Detection of methane and quantification of methanogenic archaea in faeces from young broiler chickens using real-time PCR

Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens

BACKGROUND

We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds.

RESULTS

Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet.

CONCLUSIONS

Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.

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.

Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples

Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples—or in this case, chicken droppings.

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.

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.

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.

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.

Nitro-treatment of composted poultry litter; effects on Salmonella, E. coli and nitrogen metabolism

Poultry litter is a potentially valuable crude protein feedstuff for ruminants but must be treated to kill pathogens before being fed. Composting kills pathogens but risks losses of nitrogen due to volatilization or leaching as ammonia. Treatment of poultry litter with ethyl nitroacetate, 3-nitro-1-propionate, ethyl 2-nitropropionate (at 27 µmol/g), decreased numbers of experimentally-inoculated Salmonella Typhimurium (>1.0 log₁₀ compared to controls, 4.2 ± 0.2 log₁₀ CFU/g) but not endogenous Escherichia coli early during simulated composting. By day 9 of simulated composting, Salmonella and E. coli were decreased to non-detectable levels regardless of treatment. Some nitro-treatments preserved uric acid and prevented ammonia accumulation, with 18% more uric acid remaining and 17-24% less ammonia accumulating in some nitro-treated litter than in untreated litter (18.1 ± 3.8 µmol/g and 3.4 ± 1.4 µmol/g, respectively). Results indicate that nitro-treatment may help preserve uric acid in composted litter while aiding Salmonella control.

The Preliminary Development of an in vitro Poultry Cecal Culture Model to Evaluate the Effects of Original XPCTM for the Reduction of Campylobacter jejuni and Its Potential Effects on the Microbiota

Poultry is a major reservoir for the pathogen Campylobacter jejuni. C. jejuni inhabits the poultry gastrointestinal tract as a part of the gut microbiota. The objective of this study was to evaluate both the survival of C. jejuni and the changes in the population dynamics of the cecal microbiome during an in vitro C. jejuni inoculation in the presence or absence of the functional metabolites of Diamond V Original XPC^TM (XPC). Two independent trials were conducted. Broiler chickens (n = 6 per Trial 1 and n = 3 per Trial 2) were raised according to standard industry guidelines and euthanized on Day 41. The ceca were collected aseptically, their contents removed independently and then used in an in vitro microaerobic model with 0.1% cecal contents + Campylobacter with or without 1% XPC (w/v). Before the inoculation with a chloramphenicol resistant marker strain of C. jejuni, the cecal contents were pre-incubated with XPC at 42°C for 24 h, in a shaking incubator (200 rpm) under microaerobic conditions, then experimentally inoculated with 10⁸/ml of C. jejuni into the appropriate treatment groups. At 0 and 24 h for Trial 1, and 48 h for Trial 2, sub-samples of the culture (n = 3 ceca, two technical replicates per ceca, XPC alone or ceca culture alone) were enumerated using a Petroff–Hausser counter, and the DNA was extracted for microbiome analysis. DNA was isolated using the Qiagen QIAamp Fast Stool DNA Mini Kit and sequenced using the Illumina MiSeq platform. The reads were filtered, normalized, and assigned taxonomical identities using the QIIME2 pipeline. The relative microbiota populations were identified via ANCOM. Altogether, evidence suggests that XPC alters the microbiome, and in turn reduces Campylobacter survival.

Methane emissions of geese (Anser anser) and turkeys (Meleagris gallopavo) fed pelleted lucerne

In contrast to mammalian herbivores, birds are generally perceived to produce little methane (CH₄) during digestion, and accounting for poultry in greenhouse gas inventories is considered unnecessary. We measured CH₄ emissions in six domestic geese (Anser anser, 5.0 ± 0.9 kg) and six domestic turkeys (Meleagris gallopavo, 6.3 ± 0.6 kg) kept on a diet of lucerne pellets only, using open-circuit chamber respirometry. Measurements of oxygen consumption were similar to previously published values in these species. Absolute CH₄ emissions per day were lower in geese (0.58 ± 0.10 L) than in turkeys (1.48 ± 0.16 L) and represented 0.4 ± 0.2 and 0.6 ± 0.1% of gross energy intake, respectively. These results confirm previous findings on the presence of methanogenes in the digestive tract of poultry species, and in vitro measurements performed on poultry caecal contents. In relation to mammalian herbivores in terms of absolute CH₄ emissions, CH₄ yield per dry matter or gross energy intake, or the CH₄:CO₂ ratio, the lucerne-fed geese and turkeys had comparatively low values. The emission of CH₄ in spite of the very short digesta retention times and low fibre digestibility, as measured in the same animals, gives rise to the hypothesis that that in some birds, caecal fermentation and the associated CH₄ production may be related to the microbial digestion of uric acid. The hypothesis that CH₄ emissions in poultry may depend not only on dietary fibre but also on dietary digestible protein (that is excreted as uric acid in urine and retrogradely transported from the cloaca into the caeca) remains to be tested.

Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity

OBJECTIVE

This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions.

METHODS

A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment.

RESULTS

i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens.

CONCLUSION

The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

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.

Organic Acids and Potential for Modifying the Avian Gastrointestinal Tract and Reducing Pathogens and Disease

Recently, antibiotics have been withdrawn from some poultry diets; leaving the birds at risk for increased incidence of dysbacteriosis and disease. Furthermore, mortalities occurring from disease contribute between 10 to 20% of production cost in developed countries. Currently, numerous feed supplements are being proposed as effective antibiotic alternatives in poultry diets, such as prebiotics, probiotics, acidic compounds, competitive exclusion products, herbs, essential oils, and bacteriophages. However, acidic compounds consisting of organic acids show promise as antibiotic alternatives. Organic acids have demonstrated the capability to enhance poultry performance by altering the pH of the gastrointestinal tract (GIT) and consequently changing the composition of the microbiome. In addition, organic acids, by altering the composition of the microbiome, protect poultry from pH-sensitive pathogens. Protection is further provided to poultry by the ability of organic acids to potentially enhance the morphology and physiology of the GIT and the immune system. Thus, the objective of the current review is to provide an understanding of the effects organic acids have on the microbiome of poultry and the effect those changes have on the prevalence of pathogens and diseases in poultry. From data reviewed, it can be concluded that the efficacy of organic acids on shifting microbiome composition is limited to the time of administration, the composition of the organic acid product, and the current health conditions of poultry.

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box." We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester.

High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity

Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of Methanobrevibacter smithii, followed by the Norwegian samples. One Norwegian sample contained 43 % Methanobrevibacter thaueri, whilst all other samples contained < 10 %. Vermont samples had large percentages of Methanobrevibacter ruminantium, as did two Norwegian samples. Methanosphaera stadtmanae represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % Polyplastron multivesiculatum and one contained >75 % Entodinium spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus Entodinium, especially Entodinium caudatum. Norwegian moose contained a large proportion of sequences (25–97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly Eudiplodinium rostratum (>75 %), with up to 7 % Diploplastron affine. Four of the eight Vermont samples also contained 5–12 % Entodinium spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.

Archaeal microbiota population in piglet feces shifts in response to weaning: Methanobrevibacter smithii is replaced with Methanobrevibacter boviskoreani

Methanogens commonly inhabit swine intestine. We analyzed the gut archaeal population by extracting DNA from the feces of nine piglets. We performed PCR to target the V6-V8 region of the 16S rRNA gene. Subsequent denaturing gradient gel electrophoresis (DGGE) revealed the presence of Methanobrevibacter boviskoreani, which has not previously been identified in pigs. We confirmed these data with a PCR-DGGE analysis of the mcrA gene, and subsequent sequencing. At 63 days old, the only band in fecal samples corresponded to M. boviskoreani. The DGGE analysis also showed that Methanobrevibacter smithii, which was abundant at 28 days, was dramatically reduced at 42 days, and it completely disappeared at 63 days. To confirm these data, we quantified M. smithii and the total archaeal population by quantitative PCR (qPCR); moreover, we designed a new set of species-specific primers based on the 16S rRNA gene of M. boviskoreani. The qPCR results confirmed the reduction in M. smithii over time and a simultaneous increase in M. boviskoreani. At 63 days, the total numbers of archaea and M. boviskoreani genomes were comparable, which suggested that M. boviskoreani represented the dominant archaea. This work showed that the archaeal population shifted during weaning, and M. boviskoreani replaced M. smithii.

Chicken intestinal microbiota function with a special emphasis on the role of probiotic bacteria

Bacterial colonization of the chicken gut by environmental microbes begins immediately after hatching. Composition of the intestinal microbiota is dependent on the surrounding environment, diet variation, pathological conditions, antibiotic therapy, and others. The genomes of all these intestinal microbes form a microbiome which by far outnumbers the host's genome. As a consequence, the microbiome provides additional metabolic functions to the host, including nutrient utilization and absorption, fermentation of non-digestible dietary fiber, synthesis of some vitamins, biotransformation of bile acids, and the well-being of their chicken host. Microorganisms can also directly interact with the lining of the gastrointestinal tract, which may alter the physiology and immunological status of the bird. Since newly hatched broiler chickens demonstrate delayed commensal colonization and low bacterial diversity, the most effective and harmless method available to control the development and composition of the intestinal microbiota is a competitive exclusion treatment by applying probiotic bacteria. Additionally, recent research has shown that probiotic bacteria have a variety of beneficial effects, including counteraction of dysbiosis, promotion of gut health and homeostasis, enhancement of immune defenses and antagonization of infectious agents.

Lactobacillus sakei modulates mule duck microbiota in ileum and ceca during overfeeding

The supplementation with Lactobacillus sakei as probiotic on the ileal and cecal microbiota of mule ducks during overfeeding was investigated using high-throughput 16S rRNA gene-based pyrosequencing and real-time PCR. The ducks were overfed with or without L. sakei for 12 d with 56% ground corn and 42% whole corn. Samples were collected before the overfeeding period (at 12 wk), at 13 wk (meal 12 of overfeeding), and at 14 wk (meal 24), 3 h postfeeding. Whatever the digestive segment and the level of intake, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla in the bacterial community of mule ducks (at least 90%). Before overfeeding, ileal samples were dominated by Clostridia, Bacteroidia, and Gammaproteobacteria (80% and up), and cecal samples by Bacteroidia and Clostridia (around 85%). The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding increased the relative abundance of Firmicutes and especially the Lactobacillus group in ileal samples. Nonmetric multidimensional scaling profiles separated the bacterial communities with respect to overfeeding only in cecal samples. Richness indicators decreased after L. sakei has been added at mid-overfeeding only in the ileum. In the ceca, the decrease of these indexes only occurred at the end of overfeeding. The addition of L. sakei triggers major changes in the ileum, whereas the ceca are not affected. Lactobacillus sakei decreased the relative abundance of Bacteroides at mid-overfeeding and the relative abundance of Enterobacteria at the end of overfeeding in the ileum.

Changes of poultry faecal microbiota associated with Clostridium difficile colonisation

Bacterial, fungal and archaeal microbiota was analysed in 143 chicken faecal samples from a single poultry farm. After DHPLC (denaturing high performance liquid chromatography) 15 bacterial groups, 10 fungal groups and a single archaeal species were differentiated. Samples were grouped into two clusters with significantly different frequencies of C. difficile positive and negative samples in each cluster. Acidaminococcus intestini, described here for the first time as a part of poultry faecal microbiota, was significantly more likely present in C. difficile negative samples, while presence/absence of some other microorganisms (Enterococcus cecorum, Lactobacillus galinarum, Moniliella sp. and Trichosporon asahii) was close to significance. Two other groups not reported previously for poultry, Coprobacillus sp. and Turicibacter sp. did not differ significantly between C. difficile positive and negative samples. Differences in microbiota diversity depend on animal age, but not on the presence of C. difficile. With machine learning (WEKA J48) we have defined specific combinations of microbial groups predictive for C. difficile colonisation. Microbial groups associated with C. difficile colonisation in poultry are different than those reported for humans and include bacteria as well as fungi. Also with this approach A. intestini was found to be most strongly related to C. difficile negative samples.

The microbiome of the chicken gastrointestinal tract

The modern molecular biology movement was developed in the 1960s with the conglomeration of biology, chemistry, and physics. Today, molecular biology is an integral part of studies aimed at understanding the evolution and ecology of gastrointestinal microbial communities. Molecular techniques have led to significant gains in our understanding of the chicken gastrointestinal microbiome. New advances, primarily in DNA sequencing technologies, have equipped researchers with the ability to explore these communities at an unprecedented level. A reinvigorated movement in systems biology offers a renewed promise in obtaining a more complete understanding of chicken gastrointestinal microbiome dynamics and their contributions to increasing productivity, food value, security, and safety as well as reducing the public health impact of raising production animals. Here, we contextualize the contributions molecular biology has already made to our understanding of the chicken gastrointestinal microbiome and propose targeted research directions that could further exploit molecular technologies to improve the economy of the poultry industry.

Ecology and characteristics of methanogenic archaea in animals and humans

In this review, the molecular techniques used in animal-based-methanogen studies will be discussed along with how methanogens interact not only with other microorganisms but with their animal hosts as well. These methods not only indicate the diversity and levels of methanogens, but also provide insight on their ecological functions. Most molecular techniques have been based on either 16S rRNA genes or methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens. The most predominant methanogens in animals belong to the genus Methanobrevibacter. Besides methanogens contributing to overall H2 balance, methanogens also have mutual interactions with other bacteria. In addition to shared metabolic synergism, the host animal retrieves additional energy from the diet when methanogens are co-colonized with other normal flora. By comparing genes in methanogens with other bacteria, possible gene transfer between methanogens and other bacteria in the same environments appears to occur. Finally, diets in conjunction with the genetics of methanogens and hosts may represent the biological framework that dictate the extent of methanogen prevalence in these ecosystems. In addition, host evolution including the immune system could serve as an additional selective pressure for methanogen colonization.

Archaeal characterization of bioaerosols from cage-housed and floor-housed poultry operations

Although bioaerosols from both cage-housed (CH) and floor-housed (FH) poultry operations are highly concentrated, the concentrations of dust, endotoxin, and bacteria are significantly higher in FH bioaerosols. Workers from CH operations have reported a greater prevalence of respiratory symptoms. To date, archaea have been examined in swine and dairy bioaerosols but not in poultry bioaerosols. The objective of this study was to directly compare methanogenic archaea concentrations in bioaerosols from CH and FH poultry facilities. Bioaerosols were collected from 15 CH and 15 FH poultry operations, using stationary area samplers as well as personal sampling devices. Archaea were quantified and their diversity was investigated using polymerase chain reaction (PCR) followed by denaturing gradient gel electrophoresis (DGGE) and band sequencing. Archaea were significantly higher in area and personal bioaerosols of CH poultry operations than in those from FH poultry operations (p < 0.001 and p < 0.05, respectively) and did not differ significantly between area and personal samples within each barn type. Sequences matching Methanobrevibacter woesei, an archaea previously found in poultry samples, were detected in bioaerosol samples from CH operations. Methanogenic archaea concentrations are significantly different between bioaerosols from CH and FH poultry operations.

In vitro and in vivo antimicrobial activity of propolis on the microbiota from gastrointestinal tract of chickens

The aim of this study was to examine the effect of propolis extracts on the microbial colonization of chicken gastrointestinal tract in vivo. The propolis was administered to both feed mixtures in various amounts except of the control group. The addition of 150 mg propolis to 1 kg of feed was included in the first experimental group, the addition of 450 mg.kg(-1) in the second experimental group, the addition of 600 mg.kg(-1) the third experimental group and 800 mg kg(-1) in the fourth one. The highest count of faecal enterococci was found in the third group (8.6 cfu.g(-1)) where 600 mg of propolis to 1 kg was added to the feed mixture. The highest count of lactobacilli was detected in the fourth experimental group (8.83 cfu.g(-1)) where was 800 mg of propolis added to 1 kg of feed mixture and number of Enterobacteriaceae genera count was found in control group (8.73 cfu.g(-1)). With RTQ PCR detected species from the genus Enterococcus were: E. avium, E. casseliflavus, E cecorum, E. faecalis, E. faecium, E. gallinarum, E. hirae and E. malodoratus and from genus Lactobacillus were: Lactobacillus crispatus, L. acidophilus and L. salivarius. With MALDI TOF MS Biotyper from Enterobacteriaceae genera were identified Citrobacter braakii, Raoultella ornithinolytica, Serratia fonticola, Escherichia coli and Klebsiella oxytoca. Antimicrobial activities In vitro of six species of bacteria isolated from gastrointestinal tract of chickens were also tested. The best antimicrobial effect of Citrobacter braakii on ethanolic propolis extract in all concentrations were found.

Methanogen diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis

The methanogenic communities in buffalo rumen were characterized using a culture-independent approach of a pooled sample of rumen fluid from three adult Surti buffaloes. Buffalo rumen is likely to include species of various methanogens, so 16S rDNA sequences were amplified and cloned from the sample. A total of 171 clones were sequenced to examine 16S rDNA sequence similarity. About 52.63% sequences (90 clones) had ≥ 90% similarity, whereas, 46.78% of the sequences (81 clones) were 75-89% similar to 16S rDNA database sequences, respectively. Phylogenetic analyses were also used to infer the makeup of methanogenic communities in the rumen of Surti buffalo. As a result, we distinguished 23 operational taxonomic units (OTUs) based on unique 16S rDNA sequences: 12 OTUs (52.17%) affiliated to Methanomicrobiales order, 10 OTUs (43.47%) of the order Methanobacteriales and one OTU (4.34%) of Methanosarcina barkeri like clone, respectively. In addition, the population of Methanomicrobiales and Methabacteriales orders were also observed, accounting 4% and 2.17% of total archea. This study has revealed the largest assortment of hydrogenotrophic methanogens phylotypes ever identified from rumen of Surti buffaloes.

Molecular identification of methanogenic archaea from surti buffaloes (bubalus bubalis), reveals more hydrogenotrophic methanogens phylotypes

Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in breeds of buffaloes, as well as in response to geographical location and different diets, is required. Therefore, molecular diversity of rumen methanogens in Surti buffaloes was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from three Surti buffaloes. A total of 171 clones were identified revealing 23 different sequences (phylotypes). Of these 23 sequences, twelve sequences (12 OTUs, 83 clones) and 10 sequences (10 OTUs, 83 clones) were similar to methanogens belonging to the orders Methanomicrobiales and Methanobacteriales, and the remaining 1 phylotype (5 clones) were similar to Methanosarcina barkeri. These unique sequences clustered within a distinct and strongly supported phylogenetic group. Further studies and effective strategies can be made to inhibit the growth of Methanomicrobiales and Methanobacteriales phylotypes to reduce the methane emission from rumen and thus help in preventing global warming.

High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol

Background

The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool.

Methodology/Principal Findings

Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae) yielded a sequence similarity of 99–100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences.

Conclusions/Significance

In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.

mcrA-targeted real-time quantitative PCR method to examine methanogen communities

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase alpha-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4 degrees C or 20 degrees C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.

Effects of select nitrocompounds on in vitro ruminal fermentation during conditions of limiting or excess added reductant

Ruminal methane (CH(4)) production results in the loss of up to 12% of gross energy intake and contributes nearly 20% of the United States' annual emission of this greenhouse gas. We report the effects of select nitrocompounds on ruminal fermentation after 22 h in vitro incubation (39 degrees C) with or without additions of hydrogen (H(2)), formate or both. In incubations containing no added reductant, CH(4) production was inhibited 41% by 2-nitro-1-propanol (2NPOH) and >97% by 3-nitro-1-propionic acid (3NPA), nitroethane (NE) and 2-nitroethanol (2NEOH) compared to non-treated controls and H(2) did not accumulate. With formate as the sole added reductant, nitro-treatment reduced CH(4) production by >99% and caused 42% to complete inhibition of formate catabolism compared to controls, and the accumulation of H(2) increased slightly. Nitro-treatment decreased CH(4) production 57-98% from that of controls when supplied H(2) or formate plus H(2). Formate catabolism was decreased 42-84% from that in controls by all nitro-treatments except 3NPA with both formate and H(2). Greater than 97% of the added H(2) was catabolized within controls; >84% was catabolized in nitro-treated incubations. Acetate, propionate and butyrate accumulations were unaffected by nitro-treatment irregardless of reductant; however, effects on ammonia and branched chain fatty acid accumulations varied. These results suggest that nitro-treatment inhibited formate dehydrogenase/formate hydrogen lyase and hydrogenase activity.

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

BACKGROUND

The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.

METHODOLOGY/PRINCIPAL FINDINGS

Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families.

CONCLUSION/SIGNIFICANCE

This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

Foodborne Salmonella ecology in the avian gastrointestinal tract

Foodborne Salmonella continues to be a major cause of salmonellosis with Salmonella Enteritidis and S. Typhimurium considered to be responsible for most of the infections. Investigation of outbreaks and sporadic cases has indicated that food vehicles such as poultry and poultry by-products including raw and uncooked eggs are among the most common sources of Salmonella infections. The dissemination and infection of the avian intestinal tract remain somewhat unclear. In vitro incubation of Salmonella with mammalian tissue culture cells has shown that invasion into epithelial cells is complex and involves several genetic loci and host factors. Several genes are required for the intestinal phase of Salmonella invasion and are located on Salmonella pathogenicity island 1 (SPI 1). Salmonella pathogenesis in the gastrointestinal (GI) tract and the effects of environmental stimuli on gene expression influence bacterial colonization and invasion. Furthermore, significant parameters of Salmonella including growth physiology, nutrient availability, pH, and energy status are considered contributing factors in the GI tract ecology. Approaches for limiting Salmonella colonization have been primarily based on the microbial ecology of the intestinal tract. In vitro studies have shown that the toxic effects of short chain fatty acids (SCFA) to some Enterobacteriaceae, including Salmonella, have resulted in a reduction in population. In addition, it has been established that native intestinal microorganisms such as Lactobacilli provide protective mechanisms against Salmonella in the ceca. A clear understanding of the key factors involved in Salmonella colonization in the avian GI tract has the potential to lead to better approach for more effective control of this foodborne pathogen.