Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers.

Despite the negative impacts of Salmonella intestinal colonization on human health, Salmonella is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of Salmonella across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between Salmonella enterica serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (n = 156/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators/room, 11 chicks/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators/breed, 108 total) were challenged with Salmonella Typhimurium (ST) (1 × 10 8 CFU/ml) via oral gavage while the remaining chicks (n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq. Salmonella Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7 days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (p < 0.05). Salmonella Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as Mollicutes RF39, Shuttleworthia, Flavonifractor, and Oscillibacter compared to broilers that were unchallenged with Salmonella Typhimurium (p < 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to Salmonella Typhimurium challenge. Thus, both broiler breed and Salmonella Typhimurium can impact the intestinal microbiota.

Behavior and Immune Response of Conventional and Slow-Growing Broilers to Salmonella Typhimurium.

Fast growth rate in broiler chickens comes with welfare concerns and the contribution of growth rate to pathogen resistance and sickness behavior is relatively unknown. The objective of this study was to evaluate physiological and behavioral responses of conventional (CONV) and slow-growing (SG) male broilers challenged with Salmonella Typhimurium. CONV (n = 156) and SG (n = 156) chicks were raised in a pen with wood litter shavings until day 7 of age, when birds were transferred to 24 isolators (n = 11 chicks/isolator). On day 14 of age, half of the birds (n = 12 isolators) were challenged with S. Typhimurium (ST) and the other half (n = 12 isolators) received a control (C). On days 7, 13, 17, 21, and 24, body weight was recorded, and blood, jejunum and ileum sections were collected from 2 birds/isolator (n = 48 birds/sampling) to measure plasma IgA and IgG and intestinal histomorphology, respectively. On days 12, 16, 21, and 23, video was recorded to evaluate bird postures (sitting, standing, or locomoting) and behaviors (eating, drinking, preening, stretching, sham foraging, allopreening, and aggression). CONV birds were 70 g heavier (p = 0.03) on day 21 and 140 g heavier (p = 0.007) on day 24 than SG. On day 7, CONV jejunum villus height and crypt depth were 22 and 7 µm greater (p ≤ 0.001), respectively, than SG. On day 24, ST ileum villus height was 95 µm shorter (p = 0.009) than C. IgA increased after day 17 for all birds and at day 21, CONV IgA was greater (p = 0.01) than SG. Although SG IgG was 344 µg/ml greater (p = 0.05) than CONV on day 7, CONV IgG increased with age (p < 0.0001) to greater (p ≤ 0.03) concentrations than SG on day 21 and day 24 by 689 µg/ml and 1,474 µg/ml, respectively, while SG IgG remained at similar concentrations after day 13. Generally, a greater proportion of birds sham foraged as they aged (p < 0.0001). A greater proportion of CONV tended to sit (p = 0.09) and fewer locomoted (p < 0.0001) than SG as they aged. The results illustrate conventional and slow-growing broilers differ in their behavior, immunity, and response to Salmonella.

Biological units of antimicrobial resistance and strategies for their containment in animal production.

The increasing prevalence of antimicrobial-resistant bacterial infections has ushered in a major global public health crisis. Judicious or restricted antimicrobial use in animal agriculture, aiming to confine the use for the treatment of infections, is the most commonly proposed solution to reduce selection pressure for resistant bacterial strains and resistance genes. However, a multifaceted solution will likely be required to make acceptable progress in reducing antimicrobial resistance, due to other common environmental conditions maintaining antimicrobial resistance and limited executionary potential as human healthcare and agriculture will continue to rely heavily on antimicrobials in the foreseeable future. Drawing parallels from systematic approaches to the management of infectious disease agents and biodiversity loss, we provide examples that a more comprehensive approach is required, targeting antimicrobial resistance in agroecosystems on multiple fronts simultaneously. We present one such framework, based on nested biological units of antimicrobial resistance, and describe established or innovative strategies targeting units. Some of the proposed strategies are already in use or ready to be implemented, while some require further research and discussion among scientists and policymakers. We envision that antimicrobial resistance mitigation strategies for animal agriculture combining multiple tools would constitute powerful ecosystem-level interventions necessary to mitigate antimicrobial resistance.

Composition and diversity of the seminal microbiota in bulls and its association with semen parameters.

The male bovine microbiota is a relatively unexplored area even though it has been shown to impact the fertility of not only the male but also the female. With this study, our aim was to evaluate the bacterial composition of semen from bulls with either satisfactory or unsatisfactory semen quality as represented by poor sperm motility and/or morphology. We hypothesized based on findings in human and other domestic animal studies, that the microbiota diversity and composition may be associated with decreased sperm quality. Semen samples from 45 beef bulls were collected, 32 of those bulls were classified as having satisfactory spermiograms according to Society for Theriogenology bull breeding soundness exam standards with the remaining 13 bulls being classified as unsatisfactory. Microbiota profiling was performed using 16S rRNA gene amplicon sequencing of the V4 region. The most abundant genera in the seminal microbiome include Bacteroides, Corynebacterium 1, Escherichia, Gemella, and S5-A14a (an uncultured bacterium from the Clostridiales order). Bulls with satisfactory spermiograms had a higher abundance of sequence types belonging to many genera including Bacteroides, S5-A14a, Trueperella, and two methanogenic archaea genera Methanosphaera and Methanobrevibacter. Comparatively, samples from bulls with unsatisfactory speriograms had greater abundance of sequence types belonging to Veillonellaceae, Campylobacter, and Methanobacterium. Network analysis was also performed for satisfactory and unsatisfactory samples and indicated that cooccurrence of microbial taxa was less common in the S group than in the U group. In the satisfactory group, Methanobrevibacter cooccurred with twelve amplicon sequence variants (ASVs), indicating that it may be important for maintenance of the microbiota in satisfactory samples, and members of this genus were enriched in the satisfactory group. Opportunistic pathogens such as Campylobacter, and Fusobacterium co-occurred with four and ten ASVs, respectively, in the unsatisfactory group, potentially indicating they are acting in synergy with other member of the microbial community, but only in the unsatisfactory group.

Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential.

Even though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.

Composition and diversity of the preputial microbiota in healthy bulls.

Characterization of microbial communities inhabiting the reproductive tracts of cattle may lead to a better comprehension of bovine physiology and reproductive health. To date, reported studies have utilized culture-independent 16S ribosomal RNA (rRNA) for the classification of microbiota in the vaginal tract of cows but no studies have looked at the microbiota of the prepuce or penis of the bull. The aim of this study was to elucidate the microbiota present on the epithelial surface of the penis and prepuce of the post-pubertal bull using 16S rRNA gene sequencing. Ninety-two healthy bulls of a variety of ages and breeding history, presented for routine breeding soundness examinations, were utilized in this investigation. Bacteria belonging to Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria were identified in the prepuce. From all the bulls, two major community types were found, those with low or high bacterial species richness (up to 400 operational taxonomic units in one sample). There was no animal characteristic (breed or age) or management practice (feed type, antibiotic use, co-housing, breeding history) that was correlated with the bull penile microbial community composition. However, Bradyrhizobium was a distinguishing genus only found in the low diversity samples. The bull penile microbial community includes members of genera that are common in soil, cow vagina, respiratory tract, and feces. The baseline preputial microbial community in healthy bulls is described in the current study. This knowledge can be used later when investigating the interactions between disease and the male urogenital tract microbial community.