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

Comamonas testosteroni as the cause of mortality in embryonated chicken eggs of breeding broiler hens in Costa Rica

Mortality of chicken embryos and first-week chickens was reported in a commercial incubator company in Costa Rica. Six 1-day-old Cobb chickens and twenty-four embryonated chicken eggs were examined in the Laboratory of Avian Pathology and the Laboratory of Bacteriology of the National University of Costa Rica. Twelve dead-in-shell embryos showed maceration and were immersed in a putrid, turbid, slightly thick brown liquid. Additionally, the other 12 embryonated eggs had milky yellow-orange content. The livers of those embryos had congestion, haemorrhages and multifocal cream foci of necrosis. Granulocytic infiltration was observed in the bursa of Fabricius, myocardium, liver, lung and kidney. Livers and egg yolks from six embryonated chickens and all 1-day-old chickens were aseptically collected and cultured. In addition, tissues from six better conserved embryos and all 1-day-old chickens were fixed in buffered formalin and embedded in paraffin. Biochemical and molecular tests identified Comamonas testosteroni as the cause of the early, middle and late embryo mortality. As all the eggshells from the sampled embryonated eggs were dirty with soiled a fecal matter, contamination after manipulating the eggs was considered the source of infection. C. testosteroni is an environmental microorganism that has rarely been reported to cause human disease. To our knowledge, this is the first report of C. testosteroni causing mortality in a hatchery. Cleaning and disinfection using ozone were implemented in the hatchery to eliminate the embryo mortality associated with C. testosteroni.

Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks

Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore dependent on environmental sources only. However, since chickens evolved to be hatched in nests, in this study we evaluated the importance of contact between hens and chicks for the development of chicken skin and tracheal microbiota. Sequencing of PCR amplified V3/V4 variable regions of the 16S rRNA gene showed that contact with adult hens decreased the abundance of E. coli, Proteus mirabilis and Clostridium perfringens both in skin and the trachea, and Acinetobacter johnsonii and Cutibacterium acnes in skin microbiota only. These species were replaced by Lactobacillus gallinarum, Lactobacillus aviarius, Limosilactobacillus reuteri, and Streptococcus pasterianus in the skin and tracheal microbiota of contact chicks. Lactobacilli can be therefore investigated for their probiotic effect in respiratory tract in the future. Skin and respiratory microbiota of contact chickens was also enriched for Phascolarctobacterium, Succinatimonas, Flavonifractor, Blautia, and [Ruminococcus] torque though, since these are strict anaerobes from the intestinal tract, it is likely that only DNA from nonviable cells was detected for these taxa.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.

Microbial Community and Abundance of Selected Antimicrobial Resistance Genes in Poultry Litter from Conventional and Antibiotic-Free Farms

In this study, a culture-independent approach was applied to compare the microbiome composition and the abundance of the antimicrobial resistance genes (ARGs) aadA2 for aminoglycosides, tet(A), tet(B), tet(K), and tet(M) for tetracyclines, and mcr-1 for colistin in broiler litter samples collected from conventional and antibiotic-free flocks located in Central Italy. A total of 13 flocks and 26 litter samples, collected at the beginning and at the end of each rearing cycle, were submitted to 16s rRNA sequence analysis and quantitative PCR for targeted ARGs. Firmicutes resulted in the dominant phylum in both groups of flocks, and within it, the Clostridia and Bacilli classes showed a similar distribution. Conversely, in antibiotic-free flocks, a higher frequency of Actinobacteria class and Clostridiaceae, Lactobacillaceae, Corynebacteriaceae families were reported, while in the conventional group, routinely treated with antibiotics for therapeutic purposes, the Bacteroidia class and the Enterobacteriaceae and Bacillaceae families were predominant. All investigated samples were found to be positive for at least one ARG, with the mean values of aadA2 and tet(A) the highest in conventional flocks by a significant margin. The results suggest that antibiotic use can influence the frequency of resistance determinants and the microbial community in poultry flocks, even though other environmental factors should also be investigated more deeply in order to identify additional drivers of antimicrobial resistance.

Amino acid digestibility of insect meals and effects on key bacterial groups in excreta of caecectomised laying hens

The chemical composition and amino acids (AA) digestibility were determined in insect meals from mealworms, crickets, black soldier fly (BSF) larvae and BSF prepupae, and soybean meal. Six caecectomised laying hens were individually housed in metabolism cages and fed either a basal diet or one of five assay diets. Diets and hens were arranged in a 6 × 6 Latin square design with 6 subsequent periods. In each period, the laying hens were fed their respective diet for 9 d, and excreta samples were quantitatively collected twice daily from day 5 to 8. On day 9, a sterile plastic bag was attached to the cloaca of each hen to collect excreta for microbiota analysis. The AA digestibility of the insect meals and soybean meal were calculated using a linear regression approach. Crude protein (CP) concentrations in crickets and mealworms were higher than the value in soybean meal, BSF prepupae and BSF larvae. Ether extract concentrations were high in the insect meals and low in the soybean meal. The digestibility of most essential AA in soybean meal was higher (p < 0.05) than in crickets and BSF prepupae and not different from AA digestibility in mealworms and BSF larvae (except for arginine and histidine). The gene copy number of Escherichia coli in excreta from hens fed with BSF prepupae was lower (p < 0.05) than those fed with BSF larvae, whereas the gene copy number of Bacillus spp. and Clostridium spp. in excreta from hens fed with crickets was lower (p < 0.05) than those fed with BSF larvae. In conclusion, the chemical composition and AA digestibility varied among insect meals based on insect species and life stage. The high level of AA digestibility of insect meals supports the assessment that insect meals are a suitable feed component for laying hens, but differences in AA digestibility should be considered in diet formulation.

Destruction of Mycotoxins in Poultry Waste under Anaerobic Conditions within Methanogenesis Catalyzed by Artificial Microbial Consortia

To reduce the toxicity of modern feeds polluted by mycotoxins, various sorbents are added to them when feeding animals. A part of the mycotoxins is excreted from the body of animals with these sorbents and remains in the manure. As a result, bulk animal wastes containing mixtures of mycotoxins are formed. It is known that it is partially possible to decrease the initial concentration of mycotoxins in the process of anaerobic digestion (AD) of contaminated methanogenic substrates. The aim of this review was to analyze the recent results in destruction of mycotoxins under the action of enzymes present in cells of anaerobic consortia catalyzing methanogenesis of wastes. The possible improvement of the functioning of the anaerobic artificial consortia during detoxification of mycotoxins in the bird droppings is discussed. Particular attention was paid to the possibility of effective functioning of microbial enzymes that catalyze the detoxification of mycotoxins, both at the stage of preparation of poultry manure for methanogenesis and directly in the anaerobic process itself. The sorbents with mycotoxins which appeared in the poultry wastes composed one of the topics of interest in this review. The preliminary alkaline treatment of poultry excreta before processing in AD was considered from the standpoint of effectively reducing the concentrations of mycotoxins in the waste.

The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits

This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.

A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens

Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Red osier dogwood extract vs. trimethoprim-sulfadiazine (Part 2). Pharmacodynamic effects on ileal and cecal microbiota of broiler chickens challenged orally with Salmonella Enteritidis

With the subsisting restrictions on the use of antibiotics in poultry production, the use of plant extracts has shown some promising antimicrobial capacity similar to antibiotics; however, such capacity is largely dependent on their total polyphenol concentration and profile. Given the emerging antimicrobial potential of red osier dogwood (ROD) extract, the study aimed to investigate the pharmacodynamic effect of ROD extract on the ileal and cecal microbiota of broiler chickens challenged orally with Salmonella Enteritidis (SE). A 21 d 4 × 2 factorial experiment was conducted based on 2 main factors, including diets and SE challenge. A total of 384 one-day-old mixed-sex Cobb-500 broiler chicks were randomly allotted to 4 dietary treatments; Negative control (NC), NC + 0.075 mg trimethoprim-sulfadiazine (TMP/SDZ)/kg of diet, and NC containing either 0.3 or 0.5% ROD extract. On d 1, half of the birds were orally challenged with 0.5 mL of phosphate-buffered saline (Noninfected group) and the remaining half with 0.5 mL of 3.1 × 10⁵ CFU/mL SE (Infected group). Dietary treatments were randomly assigned to 8 replicate cages at 6 birds/cage. On d 21, 10 birds/treatment were euthanized and eviscerated to collect ileal and cecal digesta for gut microbiota analysis. The ileal and cecal microbiota was dominated by phyla Firmicutes, Proteobacteria, and Actinobacteriota. The SE infection decreased (P < 0.05) the relative abundance of Proteobacteria and Actinobacteriota in the ileum and ceca, respectively, however, it increased (P < 0.05) Proteobacteria in the ceca. Both 0.3 and 0.5% ROD extracts (P < 0.05) depressed the relative abundance of Actinobacteriota in the ileum but marginally improved (P < 0.05) it in the ceca compared to the TMP/SDZ treatment. Dietary TMP/SDZ increased (P < 0.05) genus Bifidobacterium at the ileal and cecal segments compared to other treatments. Dietary 0.3 and 0.5% marginally improved (P < 0.05) Bifidobacterium in the ceca and depressed (P < 0.05) Weissella and was comparably similar to TMP/SDZ in the ileum. Regardless of the dietary treatments and SE infection, alpha diversity differed (P < 0.05) between ileal and cecal microbiota. Beta diversity was distinct (P < 0.05) in both ileal and cecal digesta along the SE infection model. Conclusively, both ROD extract levels yielded a pharmacodynamic effect similar to antibiotics on ileal and cecal microbiota.

Microbiota of Chickens and Their Environment in Commercial Production

Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.

Succession, Replacement, and Modification of Chicken Litter Microbiota

Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.

The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects

Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.

Feed Composition and Isolate of Histomonas meleagridis Alter Horizontal Transmission of Histomonosis in Turkeys. Proof of Concept

Outbreaks of histomonosis in turkeys are typically initiated by the ingestion of contaminated embryonated eggs of Heterakis gallinarum, potentially present in earthworms and mechanical vectors. Once an outbreak is started, infected turkeys can transmit the disease by horizontal transmission. Factors influencing horizontal transmission of histomonosis are poorly understood. Replication of horizontal transmission in experimental conditions has not been consistent, presenting an obstacle in searching for alternatives to prevent or treat the disease. Two pilot experiments and three validation experiments were conducted in the present study. In pilot experiment 1, one isolate of Histomonas meleagridis (named Buford) was used. Turkeys were fed a low-nutrient density diet corn-soy based (LOW-CS) and raised in floor pens. In pilot experiment 2, another isolate of H. meleagridis was used (named PHL). Turkeys were fed a low-nutrient density diet with the addition of wheat middlings (LOW-WM) and raised in floor pens. In experiment 3, conducted on floor pens, both isolates and diets were used in different groups. In experiment 4, turkeys were raised on battery cages and only the PHL isolate was used. Both diets (LOW-WM and LOW-CS) were used, in addition to a diet surpassing the nutritional needs of young poults (turkey starter, TS). In experiment 5, conducted in battery cages, only the PHL isolate was used, and the LOW-WM and TS diets were in different groups. The horizontal transmission was achieved only with the PHL isolate from all experiments. The transmission rate varied among experimental diets, with the TS diet having the lowest transmission rate in experiments 4 and 5. Variation was observed between experiments and within experimental groups.

Probiotics: Symbiotic Relationship with the Animal Host

Simple Summary

Intestinal health directly influences the profitability of animal production, and so growth-promoting antibiotics have been used in the feed or drinking water to reduce the impact of enteric diseases and improve production parameters. However, these have generated long-term bacterial resistance. In the search for natural alternatives to antibiotics, various probiotic strains have been developed to improve intestinal health and biological indicators in farm animals, which is important to provide the consumer with safe food. This review describes the main probiotic bacteria and yeasts, their in vitro properties and their impact on the antioxidant capacity and intestinal environment of animals. Furthermore, this review outlines the role of probiotics in apparently healthy ruminants, pigs and poultry, including animals with digestive diseases.

Abstract

Antibiotic growth-promoters in animal feeding are known to generate bacterial resistance on commercial farms and have proven deleterious effects on human health. This review addresses the effects of probiotics and their symbiotic relationship with the animal host as a viable alternative for producing healthy meat, eggs, and milk at present and in the future. Probiotics can tolerate the conditions of the gastrointestinal tract, such as the gastric acid, pH and bile salts, to exert beneficial effects on the host. They (probiotics) may also have a beneficial effect on productivity, health and wellbeing in different parameters of animal performance. Probiotics stimulate the native microbiota (microbes that are present in their place of origin) and production of short-chain fatty acids, with proven effects such as antimicrobial, hypocholesterolemic and immunomodulatory effects, resulting in better intestinal health, nutrient absorption capacity and productive responses in ruminant and non-ruminant animals. These beneficial effects of probiotics are specific to each microbial strain; therefore, the isolation and identification of beneficial microorganisms, as well as in vitro and in vivo testing in different categories of farm animals, will guarantee their efficacy, replicability and sustainability in the current production systems.

Dynamics and Diversity of Microbial Contamination in Poultry Bedding Materials Containing Parts of Medicinal Plants

Microorganisms thriving in poultry bedding materials during their exploitation are involved in the development of several diseases and disfunctions of animals. They can also contaminate food products and pose risks to the environment and human health. This study provides an analysis of dynamics and diversity in microbiological contamination observed during the exploitation of poultry bedding materials containing parts of medicinal plants: Satureja hortensis, Origanum vulgare, Melissa officinalis, Salvia officinalis, and Thymus vulgaris, compared with standard types of beddings: straw chaff and straw pellets. The research was carried out in two 42-day experimental cycles involving in total 2400 broiler chickens. Each week, the total count of mesophilic bacteria, fungi and yeasts, the presumptive presence and count of Staphylococcus sp., Escherichia sp., Listeria sp., Salmonella sp., and Candida sp. were determined by culturing on selective media, along with pH and moisture measurements. After 35 days of the experiment, a reduction of the total count of mesophilic bacteria above 1 log compared to the control (11.86 vs. 13.02 log CFU/g) was observed. As the count of yeasts decreased after 21 days, an increase in the total count of bacteria was reported, which indicates a strong competition between microorganisms. The results improve our understanding of the temporal effects of using materials containing parts of medicinal plants on the microbial contamination in poultry litter.

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.