Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure.

Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.

The Impact of Early-Life Cecal Microbiota Transplantation on Social Stress and Injurious Behaviors in Egg-Laying Chickens.

Injurious behaviors (i.e., aggressive pecking, feather pecking, and cannibalism) in laying hens are a critical issue facing the egg industry due to increased social stress and related health and welfare issues as well as economic losses. In humans, stress-induced dysbiosis increases gut permeability, releasing various neuroactive factors, causing neuroinflammation and related neuropsychiatric disorders via the microbiota-gut-brain axis, and consequently increasing the frequency and intensity of aggression and violent behaviors. Restoration of the imbalanced gut microbial composition has become a novel treatment strategy for mental illnesses, such as depression, anxiety, bipolar disorder, schizophrenia, impulsivity, and compulsivity. A similar function of modulating gut microbial composition following stress challenge may be present in egg-laying chickens. The avian cecum, as a multi-purpose organ, has the greatest bacterial biodiversity (bacterial diversity, richness, and species composition) along the gastrointestinal tract, with vitally important functions in maintaining physiological and behavioral homeostasis, especially during the periods of stress. To identify the effects of the gut microbiome on injurious behaviors in egg-laying chickens, we have designed and tested the effects of transferring cecal contents from two divergently selected inbred chicken lines on social stress and stress-related injurious behaviors in recipient chicks of a commercial layer strain. This article reports the outcomes from a multi-year study on the modification of gut microbiota composition to reduce injurious behaviors in egg-laying chickens. An important discovery of this corpus of experiments is that injurious behaviors in chickens can be reduced or inhibited through modifying the gut microbiota composition and brain serotonergic activities via the gut-brain axis, without donor-recipient genetic effects.

Impact of maternal live yeast supplementation to sows on intestinal inflammatory cytokine expression and tight junction proteins in suckling and weanling piglets.

Recent studies have highlighted the importance of maternal nutrition during gestation and lactation in modulating the gastrointestinal development and health of offspring. Therefore, the objective of this study was to determine the effects of live yeast (LY) supplementation to sows during late gestation and throughout lactation on markers of gut health of piglets prior to weaning and immediately postweaning. On day 77 of gestation, forty sows were allotted based on parity and expected farrowing dates to two dietary treatments: without (CON) or with (LY) supplementation at 0.05% and 0.1% of diet during gestation and lactation, respectively. On postnatal days (PND) 0, 10, 18, and postweaning days (PWD) 7 and 14, one piglet from each of 10 sows per treatment were selected for intestinal tissue collection (n = 10). Real-time PCR and western blotting analyses were used to determine the mucosal expression of immune and antioxidant-regulatory genes and tight junction markers of gut health in the duodenum, jejunum, and ileum. Inflammatory and tight junction markers on PND 0 were not affected by maternal dietary treatment. On PND 18, maternal LY supplementation increased (P < 0.05) mRNA expression of interleukin (IL)-6 and tended (P = 0.08) to increase expression of IL-10 in the ileal muocsa. Maternal LY supplementation also increased (P < 0.05) expression of IL-1ß in the ileal mucosa on PWD 14. Likewise, expression of superoxide dismutase (SOD) 1 was increased (P < 0.05) by LY on PND 10, 18, and PWD 14, with a tendency (P = 0.09) for a greater mRNA abundance of catalase on PND 14 in the ileal mucosa. Compared to CON piglets, LY piglets had a higher (P < 0.05) protein abundance of E-cadherin in the jejunal mucosa on PND 0, PWD 7, and PWD 14. Levels of occludin and claudin-4 were also higher (P < 0.05) in the jejunum of LY piglets on PWD 14. No differences were found in jejunal histomorphological measurements between treatments. In conclusion, this study shows that maternal LY supplementation affects key markers of gut health and development in the offspring that may impact the future growth potential and health of newborn piglets.

Increasing evidence supports the benefits of improving sow nutrition during gestation and lactation to promote gastrointestinal development and overall health of piglets. The objective of this research was to investigate the effects of maternal live yeast (LY) supplementation to sows during late gestation and lactation periods on the intestinal health of suckling and weaned piglets. Sows were fed LY during gestation and lactation and piglets were killed for sampling at different time points to track the temporal effect of maternal LY supplementation on changes in markers of intestinal health and development on postnatal days 0, 10, and 18, and postweaning days 7 and 14. Results showed that maternal LY supplementation affected several markers of health and development in the offspring, especially the expression of tight junction proteins, inflammatory cytokines, and antioxidant enzymes. These results indicate that nutritional intervention during gestation and lactation could serve as an effective strategy for raising piglets with better health and growth performance.

Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows (Cyprinodon variegatus).

The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). Within fish, the microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting immune function, and modulating behavior. The aim of this study was to examine if exposure to weathered oil might produce significant shifts in fish gut-associated microbial communities as determined from taxa and genes known for hydrocarbon degradation, and whether foraging behavior was affected. The gut microbiome (16S rRNA and shotgun metagenomics) of sheepshead minnow (Cyprinodon variegatus) was characterized after fish were exposed to oil in High Energy Water Accommodated Fractions (HEWAF; tPAH = 81.1 ± 12.4 µg/L) for 7 days. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome was not significantly altered in alpha or beta diversity. None of the most abundant taxa produced any significant shifts as a result of oil exposure, with only rare taxa showing significant shifts in abundance between treatments. However, several bioindicator taxa known for hydrocarbon degradation were detected in the oil treatment, primarily Sphingomonas and Acinetobacter. Notably, the genus Stenotrophomonas was detected in high abundance in 16S data, which previously was not described as a core member of fish gut microbiomes. Data also demonstrated that behavior was not significantly affected by oil exposure. Potential low bioavailability of the oil may have been a factor in our observation of minor shifts in taxa and no behavioral effects. This study lays a foundation for understanding the microbiome of captive sheepshead minnows and indicates the need for further research to elucidate the responses of the fish gut-microbiome under oil spill conditions.

Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery.

Introduction: Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery. Methods: Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing. Results: The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD. Discussion: This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.

Meta-analysis reveals the predictable dynamic development of the gut microbiota in commercial pigs.

IMPORTANCE: The swine gut microbiome undergoes an age-dependent assembly pattern with a developmental phase at early ages and a stabilization phase at later ages. Shorter time intervals and a wider range of data sources provided a clearer understanding of the gut microbiota colonization and succession and their associations with pig growth and development. The rapidly changing microbiota of suckling and weaning pigs implies potential time targets for growth and health regulation through gut microbiota manipulation. Since swine gut microbiota development is predictable, swine microbiota age can be calculated and compared between animal treatment groups rather than relying only on static time-matched comparisons.

The bovine nasal fungal community and associations with bovine respiratory disease.

Introduction: Effective identification and treatment of bovine respiratory disease (BRD) is an ongoing health and economic issue for the dairy and beef cattle industries. Bacteria pathogens Pasteurellamultocida, Mycoplasmabovis, Mannheimia haemolytica, and Histophilus somni and the virus Bovine herpesvirus-1 (BHV-1), Bovine parainfluenza-3 virus (BPIV-3), Bovine respiratory syncytial virus (BRSV), Bovine adenovirus 3 (BAdV3), bovine coronavirus (BoCV) and Bovine viral diarrhea virus (BVDV) have commonly been identified in BRD cattle; however, no studies have investigated the fungal community and how it may also relate to BRD. Methods: The objective of this study was to understand if the nasal mycobiome differs between a BRD-affected (n = 56) and visually healthy (n = 73) Holstein steers. Fungal nasal community was determined by using Internal Transcribed Spacer (ITS) sequencing. Results: The phyla, Ascomycota and Basidiomycota, and the genera, Trichosporon and Issatchenkia, were the most abundant among all animals, regardless of health status. We identified differences between healthy and BRD animals in abundance of Trichosporon and Issatchenkia orientalis at a sub-species level that could be a potential indicator of BRD. No differences were observed in the nasal fungal alpha and beta diversity between BRD and healthy animals. However, the fungal community structure was affected based on season, specifically when comparing samples collected in the summer to the winter season. We then performed a random forest model, based on the fungal community and abundance of the BRD-pathobionts (qPCR data generated from a previous study using the same animals), to classify healthy and BRD animals and determine the agreement with visual diagnosis. Classification of BRD or healthy animals using ITS sequencing was low and agreed with the visual diagnosis with an accuracy of 51.9%. A portion of the ITS-predicted BRD animals were not predicted based on the abundance of BRD pathobionts. Lastly, fungal and bacterial co-occurrence were more common in BRD animals than healthy animals. Discussion: The results from this novel study provide a baseline understanding of the fungal diversity and composition in the nasal cavity of BRD and healthy animals, upon which future interaction studies, including other nasal microbiome members to further understand and accurately diagnose BRD, can be designed.

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics.

Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.

Cecal microbiota transplantation: unique influence of cecal microbiota from divergently selected inbred donor lines on cecal microbial profile, serotonergic activity, and aggressive behavior of recipient chickens.

BACKGROUND: Accumulating evidence from human trials and rodent studies has indicated that modulation of gut microbiota affects host physiological homeostasis and behavioral characteristics. Similarly, alterations in gut microbiota could be a feasible strategy for reducing aggressive behavior and improving health in chickens. The study was conducted to determine the effects of early-life cecal microbiota transplantation (CMT) on cecal microbial composition, brain serotonergic activity, and aggressive behavior of recipient chickens. METHODS: Chicken lines 63 and 72 with nonaggressive and aggressive behavior, respectively, were used as donors and a commercial strain Dekalb XL was used as recipients for CMT. Eighty-four 1-d-old male chicks were randomly assigned to 1 of 3 treatments with 7 cages per treatment and 4 chickens per cage (n = 7): saline (control, CTRL), cecal solution of line 63 (63-CMT), and cecal solution of line 72 (72-CMT). Transplantation was conducted via oral gavage once daily from d 1 to 10, and then boosted once weekly from week 3 to 5. At weeks 5 and 16, home-cage behavior was recorded, and chickens with similar body weights were assigned to paired aggression tests between the treatments. Samples of blood, brain, and cecal content were collected from the post-tested chickens to detect CMT-induced biological and microbiota changes. RESULTS: 63-CMT chickens displayed less aggressive behavior with a higher hypothalamic serotonergic activity at week 5. Correspondingly, two amplicon sequence variants (ASVs) belonging to Lachnospiraceae and one Ruminococcaceae UCG-005 ASV were positively correlated with the levels of brain tryptophan and serotonin, respectively. 72-CMT chickens had lower levels of brain norepinephrine and dopamine at week 5 with higher levels of plasma serotonin and tryptophan at week 16. ASVs belonging to Mollicutes RF39 and GCA-900066225 in 72-CMT chickens were negatively correlated with the brain 5-hydroxyindoleacetic acid (5-HIAA) at week 5, and one Bacteroides ASV was negatively correlated with plasma serotonin at week 16. CONCLUSION: Results indicate that CMT at an early age could regulate aggressive behavior via modulating the cecal microbial composition, together with central serotonergic and catecholaminergic systems in recipient chickens. The selected CMT could be a novel strategy for reducing aggressive behavior through regulating signaling along the microbiota-gut-brain axis.

Effects of feeding Saccharomyces cerevisiae fermentation postbiotic on the fecal microbial community of Holstein dairy calves.

BACKGROUND: The livestock industry is striving to identify antibiotic alternatives to reduce the need to use antibiotics. Postbiotics, such as Saccharomyces cerevisiae fermentation product (SCFP), have been studied and proposed as potential non-antibiotic growth promoters due to their effects on animal growth and the rumen microbiome; however, little is known of their effects on the hind-gut microbiome during the early life of calves. The objective of this study was to measure the effect of in-feed SCFP on the fecal microbiome of Holstein bull calves through 4 months of age. Calves (n = 60) were separated into two treatments: CON (no SCFP added) or SCFP (SmartCare®, Diamond V, Cedar Rapids, IA, in milk replacer and NutriTek®, Diamond V, Cedar Rapids, IA, incorporated into feed), and were blocked by body weight and serum total protein. Fecal samples were collected on d 0, 28, 56, 84, and 112 of the study to characterize the fecal microbiome community. Data were analyzed as a completely randomized block design with repeated measures when applicable. A random-forest regression method was implemented to more fully understand community succession in the calf fecal microbiome of the two treatment groups. RESULTS: Richness and evenness of the fecal microbiota increased over time (P < 0.001), and SCFP calves tended to increase the evenness of the community (P = 0.06). Based on random-forest regression, calf age as predicted by microbiome composition was significantly correlated with the calf physiological age (R2 = 0.927, P < 1 × 10-15). Twenty-two "age-discriminatory" ASVs (amplicon sequence variants) were identified in the fecal microbiome that were shared between the two treatment groups. Of these, 6 ASVs (Dorea-ASV308, Lachnospiraceae-ASV288, Oscillospira-ASV311, Roseburia-ASV228, Ruminococcaceae-ASV89 and Ruminoccocaceae-ASV13) in the SCFP group reached their highest abundance in the third month, but they reached their highest abundance in the fourth month in the CON group. All other shared ASVs reached their highest abundance at the same timepoint in both treatment groups. CONCLUSIONS: Supplementation of SCFP altered the abundance dynamics of age discriminatory ASVs, suggesting a faster maturation of some members of the fecal microbiota in SCFP calves compared to CON calves. These results demonstrate the value of analyzing microbial community succession as a continuous variable to identify the effects of a dietary treatment.

Impact of ileal indigestible protein on fecal nitrogen excretion and fecal microbiota may be greater compared with total protein concentration of diets in growing pigs.

In the current study, we hypothesized that an increase in dietary ileal indigestible protein concentration induces an increase in hindgut nitrogen utilization and nitrogen excretion and a shift in fecal microbiota in growing pigs, when compared to pigs given a high total protein diet. Three diets were prepared: 1) standard protein diet based on corn and soybean meal, 2) high-indigestible protein diet in which autoclaved, low-digestible soybean meal replaced soybean meal in the first diet, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. The 3 diets were fed to 18 barrows that were fitted with T-cannula at the ileo-cecal junction (initial body weight = 63.4 ±â€…8.0 kg) in a randomized complete block design with body weight as a blocking factor. Pigs were individually housed in pens and the experiment lasted for 23 d. On days 7 and 21, fecal samples were collected by rectal massage for microbiota analysis. Grab samples of feces were collected on days 20 and 21, and ileal digesta were collected on days 22 and 23 for the determination of energy and nitrogen utilization. Lower apparent ileal digestibility of nitrogen in the high-indigestible protein diet containing autoclaved soybean meal resulted in greater ileal indigestible nitrogen concentration (P < 0.05). Apparent total tract digestibility of nitrogen was lower (P < 0.05), and correspondingly nitrogen concentration and daily fecal nitrogen output were greater (P < 0.05) in the high-indigestible protein diet compared with the other diets. Apparent post-ileal digestibility and hindgut disappearance of nitrogen and gross energy were the greatest (P < 0.05) in the high protein diet, whereas a statistical difference was not observed in those variables between the standard protein diet and the high-indigestible protein diet. Beta diversity metrics of feces in the high-indigestible protein diet on day 21 were different (q < 0.05) from those in the other two diets, which indicates a shift in microbial communities. According to the results of the DESeq2, the direction of microbiota shift induced by the high-indigestible protein diet may have reduced fiber utilization in the hindgut. In conclusion, an increase in dietary ileal indigestible protein concentration increased fecal nitrogen excretion and shifted fecal microbial communities but did not increase nitrogen utilization in the hindgut.

Dietary protein concentration has been gradually reduced because reductions in protein concentration in swine diets are known to be beneficial in terms of feed costs, nitrogen excretion, and intestinal microbiota. However, ileal indigestible protein concentration may be more influential in those variables of pigs compared with total protein concentration in diets because ileal indigestible protein considers both protein concentration and digestibility of diets. In the current study, three diets were prepared: 1) corn-soybean meal diet, 2) high-indigestible protein diet replacing soybean meal in the first diet with autoclaved soybean meal, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. The experimental diets were fed to cannulated pigs and ileal digesta and fecal samples were collected. Fecal nitrogen output was greater in pigs fed the high-indigestible protein diet. Fecal microbiota was shifted by the high-indigestible protein diet, and this shift may not be beneficial. In conclusion, the impact of changes in ileal indigestible protein on fecal nitrogen excretion and fecal microbiota may be greater compared to changes in total protein concentration of diets in growing pigs.

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.

Characterizing the Flavor Precursors and Liberation Mechanisms of Various Dry-Aging Methods in Cull Beef Loins Using Metabolomics and Microbiome Approaches.

The objective of this study was to characterize and compare the dry-aging flavor precursors and their liberation mechanisms in beef aged with different methods. Thirteen paired loins were collected at 5 days postmortem, divided into four sections, and randomly assigned into four aging methods (wet-aging (WA), conventional dry-aging (DA), dry-aging in a water-permeable bag (DWA), and UV-light dry-aging (UDA)). All sections were aged for 28 days at 2 °C, 65% RH, and a 0.8 m/s airflow before trimming and sample collection for chemical, metabolomics, and microbiome analyses. Higher concentrations of free amino acids and reducing sugars were observed in all dry-aging samples (p < 0.05). Similarly, metabolomics revealed greater short-chain peptides in the dry-aged beef (p < 0.05). The DWA samples had an increase in polyunsaturated free fatty acids (C18:2trans, C18:3n3, C20:2, and C20:5; p < 0.05) along with higher volatile compound concentrations compared to other aging methods (aldehyde, nonanal, octanal, octanol, and carbon disulfide; p < 0.05). Microbiome profiling identified a clear separation in beta diversity between dry and wet aging methods. The Pseudomonas spp. are the most prominent bacterial species in dry-aged meat, potentially contributing to the greater accumulation of flavor precursor concentrations in addition to the dehydration process during the dry-aging. Minor microbial species involvement, such as Bacillus spp., could potentially liberate unique and potent flavor precursors.

The Microbiota-Gut-Brain Axis: Gut Microbiota Modulates Conspecific Aggression in Diversely Selected Laying Hens.

The gut microbiota plays an important role in regulating brain function, influencing psychological and emotional stability. The correlations between conspecific aggression, gut microbiota, and physiological homeostasis were further studied in inbred laying chicken lines, 63 and 72, which were diversely selected for Marek's disease, and they also behave differently in aggression. Ten sixty-week-old hens from each line were sampled for blood, brain, and cecal content. Neurotransmitters, cytokines, corticosterone, and heterophil/lymphocyte ratios were determined. Cecal microbiota compositions were determined by bacterial 16s rRNA sequencing, and functional predictions were performed. Our data showed that the central serotonin and tryptophan levels were higher in line 63 compared to line 72 (p < 0.05). Plasma corticosterone, heterophil/lymphocyte ratios, and central norepinephrine were lower in line 63 (p < 0.05). The level of tumor necrosis factor α tended to be higher in line 63. Faecalibacterium, Oscillibacter, Butyricicoccus, and Bacteriodes were enriched in line 63 birds, while Clostridiales vadin BB60, Alistipes, Mollicutes RF39 were dominated in line 72. From the predicted bacterial functional genes, the kynurenine pathway was upregulated in line 72. These results suggested a functional linkage of the line differences in serotonergic activity, stress response, innate immunity, and gut microbiota populations.

Effects of early-life cecal microbiota transplantation from divergently selected inbred chicken lines on growth, gut serotonin, and immune parameters in recipient chickens.

Recent studies have revealed that fecal microbiota transplantation exerts beneficial effects on modulating stress-related inflammation and gastrointestinal health of the host. The aim of this study was to examine if cecal microbiota transplantation (CMT) presents similar efficiency in improving the health status of egg-laying strain chickens. Chicken lines 63 and 72 divergently selected for resistance or susceptibility to Marek's disease were used as CMT donors. Eighty-four d-old male recipient chicks (a commercial DeKalb XL layer strain) were randomly assigned into 3 treatments with 7 replicates per treatment and 4 birds per replicate (n = 7): saline (control, CTRL), cecal solution of line 63 (63-CMT), and cecal solution of line 72 (72-CMT) for a 16-wk trial. Cecal transplant gavage was conducted once daily from d 1 to d 10, then boosted once weekly from wk 3 to wk 5. The results indicated that 72-CMT birds had the highest body weight and ileal villus/crypt ratio among the treatments at wk 5 (P ≤ 0.05); and higher heterophil/lymphocyte ratios than that of 63-CMT birds at wk 16 (P < 0.05). 72-CMT birds also had higher levels of plasma natural IgG and Interleukin (IL)-6 at wk 16, while 63-CMT birds had higher concentrations of ileal mucosal secretory IgA at wk 5 and plasma IL-10 at wk 16 (P < 0.05), with a tendency for lower mRNA abundance of splenic IL-6 and tumor necrosis factor (TNF)-α at wk 16 (P = 0.08 and 0.07, respectively). In addition, 72-CMT birds tended to have the lowest serotonin concentrations (P = 0.07) with the highest serotonin turnover in the ileum at wk 5 (P < 0.05). There were no treatment effects on the levels of plasma corticosterone and testosterone at wk 16 (P > 0.05). In conclusion, early postnatal CMT from different donors led to different patterns of growth and health status through the regulation of ileal morphological structures, gut-derived serotonergic activities, peripheral cytokines, and antibody production in recipient chickens.

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.

Identification of bovine respiratory disease through the nasal microbiome.

BACKGROUND: Bovine respiratory disease (BRD) is an ongoing health and economic challenge in the dairy and beef cattle industries. Multiple risk factors make an animal susceptible to BRD. The presence of Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis in lung tissues have been associated with BRD mortalities, but they are also commonly present in the upper respiratory tract of healthy animals. This study aims to compare the cattle nasal microbiome (diversity, composition and community interaction) and the abundance of BRD pathogens (by qPCR) in the nasal microbiome of Holstein steers that are apparently healthy (Healthy group, n = 75) or with BRD clinical signs (BRD group, n = 58). We then used random forest models based on nasal microbial community and qPCR results to classify healthy and BRD-affected animals and determined the agreement with the visual clinical signs. Additionally, co-occurring species pairs were identified in visually BRD or healthy animal groups. RESULTS: Cattle in the BRD group had lower alpha diversity than pen-mates in the healthy group. Amplicon sequence variants (ASVs) from Trueperella pyogenes, Bibersteinia and Mycoplasma spp. were increased in relative abundance in the BRD group, while ASVs from Mycoplasma bovirhinis and Clostridium sensu stricto were increased in the healthy group. Prevalence of H. somni (98%) and P. multocida (97%) was high regardless of BRD clinical signs whereas M. haemolytica (81 and 61%, respectively) and M. bovis (74 and 51%, respectively) were more prevalent in the BRD group than the healthy group. In the BRD group, the abundance of M. haemolytica and M. bovis was increased, while H. somni abundance was decreased. Visual observation of clinical signs agreed with classification by the nasal microbial community (misclassification rate of 32%) and qPCR results (misclassification rate 34%). Co-occurrence analysis demonstrated that the nasal microbiome of BRD-affected cattle presented fewer bacterial associations than healthy cattle. CONCLUSIONS: This study offers insight into the prevalence and abundance of BRD pathogens and the differences in the nasal microbiome between healthy and BRD animals. This suggests that nasal bacterial communities provide a potential platform for future studies and potential pen-side diagnostic testing.

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.

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities.

Most dietary fibers used to shape the gut microbiota present different and unpredictable responses, presumably due to the diverse microbial communities of people. Recently, we proposed that fibers can be classified in a hierarchical way where fibers of high specificity (i.e., structurally complex and utilized by a narrow group of gut bacteria) could have more similar interindividual responses than those of low specificity (i.e., structurally simple and utilized by many gut bacteria). To test this hypothesis, we evaluated microbiota fermentation of fibers tentatively classified as low (fructooligosaccharides), low-to-intermediate (type 2 resistant starch), intermediate (pectin), and high (insoluble ß-1,3-glucan) specificity, utilizing fecal inoculum from distinct subjects, regarding interindividual similarity/dissimilarity in fiber responses. Individual shifts in target bacteria (as determined by linear discriminant analysis) confirmed that divergent fiber responses occur when utilizing both of the low-specificity dietary fibers, but fibers of intermediate and high specificity lead to more similar responses across subjects in support of targeted bacteria. The high-specificity insoluble ß-glucan promoted a large increase of the target bacteria (from 0.3 to 16.5% average for Anaerostipes sp. and 2.5 to 17.9% average for Bacteroides uniformis), which were associated with increases in ratios of related metabolites (butyrate and propionate, respectively) in every microbial community in which these bacteria were present. Also, high-specificity dietary fibers promoted more dramatic changes in microbial community structure than low-specificity ones relative to the initial microbial communities. IMPORTANCE In the face of interindividual variability and complexity of gut microbial communities, prediction of outcomes from a given fiber utilized by many microbes would require a sophisticated comprehension of all competitive interactions that occur in the gut. Results presented here suggest that high-specificity fibers potentially circumvent the competitive scope in the gut for fiber utilization, providing a promising path to targeted and predictable microbial shifts in different individuals. These findings are the first to indicate that fiber specificity is related to similarity and intensity of response in distinct human gut microbiota communities.