Contribution of the Broiler Breeders' Fecal Microbiota to the Establishment of the Eggshell Microbiota

16S amplicon-based microbiome biomapping of a commercial broiler hatchery

Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.

Essential oils mix effect on chicks ileal and caecal microbiota modulation: a metagenomics sequencing approach

Introduction

Microbiota plays a pivotal role in promoting the health and wellbeing of poultry. Essential oils (EOs) serve as an alternative solution for modulating poultry microbiota. This study aimed to investigate, using amplicon sequencing, the effect of a complex and well-defined combination of EOs feed supplement on both ileal and caecal broiler microbiota, within the context of Salmonella and Campylobacter intestinal colonization.

Material and methods

For this experiment, 150-day-old Ross chicks were randomly allocated to two groups: T+ (feed supplementation with EO mix 500 g/t) and T- (non-supplemented). At day 7, 30 birds from each group were orally inoculated with 106 CFU/bird of a Salmonella enteritidis and transferred to the second room, forming the following groups: TS+ (30 challenged birds receiving infeed EO mix at 500g/t) and TS- (30 challenged birds receiving a non-supplemented control feed). At day 14, the remaining birds in the first room were orally inoculated with 103 CFU/bird of two strains of Campylobacter jejuni, resulting in the formation of groups T+C+ and T-C+. Birds were sacrificed at day 7, D10, D14, D17, and D21. Ileal and caecal microbiota samples were analyzed using Illumina MiSeq sequencing. At D7 and D14, ileal alpha diversity was higher for treated birds (p <0.05).

Results and discussion

No significant differences between groups were observed in caecal alpha diversity (p>0.05). The ileal beta diversity exhibited differences between groups at D7 (p < 0.008), D10 (p = 0.029), D14 (p = 0.001) and D17 (p = 0.018), but not at D21 (p = 0.54). For all time points, the analysis indicated that 6 biomarkers were negatively impacted, while 10 biomarkers were positively impacted. Sellimonas and Weissella returned the lowest (negative) and highest (positive) coefficient, respectively. At each time point, treatments influenced caecal microbiota beta diversity (p < 0.001); 31 genera were associated with T+: 10 Ruminoccocaceae genera were alternatively more abundant and less abundant from D7, 7 Lachnospiraceae genera were alternatively more and less abundant from D10, 6 Oscillospiraceae genera were variable depending on the date and 4 Enterobacteriaceae differed from D7. During all the experiment, Campylobacter decreased in treated birds (p < 0.05). This study showed that EO mix modulates ileal and caecal microbiota composition both before and during challenge conditions, increasing alpha diversity, especially in ileum during the early stages of chick life.

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.

Microbiota Profiles of Hen Eggs from the Different Seasons and Different Sectors of Shanghai, China

Hen eggs are one of the most popular foods worldwide, and their safety is critical. Employing 16S rRNA full-length sequencing is an effective way to identify microorganisms on or in eggs. Here, hen eggs collected from poultry farms over four seasons, as well as from markets in Shanghai, were analyzed with third-generation sequencing. Firmicutes (44.46%) and Proteobacteria (35.78%) were the two dominant phyla, and Staphylococcus, Acinetobacter, Aerococcus, Psychrobacter, and Lactobacillus were the dominant genera. The dominant genera on the eggshell surfaces from the farms varied with the seasons, and the highest contamination of Staphylococcus (32.93%) was seen in the eggs collected during the summer. For the market samples, Pseudomonas was the most abundant in content, with Staphylococcus being the most-often genera found on the eggshell surfaces. Moreover, several potential pathogenic bacteria including Riemerella anatipestifer (species), Klebsiella (genus), and Escherichia/shigella (genus) were detected in the samples. The results revealed the impacts of weather on the microbiota deposited on an eggshell's surface, as well as the impacts due to the differences between the contents and the surface. The results can help disinfect eggs and guide antibiotic selection.

The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota

The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: (1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? (2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? (3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.

Colonization of the Gastrointestinal Tract of Chicks with Different Bacterial Microbiota Profiles

This study aimed to investigate the consequences of early-life microbiota transplantation using different caecal content sources in broiler chicks. We hypothesized that chicks receiving at-hatch microbiota from organic hens would harbour a distinct microbiota from chicks receiving industry-raised broiler microbiota after six weeks of age. Three hundred Cobb broilers eggs were randomly assigned to one of four groups according to the caecal content received: organic laying hens (Organic); autoclaved caecal content of organic laying hens (Autoclaved); conventionally grown broilers (Conventional); and sterile saline (Control). caecal microbiota transplantation was given by gavage on day 1. Ten birds/group were euthanized on days 2, 7, 14, 28, and 42. The caecal tonsils and contents were collected for cytokines and microbiota analyses. The microbiota from chicks receiving live inocula resembled the donors' microbiota from day seven until day 42. The microbiota composition from the chickens who received the Organic inoculum remained markedly different. Starting on day 7, the Organic group had higher richness. Simpson and Shannon's indices were higher in the Conventional group on days 2 and 7. Chickens in the Conventional group presented higher production of IL-1β and IL-6 in plasma on days 2 and 28, increased IL-6 expression in the caecal tonsils at days 7 and 42, and increased IL-12 expression on day 7. However, the Conventional group was infected with Eimeria spp., which likely caused inflammation. In conclusion, microbiota transplantation using different microbiota profiles persistently colonized newly hatched broiler chicks. Future studies evaluating the importance of microbiota composition during infections with common enteropathogens are necessary. This study also highlights the need for a strict screening protocol for pathogens in the donors' intestinal content.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Dynamics of Bacterial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus minor)

Eggshell bacterial communities may affect hatching success and nestling's condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation in the Oriental Tit (Parus minor). Bacterial communities on the nest material were relatively stable and remained distinct from the eggshell communities and had higher diversity and greater phylogenetic clustering than the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of bacterial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics of the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird's skin, feathers, cloaca/intestine, or uropygial secretion which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials, and the incubating bird's body.

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.

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front

Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray-Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling.

Review on skeletal disorders caused by Staphylococcus spp. in poultry

Lameness or leg weakness is the main cause of poor poultry welfare and serious economic losses in meat-type poultry production worldwide. Disorders related to the legs are often associated with multifactorial aetiology which makes diagnosis and proper treatment difficult. Among the infectious agents, bacteria of genus Staphylococcus are one of the most common causes of bone infections in poultry and are some of the oldest bacterial infections described in poultry. Staphylococci readily infect bones and joints and are associated with bacterial chondronecrosis with osteomyelitis (BCO), spondylitis, arthritis, tendinitis, tenosynovitis, osteomyelitis, turkey osteomyelitis complex (TOC), bumblefoot, dyschondroplasia with osteomyelitis and amyloid arthropathy. Overall, 61 staphylococcal species have been described so far, and 56% of them (34/61) have been isolated from clinical cases in poultry. Although Staphylococcus aureus is the principal cause of poultry staphylococcosis, other Staphylococcus species, such as S. agnetis, S. cohnii, S. epidermidis, S. hyicus, S. simulans, have also been isolated from skeletal lesions. Antimicrobial treatment of staphylococcosis is usually ineffective due to the location and type of lesion, as well as the possible occurrence of multidrug-resistant strains. Increasing demand for antibiotic-free farming has contributed to the use of alternatives to antibiotics. Other prevention methods, such as better management strategies, early feed restriction or use of slow growing broilers should be implemented to avoid rapid growth rate, which is associated with locomotor problems. This review aims to summarise and address current knowledge on skeletal disorders associated with Staphylococcus spp. infection in poultry.

Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance

Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.

Metformin modulates the gut microbiome in broiler breeder hens

Broiler breeder hens, the parent stock of commercial broiler chickens, are genetically selected for rapid growth. Due to a longer production period and the focus of genetic selection on superior carcass traits in their progeny, these hens have the propensity to gain excess adipose tissue and exhibit severe ovarian dysfunction, a phenotype that is similar to human polycystic ovary syndrome (PCOS). Metformin is an antihyperglycemic drug approved for type 2 diabetes that is prescribed off-label for PCOS with benefits on metabolic and reproductive health. An additional effect of metformin treatments in humans is modulation of gut microbiome composition, hypothesized to benefit glucose sensitivity and systemic inflammation. The effects of dietary metformin supplementation in broiler breeder hens have not been investigated, thus we hypothesized that dietary metformin supplementation would alter the gut microbiome of broiler breeder hens. Broiler breeder hens were supplemented with metformin at four different levels (0, 25, 50, and 75 mg/kg body weight) from 25 to 65 weeks of age, and a subset of hens (n = 8-10 per treatment group) was randomly selected to undergo longitudinal microbiome profiling with 16S rRNA sequencing. Metformin impacted the microbial community composition in 75 mg/kg metformin compared to controls (adjusted PERMANOVA p = 0.0006) and an additional dose-dependent difference was observed between 25 mg/kg and 75 mg/kg (adjusted PERMANOVA p = 0.001) and between 50 mg/kg and 75 mg/kg (adjusted PERMANOVA p = 0.001) but not between 25 mg/kg and 50 mg/kg (adjusted PERMANOVA p = 0.863). There were few differences in the microbiome attributed to hen age, and metformin supplementation did not alter alpha diversity. Bacteria that were identified as differentially relatively abundant between 75 mg/kg metformin treatment and the control, and between metformin doses, included Ruminococcus and members of the Clostridia family that have been previously identified in human trials of PCOS. These results demonstrate that metformin impacts the microbiome of broiler breeder hens in a dose-dependent manner and several findings were consistent with PCOS in humans and with metformin treatment in type 2 diabetes. Metformin supplementation is a potentially promising option to improve gut health and reproductive efficiency in broiler breeder hens.

Effect of Radiant Catalytic Ionization and Ozonation on Salmonella spp. on Eggshells

Three Salmonella enterica strains were used in the study (serovars: S. enteritidis, S. typhimurim and S. virchow). This study evaluated the efficacy of radiant catalytic ionization (RCI) and ozonation against Salmonella spp. on eggshell (expressed as log CFU/egg). The egg surface was contaminated three different bacterial suspension (10³ CFU/mL, 10⁵ CFU/mL and 10⁸ CFU/mL) with or without poultry manure. Experiments were conducted at 4 °C and 20 °C in three different time period: 30 min, 60 min and 120 min. Treatment with RCI reduced Salmonella numbers from 0.26 log CFU/egg in bacterial suspension 10⁸ CFU/mL, 4 °C and 20 °C, with manure for 30 min to level decrease in bacteria number below the detection limit (BDL) in bacterial suspension 10⁵ CFU/mL, 20 °C, with or without manure for 120 min. The populations of Salmonella spp. on eggs treated by ozonizer ranged from 0.20 log CFU/egg in bacteria suspension 10⁸ CFU/mL, 20 °C, with manure for 30 min to 2.73 log CFU/egg in bacterial suspension 10⁵ CFU/mL, 20 °C, with manure for 120 min. In all treatment conditions contamination with poultry manure decrease effectiveness the RCI and ozonation. In summary, RCI technology shows similar effectiveness to the ozonation, but it is safer for poultry plant workers and consumers.

Intestinal microbiota of layer hens and its association with egg quality and safety

The intestinal microbiota has attracted tremendous attention in the field of the poultry industry due to its critical role in the modulation of nutrient utilization, immune system, and consequently the improvement of the host health and production performance. Accumulating evidence implies intestinal microbiota of laying hens is a potential mediator to improve the prevalent issues in terms of egg quality decline in the late phase of laying production. However, the regulatory effect of intestinal microbiota on egg quality in laying hens remains elusive, which requires consideration of microbial baseline composition and succession during their long lifespans. Notable, although Firmicutes, Bacteroidetes, and Proteobacteria form the vast majority of intestinal microbiota in layer hens, dynamic intestinal microbiota succession occurs throughout all laying periods. In addition to the direct effects on egg safety, intestinal microbiota and its metabolites such as short-chain fatty acids, bile acids, and tryptophan derivatives, are suggested to indirectly modulate egg quality through the microbiota-gut-liver/brain-reproductive tract axis. These findings can extend our understanding of the crosstalk between intestinal microbiota and the host to improve egg quality and safety. This paper reviews the compositions of intestinal microbiota in different physiological stages of laying hens and their effects on egg quality and proposes that intestinal microbiota may become a potential target for modulating egg quality and safety by nutritional strategies in the future.

Microbiome Applications for Laying Hen Performance and Egg Production

Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions.

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.

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.

Microbiota continuum along the chicken oviduct and its association with host genetics and egg formation

The microbiota of female reproductive tract have attracted considerable attention in recent years due to their effects on host fitness. However, the microbiota throughout the chicken oviduct and its symbiotic relationships with the host have not been well characterized. Here, we characterized the microbial composition of six segments of the reproductive tract, including the infundibulum, magnum, isthmus, uterus, vagina and cloaca, in pedigreed laying hens with phenotypes of egg quality and quantity. We found that the microbial diversity gradually increased along the reproductive tract from the infundibulum to the cloaca, and the microbial communities were distinct among the cloaca, vagina and four other oviductal segments. The magnum exhibited the lowest diversity, given that the lysozyme and other antimicrobial proteins are secreted at this location. The results of correlation estimated showed that the relationship between host genetic kinship and microbial distance was negligible. Additionally, the genetically related pairwise individuals did not exhibit a more similar microbial community than unrelated pairs. Although the egg might be directly contaminated with potential pathogenic bacteria during egg formation and oviposition, some microorganisms provide long-term benefits to the host. Among these, we observed that increased abundance of vaginal Staphylococcus and Ralstonia was significantly associated with darker eggshells. Meanwhile, vaginal Romboutsia could be used as a predictor for egg number. These findings provide insight into the nature of the chicken reproductive tract microbiota and highlight the effect of oviductal bacteria on the process of egg formation.

10-Year Molecular Surveillance of Listeria monocytogenes Using Whole-Genome Sequencing in Shanghai, China, 2009-2019

Listeria monocytogenes is an etiologic agent of listeriosis, and has emerged as an important foodborne pathogen worldwide. In this study, the molecular characteristics of 155 L. monocytogenes isolates from seven food groups in Shanghai, the biggest city in China, were identified using whole-genome sequencing (WGS). Most L. monocytogenes isolates (79.3%) were obtained between May and October from 2009 to 2019. The serogroups and clonal complexes (CCs) of L. monocytogenes were found useful for identifying potential health risks linked to foods. Differences in distributions of serogroups and CCs among different food groups were analyzed using t-test. The results showed that the IIa and IVb serogroups were identified among most of food groups. However, the prevalence of serogroup IIb was significantly higher in ready-to-eat (RTE) food and raw seafood than in other food groups, similar to group IIc in raw meat and raw poultry than others. Meanwhile, the prevalence of CC9 in raw meat and raw poultry, CC8 in raw poultry, and CC87 in raw seafood significantly exceeded that of in other food groups. Specially, CC87 was the predominant CC in foodborne and clinical isolates in China, indicating that raw seafood may induce a high-risk to food safety. Also, hypervirulence pathogenicity islands LIPI-3 and LIPI-4 were found in CC3, CC1, and CC87, respectively. The clonal group CC619 carried LIPI-3 and LIPI-4, as previously reported in China. Core genome multilocus sequence typing (cgMLST) analysis suggested that CC87 isolates from the same food groups in different years had no allelic differences, indicating that L. monocytogenes could persist over years. These 10-year results in Shanghai underscore the significance of molecular epidemiological surveillance of L. monocytogenes in foodborne products in assessing the potential risk of this pathogen, and further address food safety issues in China.

Bacillus subtilis delivery route: effect on growth performance, intestinal morphology, cecal short-chain fatty acid concentration, and cecal microbiota in broiler chickens

As the poultry industry recedes from the use of antibiotic growth promoters, the need to evaluate the efficacy of possible alternatives and the delivery method that maximizes their effectiveness arises. This study aimed at expounding knowledge on the effect of the delivery method of a probiotic product (Bacillus subtilis fermentation extract) on performance and gut parameters in broiler chickens. A total of 450 fertile eggs sourced from Cobb 500 broiler breeders were randomly allotted to 3 groups: in ovo probiotic (n = 66), in ovo saline (n = 66), and noninjection (n = 200) and incubated for 21 d. On day 18.5 of incubation, 200 μL of either probiotic (10 × 10⁶ cfu) or saline was injected into the amnion. At hatch, chicks were reallotted to 6 new treatment groups: in ovo probiotic, in ovo saline, in-feed antibiotics, in-water probiotic, in-feed probiotics, and control (corn-wheat-soybean diet) in 6 replicate cages and raised for 28 d. Of all hatch parameters evaluated, only percentage pipped eggs was found significant (P < 0.05) with the noninjection group having higher percentage pipped eggs than the other groups. Treatments did not affect the incidence of necrotic enteritis on day 28 (P > 0.05). Irrespective of the delivery method, the probiotic treatments had no significant effect on growth performance. The ileum villus width of the in ovo probiotic treatment was 18% higher than the in ovo saline group (P = 0.05) but not statistically higher than other groups. The jejunum villus height was 23% higher (P = 0.000) in the in ovo probiotic group than in the control group. There was no effect of treatment on total cecal short-chain fatty acid concentration and cecal gut microbiota composition and diversity (P > 0.05), although few unique bacteria differential abundance were recorded per treatment. Conclusively, although probiotic treatments (irrespective of the delivery route) did not affect growth performance, in ovo delivery of the probiotic product enhanced intestinal morphology, without compromising hatch performance and gut homeostasis.