry is the main reservoir of Campylobacter. Despite all the efforts made, there is still no efficient vaccine to fight this bacterium directly in poultry. Recent studies have reported interactions between the chicken immune system and gut microbiota in response to Campylobacter colonisation. The present study was designed to analyse in more depth the immune responses and caecal microbiota following vaccination with a DNA prime/protein boost flagellin-based vaccine that induces some protection in specific-pathogen-free White Leghorn chickens, as shown previously. These data may help to improve future vaccination protocols against Campylobacter in poultry. Here a vaccinated and a placebo group were challenged by C. jejuni at the age of 19 days. A partial reduction in Campylobacter loads was observed in the vaccinated group. This was accompanied by the production of specific systemic and mucosal antibodies. Transient relatively higher levels of Interleukin-10 and antimicrobial peptide avian β-defensin 10 gene expressions were observed in the vaccinated and placebo groups respectively. The analysis of caecal microbiota revealed the vaccination's impact on its structure and composition. Specifically, levels of operational taxonomic units classified as Ruminococcaceae and Bacillaceae increased on day 40.

Characterization of the cecal microbiome composition of Nigerian indigenous chickens

Poultry cecum microbes are dynamic and complex. They play important roles in disease prevention, detoxification of harmful substances, nutrient processing, and ingestion harvesting. It may be possible to increase poultry productivity by better understanding and controlling the microbial population. We analyzed the composition and function of Nigerian hens' cecal microbiota using high-throughput sequencing methods. Using high-throughput sequencing of the 16S rRNA genes (V1-V9) hypervariable regions, the cecal microbiota of three Nigerian indigenous chicken genotypes (Naked neck, Frizzle, and Normal feather) was described and compared. A total of two phyla were represented among the three genotypes (Firmicutes and Proteobacteria). Microbiological diversity was found in the community, with naked neck having the most evenness, followed by normal feather, which had the least. There were a lot of similarities between the naked neck and frizzle feather chicken groups when it came to genetic diversity between them. For example, the bacterial cecal microbiota of the naked neck chickens was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. More understanding on gut microbiota roles and interactions will help Nigerian poultry farmers improve their methods and give valuable data for the study of bacteria in the chicken gut.

Stress response modulation: the key to survival of pathogenic and spoilage bacteria during poultry processing

The control of bacterial contaminants on meat is a key area of interest in the food industry. Bacteria are exposed to a variety of stresses during broiler processing which challenge bacterial structures and metabolic pathways causing death or sublethal injury. To counter these stresses, bacteria possess robust response systems that can induce shifts in the transcriptome and proteome to enable survival. Effective adaptive responses, such as biofilm formation, shock protein production and metabolic flexibility, require rapid induction and implementation at a cellular and community level to facilitate bacterial survival in adverse conditions. This review aims to provide an overview of the scientific literature pertaining to the regulation of complex adaptive processes used by bacteria to survive the processing environment, with particular focus on species that impact the quality and safety of poultry products like Campylobacter spp., Salmonella enterica and Pseudomonas spp.

A novel Lactobacillus bulgaricus isolate can maintain the intestinal health, improve the growth performance and reduce the colonization of E. coli O157:H7 in broilers

1. This study aimed at the effects of a novel Lactobacillus bulgaricus (L. bulgaricus) strain and Enterohemorrhagic Escherichia coli (E. coli) O157: H7 on intestinal flora and growth performance of broilers, and the protective effect of L. bulgaricus on broilers in challenged experiment by E. coli O157: H7.2. In vitro bacteriostatic test showed that the cell-free supernatant (CFS) of L. bulgaricus isolate had obvious inhibitory effect on E. coli O157: H7.3. Eighty 1-day-old male broilers were randomly assigned into 4 treatment groups with 4 replicate per treatment. All group received basic diet in addition to the specific treatments: NC group, gavage with normal saline; In LBP group, gavage with L. bulgaricus isolate (1×10⁹ CFU/mL) during the whole process, and challenged with E. coli O157: H7 (3×10⁹ CFU/mL); EC group, gavage with E. coli O157: H7 (3×10⁹ CFU/mL); LB Group, gavage with L. bulgaricus isolate. At the age of 21 days, broilers were weighed and feed conversion ratio (FCR) was calculated. Cecum and cecal contents, ileum and feces samples were taken after slaughter.4. The challenge of E. coli O157: H7 resulted in an increase in TLR-4, NF-κB and IL-8 mRNA in cecal tissue, a decrease in Villus: crypt ratio in ileum, a decrease in overall diversity of intestinal microflora and a poor FCR.5. The L. bulgaricus isolate decreased the mRNA expression of TLR-4, NF-κB and IL-8 induced by E. coli O157: H7, reduced the content of E. coli O157: H7 in the cecum of broilers, increased the Villus: crypt ratio, increased the abundance of beneficial bacteria and overall diversity of intestinal microflora, made good FCR.6. The L. bulgaricus isolate can maintain the intestinal health, improve the growth performance of broilers and reduce the colonization of E. coli O157:H7 in the cecum.

Selection and Optimization of High-Yielding DNA Isolation Protocol for Quantitative Analyses of Methanogenic Archaea

Methanogenic archaea are a functionally important component of the intestinal microbiota of humans and animals, participating in the utilization of detrimental hydrogen produced during gut fermentation. Despite this, archaeal DNA has rarely been found in intestinal microbiome analyses, which prompts the need to optimize detecting procedures of these microorganisms, including the DNA isolation step. Three commercially available kits for DNA isolation and one extra purification kit that removes PCR inhibitors were evaluated on chicken droppings. In addition, different variants of mechanical lysis and a double elution were tested to ensure the maximum efficiency of DNA isolation from archaea as well as bacteria. A quantitative real-time PCR was used to monitor the optimization progress. As a result, the combination of the selected Genomic Mini AX Bacteria+ kit with a 2-min-long sonication by ultrasonic probe and enzymatic pretreatment gave excellent extraction efficiency rates for DNA of methanogenic archaea (an approximate 50-fold increase compared to the standard enzymatic lysis described by the producer) and, at the same time, provided optimal protection of DNA extracted from bacteria susceptible to enzymatic lysis. The presented results indicate that the optimized protocol allows for highly efficient extraction of total DNA, which is well-suited for quantitative microbial analyses by real-time PCR.

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.

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

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

Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies

The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.

Avian leukosis virus subgroup J infection influences the gut microbiota composition in Huiyang bearded chickens

Avian leukosis virus (ALV) poses a major threat to poultry. The chicken gut microbiota plays critical roles in host performance, health and immunity. However, the effect of viral infection on the microbiota of Chinese local chickens is not well understood. In this study, we performed high-throughput 16S rRNA gene sequencing and evaluated the gut microbiota profiles using faeces from ALV subgroup J (ALV-J)-infected and healthy Huiyang bearded chickens (Chinese local chickens). At the phylum level, ALV-J infection mainly increased the abundance of Bacteroidetes and Proteobacteria and decreased that of Firmicutes. An analysis at the order, family and genus levels showed that the abundance of Lactobacillales, Lactobacillaceae and Lactobacillus was the highest in normal chicken faeces, accounting for 89·07%, 86·47% and 86·46%, respectively, of phylotypes. Moreover, samples from ALV-J-infected chickens were enriched with Bacteroidales, Clostridiales, Bacteroidaceae, Ruminococcaceae, Lachnospiraceae and Bacteroides. Our findings highlight that ALV-J infection alters the gut microbiota and disrupts the host-microbial homeostasis in chickens, which may be involved in the pathogenesis of ALV-J infection.

Impact of the gut microecology on Campylobacter presence revealed by comparisons of the gut microbiota from chickens raised on litter or in individual cages

Background

Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological impact underlying this link remains not fully clear. Here, we sought to investigate the impact of the gut microecology on the presence of Campylobacter by examining the microbiota in the duodenum, jejunum, ileum, ceca, and feces from chickens raised on commercial litter and in individual cages at 0–57 days of age.

Results

Through litter contact, the presence of Campylobacter was found to benefit from microecological competition among Lactobacillus, Helicobacter, and genera that are halotolerant and aerobic or facultatively anaerobic in the upper intestine, such as Corynebacterium and Brachybacterium. The presence was also promoted by the increased abundance in obligate anaerobic fermentation microbes, especially members of the orders Clostridiales and Bacteroidales. The longitudinal analysis supported the vertical or pseudo-vertical transmission but suggested that colonization might occur immensely at 7–28 days of age. We observed a host genetic effect on the gut microecology, which might lead to increased heterogeneity of the microecological impact on Campylobacter colonization.

Conclusions

The findings advance the understanding of the gut microecological impact on Campylobacter presence in the chicken gut under conditions of litter contact and suggest that manipulations of the gut microecology, as well as the microbes identified in the Campylobacter association networks, might be important for the development of intervention strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02353-5.

Hulless barley and β-glucanase affect ileal digesta soluble beta-glucan molecular weight and digestive tract characteristics of coccidiosis-vaccinated broilers

Exogenous β-glucanase (BGase) in barley-based feed has been shown to reduce digesta viscosity in chickens, and thereby improve performance. Less well studied is the potential for BGase to convert barley β-glucan into low molecular weight carbohydrates, which might influence digestive tract function and enteric disease. Coccidiosis-vaccinated broiler chickens were fed graded levels of hulless barley (HB) and BGase to determine their effects on β-glucan depolymerization and digestive tract characteristics. Broilers were fed high β-glucan HB (0%, 30% and 60% replacing wheat) and BGase (0%, 0.01% and 0.1%) in a 3 × 3 factorial arrangement. A total of 5,346 broilers were raised in litter floor pens and vaccinated for coccidiosis on d 5. Each treatment was assigned to 1 pen in each of 9 rooms. The significance level was set at P ≤ 0.05. At both 11 and 33 d of broiler ages, peak molecular weight of β-glucan in ileal digesta decreased with increasing BGase for 30% and 60% HB. The maximum molecular weight for the smallest 10% β-glucan molecules (MW-10%) decreased with BGase at both ages for 30% and 60% HB; for birds fed 0% HB, only 0.1% BGase decreased MW-10%. The 0.1% BGase increased caecal short chain fatty acids (SCFA) compared to the 0.01% BGase at d 11 only for the 60% HB. Ileal pH increased with increasing HB and BGase at d 11 and 33. Caecal pH was lower for 0.1% BGase than 0% BGase for 60% HB at d 11. Relative mRNA expression of interleukin 6 (IL-6) and IL-8 in the ileum increased with 0.1% BGase at d 11 and 33, respectively, whereas expression of ileal mucin 2 (MUC2) decreased with 0.1% BGase at d 33. In the caeca, interactions between HB and BGase were significant for monocarboxylate transporter 1 (MCT1) and mucin 5AC (MUC5 AC) on d 11, but no treatment effects were found at d 33. In conclusion, BGase depolymerized high molecular weight β-glucan in HB in a dose-dependent manner. Hulless barley and BGase did not increase SCFA concentrations (except for 60% HB with 0.1% BGase at d 11) and caused minor effects on digestive tract histomorphological measurements and relative mRNA gene expression.

Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg

The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica.

IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach

Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R² = 0.13, p = 10^–4, Adonis R² = 0.11, p = 10^–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.

Long-Term Grow-Out Affects Campylobacter jejuni Colonization Fitness in Coincidence With Altered Microbiota and Lipid Composition in the Cecum of Laying Hens

Campylobacter jejuni is one of the leading causes of gastrointestinal illness worldwide and is mainly transmitted from chicken through the food chain. Previous studies have provided increasing evidence that this pathogen can colonize and replicate in broiler chicken during its breeding; however, its temporal kinetics in laying hen are poorly understood. Considering the possible interaction between C. jejuni and gut microbiota, the current study was conducted to address the temporal dynamics of C. jejuni in the cecum of laying hen over 40 weeks, with possible alteration of the gut microbiota and fatty acid (FA) components. Following oral infection with C. jejuni 81-176, inocula were stably recovered from ceca for up to 8 weeks post-infection (p.i.). From 16 weeks p.i., most birds became negative for C. jejuni and remained negative up to 40 weeks p.i. 16S rRNA gene sequencing analyses revealed that most of the altered relative rRNA gene abundances occurred in the order Clostridiales, in which increased relative rRNA gene abundances were observed at >16 weeks p.i. in the families Clostridiaceae, Ruminococcaceae, Lachnospiraceae, and Peptococcaceae. Lipidome analyses revealed increased levels of sterols associated with bile acid metabolisms in the cecum at 16 and/or 24 weeks p.i. compared with those detected at 8 weeks p.i., suggesting that altered microbiota and bile acid metabolism might underlie the decreased colonization fitness of C. jejuni in the gut of laying hens.

Effect of Age on the Immune and Visceral Organ Weights and Cecal Traits in Modern Broilers

Simple Summary

Currently, due to the high developments achieved in the poultry industry especially in genetics, management, nutrition, health, and animal welfare, modern broilers reach slaughter weight at an earlier age, which in turn has brought about notable changes in the morphophysiology of these birds. The following research proposes to determine the effect of age on visceral and immune organ weight, cecal pH, and cecal lactic acid bacteria in Ross 308^® broilers, up to 10 days old. It was concluded that the immune and visceral organs increase their absolute and relative weight according to age and on days 9 and 10 the highest growth rate of the organs was found, furthermore, the colonization of the cecal lactic acid bacteria is established before 10 days of life (as the most critical stage), although with variable changes for intestinal pH. The correlation showed, in addition, a significant association between the organs evaluated, as well as for the cecum relative weight and the cecal lactic bacteria count. These results could contribute to updating knowledge on immunological activity, cecal microbiology, and the functioning of the digestive system, as well as for the development of new nutritional requirements and the optimization of dietary formulations.

Abstract

This study aimed to determine the effect of age on the immune and visceral organ weights and cecal traits in modern broilers. 200 male Ross^® 308 broilers were randomly selected, then 20 broilers were slaughtered every day (up to 10 days old) after six hours of fasting. All the organs measured had a progressive increase in absolute weight as the days progressed, apart from the spleen, which decreased its absolute weight on day 5, even though on day 10 it showed the highest values. Moreover, the small intestine relative weight increased from the fourth to the ninth day and was correlated (p ≤ 0.05) with the relative weight of the proventriculus, gizzard, small intestine, and cecum, although without statistical association with the of the heart. There was a correlation between the cecum relative weight and the cecal lactic acid bacteria, and between the primary lymphoid organs. The pH (from 5.74 to 7.40) and cecal lactic acid bacteria (from 6.11 to 8.79 log 10 CFU/g) changed according to the age of the broilers. The results could contribute to the understanding of the physiology and intestinal microbiology of the first 10 days old of modern broilers, which is crucial to improve the genetic expression of these animals.

The Effect of Antibiotics on Mesophilic Anaerobic Digestion Process of Cattle Manure

This study explored the effect of eight antimicrobials on the efficiency of biogas production in the anaerobic digestion (AD) process of cattle manure. The microbiome involved in AD, presence and number of genes mcrA, MSC and MST specific for Archaea, and antibiotic resistance genes (ARGs) concentration in digestate (D) were examined. Supplementation of antibiotics to substrate significantly lowered biogas production. Amoxicillin caused a 75% decrease in CH4 production in comparison with the control samples. Enrofloxacin, tetracycline, oxytetracycline, and chlortetracycline reduced the amount of biogas produced by 36, 39, 45 and 53%, respectively. High-throughput sequencing of 16S rRNA results revealed that bacteria dominated the Archaea microorganisms in all samples. Moreover, antibiotics led to a decrease in the abundance of the genes mcrA, MSC, MST, and induced an increase in the number of tetracyclines resistance genes. Antibiotics decreased the efficiency of the AD process and lowered the quantity of CH4 obtained, while stimulating an increase in the number of ARGs in D. This work reveals how antimicrobials affect the cattle manure AD process and changes in microbial biodiversity, number of functional genes and ARGs in the digestate due to drugs exposure. It also, provides useful, practical information about the AD process.

The distribution of antibiotic resistance genes in chicken gut microbiota commensals

Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.

Advances in Microbiome Research for Animal Health

Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.

Review: Methanogens and methane production in the digestive systems of nonruminant farm animals

The greenhouse gases (GHGs) derived from agriculture include carbon dioxide, nitrous oxide, and methane (CH₄). Of these GHGs, CH₄, in particular, constitutes a major component of the GHG emitted by the agricultural sector. Along with environmental concerns, CH₄ emission also leads to losses in gross energy intake with economic implications. While ruminants are considered the main source of CH₄ from agriculture, nonruminant animals also contribute substantially, and the CH₄ emission intensity of nonruminants remains comparable to that of ruminants. Means of mitigating CH₄ emissions from enteric fermentation have therefore been sought. Methane is produced by methanogens-archaeal microorganisms that inhabit the digestive tracts of animals and participate in fermentation processes. As the diversity of methanogen communities is thought to be responsible for the differences in CH₄ production among nonruminant animals, it is necessary to investigate the archaeal composition of specific animal species. Methanogens play an important role in energy metabolism and adipose tissue deposition in animals. Higher abundances of methanogens, along with their higher diversity, have been reported to contribute to lean phenotype in pigs. In particular, a greater abundance of Methanosphaera spp. and early dominance of Methanobrevibacter smithii have been reported to correlate with lower body fat formation in pigs. Besides the contribution of methanogens to the metabolic phenotype of their hosts, CH₄ release reduces the productivity that could be achieved through other hydrogen (H₂) disposal pathways. Enhanced participation of acetogenesis in H₂ disposal, leading to acetate formation, could be a more favorable direction for animal production and the environment. Better knowledge and understanding of the archaeal communities of the gastrointestinal tract (GIT), including their metabolism and interactions with other microorganisms, would thus allow the development of new strategies for inhibiting methanogens and shifting toward acetogenesis. There are a variety of approaches to inhibiting methanogens and mitigating methanogenesis in ruminants, which can find an application for nonruminants, such as nutritional changes through supplementation with biologically active compounds and management changes. We summarize the available reports and provide a comprehensive review of methanogens living in the GIT of various nonruminants, such as swine, horses, donkeys, rabbits, and poultry. This review will help in a better understanding of the populations and diversity of methanogens and the implications of their presence in nonruminant animals.

Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Simple Summary

Antimicrobial resistance acquired an endemic status in the Pakistan poultry sector. A cross-sectional study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant Escherichia coli using next-generation sequencing. Results show the widespread presence of diverse antibiotic resistance genes, virulence-associated genes, plasmid replicon types, and dysbiotic fecal microbial communities. Results indicate that antibiotic resistance altered the fecal microbial community structure of broiler chickens. The use of next-generation sequencing in this study documents a robust and cost-effective approach to study the fecal microbiome and resistome diversities of broiler chickens.

Abstract

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells

Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.

Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery from Salmonella enterica subsp. enterica Serovar Typhimurium Infection in Neonatal Chickens

Enrofloxacin is an important antibiotic used for prevention and treatment of Salmonella infection in poultry in many countries. However, oral administration of enrofloxacin may lead to the alterations in the microbiota and metabolome in the chicken intestine, thereby reducing colonization resistance to the Salmonella infection. To study the effect of enrofloxacin on Salmonella in the chicken cecum, we used different concentrations of enrofloxacin to feed 1-day-old chickens, followed by oral challenge with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). We then explored the distribution pattern of S. Typhimurium in cecum contents in vivo and analyzed the microbial community structure of cecum contents using microbial 16S amplicon sequencing. Untargeted metabolomics was used to explore the gut metabolome on day 14. Faecalibacterium and Anaerostipes, which are closely related to the chicken intestinal metabolome, were screened using a multi-omics technique. The abundance of S. Typhimurium was significantly higher in the enrofloxacin-treated group than in the untreated group, and S. Typhimurium persisted longer. Moreover, the cecal colony structures of the three groups exhibited different characteristics, with Lactobacillus reaching its highest abundance on day 21. Notably, S. Typhimurium infection is known to affect the fecal metabolome of chickens differently. Thus, our results suggested that enrofloxacin and Salmonella infections completely altered the intestinal microbiota and metabolism of chickens.IMPORTANCE In this study, we examined the effects of S. Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote S. Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent S. Typhimurium infection.

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.

Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period

Simple Summary

This study was conducted to characterise the caecal microbiota in two broiler management systems (fast and slow-growing) during the growing period, using 16S rRNA sequencing analysis. Because of the essential role of the caecal bacteria in poultry health and productivity, these data could be considered as a biomarker of health status and will make it possible to evaluate different treatments applied in animals. The main results demonstrated that microbiota is in constant development throughout the growing period for both management systems, and the most abundant bacteria groups are related to better productive performance and intestinal health.

Abstract

Caecal microbiota and its modulation play an important role in poultry health, productivity and disease control. Moreover, due to the emergence of antimicrobial-resistant bacteria, society is pressing for a reduction in antibiotic administration by finding effective alternatives at farm level, such as less intensified production systems. Hence, the aim of this study was to characterise the caecal microbiota in two different broiler management systems, fast and slow-growing, using 16S rRNA sequencing analysis. To this end 576 broilers were reared in two different management systems (fast and slow-growing). Results showed that Firmicutes represented the dominant phylum for both systems. At the onset, Proteobacteria was the second prevalent phylum for fast and slow-growing breeds, outnumbering the Bacteroidetes. However, during the rest of the production cycle, Bacteroidetes was more abundant than Proteobacteria in both groups. Finally, regardless of the management system, the most predominant genera identified were Oscillospira spp., Ruminococcus spp., Coprococcus spp., Lactobacillus spp. and Bacteroides spp. In conclusion, fast and slow-growing broiler microbiota are in constant development throughout rearing, being relatively stable at 21 days of age. Regarding the genus, it should be noted that the three most abundant groups for both systems, Ruminococcus spp., Lactobacillus spp. and Bacteroides spp., are related to better productive performance and intestinal health.

Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge

In poultry production, birds are raised under intensive conditions, which can enable rapid spread of infections, with Clostridium perfringens-caused necrotic enteritis (NE) being one of the most devastating for the industry. The current investigation was conducted to evaluate the effectiveness of Bacillus subtilis PB6 probiotic supplementation on bird’s post NE recovery, based on chicken performance, cecal microbiota composition, ileum histomorphometric measurements, and short-chain fatty acid production in the cecum of the birds that were challenged with NE mid-production. Birds were split into four groups, including a negative control, positive control challenged with C. perfringens, group supplemented with B. subtilis probiotic, and NE challenged birds supplemented with B. subtilis probiotic. Following NE challenge birds were allowed to reach the end of production time at 40 days, and samples were collected to estimate if probiotic supplementation resulted in better post-NE recovery. Intestinal lesion score across the duodenum, jejunum, and ileum indicated that at the end of production timeline NE challenged birds supplemented with B. subtilis probiotic had lower intestinal lesion scores compared to NE challenged birds without probiotic supplementation implying improved recovery. Probiotic supplementation improved performance of NE challenged birds only in the post-NE recovery stage. NE challenged birds had a significant increase in cecal propionic acid, which was not observed in NE challenged birds supplemented with B.subtilus. Both B. subtilis supplemented groups (challenged and unchanged) were characterized by a significant rise in cecal acetic and butyric acid. Our results demonstrate that B. subtilis supplementation can assist the birds in dealing with NE outbreak and long term recovery.

Biogeography of microbiome and short-chain fatty acids in the gastrointestinal tract of duck

It is generally accepted that domestic ducks are valuable protein sources for humans. The gastrointestinal ecosystem contains enormous and complicated microbes that have a profound effect on the nutrition, immunity, health, and production of domestic ducks. To deeply understand the gastrointestinal microbial composition of domestic ducks, we investigated the microbiomes of 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) and the short-chain fatty acids in 15 healthy muscovy ducks based on 16S rRNA gene sequencing, qPCR, and gas chromatography. As a result, 1 029 735 sequences were identified into 35 phyla and 359 genera. Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, with Bacteroidetes being most abundant in the cecum. The population of the total bacteria and the representatives of the Firmicutes, Bacteroidetes, and Bacteroides groups increased from the proximal to the distal part of the GIT. Bacteroides was the most dominant group in the cecum. Acetate, propionate, and butytrate, as well as gene copies of butyryl-CoA including acetate-CoA transferase and butyrate kinase, were significantly higher in cecum than in other sections. Isobutyrate, valerate, and isovalerate were only found in the cecum. The differences of microbial composition and the short-chain fatty acids of their metabolites among these 7 intestinal locations might be correlated with differences in gut function. All these results provide a reference for the duck gastrointestinal microbiome and a foundation for understanding the types of bacteria that promote health and enhance growth performance and decrease instances of disease in duck breeding.

Improvement of Cecal Commensal Microbiome Following the Insect Additive into Chicken Diet

Gastrointestinal microbiota play an important role in regulating the metabolic processes of animals and humans. A properly balanced cecal microbiota modulates growth parameters and the risk of infections. The study examined the effect of the addition of 0.2% and 0.3% of Tenebrio molitor and Zophobas morio on cecal microbiome of broilers. The material was the cecum digesta. The obtained DNA was analyzed using 16S rRNA next generation sequencing. The results of the study show that the addition of a relatively small amount of Z. morio and T. molitor modulates the broiler cecum microbiome composition. The most positive effect on cecal microbiota was recorded in the 0.2% Z. morio diet. A significant increase in the relative amount of genus Lactobacillus, represented by the species Lactobacillus agilis and the amount of bacteria in the Clostridia class, was observed. Moreover, the addition of 0.2% ZM resulted in a significant increase of relative abundance of the family Bifidobacteriaceae with the highest relative abundance of genus Bifidobacterium pseudolongum. The obtained results indicate that the addition of a relatively small amount of insect meal in broiler diet stimulates colonization by probiotic and commensal bacteria, which may act as barriers against infection by pathogenic bacteria.

Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms

Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.

Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes

The microbiome has entered the vernacular of the consumer as well as broiler production and is, therefore, becoming increasingly important to poultry producers to understand. The microbiome is, by definition, compositional and relates to how the microbiological organisms within the gut inhabit that ecological niche. The gut is diverse, flexible, and data acquired requires a greater understanding of the host-microbiome axes, as well as advanced bioinformatics and ecology. There are numerous microbial populations that define the gut microbiome; however, there are even more effects that can influence its composition. As management practices vary between producers, documenting these influences is an essential component of beginning to understand the microbiome. This review targets broiler production and concatenates the currently understood compositional ecology of the broiler gastrointestinal tract microbiome as well as its influences.

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.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

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.